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l variable. * gnu/packages/fonts.scm (font-meera-inimai)[native-inputs]: Adjust accordingly. --- gnu/packages/compression.scm | 6 ++++-- gnu/packages/django.scm | 1 - gnu/packages/fonts.scm | 2 +- gnu/packages/gnome.scm | 1 - gnu/packages/python-compression.scm | 20 -------------------- gnu/packages/python-web.scm | 1 - 6 files changed, 5 insertions(+), 26 deletions(-) (limited to 'gnu/packages/python-compression.scm') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index aea56a7fa9..3098230bd5 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2225,16 +2225,18 @@ (define-public brotli (define-public google-brotli (deprecated-package "google-brotli" brotli)) -(define-public python-google-brotli +(define-public python-brotli (package (inherit brotli) - (name "python-google-brotli") + (name "python-brotli") (build-system python-build-system) (arguments '()) (synopsis "Python interface to Brotli") (description "This package provides a Python interface to the @code{brotli} package, an implementation of the Brotli lossless compression algorithm."))) +(define-public python-google-brotli + (deprecated-package "python-google-brotli" python-brotli)) (define-public ucl (package diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index f8aae1e33f..3d1c9d12c3 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -37,7 +37,6 @@ (define-module (gnu packages django) #:use-module (gnu packages geo) #:use-module (gnu packages openldap) #:use-module (gnu packages python) - #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index c9a9e4f038..5cf2393177 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -2050,7 +2050,7 @@ (define-public font-meera-inimai ("harfbuzz" ,harfbuzz "bin") ("python" ,python-minimal) ("python-fonttools" ,python-fonttools) - ("python-google-brotli" ,python-google-brotli))) + ("python-brotli" ,python-brotli))) (arguments `(#:make-flags (list "PY=python3" (string-append "DESTDIR=" %output) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index af4b953cb0..a60404d370 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -170,7 +170,6 @@ (define-module (gnu packages gnome) #:use-module (gnu packages protobuf) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) - #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 30062f43c5..81e1630e81 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -261,26 +261,6 @@ (define-public python-lzstring (define-public python2-lzstring (package-with-python2 python-lzstring)) -(define-public python-brotli - (package - (name "python-brotli") - (version "1.0.9") - (source - (origin - (method url-fetch) - (uri (pypi-uri "Brotli" version ".zip")) - (sha256 - (base32 - "0f4433s4wv9masc303kkb1s0a09x81xwr8pdvj0kyxzdl05826sd")))) - (build-system python-build-system) - (native-inputs - `(("unzip" ,unzip))) - (home-page "https://github.com/google/brotli") - (synopsis "Python bindings for the Brotli compression library") - (description - "This package provides python bindings for the Brotli compression library.") - (license license:asl2.0))) - (define-public bitshuffle (package (name "bitshuffle") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b99e358e26..dcb84d0b67 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -81,7 +81,6 @@ (define-module (gnu packages python-web) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) - #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) -- cgit v1.2.3 From 8394619baceb118df92e355377fd543bb1aa501a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 13 Dec 2021 17:18:24 +0100 Subject: gnu: Simplify package inputs. This commit was obtained by running: ./pre-inst-env guix style without any additional argument. --- gnu/packages/accessibility.scm | 26 +- gnu/packages/acl.scm | 6 +- gnu/packages/ada.scm | 7 +- gnu/packages/admin.scm | 400 +- gnu/packages/adns.scm | 4 +- gnu/packages/agda.scm | 46 +- gnu/packages/aidc.scm | 16 +- gnu/packages/algebra.scm | 169 +- gnu/packages/android.scm | 136 +- gnu/packages/animation.scm | 21 +- gnu/packages/antivirus.scm | 10 +- gnu/packages/apr.scm | 7 +- gnu/packages/arcan.scm | 29 +- gnu/packages/aspell.scm | 15 +- gnu/packages/assembly.scm | 15 +- gnu/packages/astronomy.scm | 123 +- gnu/packages/audio.scm | 857 ++-- gnu/packages/augeas.scm | 6 +- gnu/packages/authentication.scm | 26 +- gnu/packages/autogen.scm | 6 +- gnu/packages/autotools.scm | 11 +- gnu/packages/avr.scm | 3 +- gnu/packages/axoloti.scm | 7 +- gnu/packages/backup.scm | 190 +- gnu/packages/bash.scm | 25 +- gnu/packages/batik.scm | 11 +- gnu/packages/bdw-gc.scm | 4 +- gnu/packages/benchmark.scm | 35 +- gnu/packages/bioconductor.scm | 7570 ++++++++++++++-------------- gnu/packages/bioinformatics.scm | 3118 ++++++------ gnu/packages/bison.scm | 10 +- gnu/packages/bittorrent.scm | 88 +- gnu/packages/boost.scm | 9 +- gnu/packages/bootloaders.scm | 39 +- gnu/packages/build-tools.scm | 30 +- gnu/packages/busybox.scm | 12 +- gnu/packages/c.scm | 77 +- gnu/packages/calcurse.scm | 4 +- gnu/packages/calendar.scm | 66 +- gnu/packages/ccache.scm | 8 +- gnu/packages/cdrom.scm | 105 +- gnu/packages/cedille.scm | 6 +- gnu/packages/certs.scm | 8 +- gnu/packages/check.scm | 276 +- gnu/packages/chemistry.scm | 92 +- gnu/packages/chez.scm | 27 +- gnu/packages/chicken.scm | 15 +- gnu/packages/ci.scm | 44 +- gnu/packages/clojure.scm | 2 +- gnu/packages/cluster.scm | 21 +- gnu/packages/cmake.scm | 11 +- gnu/packages/cobol.scm | 6 +- gnu/packages/code.scm | 75 +- gnu/packages/compression.scm | 130 +- gnu/packages/compton.scm | 62 +- gnu/packages/configuration-management.scm | 100 +- gnu/packages/conky.scm | 26 +- gnu/packages/connman.scm | 38 +- gnu/packages/convmv.scm | 2 +- gnu/packages/cook.scm | 22 +- gnu/packages/coq.scm | 90 +- gnu/packages/cpp.scm | 148 +- gnu/packages/cran.scm | 7790 +++++++++++++---------------- gnu/packages/crates-graphics.scm | 102 +- gnu/packages/crates-gtk.scm | 52 +- gnu/packages/crates-io.scm | 342 +- gnu/packages/crypto.scm | 113 +- gnu/packages/cryptsetup.scm | 14 +- gnu/packages/cups.scm | 41 +- gnu/packages/curl.scm | 24 +- gnu/packages/cvassistant.scm | 4 +- gnu/packages/cybersecurity.scm | 35 +- gnu/packages/cyrus-sasl.scm | 11 +- gnu/packages/databases.scm | 592 +-- gnu/packages/datamash.scm | 4 +- gnu/packages/datastructures.scm | 12 +- gnu/packages/dav.scm | 60 +- gnu/packages/dc.scm | 14 +- gnu/packages/debian.scm | 40 +- gnu/packages/debug.scm | 51 +- gnu/packages/dejagnu.scm | 2 +- gnu/packages/dhall.scm | 112 +- gnu/packages/dico.scm | 2 +- gnu/packages/dictionaries.scm | 27 +- gnu/packages/diffoscope.scm | 26 +- gnu/packages/direct-connect.scm | 16 +- gnu/packages/disk.scm | 176 +- gnu/packages/display-managers.scm | 59 +- gnu/packages/distributed.scm | 23 +- gnu/packages/django.scm | 261 +- gnu/packages/djvu.scm | 48 +- gnu/packages/dlang.scm | 6 +- gnu/packages/dns.scm | 124 +- gnu/packages/docbook.scm | 30 +- gnu/packages/docker.scm | 60 +- gnu/packages/documentation.scm | 29 +- gnu/packages/dunst.scm | 29 +- gnu/packages/dvtm.scm | 2 +- gnu/packages/easyrpg.scm | 34 +- gnu/packages/ebook.scm | 71 +- gnu/packages/ed.scm | 2 +- gnu/packages/education.scm | 119 +- gnu/packages/efi.scm | 22 +- gnu/packages/electronics.scm | 60 +- gnu/packages/elf.scm | 14 +- gnu/packages/elixir.scm | 3 +- gnu/packages/elm.scm | 41 +- gnu/packages/emacs-xyz.scm | 1874 +++---- gnu/packages/emacs.scm | 19 +- gnu/packages/embedded.scm | 83 +- gnu/packages/emulators.scm | 346 +- gnu/packages/enchant.scm | 11 +- gnu/packages/engineering.scm | 299 +- gnu/packages/enlightenment.scm | 43 +- gnu/packages/entr.scm | 4 +- gnu/packages/erlang.scm | 4 +- gnu/packages/esolangs.scm | 7 +- gnu/packages/fabric-management.scm | 49 +- gnu/packages/fcitx.scm | 11 +- gnu/packages/fcitx5.scm | 37 +- gnu/packages/file-systems.scm | 155 +- gnu/packages/finance.scm | 477 +- gnu/packages/firmware.scm | 14 +- gnu/packages/flashing-tools.scm | 58 +- gnu/packages/flex.scm | 5 +- gnu/packages/fltk.scm | 8 +- gnu/packages/fonts.scm | 34 +- gnu/packages/fontutils.scm | 80 +- gnu/packages/forth.scm | 2 +- gnu/packages/fpga.scm | 82 +- gnu/packages/freedesktop.scm | 293 +- gnu/packages/freeipmi.scm | 2 +- gnu/packages/fribidi.scm | 2 +- gnu/packages/ftp.scm | 33 +- gnu/packages/fvwm.scm | 20 +- gnu/packages/game-development.scm | 265 +- gnu/packages/games.scm | 2101 ++++---- gnu/packages/gawk.scm | 8 +- gnu/packages/gcc.scm | 46 +- gnu/packages/gd.scm | 9 +- gnu/packages/genealogy.scm | 40 +- gnu/packages/genimage.scm | 12 +- gnu/packages/geo.scm | 655 ++- gnu/packages/gettext.scm | 44 +- gnu/packages/ghostscript.scm | 12 +- gnu/packages/gimp.scm | 81 +- gnu/packages/gkrellm.scm | 2 +- gnu/packages/gl.scm | 137 +- gnu/packages/glib.scm | 152 +- gnu/packages/gnome-xyz.scm | 72 +- gnu/packages/gnome.scm | 2041 ++++---- gnu/packages/gnu-pw-mgr.scm | 2 +- gnu/packages/gnucash.scm | 19 +- gnu/packages/gnunet.scm | 24 +- gnu/packages/gnupg.scm | 150 +- gnu/packages/gnustep.scm | 37 +- gnu/packages/gnuzilla.scm | 28 +- gnu/packages/gobby.scm | 25 +- gnu/packages/golang.scm | 673 ++- gnu/packages/gpodder.scm | 57 +- gnu/packages/gps.scm | 55 +- gnu/packages/graph.scm | 92 +- gnu/packages/graphics.scm | 178 +- gnu/packages/graphviz.scm | 87 +- gnu/packages/groff.scm | 8 +- gnu/packages/gsasl.scm | 16 +- gnu/packages/gstreamer.scm | 84 +- gnu/packages/gtk.scm | 375 +- gnu/packages/guile-wm.scm | 12 +- gnu/packages/guile-xyz.scm | 709 ++- gnu/packages/gv.scm | 2 +- gnu/packages/gxmessage.scm | 5 +- gnu/packages/hardware.scm | 79 +- gnu/packages/haskell-apps.scm | 508 +- gnu/packages/haskell-check.scm | 304 +- gnu/packages/haskell-crypto.scm | 238 +- gnu/packages/haskell-web.scm | 1237 +++-- gnu/packages/haskell-xyz.scm | 4361 +++++++--------- gnu/packages/haskell.scm | 6 +- gnu/packages/hexedit.scm | 11 +- gnu/packages/hugs.scm | 2 +- gnu/packages/hurd.scm | 31 +- gnu/packages/hyperledger.scm | 29 +- gnu/packages/i2p.scm | 5 +- gnu/packages/ibus.scm | 61 +- gnu/packages/icu4c.scm | 6 +- gnu/packages/idris.scm | 75 +- gnu/packages/image-processing.scm | 93 +- gnu/packages/image-viewers.scm | 167 +- gnu/packages/image.scm | 168 +- gnu/packages/imagemagick.scm | 8 +- gnu/packages/inklingreader.scm | 8 +- gnu/packages/inkscape.scm | 12 +- gnu/packages/installers.scm | 2 +- gnu/packages/ipfs.scm | 144 +- gnu/packages/irc.scm | 128 +- gnu/packages/jami.scm | 78 +- gnu/packages/java-compression.scm | 9 +- gnu/packages/java-graphics.scm | 10 +- gnu/packages/java-maths.scm | 2 +- gnu/packages/java.scm | 970 ++-- gnu/packages/javascript.scm | 10 +- gnu/packages/jemalloc.scm | 2 +- gnu/packages/jose.scm | 2 +- gnu/packages/jrnl.scm | 18 +- gnu/packages/julia-jll.scm | 481 +- gnu/packages/julia-xyz.scm | 682 +-- gnu/packages/julia.scm | 2 +- gnu/packages/jupyter.scm | 234 +- gnu/packages/kawa.scm | 2 +- gnu/packages/kde-frameworks.scm | 1505 +++--- gnu/packages/kde-internet.scm | 295 +- gnu/packages/kde-multimedia.scm | 469 +- gnu/packages/kde-pim.scm | 1670 +++---- gnu/packages/kde-plasma.scm | 67 +- gnu/packages/kde-systemtools.scm | 282 +- gnu/packages/kde-utils.scm | 358 +- gnu/packages/kde.scm | 692 ++- gnu/packages/kerberos.scm | 40 +- gnu/packages/key-mon.scm | 4 +- gnu/packages/kodi.scm | 10 +- gnu/packages/language.scm | 81 +- gnu/packages/lean.scm | 2 +- gnu/packages/lego.scm | 6 +- gnu/packages/less.scm | 7 +- gnu/packages/lesstif.scm | 5 +- gnu/packages/libcanberra.scm | 6 +- gnu/packages/libedit.scm | 2 +- gnu/packages/libevent.scm | 35 +- gnu/packages/libffi.scm | 13 +- gnu/packages/libftdi.scm | 2 +- gnu/packages/libidn.scm | 2 +- gnu/packages/libphidget.scm | 2 +- gnu/packages/libreoffice.scm | 218 +- gnu/packages/libusb.scm | 76 +- gnu/packages/license.scm | 48 +- gnu/packages/lighting.scm | 19 +- gnu/packages/linphone.scm | 57 +- gnu/packages/linux.scm | 466 +- gnu/packages/lirc.scm | 7 +- gnu/packages/lisp-check.scm | 12 +- gnu/packages/lisp-xyz.scm | 540 +- gnu/packages/lisp.scm | 38 +- gnu/packages/llvm.scm | 234 +- gnu/packages/logging.scm | 14 +- gnu/packages/logo.scm | 2 +- gnu/packages/lout.scm | 2 +- gnu/packages/lsof.scm | 4 +- gnu/packages/lua.scm | 84 +- gnu/packages/lxde.scm | 188 +- gnu/packages/lxqt.scm | 526 +- gnu/packages/machine-learning.scm | 405 +- gnu/packages/magic-wormhole.scm | 52 +- gnu/packages/mail.scm | 809 ++- gnu/packages/man.scm | 29 +- gnu/packages/markup.scm | 12 +- gnu/packages/mastodon.scm | 58 +- gnu/packages/mate.scm | 492 +- gnu/packages/maths.scm | 639 +-- gnu/packages/matrix.scm | 153 +- gnu/packages/maven-parent-pom.scm | 2 +- gnu/packages/maven.scm | 861 ++-- gnu/packages/mc.scm | 17 +- gnu/packages/mcrypt.scm | 6 +- gnu/packages/medical.scm | 4 +- gnu/packages/mercury.scm | 6 +- gnu/packages/messaging.scm | 552 +- gnu/packages/microcom.scm | 5 +- gnu/packages/minetest.scm | 24 +- gnu/packages/moe.scm | 4 +- gnu/packages/monitoring.scm | 74 +- gnu/packages/mono.scm | 2 +- gnu/packages/moreutils.scm | 9 +- gnu/packages/mp3.scm | 70 +- gnu/packages/mpd.scm | 147 +- gnu/packages/mpi.scm | 13 +- gnu/packages/multiprecision.scm | 28 +- gnu/packages/music.scm | 1421 +++--- gnu/packages/ncdu.scm | 2 +- gnu/packages/ncurses.scm | 8 +- gnu/packages/nettle.scm | 4 +- gnu/packages/networking.scm | 447 +- gnu/packages/nfs.scm | 8 +- gnu/packages/nickle.scm | 2 +- gnu/packages/nicotine.scm | 4 +- gnu/packages/node-xyz.scm | 9 +- gnu/packages/node.scm | 83 +- gnu/packages/noweb.scm | 2 +- gnu/packages/nss.scm | 14 +- gnu/packages/ntp.scm | 12 +- gnu/packages/nvi.scm | 5 +- gnu/packages/ocaml.scm | 781 ++- gnu/packages/ocr.scm | 4 +- gnu/packages/onc-rpc.scm | 9 +- gnu/packages/openbox.scm | 4 +- gnu/packages/opencl.scm | 32 +- gnu/packages/opencog.scm | 31 +- gnu/packages/openkinect.scm | 14 +- gnu/packages/openldap.scm | 26 +- gnu/packages/openpgp.scm | 14 +- gnu/packages/openstack.scm | 344 +- gnu/packages/orange.scm | 89 +- gnu/packages/orpheus.scm | 14 +- gnu/packages/ots.scm | 5 +- gnu/packages/package-management.scm | 231 +- gnu/packages/pantheon.scm | 3 +- gnu/packages/parallel.scm | 36 +- gnu/packages/pascal.scm | 9 +- gnu/packages/password-utils.scm | 127 +- gnu/packages/patchutils.scm | 39 +- gnu/packages/patool.scm | 38 +- gnu/packages/pciutils.scm | 3 +- gnu/packages/pcre.scm | 8 +- gnu/packages/pdf.scm | 175 +- gnu/packages/pem.scm | 2 +- gnu/packages/pep.scm | 31 +- gnu/packages/perl-check.scm | 230 +- gnu/packages/perl-compression.scm | 11 +- gnu/packages/perl-maths.scm | 3 +- gnu/packages/perl-web.scm | 11 +- gnu/packages/perl.scm | 1619 +++--- gnu/packages/perl6.scm | 43 +- gnu/packages/phabricator.scm | 5 +- gnu/packages/photo.scm | 64 +- gnu/packages/piet.scm | 13 +- gnu/packages/pkg-config.scm | 3 +- gnu/packages/plan9.scm | 3 +- gnu/packages/plotutils.scm | 44 +- gnu/packages/poedit.scm | 21 +- gnu/packages/polkit.scm | 20 +- gnu/packages/popt.scm | 2 +- gnu/packages/presentation.scm | 17 +- gnu/packages/pretty-print.scm | 23 +- gnu/packages/profiling.scm | 41 +- gnu/packages/protobuf.scm | 52 +- gnu/packages/pulseaudio.scm | 131 +- gnu/packages/pumpio.scm | 4 +- gnu/packages/pure.scm | 4 +- gnu/packages/purescript.scm | 149 +- gnu/packages/python-build.scm | 8 +- gnu/packages/python-check.scm | 327 +- gnu/packages/python-compression.scm | 94 +- gnu/packages/python-crypto.scm | 220 +- gnu/packages/python-science.scm | 278 +- gnu/packages/python-web.scm | 1295 ++--- gnu/packages/python-xyz.scm | 3876 ++++++-------- gnu/packages/python.scm | 46 +- gnu/packages/qt.scm | 336 +- gnu/packages/racket.scm | 8 +- gnu/packages/radio.scm | 542 +- gnu/packages/rails.scm | 179 +- gnu/packages/ratpoison.scm | 3 +- gnu/packages/rcm.scm | 3 +- gnu/packages/rdesktop.scm | 25 +- gnu/packages/rdf.scm | 70 +- gnu/packages/re2c.scm | 2 +- gnu/packages/readline.scm | 8 +- gnu/packages/rednotebook.scm | 6 +- gnu/packages/robotics.scm | 35 +- gnu/packages/rocm.scm | 23 +- gnu/packages/rpc.scm | 35 +- gnu/packages/rpm.scm | 46 +- gnu/packages/rrdtool.scm | 13 +- gnu/packages/rsync.scm | 13 +- gnu/packages/ruby.scm | 1508 +++--- gnu/packages/rust-apps.scm | 52 +- gnu/packages/sagemath.scm | 46 +- gnu/packages/samba.scm | 74 +- gnu/packages/sawfish.scm | 25 +- gnu/packages/scanner.scm | 6 +- gnu/packages/scheme.scm | 74 +- gnu/packages/screen.scm | 3 +- gnu/packages/scribus.scm | 4 +- gnu/packages/sdl.scm | 69 +- gnu/packages/search.scm | 136 +- gnu/packages/security-token.scm | 176 +- gnu/packages/selinux.scm | 11 +- gnu/packages/sequoia.scm | 21 +- gnu/packages/serialization.scm | 35 +- gnu/packages/serveez.scm | 4 +- gnu/packages/shells.scm | 80 +- gnu/packages/shellutils.scm | 45 +- gnu/packages/simh.scm | 2 +- gnu/packages/simulation.scm | 46 +- gnu/packages/skarnet.scm | 24 +- gnu/packages/skribilo.scm | 15 +- gnu/packages/slang.scm | 11 +- gnu/packages/smalltalk.scm | 34 +- gnu/packages/sml.scm | 6 +- gnu/packages/solidity.scm | 4 +- gnu/packages/speech.scm | 49 +- gnu/packages/sphinx.scm | 223 +- gnu/packages/spice.scm | 110 +- gnu/packages/spreadsheet.scm | 16 +- gnu/packages/sqlite.scm | 2 +- gnu/packages/ssh.scm | 125 +- gnu/packages/sssd.scm | 87 +- gnu/packages/stalonetray.scm | 2 +- gnu/packages/statistics.scm | 1221 ++--- gnu/packages/stb.scm | 2 +- gnu/packages/stenography.scm | 20 +- gnu/packages/storage.scm | 6 +- gnu/packages/suckless.scm | 47 +- gnu/packages/swig.scm | 12 +- gnu/packages/sync.scm | 99 +- gnu/packages/syncthing.scm | 70 +- gnu/packages/syndication.scm | 148 +- gnu/packages/synergy.scm | 2 +- gnu/packages/task-management.scm | 22 +- gnu/packages/task-runners.scm | 2 +- gnu/packages/tcl.scm | 40 +- gnu/packages/telegram.scm | 46 +- gnu/packages/telephony.scm | 135 +- gnu/packages/terminals.scm | 108 +- gnu/packages/tex.scm | 621 ++- gnu/packages/texinfo.scm | 18 +- gnu/packages/text-editors.scm | 113 +- gnu/packages/textutils.scm | 34 +- gnu/packages/time.scm | 52 +- gnu/packages/tls.scm | 123 +- gnu/packages/tmux.scm | 16 +- gnu/packages/tor.scm | 93 +- gnu/packages/toys.scm | 19 +- gnu/packages/tryton.scm | 1109 ++-- gnu/packages/tv.scm | 26 +- gnu/packages/uglifyjs.scm | 3 +- gnu/packages/upnp.scm | 2 +- gnu/packages/usb-modeswitch.scm | 9 +- gnu/packages/uucp.scm | 23 +- gnu/packages/valgrind.scm | 2 +- gnu/packages/version-control.scm | 279 +- gnu/packages/video.scm | 801 ++- gnu/packages/vim.scm | 27 +- gnu/packages/virtualization.scm | 178 +- gnu/packages/vlang.scm | 2 +- gnu/packages/vnc.scm | 40 +- gnu/packages/vpn.scm | 174 +- gnu/packages/vulkan.scm | 52 +- gnu/packages/w3m.scm | 14 +- gnu/packages/wdiff.scm | 6 +- gnu/packages/web-browsers.scm | 102 +- gnu/packages/web.scm | 1450 +++--- gnu/packages/webkit.scm | 14 +- gnu/packages/wget.scm | 21 +- gnu/packages/wine.scm | 33 +- gnu/packages/wireservice.scm | 12 +- gnu/packages/wm.scm | 613 +-- gnu/packages/wordnet.scm | 3 +- gnu/packages/wv.scm | 3 +- gnu/packages/wxwidgets.scm | 30 +- gnu/packages/xdisorg.scm | 448 +- gnu/packages/xfce.scm | 449 +- gnu/packages/xfig.scm | 6 +- gnu/packages/xiph.scm | 81 +- gnu/packages/xml.scm | 260 +- gnu/packages/xnee.scm | 14 +- gnu/packages/xorg.scm | 1070 ++-- gnu/packages/zig.scm | 6 +- gnu/packages/zile.scm | 4 +- gnu/packages/zwave.scm | 9 +- 460 files changed, 37971 insertions(+), 50054 deletions(-) (limited to 'gnu/packages/python-compression.scm') diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm index f3bd094c92..02159cbfcc 100644 --- a/gnu/packages/accessibility.scm +++ b/gnu/packages/accessibility.scm @@ -223,19 +223,17 @@ (define-public florence "--without-docs" "--with-notification"))) (inputs - `(("libxml2" ,libxml2) - ("libglade" ,libglade) - ("librsvg" ,librsvg) - ("gstreamer" ,gstreamer) - ("cairo" ,cairo) - ("gtk+" ,gtk+) - ("libxtst" ,libxtst) - ("libxcomposite" ,libxcomposite) - ("libnotify" ,libnotify))) + (list libxml2 + libglade + librsvg + gstreamer + cairo + gtk+ + libxtst + libxcomposite + libnotify)) (native-inputs - `(("gettext-minimal" ,gettext-minimal) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list gettext-minimal intltool pkg-config)) (home-page "http://florence.sourceforge.net/") (synopsis "Extensible, scalable virtual keyboard for X11") (description @@ -268,9 +266,9 @@ (define-public footswitch "14pyzc4ws1mj859xs9n4x83wzxxvd3bh5bdxzr6nv267xwx1mq68")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("hidapi" ,hidapi))) + (list hidapi)) (arguments `(#:tests? #f ; no tests #:make-flags (list (string-append "CC=" ,(cc-for-target))) diff --git a/gnu/packages/acl.scm b/gnu/packages/acl.scm index b299e7d284..da6dead3c2 100644 --- a/gnu/packages/acl.scm +++ b/gnu/packages/acl.scm @@ -86,7 +86,7 @@ (define-public acl ((".*test/cp\\.test.*") "") ((".*test/setfacl-X\\.test.*") "")) #t))))) - (inputs `(("attr" ,attr))) + (inputs (list attr)) (native-inputs `(("gettext" ,gettext-minimal) ("perl" ,perl))) @@ -125,8 +125,8 @@ (define-public python-pylibacl (when tests? (add-installed-pythonpath inputs outputs) (invoke "pytest" "tests"))))))) - (inputs `(("acl" ,acl))) - (native-inputs `(("python-pytest" ,python-pytest))) + (inputs (list acl)) + (native-inputs (list python-pytest)) (home-page "https://pylibacl.k1024.org/") (synopsis "POSIX.1e @acronym{ACLs, access control lists} for Python") (description diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm index 8f8b68d80d..a3bba245ec 100644 --- a/gnu/packages/ada.scm +++ b/gnu/packages/ada.scm @@ -134,7 +134,7 @@ (define-public ada/ed (find-files "share" "."))) #t))))))) (native-inputs - `(("sed" ,sed))) + (list sed)) (home-page (string-append "https://web.archive.org/web/20140902150609/" "http://www2.informatik.uni-stuttgart.de/iste/ps/" "ada-software/html/dos_ada.html")) @@ -167,10 +167,7 @@ (define-public python2-langkit (file-name (string-append name "-" version "-checkout")))) (build-system python-build-system) (propagated-inputs - `(("python2-docutils" ,python2-docutils) - ("python2-enum34" ,python2-enum34) - ("python2-funcy" ,python2-funcy) - ("python2-mako" ,python2-mako))) + (list python2-docutils python2-enum34 python2-funcy python2-mako)) (arguments `(#:python ,python-2 #:tests? #f)) ; Tests would requite gprbuild (Ada). diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index afb3afac75..4ed1f1abf3 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -180,13 +180,9 @@ (define-public ktsuss "supath=/run/setuid-programs/su")) #t))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("glib" ,glib) - ("gtk+" ,gtk+-2))) + (list glib gtk+-2)) (synopsis "Graphical front end for @command{su}") (description "Ktsuss stands for ``Keep the @command{su} simple, stupid''. @@ -208,8 +204,7 @@ (define-public aide (base32 "15xp47sz7kk1ciffw3f5xw2jg2mb2lqrbr3q6p4bkbz5dap9iy8p")))) (build-system gnu-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex))) + (list bison flex)) (inputs `(("libgcrypt" ,libgcrypt) ("libgpg-error" ,libgpg-error) @@ -244,10 +239,9 @@ (define-public progress (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("which" ,which))) + (list pkg-config which)) (inputs - `(("ncurses" ,ncurses))) + (list ncurses)) (arguments `(#:tests? #f ; no test suite #:make-flags @@ -292,17 +286,15 @@ (define-public shepherd '(#:configure-flags '("--localstatedir=/var") #:make-flags '("GUILE_AUTO_COMPILE=0"))) (native-inputs - `(("pkg-config" ,pkg-config) - - ;; This is the Guile we use as a cross-compiler... - ("guile" ,guile-3.0))) + (list pkg-config + ;; This is the Guile we use as a cross-compiler... + guile-3.0)) (inputs ;; ... and this is the one that appears in shebangs when cross-compiling. - `(("guile" ,guile-3.0) - - ;; The 'shepherd' command uses Readline when used interactively. It's - ;; an unusual use case though, so we don't propagate it. - ("guile-readline" ,guile-readline))) + (list guile-3.0 + ;; The 'shepherd' command uses Readline when used interactively. It's + ;; an unusual use case though, so we don't propagate it. + guile-readline)) (synopsis "System service manager") (description "The GNU Shepherd is a daemon-managing daemon, meaning that it supervises @@ -317,22 +309,18 @@ (define-public guile2.2-shepherd (inherit shepherd) (name "guile2.2-shepherd") (native-inputs - `(("pkg-config" ,pkg-config) - ("guile" ,guile-2.2))) + (list pkg-config guile-2.2)) (inputs - `(("guile" ,guile-2.2) - ("guile2.2-readline" ,guile2.2-readline))))) + (list guile-2.2 guile2.2-readline)))) (define-public guile2.0-shepherd (package (inherit shepherd) (name "guile2.0-shepherd") (native-inputs - `(("help2man" ,help2man) - ("pkg-config" ,pkg-config) - ("guile" ,guile-2.0))) + (list help2man pkg-config guile-2.0)) (inputs - `(("guile" ,guile-2.0))) + (list guile-2.0)) (arguments `(#:phases (modify-phases %standard-phases @@ -409,8 +397,7 @@ (define-public cloud-utils ,(dirname (which "readlink")))))) #t))))) (inputs - `(("python" ,python) - ("util-linux" ,util-linux))) ; contains sfdisk for growpart + (list python util-linux)) ; contains sfdisk for growpart (home-page "https://launchpad.net/cloud-utils") (synopsis "Set of utilities for cloud computing environments") (description @@ -656,7 +643,7 @@ (define-public htop (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("ncurses" ,ncurses))) + (list ncurses)) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -704,7 +691,7 @@ (define-public bpytop (base32 "1fwmiwvs8ax9az3hbp1p79x6m3wq73pn3vkbhcg9jvps4wv8wcwb")))) (build-system python-build-system) (inputs - `(("python-psutil" ,python-psutil))) + (list python-psutil)) (arguments `(#:phases (modify-phases %standard-phases @@ -931,7 +918,7 @@ (define-public mingetty (mkdir-p man8)) #t))) #:tests? #f)) ; no tests - (inputs `(("shadow" ,shadow))) + (inputs (list shadow)) (home-page "https://sourceforge.net/projects/mingetty") (synopsis "Getty for the text console") @@ -980,8 +967,7 @@ (define-public net-base (map (cut string-append etc "/" <>) '("services" "protocols" "rpc"))) #t)))) - (native-inputs `(("tar" ,tar) - ("xz" ,xz))) + (native-inputs (list tar xz)) (synopsis "IANA protocol, port, and RPC number assignments") (description "This package provides the /etc/services, /etc/protocols, and /etc/rpc @@ -1056,9 +1042,8 @@ (define-public netcat-openbsd (install-file "nc.1" man) (install-file "debian/copyright" doc) (copy-recursively "debian/examples" examples))))))) - (inputs `(("libbsd" ,libbsd))) - (native-inputs `(("pkg-config" ,pkg-config) - ("quilt" ,quilt))) + (inputs (list libbsd)) + (native-inputs (list pkg-config quilt)) (home-page "https://packages.debian.org/sid/netcat-openbsd") (synopsis "Read and write data over TCP/IP") (description @@ -1140,7 +1125,7 @@ (define-public prips (let ((out (assoc-ref outputs "out"))) (install-file "prips" (string-append out "/bin")))))))) - (native-inputs `(("perl-test-harness" ,perl-test-harness))) + (native-inputs (list perl-test-harness)) (synopsis "Tool that prints the IP addresses in a given range") (description "Prips can be used to print all of the IP addresses in a given range. This allows the enhancement of tools only work @@ -1161,8 +1146,7 @@ (define-public alive "053hfp7s66lnilm1ii4jrjmy44wpa2cwwh6f0sl8cyz0mm813x4b")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("alive_cv_nice_ping=yes"))) - (inputs `(("guile" ,guile-2.0) - ("inetutils" ,inetutils))) + (inputs (list guile-2.0 inetutils)) (home-page "https://www.gnu.org/software/alive/") (synopsis "Autologin and keep-alive daemon") (description @@ -1309,8 +1293,7 @@ (define-public isc-dhcp #t)))))) (native-inputs - `(("perl" ,perl) - ("file" ,file))) + (list perl file)) (inputs `(("inetutils" ,inetutils) ;; TODO(core-updates): simply make this unconditional @@ -1361,12 +1344,12 @@ (define-public radvd (base32 "1df827m3vkjq2bcs5y9wg2cygvpdwl8ppl446qqhyym584gz54nl")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("bison" ,bison) - ("check" ,check) - ("flex" ,flex) - ("pkg-config" ,pkg-config))) + (list autoconf + automake + bison + check + flex + pkg-config)) (arguments `(#:configure-flags '("--with-check"))) (home-page "https://radvd.litech.org/") @@ -1391,8 +1374,7 @@ (define-public libpcap "1m5x26vlbymp90k1qh0w3nj2nxzyvfrmfmwpj17k81dgri55ya7d")))) (build-system gnu-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex))) + (list bison flex)) (arguments ;; There are some tests in testprogs/, but no automated test suite. `(#:tests? #f @@ -1426,9 +1408,8 @@ (define-public tcpdump (base32 "1ghfs5gifzrk3813zf9zalfbjs70wg6llz6q31k180r7zf2nkcvr")))) (build-system gnu-build-system) - (inputs `(("libpcap" ,libpcap) - ("openssl" ,openssl))) - (native-inputs `(("perl" ,perl))) ; for tests + (inputs (list libpcap openssl)) + (native-inputs (list perl)) ; for tests (home-page "https://www.tcpdump.org/") (synopsis "Network packet analyzer") (description @@ -1451,11 +1432,9 @@ (define-public jnettop "1855np7c4b0bqzhf1l1dyzxb90fpnvrirdisajhci5am6als31z9")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("glib" ,glib) - ("ncurses" ,ncurses) - ("libpcap" ,libpcap))) + (list glib ncurses libpcap)) (home-page "https://web.archive.org/web/20160703195221/http://jnettop.kubs.info/wiki/") (synopsis "Visualize network traffic by bandwidth use") @@ -1524,26 +1503,26 @@ (define-public clusterssh (find-files "." ".*"))) #t)))))) (native-inputs - `(("perl-cpan-changes" ,perl-cpan-changes) - ("perl-file-slurp" ,perl-file-slurp) - ("perl-file-which" ,perl-file-which) - ("perl-module-build" ,perl-module-build) - ("perl-readonly" ,perl-readonly) - ("perl-test-differences" ,perl-test-differences) - ("perl-test-distmanifest" ,perl-test-distmanifest) - ("perl-test-perltidy" ,perl-test-perltidy) - ("perl-test-pod" ,perl-test-pod) - ("perl-test-pod-coverage" ,perl-test-pod-coverage) - ("perl-test-trap" ,perl-test-trap) - ("perltidy" ,perltidy))) + (list perl-cpan-changes + perl-file-slurp + perl-file-which + perl-module-build + perl-readonly + perl-test-differences + perl-test-distmanifest + perl-test-perltidy + perl-test-pod + perl-test-pod-coverage + perl-test-trap + perltidy)) (inputs - `(("perl-exception-class" ,perl-exception-class) - ("perl-sort-naturally" ,perl-sort-naturally) - ("perl-tk" ,perl-tk) - ("perl-try-tiny" ,perl-try-tiny) - ("perl-x11-protocol" ,perl-x11-protocol) - ("perl-x11-protocol-other" ,perl-x11-protocol-other) - ("xterm" ,xterm))) + (list perl-exception-class + perl-sort-naturally + perl-tk + perl-try-tiny + perl-x11-protocol + perl-x11-protocol-other + xterm)) ;; The clusterssh.sourceforge.net address requires login to view (home-page "https://sourceforge.net/projects/clusterssh/") (synopsis "Secure concurrent multi-server terminal control") @@ -1589,10 +1568,7 @@ (define-public realmd ("pkg-config" ,pkg-config) ("python" ,python))) (inputs - `(("glib" ,glib) - ("mit-krb5" ,mit-krb5) - ("openldap" ,openldap) - ("polkit" ,polkit))) + (list glib mit-krb5 openldap polkit)) (synopsis "DBus service for network authentication") (description "This package provides an on demand system DBus service. It allows callers to configure network authentication and domain membership @@ -1633,9 +1609,7 @@ (define-public rename (find-files "." ".*"))) #t)))))) (native-inputs - `(("perl-module-build" ,perl-module-build) - ("perl-test-pod" ,perl-test-pod) - ("perl-test-pod-coverage" ,perl-test-pod-coverage))) + (list perl-module-build perl-test-pod perl-test-pod-coverage)) (home-page "https://metacpan.org/pod/distribution/File-Rename/rename.PL") (synopsis "Perl extension for renaming multiple files") (description @@ -1717,9 +1691,7 @@ (define-public rottlog (add-after 'install 'install-info (lambda _ (invoke "make" "install-info")))))) - (native-inputs `(("texinfo" ,texinfo) - ("automake" ,automake) - ("util-linux" ,util-linux))) ; for 'cal' + (native-inputs (list texinfo automake util-linux)) ; for 'cal' (inputs `(("coreutils*" ,coreutils) ("mailutils" ,mailutils))) (home-page "https://www.gnu.org/software/rottlog/") @@ -1808,7 +1780,7 @@ (define-public sudo ;; the chroot's /etc/passwd doesn't have it. Turn off the tests. #:tests? #f)) (native-inputs - `(("groff" ,groff))) + (list groff)) (inputs `(("coreutils" ,coreutils) ,@(if (hurd-target?) @@ -1872,7 +1844,7 @@ (define-public opendoas (list (string-append "CC=" ,(cc-for-target))) #:tests? #f)) ; no test suite (native-inputs - `(("bison" ,bison))) + (list bison)) (home-page "https://github.com/Duncaen/OpenDoas") (synopsis "Portable version of OpenBSD's doas command") (description "Doas is a minimal replacement for the venerable sudo. It was @@ -1967,11 +1939,9 @@ (define (copy-man-page target) "/lib")) #:tests? #f)) (inputs - `(("readline" ,readline) - ("libnl" ,libnl) - ("openssl" ,openssl))) + (list readline libnl openssl)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://w1.fi/wpa_supplicant/") (synopsis "Connecting to WPA and WPA2-protected wireless networks") (description @@ -1992,8 +1962,8 @@ (define (copy-man-page target) (define-public wpa-supplicant (package (inherit wpa-supplicant-minimal) (name "wpa-supplicant") - (inputs `(("dbus" ,dbus) - ,@(package-inputs wpa-supplicant-minimal))) + (inputs (modify-inputs (package-inputs wpa-supplicant-minimal) + (prepend dbus))) (arguments (substitute-keyword-arguments (package-arguments wpa-supplicant-minimal) ((#:phases phases) @@ -2019,14 +1989,12 @@ (define-public wpa-supplicant-gui (package (inherit wpa-supplicant) (name "wpa-supplicant-gui") - (inputs `(("qtbase" ,qtbase-5) - ("qtsvg" ,qtsvg) - ,@(package-inputs wpa-supplicant))) + (inputs (modify-inputs (package-inputs wpa-supplicant) + (prepend qtbase-5 qtsvg))) (native-inputs ;; For icons. - `(("imagemagick" ,imagemagick) - ("inkscape" ,inkscape) - ,@(package-native-inputs wpa-supplicant))) + (modify-inputs (package-native-inputs wpa-supplicant) + (prepend imagemagick inkscape))) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'chdir @@ -2118,11 +2086,10 @@ (define (copy-man-page target) (string-append "LIBDIR=" (assoc-ref %outputs "out") "/lib")) #:tests? #f)) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) ;; There's an optional dependency on SQLite. - (inputs `(("openssl" ,openssl) - ("libnl" ,libnl))) + (inputs (list openssl libnl)) (home-page "https://w1.fi/hostapd/") (synopsis "Daemon for Wi-Fi access points and authentication servers") (description @@ -2217,8 +2184,7 @@ (define-public acpica (base32 "06wsrl1118sl9z76p9sh53zvzv5hpm82qks896d8slx5dgnzrrll")))) (build-system gnu-build-system) - (native-inputs `(("flex" ,flex) - ("bison" ,bison))) + (native-inputs (list flex bison)) (arguments `(#:make-flags (list (string-append "PREFIX=" %output) (string-append "CC=" ,(cc-for-target)) @@ -2252,8 +2218,7 @@ (define-public s-tui (base32 "1l2ik5iwmb8vxa2aqdy62zfy3zfzbpq5a0pgpka2vvlw9ivpqy5p")))) (build-system python-build-system) (inputs - `(("python-psutil" ,python-psutil) - ("python-urwid" ,python-urwid))) + (list python-psutil python-urwid)) (home-page "https://github.com/amanusk/s-tui") (synopsis "Interactive terminal stress test and monitoring tool") (description @@ -2274,8 +2239,7 @@ (define-public stress "09shpd85g8dvpiw0mnwykss676g0s7lbi8ab37xjinb5lfff960p")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (home-page "https://packages.debian.org/sid/stress") (synopsis "Impose load on and stress test a computer system") (description @@ -2305,9 +2269,7 @@ (define-public detox "116bgpbkh3c96h6vq0880rmnpb5kbnnlvvkpsrcib6928bj8lfvi")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("flex" ,flex))) + (list autoconf automake flex)) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'delete-configure @@ -2497,7 +2459,7 @@ (define-public smartmontools (base32 "1mlc25sd5rgj5xmzcllci47inmfdw7cp185fday6hc9rwqkqmnaw")))) (build-system gnu-build-system) - (inputs `(("libcap-ng" ,libcap-ng))) + (inputs (list libcap-ng)) (home-page "https://www.smartmontools.org/") (synopsis "S.M.A.R.T. harddisk control and monitoring tools") (description @@ -2522,8 +2484,7 @@ (define-public fdupes (base32 "1g9p50xhi2sp0hqxml4w2k0kq9jv988q2yxm347z5349dlxvap6d")))) (build-system gnu-build-system) (inputs - `(("ncurses" ,ncurses) - ("pcre2" ,pcre2))) + (list ncurses pcre2)) (home-page "https://github.com/adrianlopezroche/fdupes") (synopsis "Identify duplicate files") (description @@ -2653,27 +2614,24 @@ (define bin (string-append (assoc-ref outputs "out") "/bin")) ;; devel/test/utils/shippable/shippable.sh. (invoke "ansible-test" "units" "-v"))))))) (native-inputs - `(("openssh" ,openssh) - ("openssl" ,openssl) - ("python-mock" ,python-mock) - ("python-pycrypto" ,python-pycrypto) - ("python-pytest" ,python-pytest) - ("python-pytest-forked" ,python-pytest-forked) - ("python-pytest-mock" ,python-pytest-mock) - ("python-pytest-xdist" ,python-pytest-xdist) - ("python-pytz" ,python-pytz))) + (list openssh + openssl + python-mock + python-pycrypto + python-pytest + python-pytest-forked + python-pytest-mock + python-pytest-xdist + python-pytz)) (inputs ;optional dependencies captured in wrap scripts - `(("libselinux" ,libselinux) - ("python-paramiko" ,python-paramiko) - ("python-passlib" ,python-passlib) - ("python-pexpect" ,python-pexpect) - ("sshpass" ,sshpass))) + (list libselinux python-paramiko python-passlib python-pexpect + sshpass)) (propagated-inputs ;core dependencies listed in egg-info/requires.txt - `(("python-cryptography" ,python-cryptography) - ("python-jinja2" ,python-jinja2) - ("python-pyyaml" ,python-pyyaml) - ("python-packaging" ,python-packaging) ;for version number parsing - ("python-resolvelib" ,python-resolvelib-0.5))) + (list python-cryptography + python-jinja2 + python-pyyaml + python-packaging ;for version number parsing + python-resolvelib-0.5)) (home-page "https://www.ansible.com/") (synopsis "Radically simple IT automation") (description "Ansible aims to be a radically simple IT automation system. @@ -2709,7 +2667,7 @@ (define-public ansible (base32 "0aab9id6dqfw2111r731c7y1p77dpzczynmgl4d989p3a7n54z0b")))) (build-system python-build-system) (propagated-inputs - `(("ansible-core" ,ansible-core))) + (list ansible-core)) ;; The Ansible collections are found by ansible-core via PYTHONPATH; the ;; following search path ensures that they are found even when Python is ;; not present in the profile. @@ -2749,18 +2707,17 @@ (define-public debops "debops-debops-defaults-fall-back-to-less.patch")))) (build-system python-build-system) (native-inputs - `(("git" ,git))) + (list git)) (inputs - `(("ansible" ,ansible) - ("encfs" ,encfs) - ("fuse" ,fuse) - ("util-linux" ,util-linux) ;; for umount - ("findutils" ,findutils) - ("gnupg" ,gnupg) - ("which" ,which))) + (list ansible + encfs + fuse + util-linux ;; for umount + findutils + gnupg + which)) (propagated-inputs - `(("python-future" ,python-future) - ("python-distro" ,python-distro))) + (list python-future python-distro)) (arguments `(#:tests? #f #:phases @@ -2911,8 +2868,7 @@ (define-public autojump (base32 "1rgpsh70manr2dydna9da4x7p8ahii7dgdgwir5fka340n1wrcws")))) (build-system gnu-build-system) (native-inputs ; for tests - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + (list python-mock python-pytest)) (inputs `(("python" ,python-wrapper))) (arguments @@ -2985,8 +2941,7 @@ (define-public iftop "15sgkdyijb7vbxpxjavh5qm5nvyii3fqcg9mzvw7fx8s6zmfwczp")))) (build-system gnu-build-system) (inputs - `(("libpcap" ,libpcap) - ("ncurses" ,ncurses))) + (list libpcap ncurses)) (arguments ;; Fix build failure with GCC 10 '(#:configure-flags '("CFLAGS=-O2 -g -fcommon"))) @@ -3020,8 +2975,7 @@ (define-public munge "")) #t)))) (inputs - `(("openssl" ,openssl) - ("libgcrypt" ,libgcrypt))) + (list openssl libgcrypt)) (build-system gnu-build-system) (arguments '(#:configure-flags @@ -3256,16 +3210,10 @@ (define-public thefuck (("settings\\.init\\(\\)") "")) (invoke "py.test" "-v")))))) (propagated-inputs - `(("python-colorama" ,python-colorama) - ("python-decorator" ,python-decorator) - ("python-psutil" ,python-psutil) - ("python-pyte" ,python-pyte) - ("python-six" ,python-six))) + (list python-colorama python-decorator python-psutil python-pyte + python-six)) (native-inputs - `(("go" ,go) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) + (list go python-mock python-pytest python-pytest-mock)) (home-page "https://github.com/nvbn/thefuck") (synopsis "Correct mistyped console command") (description @@ -3330,7 +3278,7 @@ (define-public cbatticon ("gettext" ,gettext-minimal) ("libnotify" ,libnotify))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Lightweight battery icon for the system tray") (description "cbatticon is a lightweight battery icon that displays the status of your battery in the system tray.") @@ -3361,9 +3309,9 @@ (define-public interrobang #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))))) (inputs - `(("libx11" ,libx11))) + (list libx11)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Scriptable launcher menu") (description "Interrobang is a scriptable launcher menu with a customizable shortcut syntax and completion options.") @@ -3400,11 +3348,9 @@ (define-public pam-krb5 (("pam-util/vector\n") "")) #t))))) (inputs - `(("linux-pam" ,linux-pam) - ("mit-krb5" ,mit-krb5))) + (list linux-pam mit-krb5)) (native-inputs - `(("perl" ,perl) - ("perl-test-pod" ,perl-test-pod))) ; required for tests + (list perl perl-test-pod)) ; required for tests (synopsis "Kerberos PAM module") (description "Pam-krb5 is a Kerberos PAM module for either MIT Kerberos or Heimdal. @@ -3481,10 +3427,9 @@ (define-public sunxi-tools (source (sunxi-tools-source version)) (native-inputs - `(("sunxi-target-tools" ,sunxi-target-tools) - ("pkg-config" ,pkg-config))) + (list sunxi-target-tools pkg-config)) (inputs - `(("libusb" ,libusb))) + (list libusb)) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests exist @@ -3605,18 +3550,16 @@ (define-public igt-gpu-tools (arguments `(#:tests? #f)) ; many of the tests try to load kernel modules (inputs - `(("cairo" ,cairo) - ("elfutils" ,elfutils) ; libdw - ("eudev" ,eudev) - ("kmod" ,kmod) - ("libdrm" ,libdrm) - ("libpciaccess" ,libpciaccess) - ("libunwind" ,libunwind) - ("procps" ,procps))) + (list cairo + elfutils ; libdw + eudev + kmod + libdrm + libpciaccess + libunwind + procps)) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("pkg-config" ,pkg-config))) + (list bison flex pkg-config)) (home-page "https://gitlab.freedesktop.org/drm/igt-gpu-tools") (synopsis "Tools for development and testing of the Intel DRM driver") (description "IGT GPU Tools is a collection of tools for development and @@ -3704,11 +3647,7 @@ (define-public screenfetch (search-input-file %build-inputs "/bin/bash")))))))) (inputs - `(("bash" ,bash) - ("bc" ,bc) - ("scrot" ,scrot) - ("xdpyinfo" ,xdpyinfo) - ("xprop" ,xprop))) + (list bash bc scrot xdpyinfo xprop)) (home-page "https://github.com/KittyKatt/screenFetch") (synopsis "System information script") (description "Bash screenshot information tool which can be used to @@ -3781,7 +3720,7 @@ (define-public pfetch (base32 "1md40av6i3xvvwig5jzhy4kf3s5sgxxk35r0vcyrjd8qyndk927l")))) (build-system trivial-build-system) - (inputs `(("bash" ,bash))) + (inputs (list bash)) (arguments `(#:modules ((guix build utils)) #:builder @@ -3817,10 +3756,9 @@ (define-public nnn (base32 "0lqn7pyy8c1vy29vn8ad4x23cw67cy1d21ghns6f3w9a1h7kyjp0")))) (build-system gnu-build-system) (inputs - `(("ncurses" ,ncurses) - ("readline" ,readline))) + (list ncurses readline)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (arguments `(#:tests? #f ; no tests #:phases @@ -3869,18 +3807,14 @@ (define-public thermald (lambda _ (setenv "NO_CONFIGURE" "yet")))))) (native-inputs - `(("autoconf" ,autoconf) - ("autoconf-archive" ,autoconf-archive) - ("automake" ,automake) - ("glib" ,glib "bin") ; for glib-genmarshal, etc. - ("gtk-doc" ,gtk-doc) - ("pkg-config" ,pkg-config))) + (list autoconf + autoconf-archive + automake + `(,glib "bin") ; for glib-genmarshal, etc. + gtk-doc + pkg-config)) (inputs - `(("dbus-glib" ,dbus-glib) - ("libevdev" ,libevdev) - ("libxml2" ,libxml2) - ("upower" ,upower) - ("xz" ,xz))) + (list dbus-glib libevdev libxml2 upower xz)) (home-page "https://01.org/linux-thermal-daemon/") (synopsis "CPU scaling for thermal management") (description "The Linux Thermal Daemon helps monitor and control temperature @@ -3904,7 +3838,7 @@ (define-public masscan (base32 "0q0c7bsf0pbl8napry1qyg0gl4pd8wn872h4mz9b56dx4rx90vqg")))) (build-system gnu-build-system) (inputs - `(("libpcap" ,libpcap))) + (list libpcap)) (arguments `(#:test-target "regress" #:make-flags @@ -4052,7 +3986,7 @@ (define-public inxi-minimal ("perl" ,perl) ("procps" ,procps))) (native-inputs - `(("gzip" ,gzip))) + (list gzip)) (arguments `(#:modules ((guix build utils)) #:builder @@ -4158,11 +4092,9 @@ (define-public pscircle (base32 "1sm99423hh90kr4wdjqi9sdrrpk65j2vz2hzj65zcxfxyr6khjci")))) (build-system meson-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("cairo" ,cairo) - ("libpng" ,libpng) - ("libx11" ,libx11))) + (list cairo libpng libx11)) (home-page "https://gitlab.com/mildlyparallel/pscircle") (synopsis "Visualize Linux processes in a form of radial tree") (description @@ -4196,15 +4128,12 @@ (define-public python-pyudev (("= find_library") "= ")) #t)))))) (inputs - `(("eudev" ,eudev))) + (list eudev)) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (native-inputs - `(("python-docutils" ,python-docutils) - ("python-hypothesis" ,python-hypothesis) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-sphinx" ,python-sphinx))) + (list python-docutils python-hypothesis python-mock python-pytest + python-sphinx)) (home-page "https://pyudev.readthedocs.io/") (synopsis "Python udev binding") (description "This package provides @code{udev} bindings for Python.") @@ -4225,7 +4154,7 @@ (define-public vmtouch (base32 "08da6apzfkfjwasn4dxrlfxqfx7arl28apdzac5nvm0fhvws0dxk")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + (list perl)) (arguments `(#:tests? #f ; no tests #:make-flags @@ -4263,15 +4192,14 @@ (define-public solaar (lambda _ (setenv "PYTHONPATH" "lib")))))) (propagated-inputs - `(("python-pygobject" ,python-pygobject) - ("python-pyudev" ,python-pyudev) - - ;; For GUI. - ("python-pyyaml" ,python-pyyaml) - ("python-psutil" ,python-psutil) - ("python-xlib" ,python-xlib) - ("gtk+" ,gtk+) - ("python-pygobject" ,python-pygobject))) + (list python-pygobject + python-pyudev + ;; For GUI. + python-pyyaml + python-psutil + python-xlib + gtk+ + python-pygobject)) (home-page "https://pwr-solaar.github.io/Solaar/") (synopsis "Linux devices manager for the Logitech Unifying Receiver") (description "This package provides tools to manage clients of the @@ -4369,7 +4297,7 @@ (define-public ngrep "1x2fyd7wdqlj1r76ilal06cl2wmbz0ws6i3ys204sbjh1cj6dcl7")))) (build-system gnu-build-system) (inputs - `(("libpcap" ,libpcap))) + (list libpcap)) (arguments `(#:tests? #f ;; No tests. #:configure-flags (list (string-append "--with-pcap-includes=" @@ -4399,8 +4327,7 @@ (define-public pam-mount (base32 "0832nh2qf9pisgwnbgx6hkylx5d7i416l19y3ly4ifv7k1p7mxqa")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list perl pkg-config)) (inputs `(("cryptsetup" ,cryptsetup) ("libhx" ,libhx) @@ -4463,9 +4390,7 @@ (define-public jc (base32 "0rwvyyrdnw43pixp8h51rncq2inc9pbbj1j2191y5si00pjw34zr")))) (build-system python-build-system) (propagated-inputs - `(("python-pygments" ,python-pygments) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-xmltodict" ,python-xmltodict))) + (list python-pygments python-ruamel.yaml python-xmltodict)) (home-page "https://github.com/kellyjonbrazil/jc") (synopsis "Convert the output of command-line tools to JSON") (description "@code{jc} JSONifies the output of many CLI tools and @@ -4487,7 +4412,7 @@ (define-public jtbl "19i21fqz2m40cds9pb17brjxkczqagmx2f7mfb0xdvbygaply5wz")))) (build-system python-build-system) (inputs - `(("python-tabulate" ,python-tabulate))) + (list python-tabulate)) (home-page "https://github.com/kellyjonbrazil/jtbl") (synopsis "Command-line tool to print JSON data as a table in the terminal") (description "@code{jtbl} accepts piped JSON data from stdin and outputs a @@ -4585,10 +4510,9 @@ (define-public nmrpflash (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libnl" ,libnl) - ("libpcap" ,libpcap))) + (list libnl libpcap)) (arguments `(#:tests? #f ; None exist #:make-flags @@ -4747,7 +4671,7 @@ (define-public novena-eeprom (install-file "novena-eeprom" out-bin) (install-file "novena-eeprom.8" out-share-man))))))) (inputs - `(("i2c-tools" ,i2c-tools))) + (list i2c-tools)) (synopsis "Novena EEPROM editor") (description "This package provides an editor for the Novena EEPROM. Novena boards contain a device-dependent descriptive EEPROM that defines @@ -4799,7 +4723,7 @@ (define-public nq (base32 "0sdamjzvmf6cxhjmd1rjvn7zm6k10fp5n6vabyxd3yl30cgrxw2i")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + (list perl)) (arguments `(#:make-flags (list (string-append "CC=" ,(cc-for-target)) (string-append "PREFIX=" (assoc-ref %outputs "out"))) @@ -4830,7 +4754,7 @@ (define-public lsofgraph "058x04yp6bc77hbl3qchqm7pa8f9vqfl9jryr88m8pzl7kvpif54")))) (build-system trivial-build-system) (inputs - `(("lua" ,lua))) + (list lua)) (arguments `(#:modules ((guix build utils)) #:builder diff --git a/gnu/packages/adns.scm b/gnu/packages/adns.scm index ef3bf68e71..5703016549 100644 --- a/gnu/packages/adns.scm +++ b/gnu/packages/adns.scm @@ -52,7 +52,7 @@ (define-public adns ;; XXX: Tests expect real name resolution to work. #:tests? #f)) (native-inputs - `(("m4" ,m4))) + (list m4)) (home-page "https://www.gnu.org/software/adns/") (synopsis "Asynchronous DNS client library and utilities") (description @@ -85,7 +85,7 @@ (define-public c-ares ;; Filter tests that require internet access. (setenv "GTEST_FILTER" "-*.Live*:*.FamilyV4*")))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://c-ares.haxx.se/") (synopsis "C library for asynchronous DNS requests") (description diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index de7454c4e8..606b0e48b5 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -49,28 +49,28 @@ (define-public agda "159hznnsxg7hlp80r1wqizyd7gwgnq0j13cm4d27cns0ganslb07")))) (build-system haskell-build-system) (inputs - `(("ghc-aeson" ,ghc-aeson) - ("ghc-alex" ,ghc-alex) - ("ghc-async" ,ghc-async) - ("ghc-blaze-html" ,ghc-blaze-html) - ("ghc-boxes" ,ghc-boxes) - ("ghc-case-insensitive" ,ghc-case-insensitive) - ("ghc-data-hash" ,ghc-data-hash) - ("ghc-edit-distance" ,ghc-edit-distance) - ("ghc-equivalence" ,ghc-equivalence) - ("ghc-gitrev" ,ghc-gitrev) - ("ghc-happy" ,ghc-happy) - ("ghc-hashable" ,ghc-hashable) - ("ghc-hashtables" ,ghc-hashtables) - ("ghc-monad-control" ,ghc-monad-control) - ("ghc-murmur-hash" ,ghc-murmur-hash) - ("ghc-parallel" ,ghc-parallel) - ("ghc-regex-tdfa" ,ghc-regex-tdfa) - ("ghc-split" ,ghc-split) - ("ghc-strict" ,ghc-strict) - ("ghc-unordered-containers" ,ghc-unordered-containers) - ("ghc-uri-encode" ,ghc-uri-encode) - ("ghc-zlib" ,ghc-zlib))) + (list ghc-aeson + ghc-alex + ghc-async + ghc-blaze-html + ghc-boxes + ghc-case-insensitive + ghc-data-hash + ghc-edit-distance + ghc-equivalence + ghc-gitrev + ghc-happy + ghc-hashable + ghc-hashtables + ghc-monad-control + ghc-murmur-hash + ghc-parallel + ghc-regex-tdfa + ghc-split + ghc-strict + ghc-unordered-containers + ghc-uri-encode + ghc-zlib)) (arguments `(#:modules ((guix build haskell-build-system) (guix build utils) @@ -139,7 +139,7 @@ (define-public agda-ial "0dlis6v6nzbscf713cmwlx8h9n2gxghci8y21qak3hp18gkxdp0g")))) (build-system gnu-build-system) (inputs - `(("agda" ,agda))) + (list agda)) (arguments `(#:parallel-build? #f #:phases diff --git a/gnu/packages/aidc.scm b/gnu/packages/aidc.scm index ac85dca4b0..ec038c5d33 100644 --- a/gnu/packages/aidc.scm +++ b/gnu/packages/aidc.scm @@ -64,8 +64,7 @@ (define-public zxing-cpp "1yl2cpaqiv1g4nq9v0xfj1vd5faz55k4541vz6hsffvcxgn9nmc5")))) (build-system cmake-build-system) (native-inputs - `(("fmt" ,fmt) - ("googletest" ,googletest))) + (list fmt googletest)) (synopsis "C++ port of ZXing") (description "ZXing-CPP is a barcode scanning library.") (home-page "https://github.com/nu-book/zxing-cpp") @@ -133,8 +132,8 @@ (define-public qrencode (with-directory-excursion "tests" (invoke "./test_basic.sh"))) #t))))) - (inputs `(("libpng" ,libpng))) - (native-inputs `(("pkg-config" ,pkg-config))) + (inputs (list libpng)) + (native-inputs (list pkg-config)) (synopsis "Encode data into a QR Code symbol") (description "Libqrencode is a C library for encoding data in a QR Code symbol, a kind of 2D symbology that can be scanned by handy terminals such as @@ -161,10 +160,7 @@ (define-public libdmtx ;; XXX Test suite is broken: https://github.com/dmtx/libdmtx/issues/22 `(#:tests? #f)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "https://github.com/dmtx") (synopsis "Library for reading and writing Data Matrix 2D barcodes") (description "libdmtx is software for reading and writing Data Matrix 2D @@ -213,9 +209,7 @@ (define-public zbar ("v4l-utils" ,v4l-utils))) (propagated-inputs ;; These are in 'requires' field of .pc files. - `(("glib" ,glib) - ("gtk+" ,gtk+) - ("qtbase" ,qtbase-5))) + (list glib gtk+ qtbase-5)) (synopsis "Bar code reader") (description "ZBar can read barcodes from various sources, such as video streams, diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index d30b9b7930..6717a2ce2e 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -89,9 +89,7 @@ (define-public mpfrcx "1545vgizpypqi2rrriad0ybqv0qwbn9zr0ibxpk00gha9ihv7acx")))) (build-system gnu-build-system) (propagated-inputs - `(("gmp" ,gmp) - ("mpfr" ,mpfr) - ("mpc" ,mpc))) ; Header files are included by mpfrcx.h. + (list gmp mpfr mpc)) ; Header files are included by mpfrcx.h. (synopsis "Arithmetic of polynomials over arbitrary precision numbers") (description "Mpfrcx is a library for the arithmetic of univariate polynomials over @@ -138,10 +136,9 @@ (define-public cm "0qq6b1kwb1byj8ws33ya5awq0ilkpm32037pi1l4cf2737fg9m42")))) (build-system gnu-build-system) (propagated-inputs - `(("mpfrcx" ,mpfrcx) - ("zlib" ,zlib))) ; Header files included from cm_common.h. + (list mpfrcx zlib)) ; Header files included from cm_common.h. (inputs - `(("pari-gp" ,pari-gp))) + (list pari-gp)) (synopsis "CM constructions for elliptic curves") (description "The CM software implements the construction of ring class fields of @@ -168,13 +165,9 @@ (define-public fplll (patches (search-patches "fplll-std-fenv.patch")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (propagated-inputs ; header files pulled in by fplll/defs.h - `(("gmp" ,gmp) - ("mpfr" ,mpfr))) + (list gmp mpfr)) (home-page "https://github.com/fplll/fplll") (synopsis "Library for LLL-reduction of euclidean lattices") (description @@ -219,10 +212,7 @@ (define-public python-fpylll "1a25iibihph626jl4wbs4b77xc4a2c4nfc2ypscf9wpani3dnhjf")))) (build-system python-build-system) (inputs - `(("fplll" ,fplll) - ("gmp" ,gmp) - ("mpfr" ,mpfr) - ("pari-gp" ,pari-gp))) + (list fplll gmp mpfr pari-gp)) (propagated-inputs `(("cysignals" ,python-cysignals) ("cython" ,python-cython) @@ -250,10 +240,7 @@ (define-public pari-gp (native-inputs `(("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts))))) - (inputs `(("gmp" ,gmp) - ("libx11" ,libx11) - ("perl" ,perl) - ("readline" ,readline))) + (inputs (list gmp libx11 perl readline)) (arguments '(#:make-flags '("all") #:test-target "dobench" @@ -289,8 +276,8 @@ (define-public gp2c (base32 "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl))) - (inputs `(("pari-gp" ,pari-gp))) + (native-inputs (list perl)) + (inputs (list pari-gp)) (arguments '(#:configure-flags (list (string-append "--with-paricfg=" @@ -324,12 +311,12 @@ (define-public cmh "1ws2yhzxmm2l5xqqqcjcimmg40f9qq5l9i6d4i5434an9v9s8531")))) (build-system gnu-build-system) (inputs - `(("gmp" ,gmp) - ("mpfr" ,mpfr) - ("mpc" ,mpc) - ("mpfrcx" ,mpfrcx) - ("fplll" ,fplll) - ("pari-gp" ,pari-gp))) + (list gmp + mpfr + mpc + mpfrcx + fplll + pari-gp)) (synopsis "Igusa class polynomial computations") (description "The CMH software computes Igusa (genus 2) class polynomials, which @@ -440,10 +427,9 @@ (define-public flint (base32 "1gp4wm2s8c27g2hh53d09cys62da1bsxfwbcsj9cd7cfikm95pv1")))) (build-system gnu-build-system) (inputs - `(("ntl" ,ntl))) + (list ntl)) (propagated-inputs - `(("gmp" ,gmp) - ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h + (list gmp mpfr)) ; header files from both are included by flint/arith.h (arguments `(#:parallel-tests? #f ; seems to be necessary on arm #:phases @@ -497,10 +483,9 @@ (define-public arb "1lmcl122qy6mr1g1y65bm7dk9fj0sym7gzmvar5vdgk7ln03c5iq")))) (build-system gnu-build-system) (propagated-inputs - `(("flint" ,flint))) ; flint.h is included by arf.h + (list flint)) ; flint.h is included by arf.h (inputs - `(("gmp" ,gmp) - ("mpfr" ,mpfr))) + (list gmp mpfr)) (arguments `(#:phases (modify-phases %standard-phases @@ -542,12 +527,11 @@ (define-public python-flint (patches (search-patches "python-flint-includes.patch")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("arb" ,arb) - ("flint" ,flint))) + (list arb flint)) (synopsis "Python module wrapping ARB and FLINT") (description "Python-flint is a Python extension module wrapping FLINT @@ -576,11 +560,9 @@ (define-public ntl #t)))) (build-system gnu-build-system) (native-inputs - `(("libtool" ,libtool) - ("perl" ,perl))) ; for configuration + (list libtool perl)) ; for configuration (inputs - `(("gmp" ,gmp) - ("gf2x" ,gf2x))) + (list gmp gf2x)) (arguments `(#:phases (modify-phases %standard-phases @@ -627,9 +609,7 @@ (define-public singular "13gy1gdng8zijwlr1fn5sixw53z0zf9czzlg0vh1dcc59zw6v998")))) (build-system gnu-build-system) (native-inputs - `(("doxygen" ,doxygen) - ("graphviz" ,graphviz) - ("perl" ,perl))) + (list doxygen graphviz perl)) (inputs `(("cddlib" ,cddlib) ("gmp" ,gmp) @@ -668,7 +648,7 @@ (define-public gmp-ecm "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc")))) (build-system gnu-build-system) (inputs - `(("gmp" ,gmp))) + (list gmp)) (arguments `(#:configure-flags '("--enable-shared" ;; Disable specific assembly routines, which depend @@ -698,13 +678,9 @@ (define-public bc (patches (search-patches "bc-fix-cross-compilation.patch")))) (build-system gnu-build-system) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf) - ("ed" ,ed) - ("flex" ,flex) - ("texinfo" ,texinfo))) + (list automake autoconf ed flex texinfo)) (inputs - `(("readline" ,readline))) + (list readline)) (arguments '(#:configure-flags (list "--with-readline") @@ -784,7 +760,7 @@ (define-public fftw ;; available on the user's machine when that package is built on a ;; different machine. "ax_cv_c_flags__mtune_native=no"))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) (home-page "http://fftw.org") (synopsis "Computing the discrete Fourier transform") (description @@ -855,8 +831,7 @@ (define-public java-la4j "**/SparseVectorTest.java" "**/DenseVectorTest.java"))) (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-junit java-hamcrest-core)) (home-page "http://la4j.org/") (synopsis "Java library that provides Linear Algebra primitives and algorithms") (description "The la4j library is a Java library that provides Linear @@ -893,7 +868,7 @@ (define-public java-jlargearrays #:tests? #f ; tests are not included in the release archive #:jdk ,icedtea-8)) (propagated-inputs - `(("java-commons-math3" ,java-commons-math3))) + (list java-commons-math3)) (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays") (synopsis "Library of one-dimensional arrays that can store up to 263 elements") (description "JLargeArrays is a Java library of one-dimensional arrays @@ -918,8 +893,7 @@ (define-public java-jtransforms #:tests? #f ; tests are not included in the release archive #:jdk ,icedtea-8)) (propagated-inputs - `(("java-commons-math3" ,java-commons-math3) - ("java-jlargearrays" ,java-jlargearrays))) + (list java-commons-math3 java-jlargearrays)) (home-page "https://github.com/wendykierp/JTransforms") (synopsis "Multithreaded FFT library written in pure Java") (description "JTransforms is a multithreaded FFT library written in pure @@ -943,7 +917,7 @@ (define-public lmfit "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf")))) (build-system cmake-build-system) (native-inputs - `(("perl" ,perl))) ; for pod2man + (list perl)) ; for pod2man (home-page "https://jugit.fz-juelich.de/mlz/lmfit") (synopsis "Levenberg-Marquardt minimization and least-squares fitting") (description "lmfit is a C library for Levenberg-Marquardt least-squares @@ -976,10 +950,7 @@ (define-public symengine "-DWITH_SYMENGINE_THREAD_SAFE=on" "-DBUILD_SHARED_LIBS=on"))) ;also build libsymengine (inputs - `(("flint" ,flint) - ("gmp" ,gmp) - ("mpc" ,mpc) - ("mpfr" ,mpfr))) + (list flint gmp mpc mpfr)) (home-page "https://github.com/symengine/symengine") (synopsis "Fast symbolic manipulation library") (description @@ -1008,8 +979,7 @@ (define-public ginac ("pkg-config" ,pkg-config) ("python" ,python-wrapper))) ; Python is required (inputs - `(("cln" ,cln) - ("readline" ,readline))) + (list cln readline)) (home-page "https://www.ginac.de/") (synopsis "Library for symbolic computation") (description "GiNaC is a C++ library for symbolic computation. Contrary @@ -1144,8 +1114,7 @@ (define-public xtensor (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("googletest" ,googletest) - ("xtl" ,xtl))) + (list googletest xtl)) (arguments `(#:configure-flags '("-DBUILD_TESTS=ON") @@ -1226,9 +1195,7 @@ (define-public gap #t)))) (build-system gnu-build-system) (inputs - `(("gmp" ,gmp) - ("readline" ,readline) - ("zlib" ,zlib))) + (list gmp readline zlib)) (arguments `(#:modules ((ice-9 ftw) (srfi srfi-26) @@ -1315,9 +1282,7 @@ (define-public gappa "0q1wdiwqj6fsbifaayb1zkp20bz8a1my81sqjsail577jmzwi07w")))) (build-system gnu-build-system) (inputs - `(("boost" ,boost) - ("gmp" ,gmp) - ("mpfr" ,mpfr))) + (list boost gmp mpfr)) (arguments `(#:phases (modify-phases %standard-phases @@ -1358,11 +1323,9 @@ (define-public givaro "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (propagated-inputs - `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h + (list gmp)) ; gmp++.h includes gmpxx.h (synopsis "Algebraic computations with exact rings and fields") (description "Givaro is a C++ library implementing the basic arithmetic of various @@ -1389,14 +1352,11 @@ (define-public fflas-ffpack "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("openblas" ,openblas))) + (list openblas)) (propagated-inputs - `(("givaro" ,givaro))) ; required according to the .pc file + (list givaro)) ; required according to the .pc file (arguments `(#:configure-flags (list (string-append "--with-blas-libs=" @@ -1432,12 +1392,9 @@ (define-public linbox (patches (search-patches "linbox-fix-pkgconfig.patch")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (propagated-inputs - `(("fflas-ffpack" ,fflas-ffpack))) + (list fflas-ffpack)) (synopsis "C++ library for linear algebra over exact rings") (description "LinBox is a C++ template library for exact linear algebra computation @@ -1461,12 +1418,9 @@ (define-public m4ri "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("libpng" ,libpng))) + (list libpng)) (synopsis "Arithmetic of dense matrices over F_2") (description "M4RI is a library for fast arithmetic with dense matrices over F2. The name M4RI comes from the first implemented algorithm: The @@ -1551,11 +1505,9 @@ (define-public m4rie "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("m4ri" ,m4ri))) + (list m4ri)) (synopsis "Arithmetic of dense matrices over F_{2^e}") (description "M4RI is a library for fast arithmetic with dense matrices over finite fields of characteristic 2. So it extends the functionality @@ -1578,12 +1530,9 @@ (define-public eclib "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("ntl" ,ntl) - ("pari-gp" ,pari-gp))) + (list ntl pari-gp)) (synopsis "Ranks of elliptic curves and modular symbols") (description "The eclib package includes mwrank (for 2-descent on elliptic curves over Q) and modular symbol code; it has been written by @@ -1608,9 +1557,7 @@ (define-public lrcalc (patches (search-patches "lrcalc-includes.patch")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (arguments `(#:phases (modify-phases %standard-phases @@ -1720,12 +1667,12 @@ (define-public sollya "11290ivi9h665cxi8f1shlavhy10vzb8s28m57hrcgnxyxqmhx0m")))) (build-system gnu-build-system) (inputs - `(("fplll" ,fplll) - ("gmp" ,gmp) - ("gnuplot" ,gnuplot) - ("libxml2" ,libxml2) - ("mpfi" ,mpfi) - ("mpfr" ,mpfr))) + (list fplll + gmp + gnuplot + libxml2 + mpfi + mpfr)) (arguments `(#:configure-flags (list (string-append "--docdir=${datadir}/doc/sollya-" ,version)) diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm index e390001d06..5fa4e6c8e9 100644 --- a/gnu/packages/android.scm +++ b/gnu/packages/android.scm @@ -311,7 +311,7 @@ (define-public android-libsparse (add-after 'unpack 'enter-source (lambda _ (chdir "libsparse") #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://developer.android.com/") (synopsis "Android platform sparse library") (description "@code{android-libsparse} is a library in common use by the @@ -342,11 +342,9 @@ (define-public android-libziparchive (string-append out "/include/ziparchive")) #t)))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("android-libbase" ,android-libbase) - ("android-libutils" ,android-libutils) - ("android-liblog" ,android-liblog))) + (list android-libbase android-libutils android-liblog)) (home-page "https://developer.android.com/") (synopsis "Android platform ZIP library") (description "@code{android-libziparchive} is a library in common use by the @@ -389,10 +387,7 @@ (define-public adb (install-file "diagnose_usb.h" (string-append (assoc-ref outputs "out") "/include")) #t))))) (inputs - `(("android-libbase" ,android-libbase) - ("android-libcutils" ,android-libcutils) - ("android-liblog" ,android-liblog) - ("openssl" ,openssl))) + (list android-libbase android-libcutils android-liblog openssl)) (home-page "https://developer.android.com/studio/command-line/adb.html") (synopsis "Android Debug Bridge") (description @@ -511,11 +506,11 @@ (define-public android-libselinux (("#ifdef HOST") "#ifdef XXX")) #t))))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (native-inputs - `(("android-bionic-uapi" ,android-bionic-uapi) - ;; pcre is inlined by our package. - ("pcre" ,pcre))) + (list android-bionic-uapi + ;; pcre is inlined by our package. + pcre)) (home-page "https://developer.android.com/") (synopsis "Android version of the SELinux libraries and utilities") (description @@ -561,11 +556,8 @@ (define-public android-ext4-utils (copy-recursively "." (string-append out "/include"))) #t))))) (inputs - `(("android-libcutils" ,android-libcutils) - ("android-liblog" ,android-liblog) - ("android-libselinux" ,android-libselinux) - ("android-libsparse" ,android-libsparse) - ("zlib" ,zlib))) + (list android-libcutils android-liblog android-libselinux + android-libsparse zlib)) (native-inputs `(("android-core" ,(android-platform-system-core version)))) (home-page "https://developer.android.com/") @@ -603,11 +595,8 @@ (define-public android-f2fs-utils (install-file "mkf2fsuserimg.sh" bin) #t)))))) (inputs - `(("f2fs-tools" ,f2fs-tools-1.7) - ("android-libselinux" ,android-libselinux) - ("android-libsparse" ,android-libsparse) - ("android-libcutils" ,android-libcutils) - ("zlib" ,zlib))) + (list f2fs-tools-1.7 android-libselinux android-libsparse + android-libcutils zlib)) (home-page "https://developer.android.com/") (synopsis "Android f2fs utils") (description "@code{android-f2fs-utils} is a library in common use by the @@ -644,8 +633,7 @@ (define-public android-libutils (lambda* (#:key inputs outputs #:allow-other-keys) (copy-recursively "../include/utils" (string-append (assoc-ref outputs "out") "/include/utils"))))))) (inputs - `(("android-safe-iop" ,android-safe-iop) - ("android-libcutils" ,android-libcutils))) + (list android-safe-iop android-libcutils)) (native-inputs `(("android-bionic-uapi" ,android-bionic-uapi) ("android-liblog" ,android-liblog) @@ -682,22 +670,22 @@ (define-public fastboot (install-file "fastboot" bin) #t)))))) (inputs - `(("adb" ,adb) - ("android-safe-iop" ,android-safe-iop) - ("android-ext4-utils" ,android-ext4-utils) - ("android-f2fs-utils" ,android-f2fs-utils) - ("android-libbase" ,android-libbase) - ("android-libcutils" ,android-libcutils) - ("android-liblog" ,android-liblog) - ("android-libutils" ,android-libutils) - ("android-libsparse" ,android-libsparse) - ("android-libziparchive" ,android-libziparchive) - ("android-libselinux" ,android-libselinux) - ("pcre" ,pcre) - ("mkbootimg" ,mkbootimg) - ("zlib" ,zlib))) + (list adb + android-safe-iop + android-ext4-utils + android-f2fs-utils + android-libbase + android-libcutils + android-liblog + android-libutils + android-libsparse + android-libziparchive + android-libselinux + pcre + mkbootimg + zlib)) (native-inputs - `(("xz" ,xz))) + (list xz)) (home-page "https://developer.android.com/studio/command-line/") (synopsis "Android image flasher") (description @@ -897,21 +885,18 @@ (define-public python-androguard (invoke "nosetests" "--with-coverage" "--with-timer" "--timer-top-n" "50")))))) (native-inputs - `(("python-codecov" ,python-codecov) - ("python-coverage" ,python-coverage) - ("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-nose-timer" ,python-nose-timer))) + (list python-codecov python-coverage python-mock python-nose + python-nose-timer)) (propagated-inputs - `(("python-asn1crypto" ,python-asn1crypto) - ("python-colorama" ,python-colorama) - ("python-future" ,python-future) - ("python-ipython" ,python-ipython) - ("python-lxml" ,python-lxml) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-pygments" ,python-pygments) - ("python-pyperclip" ,python-pyperclip))) + (list python-asn1crypto + python-colorama + python-future + python-ipython + python-lxml + python-matplotlib + python-networkx + python-pygments + python-pyperclip)) (home-page "https://github.com/androguard/androguard") (synopsis "Python tool to play with Android files") (description @@ -946,28 +931,25 @@ (define-public fdroidserver (("docker-py >= 1.9, < 2.0") "docker >= 1.9")) #t))))) (propagated-inputs - `(("python-androguard" ,python-androguard) - ("python-apache-libcloud" ,python-apache-libcloud) - ("python-clint" ,python-clint) - ("python-defusedxml" ,python-defusedxml) - ("python-docker" ,python-docker) - ("python-gitpython" ,python-gitpython) - ("python-mwclient" ,python-mwclient) - ("python-paramiko" ,python-paramiko) - ("python-pillow" ,python-pillow) - ("python-pyasn1" ,python-pyasn1) - ("python-pyasn1-modules" ,python-pyasn1-modules) - ("python-pyyaml" ,python-pyyaml) - ("python-qrcode" ,python-qrcode) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-requests" ,python-requests) - ("python-vagrant" ,python-vagrant))) + (list python-androguard + python-apache-libcloud + python-clint + python-defusedxml + python-docker + python-gitpython + python-mwclient + python-paramiko + python-pillow + python-pyasn1 + python-pyasn1-modules + python-pyyaml + python-qrcode + python-ruamel.yaml + python-requests + python-vagrant)) (native-inputs - `(("python-babel" ,python-babel) - ("python-bcrypt" ,python-bcrypt) - ("python-docker-pycreds" ,python-docker-pycreds) - ("python-pynacl" ,python-pynacl) - ("python-websocket-client" ,python-websocket-client))) + (list python-babel python-bcrypt python-docker-pycreds python-pynacl + python-websocket-client)) (home-page "https://f-droid.org") (synopsis "F-Droid server tools") (description @@ -996,7 +978,7 @@ (define-public fdroidcl #:tests? #f ; TODO: Inputs missing. #:install-source? #f)) (inputs - `(("go-github-com-kr-pretty" ,go-github-com-kr-pretty))) + (list go-github-com-kr-pretty)) ;(native-inputs ; `(("go-github-com-rogpeppe-go-internal-testscript" ; ,go-github-com-rogpeppe-go-internal-testscript))) @@ -1049,7 +1031,7 @@ (define-public enjarify (mkdir-p (string-append out "/bin/")) (copy-file "enjarify.sh" (string-append out "/bin/enjarify")) #t)))))) - (native-inputs `(("openjdk" ,openjdk12))) + (native-inputs (list openjdk12)) (synopsis "Translate Dalvik bytecode to equivalent Java bytecode") (description "Android applications are Java programs that run on a customized virtual machine, which is part of the Android operating system, the diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm index 063103e433..c281772563 100644 --- a/gnu/packages/animation.scm +++ b/gnu/packages/animation.scm @@ -82,8 +82,7 @@ (define-public rlottie "-Dlog=true" "-Dtest=true"))) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (synopsis "Lottie Animation Library") (description "Rlottie is a platform independent standalone c++ library for rendering vector based animations and art in realtime.") @@ -182,8 +181,7 @@ (define-public synfig ("openexr" ,openexr-2) ("pango" ,pango))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (home-page "https://www.synfig.org") (synopsis "Vector-based 2D animation renderer") (description @@ -225,13 +223,9 @@ (define-public synfigstudio `("XDG_DATA_DIRS" ":" prefix (,gtk-share))) #t)))))) (inputs - `(("gtkmm" ,gtkmm-3) - ("gtk+" ,gtk+) - ("libsigc++" ,libsigc++) - ("synfig" ,synfig))) + (list gtkmm-3 gtk+ libsigc++ synfig)) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool))) + (list pkg-config intltool)) (home-page "https://www.synfig.org") (synopsis "Vector-based 2D animation package (GUI)") (description @@ -454,7 +448,7 @@ (define-public papagayo ("qtmultimedia" ,qtmultimedia) ("libsndfile" ,libsndfile))) (native-inputs - `(("qttools" ,qttools))) + (list qttools)) (home-page "https://www.lostmarble.com/papagayo/") (synopsis "Lip-syncing for animations") (description @@ -480,10 +474,7 @@ (define-public pencil2d "0b1nwiwyg01087q318vymg4si76dw41ykxbn2zwd6dqbxzbpr1dh")))) (build-system gnu-build-system) (inputs - `(("qtbase" ,qtbase-5) - ("qtxmlpatterns" ,qtxmlpatterns) - ("qtmultimedia" ,qtmultimedia) - ("qtsvg" ,qtsvg))) + (list qtbase-5 qtxmlpatterns qtmultimedia qtsvg)) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/antivirus.scm b/gnu/packages/antivirus.scm index 368b0efde7..80126a5b59 100644 --- a/gnu/packages/antivirus.scm +++ b/gnu/packages/antivirus.scm @@ -66,11 +66,11 @@ (define-public clamav "clamav-config-llvm-libs.patch")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("check" ,check) ; for tests - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf + automake + check ; for tests + libtool + pkg-config)) (inputs `(("bzip2" ,bzip2) ("libcurl" ,curl) diff --git a/gnu/packages/apr.scm b/gnu/packages/apr.scm index 5ef1488218..3b4968089b 100644 --- a/gnu/packages/apr.scm +++ b/gnu/packages/apr.scm @@ -48,8 +48,7 @@ (define-public apr ;; Thus, build sequentially. '(#:parallel-build? #f #:parallel-tests? #f)) - (inputs `(("perl" ,perl) - ("libltdl" ,libltdl))) + (inputs (list perl libltdl)) (home-page "http://apr.apache.org/") (synopsis "The Apache Portable Runtime Library") (description @@ -75,9 +74,9 @@ (define-public apr-util "0nq3s1yn13vplgl6qfm09f7n0wm08malff9s59bqf9nid9xjzqfk")))) (build-system gnu-build-system) (inputs - `(("apr" ,apr))) + (list apr)) (propagated-inputs - `(("expat" ,expat))) + (list expat)) (arguments '(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/arcan.scm b/gnu/packages/arcan.scm index 721cd7fd70..c25d64903c 100644 --- a/gnu/packages/arcan.scm +++ b/gnu/packages/arcan.scm @@ -151,8 +151,7 @@ (define-public arcan (base32 "0dcxcnqjkyyqdr2yk84mprvkncy5g172kfs6vc4zrkklsbkr8yi2")))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("ruby" ,ruby))) ; For documentation and testing + (list pkg-config ruby)) ; For documentation and testing (home-page "https://arcan-fe.com") (synopsis "Display server, multimedia framework and game engine (egl-dri)") (description "Arcan is a development framework for creating virtually @@ -171,9 +170,9 @@ (define-public arcan-sdl (inherit arcan) (name "arcan-sdl") (inputs - `(("sdl" ,sdl) - ,@(fold alist-delete (package-inputs arcan) - '("libdrm")))) + (modify-inputs (package-inputs arcan) + (delete "libdrm") + (prepend sdl))) (arguments `(,@(ensure-keyword-arguments (package-arguments arcan) @@ -219,11 +218,7 @@ (define-public xarcan ,(string-append "--with-xkb-output=" "/tmp")))) ; FIXME: Copied from xorg (native-inputs - `(("pkg-config" ,pkg-config) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("util-macros" ,util-macros))) + (list pkg-config autoconf automake libtool util-macros)) (inputs `(("arcan" ,arcan) ("font-util" ,font-util) @@ -251,14 +246,14 @@ (define-public arcan-wayland (inherit arcan) (name "arcan-wayland") (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("arcan" ,arcan) - ("libseccomp" ,libseccomp) - ("libxkbcommon" ,libxkbcommon) - ("mesa" ,mesa) - ("wayland" ,wayland) - ("wayland-protocols" ,wayland-protocols))) + (list arcan + libseccomp + libxkbcommon + mesa + wayland + wayland-protocols)) (arguments `(#:tests? #f #:phases diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index a86984b28c..753f65642d 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -73,7 +73,7 @@ (define-public aspell (string-append "\"filter-path" middle "\"" libdir "\""))) #t)))))) - (inputs `(("perl" ,perl))) + (inputs (list perl)) (native-search-paths ;; This is a Guix-specific environment variable that takes a single @@ -131,8 +131,7 @@ (define* (aspell-dictionary dict-name full-name (list (string-append "dictdir=" out "/lib/aspell") (string-append "datadir=" out "/lib/aspell"))) #:tests? #f)) - (native-inputs `(("aspell" ,aspell) - ("which" ,which))) + (native-inputs (list aspell which)) (synopsis (string-append full-name " dictionary for GNU Aspell")) ; XXX: i18n (description "This package provides a dictionary for the GNU Aspell spell checker.") @@ -389,10 +388,7 @@ (define* (aspell-word-list language synopsis (base32 "11lkrnhwrf5mvrrq45k4mads3n9aswgac8dc25ba61c75alxb5rs")))) (native-inputs - `(("tar" ,tar) - ("gzip" ,gzip) - ("perl" ,perl) - ("aspell" ,aspell))) + (list tar gzip perl aspell)) (build-system gnu-build-system) (arguments `(#:phases @@ -522,10 +518,9 @@ (define-public ispell (format port "#define MAN45DIR \"~a/share/man/man5\"~%" out)))) #t))))) (inputs - `(("grep" ,grep) - ("ncurses" ,ncurses))) + (list grep ncurses)) (native-inputs - `(("bison" ,bison))) + (list bison)) (synopsis "Interactive spell-checking tool for Unix") (description "Ispell is an interactive spell-checking tool supporting many European languages.") diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index 675663047e..bcb42a083f 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -68,8 +68,8 @@ (define-public nasm (base32 "0gqand86b0r86k3h46dh560lykxmxqqywz5m55kgjfq7q4lngbrw")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl) ;for doc and test target - ("texinfo" ,texinfo))) + (native-inputs (list perl ;for doc and test target + texinfo)) (arguments `(#:test-target "test" #:phases @@ -140,7 +140,7 @@ (define-public lightning (base32 "1jgxbq2cm51dzi3zhz38mmgwdcgs328mfl8iviw8dxn6dn36p1gd")))) (build-system gnu-build-system) - (native-inputs `(("zlib" ,zlib))) + (native-inputs (list zlib)) (arguments ;; Some tests fail when run in parallel. `(#:parallel-tests? #f)) @@ -324,12 +324,9 @@ (define-public rgbds ,(string-append "PREFIX=" (assoc-ref %outputs "out"))))) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("pkg-config" ,pkg-config) - ("util-linux" ,util-linux))) + (list bison flex pkg-config util-linux)) (inputs - `(("libpng" ,libpng))) + (list libpng)) (home-page "https://github.com/gbdev/rgbds") (synopsis "Rednex Game Boy Development System") (description @@ -402,7 +399,7 @@ (define-public xa (modify-phases %standard-phases (delete 'configure)) ; no "configure" script #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out"))))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) (home-page "https://www.floodgap.com/retrotech/xa/") (synopsis "Two-pass portable cross-assembler") (description diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 9675d09c6e..0a1c556b85 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -144,8 +144,7 @@ (define-public python-fitsio (substitute* "fitsio/test.py" (("'SKIP_BZIP_TEST' in os.environ") "True"))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("cfitsio" ,cfitsio))) + (list python-numpy cfitsio)) (home-page "https://github.com/esheldon/fitsio") (synopsis "Python library to read from and write to FITS files") @@ -250,7 +249,7 @@ (define-public wcslib (sha256 (base32 "1536gmcpm6pckn9xrb6j8s4pm1vryjhzvhfaj9wx3jwxcpbdy0dw")))) (inputs - `(("cfitsio" ,cfitsio))) + (list cfitsio)) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -321,8 +320,7 @@ (define-public gnuastro ("wcslib" ,wcslib) ("zlib" ,zlib))) (native-inputs - `(("libtool" ,libtool) - ("lzip" ,lzip))) + (list libtool lzip)) (home-page "https://www.gnu.org/software/gnuastro/") (synopsis "Astronomy utilities") (description "The GNU Astronomy Utilities (Gnuastro) is a suite of @@ -360,9 +358,7 @@ (define-public sextractor (string-append "--with-fftw-incdir=" (assoc-ref %build-inputs "fftw") "/include")))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs `(("openblas" ,openblas) ("fftw" ,fftwf))) @@ -454,11 +450,9 @@ (define-public stackistry (copy-recursively "lang" lang)) #t))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("gtkmm" ,gtkmm-3) - ("libskry" ,libskry) - ("ffmpeg" ,ffmpeg))) + (list gtkmm-3 libskry ffmpeg)) (home-page "https://github.com/GreatAttractor/stackistry") (synopsis "Astronomical lucky imaging/image stacking tool") (description @@ -483,12 +477,12 @@ (define-public stellarium (base32 "049jlc8vx06pad5h2syrmf7f1l346yr5iraai0wkn8s8pk30j8q7")))) (build-system cmake-build-system) (inputs - `(("qtbase" ,qtbase-5) - ("qtlocation" ,qtlocation) - ("qtmultimedia" ,qtmultimedia) - ("qtscript" ,qtscript) - ("qtserialport" ,qtserialport) - ("zlib" ,zlib))) + (list qtbase-5 + qtlocation + qtmultimedia + qtscript + qtserialport + zlib)) (native-inputs `(("gettext" ,gettext-minimal) ; xgettext is used at compile time ("perl" ,perl) ; for pod2man @@ -591,7 +585,7 @@ (define-public celestia ;; glut: for glut interface ("freeglut" ,freeglut))) (propagated-inputs - `(("lua" ,lua))) + (list lua)) (arguments `(#:configure-flags '("-DENABLE_GLUT=ON" "-DENABLE_QT=OFF") #:tests? #f)) ;no tests @@ -683,27 +677,23 @@ (define-public python-astropy ;; Skip tests that need remote data. "-m" "not remote_data"))))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-coverage" ,python-coverage) - ("python-cython" ,python-cython) - ("python-extension-helpers" ,python-extension-helpers) - ("python-ipython" ,python-ipython) - ("python-jplephem" ,python-jplephem) - ("python-objgraph" ,python-objgraph) - ("python-pytest" ,python-pytest) - ("python-pytest-astropy" ,python-pytest-astropy) - ("python-pytest-xdist" ,python-pytest-xdist) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-sgp4" ,python-sgp4) - ("python-skyfield" ,python-skyfield))) + (list pkg-config + python-coverage + python-cython + python-extension-helpers + python-ipython + python-jplephem + python-objgraph + python-pytest + python-pytest-astropy + python-pytest-xdist + python-setuptools-scm + python-sgp4 + python-skyfield)) (inputs - `(("cfitsio" ,cfitsio) - ("expat" ,expat))) + (list cfitsio expat)) (propagated-inputs - `(("python-configobj" ,python-configobj) - ("python-numpy" ,python-numpy) - ("python-ply" ,python-ply) - ("python-pyerfa" ,python-pyerfa))) + (list python-configobj python-numpy python-ply python-pyerfa)) (home-page "https://www.astropy.org/") (synopsis "Core package for Astronomy in Python") (description @@ -736,9 +726,7 @@ (define-public libnova (("/bin/sh") (which "sh"))) #t))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (synopsis "Celestial mechanics, astrometry and astrodynamics library") (description "Libnova is a general purpose, double precision, Celestial Mechanics, Astrometry and Astrodynamics library.") @@ -779,7 +767,7 @@ (define-public libskry (copy-recursively "include" include)) #t))))) (inputs - `(("ffmpeg" ,ffmpeg))) + (list ffmpeg)) (home-page "https://github.com/GreatAttractor/libskry") (synopsis "Astronimical lucky imaging library") (description @@ -885,7 +873,7 @@ (define-public xplanet "xplanet-1.3.1-xpUtil-Add2017LeapSecond.cpp.patch")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("libx11" ,libx11) ("libxscrnsaver" ,libxscrnsaver) @@ -933,10 +921,7 @@ (define-public gpredict ("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config))) (inputs - `(("curl" ,curl) - ("glib" ,glib) - ("goocanvas" ,goocanvas) - ("gtk+" ,gtk+))) + (list curl glib goocanvas gtk+)) (arguments `(#:configure-flags '("CFLAGS=-O2 -g -fcommon") #:phases @@ -1020,13 +1005,9 @@ (define-public imppg (string-append "-DCMAKE_INSTALL_PREFIX=" (assoc-ref outputs "out")) "..")))))) (native-inputs - `(("boost" ,boost) - ("pkg-config" ,pkg-config))) + (list boost pkg-config)) (inputs - `(("cfitsio" ,cfitsio) - ("freeimage" ,freeimage) - ("glew" ,glew) - ("wxwidgets" ,wxwidgets))) + (list cfitsio freeimage glew wxwidgets)) (home-page "https://github.com/GreatAttractor/imppg") (synopsis "Astronomical Image Post-Proccessor (ImPPG)") (description @@ -1076,17 +1057,17 @@ (define-public indi (let ((out (assoc-ref outputs "out"))) (mkdir-p (string-append out "/lib/udev/rules.d")))))))) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (inputs - `(("cfitsio" ,cfitsio) - ("curl" ,curl) - ("fftw" ,fftw) - ("gsl" ,gsl) - ("libjpeg-turbo" ,libjpeg-turbo) - ("libnova" ,libnova) - ("libtiff" ,libtiff) - ("libusb" ,libusb) - ("zlib" ,zlib))) + (list cfitsio + curl + fftw + gsl + libjpeg-turbo + libnova + libtiff + libusb + zlib)) (home-page "https://www.indilib.org") (synopsis "Library for astronimical intrumentation control") (description @@ -1144,12 +1125,9 @@ (define-public sunclock (invoke "xmkmf")))) #:tests? #f)) ; No check target. (inputs - `(("libjpeg-turbo" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libx11" ,libx11) - ("libxpm" ,libxpm))) + (list libjpeg-turbo libpng libx11 libxpm)) (native-inputs - `(("imake" ,imake))) + (list imake)) (home-page "https://github.com/nongiach/Sunclock") (synopsis "Map of the Earth that shows which portion is illuminated by the Sun") @@ -1184,7 +1162,7 @@ (define-public python-jplephem (setenv "PATH" (string-append out "/bin:" (getenv "PATH"))) (invoke "python" "-m" "unittest" "discover" "-s" "test")))))))) (inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/brandon-rhodes/python-jplephem") (synopsis "Python version of NASA DE4xx ephemerides") (description @@ -1223,7 +1201,7 @@ (define-public python-pyerfa (inputs `(("liberfa" ,erfa))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/liberfa/pyerfa") (synopsis "Python bindings for ERFA") (description @@ -1333,10 +1311,7 @@ (define-public python-skyfield ;; framework https://github.com/brandon-rhodes/assay `(#:tests? #f)) (inputs - `(("python-certifi" ,python-certifi) - ("python-jplephem" ,python-jplephem) - ("python-numpy" ,python-numpy) - ("python-sgp4" ,python-sgp4))) + (list python-certifi python-jplephem python-numpy python-sgp4)) (home-page "https://rhodesmill.org/skyfield/") (synopsis "Astronomy for Python") (description diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 43259c5989..eeae55efcb 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -374,9 +374,7 @@ (define-public libopenmpt (for-each delete-file (find-files lib "\\.a$")) #t)))))) (native-inputs - `(("doxygen" ,doxygen) - ("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list doxygen perl pkg-config)) (inputs `(("alsa" ,alsa-lib) ("flac" ,flac) @@ -413,12 +411,11 @@ (define-public libofa "libofa-ftbfs-2.diff")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("expat" ,expat))) + (list curl expat)) (propagated-inputs - `(("fftw" ,fftw))) + (list fftw)) (synopsis "Open Fingerprint Architecture") (description "LibOFA is an audio fingerprint library, created and provided by MusicIP.") @@ -439,10 +436,7 @@ (define-public faac (base32 "1lmj0dib3mjp84jhxc5ddvydkzzhb0gfrdh3ikcidjlcb378ghxd")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (synopsis "Freeware Advanced Audio Coder") (description "FAAC is an MPEG-4 and MPEG-2 AAC encoder.") (home-page "https://www.audiocoding.com/faac.html") @@ -469,9 +463,9 @@ (define-public libtimidity (arguments `(#:tests? #f)) ; XXX: LibTiMidity could not be initialised (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("ao" ,ao))) + (list ao)) (synopsis "MIDI to WAVE converter library") (description "LibTiMidity is a MIDI to WAVE converter library that uses Gravis Ultrasound-compatible patch files to generate digital audio data from @@ -536,18 +530,17 @@ (define-public alsa-modular-synth "056dn6b9c5nsw2jdww7z1kxrjqqfvxjzxhsd5x9gi4wkwyiv21nz")))) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ;; We cannot use zita-alsa-pcmi (the successor of clalsadrv) due to - ;; license incompatibility. - ("clalsadrv" ,clalsadrv) - ("fftw" ,fftw) - ("jack" ,jack-1) - ("ladspa" ,ladspa) - ("liblo" ,liblo) - ("qtbase" ,qtbase-5))) + (list alsa-lib + ;; We cannot use zita-alsa-pcmi (the successor of clalsadrv) due to + ;; license incompatibility. + clalsadrv + fftw + jack-1 + ladspa + liblo + qtbase-5)) (native-inputs - `(("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list pkg-config qttools)) (home-page "http://alsamodular.sourceforge.net/") (synopsis "Realtime modular synthesizer and effect processor") (description @@ -582,13 +575,9 @@ (define-public aubio "--enable-avcodec") #:python ,python-2)) (inputs - `(("jack" ,jack-1) - ("libsndfile" ,libsndfile) - ("libsamplerate" ,libsamplerate) - ("fftwf" ,fftwf) - ("ffmpeg" ,ffmpeg))) ; for libavcodec + (list jack-1 libsndfile libsamplerate fftwf ffmpeg)) ; for libavcodec (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://aubio.org/") (synopsis "Library for audio labelling") (description @@ -672,48 +661,48 @@ (define-public ardour #t))) #:test-target "test")) (inputs - `(("alsa-lib" ,alsa-lib) - ("atkmm" ,atkmm) - ("aubio" ,aubio) - ("boost" ,boost) - ("cairomm" ,cairomm) - ("curl" ,curl) - ("dbus" ,dbus) - ("eudev" ,eudev) - ("fftw" ,fftw) - ("fftwf" ,fftwf) - ("flac" ,flac) - ("glibmm" ,glibmm) - ("gtkmm" ,gtkmm-2) - ("jack" ,jack-1) - ("libarchive" ,libarchive) - ("libart-lgpl" ,libart-lgpl) - ("libgnomecanvasmm" ,libgnomecanvasmm) - ("liblo" ,liblo) - ("libogg" ,libogg) - ("libsamplerate" ,libsamplerate) - ("libsndfile" ,libsndfile) - ("libusb" ,libusb) - ("libvorbis" ,libvorbis) - ("libwebsockets" ,libwebsockets) - ("libxml2" ,libxml2) - ("lilv" ,lilv) - ("lrdf" ,lrdf) - ("lv2" ,lv2) - ("openssl" ,openssl) ; Required by libwebsockets. - ("pangomm" ,pangomm) - ("python-rdflib" ,python-rdflib) - ("pulseaudio" ,pulseaudio) - ("readline" ,readline) - ("redland" ,redland) - ("rubberband" ,rubberband) - ("serd" ,serd) - ("sord" ,sord) - ("soundtouch" ,soundtouch) - ("sratom" ,sratom) - ("suil" ,suil) - ("taglib" ,taglib) - ("vamp" ,vamp))) + (list alsa-lib + atkmm + aubio + boost + cairomm + curl + dbus + eudev + fftw + fftwf + flac + glibmm + gtkmm-2 + jack-1 + libarchive + libart-lgpl + libgnomecanvasmm + liblo + libogg + libsamplerate + libsndfile + libusb + libvorbis + libwebsockets + libxml2 + lilv + lrdf + lv2 + openssl ; Required by libwebsockets. + pangomm + python-rdflib + pulseaudio + readline + redland + rubberband + serd + sord + soundtouch + sratom + suil + taglib + vamp)) (native-inputs `(("cppunit" ,cppunit) ("gettext" ,gettext-minimal) @@ -769,27 +758,27 @@ (define-public audacity #t)))) (build-system cmake-build-system) (inputs - `(("wxwidgets" ,wxwidgets) - ("gtk+" ,gtk+) - ("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("expat" ,expat) - ("ffmpeg" ,ffmpeg) - ("lame" ,lame) - ("flac" ,flac) - ("libid3tag" ,libid3tag) - ("libmad" ,libmad) - ;;("libsbsms" ,libsbsms) ;bundled version is modified - ("libsndfile" ,libsndfile) - ("soundtouch" ,soundtouch) - ("soxr" ,soxr) ;replaces libsamplerate - ("twolame" ,twolame) - ("vamp" ,vamp) - ("libvorbis" ,libvorbis) - ("lv2" ,lv2) - ("lilv" ,lilv) ;for lv2 - ("suil" ,suil) ;for lv2 - ("portmidi" ,portmidi))) + (list wxwidgets + gtk+ + alsa-lib + jack-1 + expat + ffmpeg + lame + flac + libid3tag + libmad + ;;("libsbsms" ,libsbsms) ;bundled version is modified + libsndfile + soundtouch + soxr ;replaces libsamplerate + twolame + vamp + libvorbis + lv2 + lilv ;for lv2 + suil ;for lv2 + portmidi)) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -890,7 +879,7 @@ (define-public audiofile "CVE-2017-6831" "CVE-2017-6833")))) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib))) + (list alsa-lib)) (home-page "https://audiofile.68k.org/") (synopsis "Library to handle various audio file formats") (description "This is an open-source version of SGI's audiofile library. @@ -931,7 +920,7 @@ (define-public autotalent (string-append (assoc-ref outputs "out") "/lib/ladspa"))) #t))))) (inputs - `(("ladspa" ,ladspa))) + (list ladspa)) (home-page "http://tombaran.info/autotalent.html") (synopsis "Pitch-correction LADSPA audio plugin") (description @@ -970,12 +959,9 @@ (define-public azr3 (utime "azr3.1" early-1980 early-1980)) #t))))) (inputs - `(("gtkmm" ,gtkmm-2) - ("lvtk" ,lvtk) - ("jack" ,jack-1) - ("lash" ,lash))) + (list gtkmm-2 lvtk jack-1 lash)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://ll-plugins.nongnu.org/azr3/") (synopsis "Tonewheel organ synthesizer") (description @@ -1010,7 +996,7 @@ (define-public calf ("ladspa" ,ladspa) ("fftw" ,fftw))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (native-search-paths (list (search-path-specification (variable "LV2_PATH") @@ -1055,7 +1041,7 @@ (define-public caps-plugins-lv2 (("/usr/local")(assoc-ref outputs "out"))) #t))))) (inputs - `(("lv2" ,lv2))) + (list lv2)) ;; home-page of the original LADSPA version: http://quitte.de/dsp/caps.html (home-page "https://github.com/moddevices/caps-lv2") (synopsis "LV2 port of the CAPS audio plugin collection") @@ -1095,13 +1081,9 @@ (define-public infamous-plugins (("_LV2UI_Descriptor") "LV2UI_Descriptor")) #t))))) (inputs - `(("cairo" ,cairo) - ("fftwf" ,fftwf) - ("lv2" ,lv2) - ("ntk" ,ntk) - ("zita-resampler" ,zita-resampler))) + (list cairo fftwf lv2 ntk zita-resampler)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://ssj71.github.io/infamousPlugins") (synopsis "LV2 plugins for live use") (description @@ -1127,16 +1109,16 @@ (define-public snapcast (arguments '(#:tests? #f)) ; no included tests (inputs - `(("boost" ,boost) - ("libvorbis" ,libvorbis) - ("soxr" ,soxr) - ("alsa-lib" ,alsa-lib) - ("avahi" ,avahi) - ("pulseaudio" ,pulseaudio) - ("flac" ,flac) - ("opus" ,opus))) + (list boost + libvorbis + soxr + alsa-lib + avahi + pulseaudio + flac + opus)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/badaix/snapcast") (synopsis "Synchronous multiroom audio player") (description @@ -1166,8 +1148,7 @@ (define-public swh-plugins ("pkg-config" ,pkg-config) ("which" ,which))) (inputs - `(("fftwf" ,fftwf) - ("perl-xml-parser" ,perl-xml-parser))) + (list fftwf perl-xml-parser)) (build-system gnu-build-system) (home-page "http://plugin.org.uk") (synopsis "The SWH Plugins package for the LADSPA plugin system") @@ -1205,11 +1186,9 @@ (define-public swh-plugins-lv2 (("install:") "install: install-system")) #t))))) (inputs - `(("lv2" ,lv2) - ("fftwf" ,fftwf))) + (list lv2 fftwf)) (native-inputs - `(("libxslt" ,libxslt) - ("pkg-config" ,pkg-config))) + (list libxslt pkg-config)) (home-page "http://plugin.org.uk") (synopsis "SWH plugins in LV2 format") (description @@ -1241,11 +1220,9 @@ (define-public libdjinterop (lambda _ (for-each make-file-writable (find-files "."))))))) (native-inputs - `(("boost" ,boost) - ("pkg-config" ,pkg-config))) + (list boost pkg-config)) (inputs - `(("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list sqlite zlib)) (home-page "https://github.com/xsco/libdjinterop") (synopsis "C++ library for access to DJ record libraries") (description @@ -1343,13 +1320,13 @@ (define-public csound ("gettext" ,gettext-minimal) ("zlib" ,zlib))) (inputs - `(("alsa-lib" ,alsa-lib) - ("boost" ,boost) - ("jack" ,jack-1) - ("ladspa" ,ladspa) - ("liblo" ,liblo) - ("libsndfile" ,libsndfile) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib + boost + jack-1 + ladspa + liblo + libsndfile + pulseaudio)) (home-page "https://csound.com/") (synopsis "Sound and music computing system") (description @@ -1423,8 +1400,7 @@ (define-public clalsadrv ;; no configure script (delete 'configure)))) (inputs - `(("alsa-lib" ,alsa-lib) - ("fftw" ,fftw))) + (list alsa-lib fftw)) (home-page "https://kokkinizita.linuxaudio.org") (synopsis "C++ wrapper around the ALSA API") (description @@ -1771,15 +1747,15 @@ (define-public fluidsynth "LIB_SUFFIX \"\"")) #t))))) (inputs - `(("libsndfile" ,libsndfile) - ("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("ladspa" ,ladspa) - ("lash" ,lash) - ("readline" ,readline) - ("glib" ,glib))) + (list libsndfile + alsa-lib + jack-1 + ladspa + lash + readline + glib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.fluidsynth.org/") (synopsis "SoundFont synthesizer") (description @@ -1859,7 +1835,7 @@ (define-public faust (find-files "architecture/max-msp" ".*")) #t))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://faust.grame.fr/") (synopsis "Signal processing language") (description @@ -1891,11 +1867,7 @@ (define-public faust-2 ("ctags" ,emacs-minimal) ; for ctags ("pkg-config" ,pkg-config))) (inputs - `(("libsndfile" ,libsndfile) - ("libmicrohttpd" ,libmicrohttpd) - ("ncurses" ,ncurses) - ("openssl" ,openssl) - ("zlib" ,zlib))))) + (list libsndfile libmicrohttpd ncurses openssl zlib)))) (define-public freepats (package @@ -1927,8 +1899,7 @@ (define-public freepats (copy-recursively "." out) #t)))) (native-inputs - `(("tar" ,tar) - ("bzip2" ,bzip2))) + (list tar bzip2)) (home-page "http://freepats.zenvoid.org") (synopsis "GUS compatible patches for MIDI players") (description @@ -1957,21 +1928,21 @@ (define-public guitarix ;; Add the output lib directory to the RUNPATH. (string-append "--ldflags=-Wl,-rpath=" %output "/lib")))) (inputs - `(("libsndfile" ,libsndfile) - ("boost" ,boost) - ("curl" ,curl) - ("avahi" ,avahi) - ("eigen" ,eigen) - ("lv2" ,lv2) - ("lilv" ,lilv) - ("ladspa" ,ladspa) - ("jack" ,jack-1) - ("gtkmm" ,gtkmm-3) - ("gtk+" ,gtk+) - ("fftwf" ,fftwf) - ("lrdf" ,lrdf) - ("zita-resampler" ,zita-resampler) - ("zita-convolver" ,zita-convolver))) + (list libsndfile + boost + curl + avahi + eigen + lv2 + lilv + ladspa + jack-1 + gtkmm-3 + gtk+ + fftwf + lrdf + zita-resampler + zita-convolver)) (native-inputs `(("gperf" ,gperf) ("faust" ,faust) @@ -2082,14 +2053,14 @@ (define-public ir (("_LV2UI_Descriptor") "LV2UI_Descriptor")) #t))))) (inputs - `(("libsndfile" ,libsndfile) - ("libsamplerate" ,libsamplerate) - ("lv2" ,lv2) - ("glib" ,glib) - ("gtk+" ,gtk+-2) - ("zita-convolver" ,zita-convolver))) + (list libsndfile + libsamplerate + lv2 + glib + gtk+-2 + zita-convolver)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (native-search-paths (list (search-path-specification (variable "LV2_PATH") @@ -2126,15 +2097,14 @@ (define-public jack-1 (("libnn=lib64") "libnn=lib")) #t))))) (inputs - `(("alsa-lib" ,alsa-lib) - ("readline" ,readline))) + (list alsa-lib readline)) ;; uuid.h is included in the JACK type headers ;; db.h is included in the libjack metadata headers (propagated-inputs `(("libuuid" ,util-linux "lib") ("bdb" ,bdb))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://jackaudio.org/") (synopsis "JACK audio connection kit") (description @@ -2193,15 +2163,15 @@ (define-public jack-2 `("GUIX_PYTHONPATH" ":" prefix (,path)))) #t))))) (inputs - `(("alsa-lib" ,alsa-lib) - ("dbus" ,dbus) - ("expat" ,expat) - ("libsamplerate" ,libsamplerate) - ("opus" ,opus) - ("python-dbus" ,python-dbus) - ("readline" ,readline))) + (list alsa-lib + dbus + expat + libsamplerate + opus + python-dbus + readline)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) ;; Most files are under GPLv2+, but some headers are under LGPLv2.1+ (license (list license:gpl2+ license:lgpl2.1+)))) @@ -2230,7 +2200,7 @@ (define-public jalv ("qtbase" ,qtbase-5) ("jack" ,jack-1))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://drobilla.net/software/jalv/") (synopsis "Simple LV2 host for JACK") (description @@ -2326,11 +2296,9 @@ (define-public lash ;; According to pkg-config, packages depending on lash also need to have ;; at least the following packages declared as inputs. (propagated-inputs - `(("alsa-lib" ,alsa-lib) - ("dbus" ,dbus) - ("libxml2" ,libxml2))) + (list alsa-lib dbus libxml2)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.nongnu.org/lash/") (synopsis "Audio application session manager") (description @@ -2352,8 +2320,8 @@ (define-public libbs2b (base32 "1mcc4gjkmphczjybnsrip3gq1f974knzys7x49bv197xk3fn8wdr")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("libsndfile" ,libsndfile))) + (native-inputs (list pkg-config)) + (inputs (list libsndfile)) (home-page "https://sourceforge.net/projects/bs2b/") (synopsis "Bauer stereophonic-to-binaural DSP") (description @@ -2376,9 +2344,8 @@ (define-public ladspa-bs2b (base32 "1b4aipbj1ba5k99gbc7gmgy14sywyrjd8rpyqj5l905j0mjv8jg2")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("ladspa" ,ladspa) - ("libbs2b" ,libbs2b))) + (native-inputs (list pkg-config)) + (inputs (list ladspa libbs2b)) (home-page "https://sourceforge.net/projects/bs2b/") (synopsis "Bauer stereophonic-to-binaural DSP - LADSPA plugin") (description "The Bauer stereophonic-to-binaural DSP (bs2b) library and @@ -2438,11 +2405,9 @@ (define-public rtaudio (rename-file (string-append inc "/RtAudio.h") (string-append inc "/rtaudio/RtAudio.h")))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib jack-1 pulseaudio)) (synopsis "Common API for real-time audio I/O") (description "RtAudio is a set of C++ classes that provides a common API for real-time @@ -2478,7 +2443,7 @@ (define-public python-pyaudio "0x7vdsigm7xgvyg3shd3lj113m8zqj2pxmrgdyj66kmnw0qdxgwk")))) (build-system python-build-system) (inputs - `(("portaudio" ,portaudio))) + (list portaudio)) (home-page "https://people.csail.mit.edu/hubert/pyaudio/") (synopsis "Bindings for PortAudio v19") (description "This package provides bindings for PortAudio v19, the @@ -2502,9 +2467,9 @@ (define-public python-pyliblo (build-system python-build-system) (arguments `(#:tests? #f)) ;no tests (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (inputs - `(("liblo" ,liblo))) + (list liblo)) (home-page "http://das.nasophon.de/pyliblo/") (synopsis "Python bindings for liblo") (description @@ -2530,11 +2495,9 @@ (define-public python-soundfile "0yqhrfz7xkvqrwdxdx2ydy4h467sk7z3gf984y1x2cq7cm1gy329")))) (build-system python-build-system) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-numpy" ,python-numpy) - ("libsndfile" ,libsndfile))) + (list python-cffi python-numpy libsndfile)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (arguments `(#:tests? #f ; missing OGG support #:phases @@ -2585,15 +2548,15 @@ (define-public audio-to-midi "12wf17abn3psbsg2r2lk0xdnk8n5cd5rrvjlpxjnjfhd09n7qqgm")))) (build-system python-build-system) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-cython" ,python-cython) - ("python-numpy" ,python-numpy) - ("python-progressbar2" ,python-progressbar2) - ("python-pycparser" ,python-pycparser) - ("python-python3-midi" ,python-python3-midi) - ("python-soundfile" ,python-soundfile))) + (list python-cffi + python-cython + python-numpy + python-progressbar2 + python-pycparser + python-python3-midi + python-soundfile)) (native-inputs - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (arguments `(#:phases (modify-phases %standard-phases @@ -2639,13 +2602,9 @@ (define-public lilv "/lib/liblilv-0.so"))))))))) ;; Required by lilv-0.pc. (propagated-inputs - `(("lv2" ,lv2) - ("serd" ,serd) - ("sord" ,sord) - ("sratom" ,sratom))) + (list lv2 serd sord sratom)) (native-inputs - `(("python" ,python) - ("pkg-config" ,pkg-config))) + (list python pkg-config)) (home-page "https://drobilla.net/software/lilv") (synopsis "Library to simplify use of LV2 plugins in applications") (description @@ -2671,9 +2630,9 @@ (define-public lv2 #:configure-flags '("--no-plugins"))) (inputs ;; Leaving off cairo and gtk+-2.0 which are needed for example plugins - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://lv2plug.in/") (synopsis "LV2 audio plugin specification") (description @@ -2704,10 +2663,9 @@ (define-public lv2-mda-piano #:tests? #f ; no check target #:phases (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("lv2" ,lv2) - ("lvtk" ,lvtk))) + (list lv2 lvtk)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (native-search-paths (list (search-path-specification (variable "LV2_PATH") @@ -2752,11 +2710,9 @@ (define-public lvtk (assoc-ref %build-inputs "boost") "/include")))) (inputs - `(("boost" ,boost) - ("gtkmm" ,gtkmm-2) - ("lv2" ,lv2))) + (list boost gtkmm-2 lv2)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/lvtk/lvtk") (synopsis "C++ libraries for LV2 plugins") (description @@ -2799,8 +2755,7 @@ (define-public openal "\")"))) #t))))) (inputs - `(("alsa-lib" ,alsa-lib) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib pulseaudio)) (synopsis "3D audio API") (description "OpenAL provides capabilities for playing audio in a virtual 3D @@ -2832,7 +2787,7 @@ (define-public freealut (arguments `(#:tests? #f)) ; no check target (inputs - `(("openal" ,openal))) + (list openal)) (synopsis "Free implementation of OpenAL's ALUT standard") (description "freealut is the OpenAL Utility Toolkit.") (home-page "https://kcat.strangesoft.net/openal.html") @@ -2854,15 +2809,15 @@ (define-public patchage (arguments `(#:tests? #f)) ; no check target (inputs - `(("alsa-lib" ,alsa-lib) - ("boost" ,boost) - ("jack" ,jack-1) - ("ganv" ,ganv) - ("glibmm" ,glibmm) - ("gtkmm" ,gtkmm-2) - ("dbus-glib" ,dbus-glib))) + (list alsa-lib + boost + jack-1 + ganv + glibmm + gtkmm-2 + dbus-glib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://drobilla.net/software/patchage.html") (synopsis "Modular patch bay for audio and MIDI systems") (description @@ -2886,14 +2841,9 @@ (define-public pcaudiolib (arguments `(#:configure-flags '("--disable-static"))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("which" ,which))) + (list autoconf automake libtool pkg-config which)) (inputs - `(("alsa-lib" ,alsa-lib) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib pulseaudio)) (synopsis "Portable C audio library") (description "The Portable C Audio Library (pcaudiolib) provides a C@tie{}API to @@ -2918,14 +2868,9 @@ (define-public qjackctl (arguments '(#:tests? #f)) ; no check target (inputs - `(("jack" ,jack-1) - ("alsa-lib" ,alsa-lib) - ("portaudio" ,portaudio) - ("qtbase" ,qtbase-5) - ("qtx11extras" ,qtx11extras))) + (list jack-1 alsa-lib portaudio qtbase-5 qtx11extras)) (native-inputs - `(("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list pkg-config qttools)) (home-page "https://qjackctl.sourceforge.io/") (synopsis "Jack server control application") (description "Control a Jack server. Allows you to plug various sources @@ -2955,11 +2900,9 @@ (define-public qjackrcd (string-append "PREFIX=" (assoc-ref outputs "out")))))))) (native-inputs - `(("qtbase" ,qtbase-5))) ; for qmake + (list qtbase-5)) ; for qmake (inputs - `(("jack" ,jack-1) - ("libsndfile" ,libsndfile) - ("qtbase" ,qtbase-5))) + (list jack-1 libsndfile qtbase-5)) (home-page "https://sourceforge.net/projects/qjackrcd/") (synopsis "Stereo audio recorder for JACK") (description "QJackRcd is a simple graphical stereo recorder for JACK @@ -3051,10 +2994,7 @@ (define-public supercollider (delete-file scide) #t)))))) (native-inputs - `(("ableton-link" ,ableton-link) - ("pkg-config" ,pkg-config) - ("qttools" ,qttools) - ("xorg-server" ,xorg-server-for-tests))) + (list ableton-link pkg-config qttools xorg-server-for-tests)) (inputs `(("jack" ,jack-1) ("libsndfile" ,libsndfile) @@ -3074,7 +3014,7 @@ (define-public supercollider ("qtwebchannel" ,qtwebchannel) ("qtwebsockets" ,qtwebsockets))) (propagated-inputs ;to get native-search-path - `(("qtwebengine" ,qtwebengine))) + (list qtwebengine)) (home-page "https://github.com/supercollider/supercollider") (synopsis "Synthesis engine and programming language") (description "SuperCollider is a synthesis engine (@code{scsynth} or @@ -3100,12 +3040,9 @@ (define-public libshout-idjc (base32 "1r9z8ggxylr2ab0isaljbm574rplnlcb12758j994h54nh2vikwb")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libogg" ,libogg) - ("libtheora" ,libtheora) - ("libvorbis" ,libvorbis) - ("speex" ,speex))) + (list libogg libtheora libvorbis speex)) (home-page "http://idjc.sourceforge.net/") (synopsis "Broadcast streaming library with IDJC extensions") (description "This package provides libshout plus IDJC extensions.") @@ -3128,10 +3065,9 @@ (define-public raul `(#:python ,python-2 #:tests? #f)) ; no check target (inputs - `(("glib" ,glib) - ("boost" ,boost))) + (list glib boost)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://drobilla.net/software/raul/") (synopsis "Real-time audio utility library") (description @@ -3169,10 +3105,7 @@ (define-public resample "074zj8ydp05yy1hjcglfv3hkvj4cm50f9nralka1992pm6yf8yvy")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("libtool" ,libtool))) + (list autoconf automake pkg-config libtool)) (synopsis "Sampling rate conversion and filter design utilities") (description "This package contains the @command{resample} and @command{windowfilter} command line utilities. The @command{resample} command @@ -3209,11 +3142,9 @@ (define-public rubberband ((".*cp -f \\$\\(JNI_TARGET\\).*") "")) #t))))) (inputs - `(("ladspa" ,ladspa) - ("libsamplerate" ,libsamplerate) - ("vamp" ,vamp))) + (list ladspa libsamplerate vamp)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://breakfastquay.com/rubberband/") (synopsis "Audio time-stretching and pitch-shifting library") (description @@ -3235,13 +3166,9 @@ (define-public rtmidi "1k962ljpnwyjw9jjiky2372khhri1wqvrj5qsalfpys31xqzw31p")))) (build-system gnu-build-system) (inputs - `(("jack" ,jack-1) - ("alsa-lib" ,alsa-lib))) + (list jack-1 alsa-lib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "https://www.music.mcgill.ca/~gary/rtmidi") (synopsis "Cross-platform MIDI library for C++") (description @@ -3265,11 +3192,9 @@ (define-public sratom (arguments `(#:tests? #f)) ;no check target (propagated-inputs ;; In Requires of sratom-0.pc. - `(("lv2" ,lv2) - ("serd" ,serd) - ("sord" ,sord))) + (list lv2 serd sord)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://drobilla.net/software/sratom/") (synopsis "Library for serialising LV2 atoms to/from RDF") (description @@ -3297,7 +3222,7 @@ (define-public suil ("gtk+" ,gtk+) ("qt" ,qtbase-5))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://drobilla.net/software/suil/") (synopsis "Library for loading and wrapping LV2 plugin UIs") (description @@ -3373,17 +3298,17 @@ (define-public timidity++ "/share/freepats/freepats.cfg"))))) #t))))) (inputs - `(("alsa-lib" ,alsa-lib) - ("ao" ,ao) - ("flac" ,flac) - ("jack" ,jack-1) - ("libogg" ,libogg) - ("libvorbis" ,libvorbis) - ("speex" ,speex) - ("ncurses" ,ncurses) - ("freepats" ,freepats))) + (list alsa-lib + ao + flac + jack-1 + libogg + libvorbis + speex + ncurses + freepats)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://timidity.sourceforge.net/") (synopsis "Software synthesizer for playing MIDI files") (description @@ -3421,9 +3346,9 @@ (define-public vamp (string-append out "/lib/libvamp-hostsdk.la")))) #t))))) (inputs - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://vamp-plugins.org") (synopsis "Modular and extensible audio processing system") (description @@ -3446,7 +3371,7 @@ (define-public libsbsms (sha256 (base32 "1vmf84iy4dkwxv887grnlsfk43fmhd9gbg26gc2kgcv40sbkvayf")))) (build-system gnu-build-system) - (native-inputs `(("automake" ,automake))) + (native-inputs (list automake)) (arguments `(#:configure-flags ;; Disable the use of SSE unless on x86_64. @@ -3494,7 +3419,7 @@ (define-public libkeyfinder (native-inputs `(("catch" ,catch-framework2))) (inputs - `(("fftw" ,fftw))) + (list fftw)) (home-page "https://mixxxdj.github.io/libkeyfinder/") (synopsis "Musical key detection for digital audio") (description @@ -3588,10 +3513,9 @@ (define-public xmp "17i8fc7x7yn3z1x963xp9iv108gxfakxmdgmpv3mlm438w3n3g8x")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libxmp" ,libxmp) - ("pulseaudio" ,pulseaudio))) + (list libxmp pulseaudio)) (home-page "http://xmp.sourceforge.net/") (synopsis "Extended module player") (description @@ -3615,10 +3539,7 @@ (define-public soundtouch (base32 "12i6yg8vvqwyk412lxl2krbfby6hnxld8qxy0k4m5xp4g94jiq4p")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("file" ,file))) + (list autoconf automake libtool file)) (home-page "https://www.surina.net/soundtouch/") (synopsis "Audio processing library for changing tempo, pitch and playback rate") @@ -3647,18 +3568,18 @@ (define-public sox ;; bug reports. '("--with-distro=Guix System Distribution"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("ao" ,ao) - ("flac" ,flac) - ("lame" ,lame) - ("libid3tag" ,libid3tag) - ("libltdl" ,libltdl) - ("libmad" ,libmad) - ("libpng" ,libpng) - ("libvorbis" ,libvorbis) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib + ao + flac + lame + libid3tag + libltdl + libmad + libpng + libvorbis + pulseaudio)) (home-page "http://sox.sourceforge.net") (synopsis "Sound processing utility") (description @@ -3704,10 +3625,9 @@ (define-public twolame (base32 "0zf8sxqb02w07ah55b1y7ab643zmpbhn62spa9pqra0rc17l4dfc")))) (build-system gnu-build-system) (inputs - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (native-inputs - `(("perl" ,perl) - ("which" ,which))) ;used in tests/test.pl + (list perl which)) ;used in tests/test.pl (home-page "https://www.twolame.org/") (synopsis "MPEG Audio Layer 2 (MP2) encoder") (description @@ -3733,15 +3653,11 @@ (define-public portaudio (build-system gnu-build-system) (inputs ;; TODO: Add ASIHPI. - `(("alsa-lib" ,alsa-lib) - ("jack" ,jack-1))) + (list alsa-lib jack-1)) ;; Autoreconf is necessary because the audacity-compat patch modifies .in ;; files. (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (arguments '(#:tests? #f ;no 'check' target #:parallel-build? #f ;fails on some systems @@ -3794,12 +3710,9 @@ (define-public qsynth (arguments `(#:tests? #f)) ; no "check" phase (native-inputs - `(("qttools" ,qttools) - ("pkg-config" ,pkg-config))) + (list qttools pkg-config)) (inputs - `(("fluidsynth" ,fluidsynth) - ("qtbase" ,qtbase-5) - ("qtx11extras" ,qtx11extras))) + (list fluidsynth qtbase-5 qtx11extras)) (home-page "https://qsynth.sourceforge.io") (synopsis "Graphical user interface for FluidSynth") (description @@ -3822,13 +3735,13 @@ (define-public rsound (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf")))) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("ao" ,ao) - ("libsamplerate" ,libsamplerate) - ("openal" ,openal) - ("portaudio" ,portaudio) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib + jack-1 + ao + libsamplerate + openal + portaudio + pulseaudio)) (arguments '(#:phases (modify-phases %standard-phases @@ -3866,12 +3779,9 @@ (define-public xjackfreak (list (string-append "docdir=" (assoc-ref %outputs "out") "/share/doc/xjackfreak")))) (inputs - `(("jack" ,jack-1) - ("libx11" ,libx11) - ("libxt" ,libxt) - ("libxext" ,libxext))) + (list jack-1 libx11 libxt libxext)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/johnhldavis/xjackfreak") (synopsis "JACK audio frequency analyzer and display") (description @@ -3923,7 +3833,7 @@ (define-public zita-convolver #t)) ;; no configure script (delete 'configure)))) - (inputs `(("fftwf" ,fftwf))) + (inputs (list fftwf)) (home-page "https://kokkinizita.linuxaudio.org") (synopsis "Fast, partitioned convolution engine library") (description @@ -4021,8 +3931,7 @@ (define-public zita-alsa-pcmi ;; no configure script (delete 'configure)))) (inputs - `(("alsa-lib" ,alsa-lib) - ("fftw" ,fftw))) + (list alsa-lib fftw)) (home-page "https://kokkinizita.linuxaudio.org") (synopsis "C++ wrapper around the ALSA API") (description @@ -4048,10 +3957,7 @@ (define-public cuetools (build-system gnu-build-system) ;; The source checkout is not bootstrapped. (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("flex" ,flex) - ("bison" ,bison))) + (list autoconf automake flex bison)) (synopsis "Cue and toc file parsers and utilities") (description "Cuetools is a set of programs that are useful for manipulating and using CUE sheet (cue) files and Table of Contents (toc) files. CUE and TOC @@ -4177,8 +4083,7 @@ (define-public bs1770gain ,home-page)) #t)))) (build-system gnu-build-system) - (inputs `(("ffmpeg" ,ffmpeg) - ("sox" ,sox))) + (inputs (list ffmpeg sox)) (synopsis "Tool to adjust loudness of media files") (description "BS1770GAIN is a loudness scanner compliant with ITU-R BS.1770 and its @@ -4285,7 +4190,7 @@ (define-public python-pyalsaaudio (arguments `(#:tests? #f)) ; tests require access to ALSA devices. (inputs - `(("alsa-lib" ,alsa-lib))) + (list alsa-lib)) (home-page "https://larsimmisch.github.io/pyalsaaudio/") (synopsis "ALSA wrappers for Python") (description @@ -4344,20 +4249,17 @@ (define-public bluez-alsa (assoc-ref %outputs "out") "/etc/dbus-1/system.d")))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("bluez" ,bluez) - ("dbus" ,dbus) - ("glib" ,glib) - ("ldacbt" ,ldacbt) - ("libbsd" ,libbsd) - ("ncurses" ,ncurses) - ("ortp" ,ortp) - ("sbc" ,sbc))) + (list alsa-lib + bluez + dbus + glib + ldacbt + libbsd + ncurses + ortp + sbc)) (home-page "https://github.com/Arkq/bluez-alsa") (synopsis "Bluetooth ALSA backend") (description "This project is a rebirth of a direct integration between @@ -4406,23 +4308,23 @@ (define-public snd (copy-recursively "pix" (string-append doc "/pix")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("fftw" ,fftw) - ("flac" ,flac) - ("gmp" ,gmp) - ("gsl" ,gsl) - ("gtk+" ,gtk+) - ("jack" ,jack-1) - ("libsamplerate" ,libsamplerate) - ("mpc" ,mpc) - ("mpfr" ,mpfr) - ("mpg123" ,mpg123) - ("speex" ,speex) - ("timidity++" ,timidity++) - ("vorbis-tools" ,vorbis-tools) - ("wavpack" ,wavpack))) + (list alsa-lib + fftw + flac + gmp + gsl + gtk+ + jack-1 + libsamplerate + mpc + mpfr + mpg123 + speex + timidity++ + vorbis-tools + wavpack)) (synopsis "Sound editor") (home-page "https://ccrma.stanford.edu/software/snd/") (description @@ -4450,10 +4352,9 @@ (define-public noise-repellent (list (string-append "--prefix=" (assoc-ref %outputs "out") "/lib/lv2")))) (inputs - `(("lv2" ,lv2) - ("fftwf" ,fftwf))) + (list lv2 fftwf)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/lucianodato/noise-repellent") (synopsis "LV2 plugin for broadband noise reduction") (description "Noise Repellent is an LV2 plugin to reduce noise. It has @@ -4518,12 +4419,9 @@ (define-public lv2-speech-denoiser (invoke "make") (setenv "CFLAGS" old-CFLAGS)))))))) (inputs - `(("lv2" ,lv2))) + (list lv2)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "https://github.com/werman/noise-suppression-for-voice") (synopsis "Speech denoise LV2 plugin based on Xiph's RNNoise library") (description "RNNoise is a library that uses deep learning to apply @@ -4547,12 +4445,10 @@ (define-public cli-visualizer (build-system cmake-build-system) (native-inputs ;; TODO: Try using the latest googletest for versions > 1.8. - `( ;; ("googletest" ,googletest-1.8) - ("which" ,which))) + (list ;; ("googletest" ,googletest-1.8) + which)) (inputs - `(("fftw" ,fftw) - ("ncurses" ,ncurses) - ("pulseaudio" ,pulseaudio))) + (list fftw ncurses pulseaudio)) (arguments '(#:tests? #f ;; XXX Enable tests after patching them to use the system googletest. @@ -4592,13 +4488,9 @@ (define-public cava "1mziklmqifhnb4kg9ia2r56r8wjn6xp40bkpf484hsgqvnrccl86")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("fftw" ,fftw) - ("ncurses" ,ncurses) - ("pulseaudio" ,pulseaudio))) + (list fftw ncurses pulseaudio)) (arguments `(#:configure-flags (list (string-append "PREFIX=" %output) @@ -4679,9 +4571,7 @@ (define-public libfdk "1fkrnzs78fmj11n9z3l0w53i2fl16jcfiyavwidck9bzmkmsf486")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (home-page "https://github.com/mstorsjo/fdk-aac") (synopsis "Fraunhofer FDK AAC library") (description "FDK is a library for encoding and decoding Advanced Audio @@ -4709,13 +4599,13 @@ (define-public libopenshot-audio "03dygh85riljk7dpn5a5a0d22a2kz45fs13gzwqgnbzzr1k17p2y")))) (build-system cmake-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ;; The following are for JUCE GUI components: - ("libx11" ,libx11) - ("freetype" ,freetype) - ("libxrandr" ,libxrandr) - ("libxinerama" ,libxinerama) - ("libxcursor" ,libxcursor))) + (list alsa-lib + ;; The following are for JUCE GUI components: + libx11 + freetype + libxrandr + libxinerama + libxcursor)) (arguments `(#:tests? #f ;there are no tests #:configure-flags @@ -4746,10 +4636,8 @@ (define-public faudio '(#:tests? #f ; No tests. #:configure-flags '("-DGSTREAMER=ON"))) (build-system cmake-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("gstreamer" ,gstreamer) - ("gst-plugins-base" ,gst-plugins-base) - ("sdl2" ,sdl2))) + (native-inputs (list pkg-config)) + (inputs (list gstreamer gst-plugins-base sdl2)) (home-page "https://github.com/FNA-XNA/FAudio") (synopsis "XAudio reimplementation") (description "FAudio is an XAudio reimplementation that focuses solely on @@ -4774,12 +4662,9 @@ (define-public gnaural "1gq519c0imsh57zklyi0f8h64l3ai48lh672c834470z8c6kvbfi")))) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ("gtk+" ,gtk+-2) - ("libsndfile" ,libsndfile) - ("portaudio" ,portaudio))) + (list alsa-lib gtk+-2 libsndfile portaudio)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://gnaural.sourceforge.net/") (synopsis "Binaural beat synthesizer") (description "Gnaural is a programmable auditory binaural beat synthesizer @@ -4802,15 +4687,15 @@ (define-public darkice (base32 "05yq7lggxygrkd76yiqby3msrgdn082p0qlvmzzv9xbw8hmyra76")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("lame" ,lame) - ("libvorbis" ,libvorbis) - ("opus" ,opus) - ("twolame" ,twolame) - ("alsa-lib" ,alsa-lib) - ("pulseaudio" ,pulseaudio) - ("jack" ,jack-1) - ("libsamplerate" ,libsamplerate))) + (native-inputs (list pkg-config)) + (inputs (list lame + libvorbis + opus + twolame + alsa-lib + pulseaudio + jack-1 + libsamplerate)) (arguments `(#:configure-flags (list (string-append "--with-lame-prefix=" @@ -4839,8 +4724,7 @@ (define-public libltc (arguments `(#:parallel-tests? #f)) ;tests fail otherwise (native-inputs - `(("doxygen" ,doxygen) - ("pkg-config" ,pkg-config))) + (list doxygen pkg-config)) (synopsis "Encode or decode Linear/Longitudinal Time Code (LTC) audio") (description "Libltc is a POSIX-C Library for handling @dfn{Linear/Longitudinal Time Code} (LTC) data.") @@ -4904,11 +4788,9 @@ (define-public libsoundio (arguments `(#:tests? #f)) ;no tests included (inputs - `(("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib jack-1 pulseaudio)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://libsound.io") (synopsis "C library for real-time audio input and output") (description "@code{libsoundio} is a C library providing audio input and @@ -4933,9 +4815,9 @@ (define-public redkite (arguments `(#:tests? #f)) ;no tests included (propagated-inputs - `(("cairo" ,cairo))) + (list cairo)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Small GUI toolkit") (description "Redkite is a small GUI toolkit developed in C++17 and inspired from other well known GUI toolkits such as Qt and GTK. It is @@ -5006,7 +4888,7 @@ (define-public carla ;; For WRAP-SCRIPT above. ("guile" ,guile-2.2))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://kx.studio/Applications:Carla") (synopsis "Audio plugin host") (description "Carla is a modular audio plugin host, with features like @@ -5027,22 +4909,22 @@ (define-public ecasound (sha256 (base32 "1m7njfjdb7sqf0lhgc4swihgdr4snkg8v02wcly08wb5ar2fr2s6")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) ;; It would be nice to add mikmod to inputs if that gets packaged ;; eventually. - (inputs `(("alsa-lib" ,alsa-lib) - ("jack" ,jack-1) - ("mpg123" ,mpg123) - ("lame" ,lame) - ("vorbis-tools" ,vorbis-tools) - ("faad2" ,faad2) - ("flac" ,flac) - ("timidity++" ,timidity++) - ("libsndfile" ,libsndfile) - ("libsamplerate" ,libsamplerate) - ("ncurses" ,ncurses) - ("ladspa" ,ladspa) - ("lilv" ,lilv))) + (inputs (list alsa-lib + jack-1 + mpg123 + lame + vorbis-tools + faad2 + flac + timidity++ + libsndfile + libsamplerate + ncurses + ladspa + lilv)) (home-page "https://nosignal.fi/ecasound/index.php") (synopsis "Multitrack audio processing") (description "Ecasound is a software package designed for multitrack audio @@ -5079,10 +4961,9 @@ (define-public libaudec ;; Build the tests. `("-Dtests=true"))) (inputs - `(("libsamplerate" ,libsamplerate) - ("libsndfile" ,libsndfile))) + (list libsamplerate libsndfile)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Library for reading and resampling audio files") (description "libaudec is a wrapper library over ffmpeg, sndfile and libsamplerate for reading and resampling audio files, based on Robin Gareus' @@ -5110,11 +4991,9 @@ (define-public lv2lint `("-Delf-tests=true" ; for checking symbol visibility "-Donline-tests=true"))) ; for checking URI existence (inputs - `(("curl" ,curl) - ("libelf" ,libelf) - ("lilv" ,lilv))) + (list curl libelf lilv)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "LV2 plugin lint tool") (description "lv2lint is an LV2 lint-like tool that checks whether a given plugin and its UI(s) match up with the provided metadata and adhere @@ -5145,11 +5024,9 @@ (define-public lv2toweb (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("jalv" ,jalv) - ("lilv" ,lilv))) + (list jalv lilv)) (native-inputs - `(("help2man" ,help2man) - ("pkg-config" ,pkg-config))) + (list help2man pkg-config)) (synopsis "Documentation generator for LV2 plugins") (description "lv2toweb allows the user to create an xhtml page with information @@ -5174,12 +5051,11 @@ (define-public ztoolkit "07xl3cmdaf7k9mm58m93cn8i1jvgimmiifdw1w7v2jl88nx60pm1")))) (build-system meson-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) ;; These are listed as propagated inputs because they are dependencies ;; in pkgconfig. (propagated-inputs - `(("cairo" ,cairo) - ("libx11" ,libx11))) + (list cairo libx11)) (synopsis "GUI toolkit for LV2 plugins") (description "ZToolkit (Ztk) is a cross-platform GUI toolkit heavily inspired by GTK. It handles events and low level drawing on behalf of @@ -5210,8 +5086,7 @@ (define-public libinstpatch `(("glib:bin" ,glib "bin") ("pkg-config" ,pkg-config))) (inputs - `(("glib" ,glib) - ("libsndfile" ,libsndfile))) + (list glib libsndfile)) (home-page "http://www.swamiproject.org/") (synopsis "Instrument file software library") (description @@ -5282,9 +5157,7 @@ (define-public codec2 (base32 "1jpvr7bra8srz8jvnlbmhf8andbaavq5v01qjnp2f61za93rzwba")))) (build-system cmake-build-system) (native-inputs - `(("bc" ,bc) - ("octave" ,octave) - ("valgrind" ,valgrind))) + (list bc octave valgrind)) (arguments `(#:tests? #f ; TODO: Fix tests (paths, graphic toolkit, octave modules). #:phases @@ -5355,19 +5228,19 @@ (define-public ableton-link #t)))) (build-system cmake-build-system) (native-inputs - `(("catch" ,catch-framework) - ("python" ,python) ;for running tests - ("portaudio" ,portaudio) ;for portaudio examples - ("qtbase" ,qtbase-5) ;for Qt examples - ("qtdeclarative" ,qtdeclarative) - ("qttools" ,qttools))) + (list catch-framework + python ;for running tests + portaudio ;for portaudio examples + qtbase-5 ;for Qt examples + qtdeclarative + qttools)) (inputs - `(("jack" ,jack-1) ;for JACK examples - ("qtquickcontrols" ,qtquickcontrols))) ;for Qt examples + (list jack-1 ;for JACK examples + qtquickcontrols)) ;for Qt examples (propagated-inputs ;; This is because include/ableton/platforms/asio/AsioWrapper.hpp ;; contains '#include '. - `(("asio" ,asio))) + (list asio)) (arguments `(#:configure-flags '("-DLINK_BUILD_QT_EXAMPLES=ON" @@ -5521,7 +5394,7 @@ (define-public siggen (list "/bin" "/share/man/man1" "/share/man/man5")) (apply invoke "make" "sysinstall" make-flags))))))) (inputs - `(("ncurses" ,ncurses))) + (list ncurses)) (native-inputs `(("groff" ,groff-minimal) ; for nroff ("util-linux" ,util-linux))) ; for col @@ -5569,13 +5442,9 @@ (define-public python-pysox (add-installed-pythonpath inputs outputs) (invoke "pytest"))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-typing-extensions" ,python-typing-extensions))) + (list python-numpy python-typing-extensions)) (native-inputs - `(("sox" ,sox) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-soundfile" ,python-soundfile))) + (list sox python-pytest python-pytest-cov python-soundfile)) (home-page "https://github.com/rabitt/pysox") (synopsis "Python wrapper around SoX") (description "@code{python-pysox} is a wrapper around the @command{sox} @@ -5604,9 +5473,9 @@ (define-public mda-lv2 (list (string-append "--prefix=" (assoc-ref %outputs "out"))))) (inputs - `(("lv2" ,lv2))) + (list lv2)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (native-search-paths (list (search-path-specification (variable "LV2_PATH") diff --git a/gnu/packages/augeas.scm b/gnu/packages/augeas.scm index b3c4803e04..2fd933604c 100644 --- a/gnu/packages/augeas.scm +++ b/gnu/packages/augeas.scm @@ -44,11 +44,11 @@ (define-public augeas (build-system gnu-build-system) ;; Marked as "required" in augeas.pc. (propagated-inputs - `(("libxml2" ,libxml2))) + (list libxml2)) (inputs - `(("readline" ,readline))) + (list readline)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://augeas.net") (synopsis "Edit configuration files programmatically") (description diff --git a/gnu/packages/authentication.scm b/gnu/packages/authentication.scm index a8070f4789..f5fba35031 100644 --- a/gnu/packages/authentication.scm +++ b/gnu/packages/authentication.scm @@ -59,14 +59,11 @@ (define-public oath-toolkit (for-each delete-file (find-files lib "\\.a$")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config) - - ;; XXX: Perhaps this should be propagated from xmlsec. - ("libltdl" ,libltdl))) + (list pkg-config + ;; XXX: Perhaps this should be propagated from xmlsec. + libltdl)) (inputs - `(("linux-pam" ,linux-pam) - ("openssl" ,openssl) - ("xmlsec-openssl" ,xmlsec-openssl))) + (list linux-pam openssl xmlsec-openssl)) (home-page "https://www.nongnu.org/oath-toolkit/") (synopsis "One-time password (OTP) components") (description @@ -111,16 +108,9 @@ (define-public yubico-pam ;; The pam_test fails because ykclient fails to build a Curl handle. '(#:make-flags '("TESTS=util_test"))) (inputs - `(("linux-pam" ,linux-pam) - ("libyubikey" ,libyubikey) - ("ykclient" ,ykclient) - ("yubikey-personalization" ,yubikey-personalization))) + (list linux-pam libyubikey ykclient yubikey-personalization)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("asciidoc" ,asciidoc) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool asciidoc pkg-config)) (home-page "https://developers.yubico.com/yubico-pam") (synopsis "Yubico pluggable authentication module") (description "The Yubico PAM module provides an easy way to integrate the @@ -141,9 +131,9 @@ (define-public pamtester (base32 "1mdj1wj0adcnx354fs17928yn2xfr1hj5mfraq282dagi873sqw3")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("linux-pam" ,linux-pam))) + (list linux-pam)) (home-page "http://pamtester.sourceforge.net/") (synopsis "Utility for testing pluggable authentication modules (PAM) facility") (description diff --git a/gnu/packages/autogen.scm b/gnu/packages/autogen.scm index 968337ad8d..1fe742bbae 100644 --- a/gnu/packages/autogen.scm +++ b/gnu/packages/autogen.scm @@ -42,10 +42,8 @@ (define-public autogen (sha256 (base32 "16mlbdys8q4ckxlvxyhwkdnh1ay9f6g0cyp1kylkpalgnik398gq")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config) - ("which" ,which))) - (inputs `(("guile" ,guile-2.2) - ("perl" ,perl))) ; for doc generator mdoc + (native-inputs (list pkg-config which)) + (inputs (list guile-2.2 perl)) ; for doc generator mdoc (arguments '(#:configure-flags ;; XXX Needed to build 5.18.16. ./configure fails without it: diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm index 57efc4c477..a8bf36a966 100644 --- a/gnu/packages/autotools.scm +++ b/gnu/packages/autotools.scm @@ -63,8 +63,7 @@ (define-public autoconf-2.69 ("perl" ,perl) ("m4" ,m4))) (native-inputs - `(("perl" ,perl) - ("m4" ,m4))) + (list perl m4)) (arguments `(;; XXX: testsuite: 209 and 279 failed. The latter is an impurity. It ;; should use our own "cpp" instead of "/lib/cpp". @@ -313,7 +312,7 @@ (define-public autobuild (base32 "0gv7g61ja9q9zg1m30k4snqwwy1kq7b4df6sb7d2qra7kbdq8af1")))) (build-system gnu-build-system) - (inputs `(("perl" ,perl))) + (inputs (list perl)) (synopsis "Process generated build logs") (description "Autobuild is a package that processes build logs generated when building software. Autobuild is primarily focused on packages using @@ -465,7 +464,7 @@ (define-public libtool "0vxj52zm709125gwv9qqlw02silj8bnjnh4y07arrz60r31ai1vw")) (patches (search-patches "libtool-skip-tests2.patch")))) (build-system gnu-build-system) - (propagated-inputs `(("m4" ,m4))) + (propagated-inputs (list m4)) (native-inputs `(("m4" ,m4) ("perl" ,perl) ;; XXX: this shouldn't be necessary, but without it test @@ -562,7 +561,7 @@ (define-public config (install-file "doc/config.sub.1" man1) #t)))))) (native-inputs - `(("help2man" ,help2man))) + (list help2man)) (home-page "https://savannah.gnu.org/projects/config") (synopsis "Ubiquitous config.guess and config.sub scripts") (description "The `config.guess' script tries to guess a canonical system triple, @@ -618,7 +617,7 @@ (define-public pyconfigure (("/usr/bin/env python") (which "python3"))) #t))))) (inputs - `(("python" ,python-3))) + (list python-3)) (synopsis "@command{configure} interface for Python-based packages") (description "GNU pyconfigure provides template files for easily implementing diff --git a/gnu/packages/avr.scm b/gnu/packages/avr.scm index c113707283..3cc5a6964e 100644 --- a/gnu/packages/avr.scm +++ b/gnu/packages/avr.scm @@ -168,8 +168,7 @@ (define-public microscheme #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))))) (native-inputs - `(("unzip" ,unzip) - ("xxd" ,xxd))) + (list unzip xxd)) (home-page "https://github.com/ryansuchocki/microscheme/") (synopsis "Scheme subset for Atmel microcontrollers") (description diff --git a/gnu/packages/axoloti.scm b/gnu/packages/axoloti.scm index 411ebbc610..f680d6fb83 100644 --- a/gnu/packages/axoloti.scm +++ b/gnu/packages/axoloti.scm @@ -205,7 +205,7 @@ (define-public axoloti-runtime ;; for uploading compiled patches and firmware ("dfu-util" ,dfu-util-for-axoloti))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "http://www.axoloti.com/") (synopsis "Audio development environment for the Axoloti core board") (description @@ -351,9 +351,8 @@ (define-public axoloti-patcher ("java-jgit" ,java-jgit-4.2) ("axoloti-runtime" ,axoloti-runtime))) (native-inputs - `(("ant" ,ant) - ("zip" ,zip) ; for repacking the jar - ("unzip" ,unzip))) + (list ant zip ; for repacking the jar + unzip)) (description "The Axoloti patcher offers a “patcher” environment similar to Pure Data for sketching digital audio algorithms. The patches run on a standalone diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 5e147113b1..fdb84898bb 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -118,11 +118,11 @@ (define-public duplicity ("pygobject" ,python-pygobject) ("urllib3" ,python-urllib3))) (inputs - `(("dbus" ,dbus) ; dbus-launch (Gio backend) - ("librsync" ,librsync) - ("lftp" ,lftp) - ("gnupg" ,gnupg) ; gpg executable needed - ("util-linux" ,util-linux))) ; for setsid + (list dbus ; dbus-launch (Gio backend) + librsync + lftp + gnupg ; gpg executable needed + util-linux)) ; for setsid (arguments `(#:test-target "test" #:phases @@ -173,8 +173,7 @@ (define-public par2cmdline (base32 "11mx8q29cr0sryd11awab7y4mhqgbamb1ss77rffjj6in8pb4hdk")))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf))) + (list automake autoconf)) (build-system gnu-build-system) (synopsis "File verification and repair tools") (description "Par2cmdline uses Reed-Solomon error-correcting codes to @@ -200,14 +199,14 @@ (define-public hdup (base32 "02bnczg01cyhajmm4rhbnc0ja0dd9ikv9fwv28asxh1rlx9yr0b7")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (inputs - `(("glib" ,glib) - ("tar" ,tar) - ("lzop" ,lzop) - ("mcrypt" ,mcrypt) - ("openssh" ,openssh) - ("gnupg" ,gnupg-1))) + (list glib + tar + lzop + mcrypt + openssh + gnupg-1)) (arguments `(#:configure-flags `(,(string-append "--sbindir=" (assoc-ref %outputs "out") "/bin")) @@ -239,13 +238,13 @@ (define-public libarchive "16r95rlmikll1k8vbhh06vq6x3srkc10hzxjjf3021mjs2ld65qf")))) (build-system gnu-build-system) (inputs - `(("bzip2" ,bzip2) - ("libxml2" ,libxml2) - ("lzo" ,lzo) - ("nettle" ,nettle) - ("xz" ,xz) - ("zlib" ,zlib) - ("zstd" ,zstd "lib"))) + (list bzip2 + libxml2 + lzo + nettle + xz + zlib + `(,zstd "lib"))) (arguments `(#:configure-flags '("--disable-static") #:phases @@ -337,21 +336,15 @@ (define-public rdup (base32 "0bzyv6qmnivxnv9nw7lnfn46k0m1dlxcjj53zcva6v8y8084l1iw")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - - ;; For tests. - ("dejagnu" ,dejagnu))) + (list autoconf automake pkg-config + ;; For tests. + dejagnu)) (inputs ;; XXX Compiling with nettle (encryption) support requires patching out ;; -Werror from GNUmakefile.in. Then, rdup-tr-{en,de}crypt tests fail: ;; free(): invalid pointer ;; ** rdup-tr: SIGPIPE received, exiting - `(("glib" ,glib) - ("pcre" ,pcre) - ("libarchive" ,libarchive) - ("mcrypt" ,mcrypt))) + (list glib pcre libarchive mcrypt)) (arguments `(#:parallel-build? #f ;race conditions #:phases @@ -414,13 +407,11 @@ (define-public snapraid (setenv "VERSION" ,version) (patch-shebang "autover.sh")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf) - - ;; For the tests. - ("valgrind" ,valgrind))) + (list automake autoconf + ;; For the tests. + valgrind)) (inputs - `(("util-linux" ,util-linux "lib"))) ; libblkid + (list `(,util-linux "lib"))) ; libblkid (home-page "https://www.snapraid.it/") (synopsis "Efficient backups using parity snapshots across disk arrays") (description @@ -462,7 +453,7 @@ (define-public btar "0miklk4bqblpyzh1bni4x6lqn88fa8fjn15x1k1n8bxkx60nlymd")))) (build-system gnu-build-system) (inputs - `(("librsync" ,librsync-0.9))) + (list librsync-0.9)) (arguments `(#:make-flags `(,(string-append "PREFIX=" (assoc-ref %outputs "out")) ,(string-append "CC=" ,(cc-for-target))) @@ -493,10 +484,9 @@ (define-public rdiff-backup (base32 "11rvjcp77zwgkphz1kyf5yqgr3rlss7dm9xzmvpvc4lp99xq7drb")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (inputs - `(("python" ,python) - ("librsync" ,librsync))) + (list python librsync)) (arguments `(#:tests? #f)) ; Tests require root/sudo (home-page "https://rdiff-backup.net/") @@ -535,8 +525,7 @@ (define-public rsnapshot (lambda _ (invoke "make" "test")))))) (inputs - `(("perl" ,perl) - ("rsync" ,rsync))) + (list perl rsync)) (home-page "https://rsnapshot.org") (synopsis "Deduplicating snapshot backup utility based on rsync") (description "rsnapshot is a file system snapshot utility based on rsync. @@ -600,22 +589,20 @@ (define-public libchop ;; some obscure reason. Better skip it. (setenv "XFAIL_TESTS" "utils/block-server")))))) (native-inputs - `(("guile" ,guile-2.0) - ("gperf" ,gperf-3.0) ;see - ("pkg-config" ,pkg-config) - ("rpcsvc-proto" ,rpcsvc-proto))) ;for 'rpcgen' + (list guile-2.0 gperf-3.0 ;see + pkg-config rpcsvc-proto)) ;for 'rpcgen' (inputs - `(("guile" ,guile-2.0) - ("util-linux" ,util-linux) - ("libtirpc" ,libtirpc) - ("gnutls" ,gnutls) - ("tdb" ,tdb) - ("bdb" ,bdb) - ("gdbm" ,gdbm) - ("libgcrypt" ,libgcrypt) - ("lzo" ,lzo) - ("bzip2" ,bzip2) - ("zlib" ,zlib))) + (list guile-2.0 + util-linux + libtirpc + gnutls + tdb + bdb + gdbm + libgcrypt + lzo + bzip2 + zlib)) (home-page "https://nongnu.org/libchop/") (synopsis "Tools & library for data backup and distributed storage") (description @@ -740,16 +727,14 @@ (define-public borg (string-append share "/fish/vendor_completions.d"))) #t)))))) (native-inputs - `(("python-cython" ,python-cython) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-pytest" ,python-pytest))) + (list python-cython python-setuptools-scm python-pytest)) (inputs - `(("acl" ,acl) - ("libb2" ,libb2) - ("lz4" ,lz4) - ("openssl" ,openssl) - ("python-llfuse" ,python-llfuse) - ("zstd" ,zstd "lib"))) + (list acl + libb2 + lz4 + openssl + python-llfuse + `(,zstd "lib"))) (synopsis "Deduplicated, encrypted, authenticated and compressed backups") (description "Borg is a deduplicating backup program. Optionally, it supports compression and authenticated encryption. The main goal of Borg is to @@ -773,12 +758,9 @@ (define-public wimlib "04ny5s5z05gk6davbwkjkraan781k2xzw6kjwp75h6ncv45dv1sb")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("fuse" ,fuse) - ("libxml2" ,libxml2) - ("ntfs-3g" ,ntfs-3g) - ("openssl" ,openssl))) + (list fuse libxml2 ntfs-3g openssl)) (arguments `(#:configure-flags (list "--disable-static" @@ -889,10 +871,7 @@ (define write-man (for-each write-man man-pages) #t)))))) (inputs - `(("perl" ,perl) - ("rsync" ,rsync) - ("perl-libtime-period" ,perl-libtime-period) - ("perl-libtime-parsedate" ,perl-libtime-parsedate))) + (list perl rsync perl-libtime-period perl-libtime-parsedate)) (home-page "http://dirvish.org/") (synopsis "Fast, disk based, rotating network backup system") (description @@ -1038,11 +1017,7 @@ (define-public zbackup (arguments `(#:tests? #f)) ;no test (inputs - `(("lzo" ,lzo) - ("libressl" ,libressl) - ("protobuf" ,protobuf) - ("xz" ,xz) - ("zlib" ,zlib))) + (list lzo libressl protobuf xz zlib)) (home-page "http://zbackup.org") (synopsis "Versatile deduplicating backup tool") (description @@ -1076,12 +1051,10 @@ (define-public dump "--disable-readline" "--disable-rmt"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl) - ("zlib" ,zlib) - ("util-linux" ,util-linux "lib") - ("e2fsprogs" ,e2fsprogs))) + (list openssl zlib + `(,util-linux "lib") e2fsprogs)) (home-page "https://dump.sourceforge.io/") (synopsis "Ext2/3/4 file system dump/restore utilities") (description "Dump examines files in a file system, determines which ones @@ -1118,17 +1091,14 @@ (define-public burp (string-append prefix " 3600" suffix "\n"))) #t))))) (inputs - `(("acl" ,acl) - ("librsync" ,librsync) - ("ncurses" ,ncurses) ; for the live status monitor - ("openssl" ,openssl) - ("uthash" ,uthash) - ("zlib" ,zlib))) + (list acl + librsync + ncurses ; for the live status monitor + openssl + uthash + zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("check" ,check-0.14) - ("pkg-config" ,pkg-config))) + (list autoconf automake check-0.14 pkg-config)) (home-page "https://burp.grke.org") (synopsis "Differential backup and restore") (description "Burp is a network backup and restore program. It attempts @@ -1149,17 +1119,16 @@ (define-public disarchive "0jgc53rrbas8i4z13l2ii99cpav1ma73spsjg70ygihf0635r3dh")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("guile" ,guile-3.0) ;for cross-compilation - ("guile-gcrypt" ,guile-gcrypt) - ("guile-quickcheck" ,guile-quickcheck))) + (list autoconf + automake + pkg-config + guile-3.0 ;for cross-compilation + guile-gcrypt + guile-quickcheck)) (inputs - `(("guile" ,guile-3.0) - ("zlib" ,zlib))) + (list guile-3.0 zlib)) (propagated-inputs - `(("guile-gcrypt" ,guile-gcrypt))) + (list guile-gcrypt)) (home-page "https://ngyro.com/software/disarchive.html") (synopsis "Software archive disassembler") (description "Disarchive can disassemble software archives into data @@ -1200,15 +1169,10 @@ (define-public borgmatic ":" (getenv "PATH"))) (invoke "pytest"))))))) (inputs - `(("borg" ,borg) - ("python-colorama" ,python-colorama) - ("python-jsonschema" ,python-jsonschema) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml))) + (list borg python-colorama python-jsonschema python-requests + python-ruamel.yaml)) (native-inputs - `(("python-flexmock" ,python-flexmock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-flexmock python-pytest python-pytest-cov)) (home-page "https://torsion.org/borgmatic/") (synopsis "Simple, configuration-driven backup software") (description diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index 7e98367bbb..cf40ee94f6 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -137,8 +137,7 @@ (define-public bash (outputs '("out" "doc" ;1.7 MiB of HTML and extra files "include")) ;headers used by extensions - (inputs `(("readline" ,readline) - ("ncurses" ,ncurses))) ;TODO: add texinfo + (inputs (list readline ncurses)) ;TODO: add texinfo (arguments `(;; When cross-compiling, `configure' incorrectly guesses that job ;; control is missing. @@ -285,7 +284,7 @@ (define-public bash-completion (patches (search-patches "bash-completion-directories.patch")))) (build-system gnu-build-system) - (native-inputs `(("util-linux" ,util-linux))) + (native-inputs (list util-linux)) (arguments `(#:phases (modify-phases %standard-phases (add-after @@ -378,10 +377,8 @@ (define-public bats (base32 "0f59zh4d4pa1a7ybs5zl6h0csbqqv11lbnq0jl1dgwm1s6p49bsq")))) (inputs - `(("bash" ,bash) - ("coreutils" ,coreutils) - ("guile" ,guile-3.0) ;for wrap-script - ("grep" ,grep))) + (list bash coreutils guile-3.0 ;for wrap-script + grep)) (arguments `(#:modules ((guix build utils)) #:builder @@ -428,14 +425,14 @@ (define-public bash-ctypes (base32 "0s1sifqzqmr0dnciv06yqrpzgj11d7n0gy5zaxh6b3x8bx7k75l8")))) (build-system gnu-build-system) (inputs - `(("elfutils" ,elfutils) - ("libelf" ,libelf) - ("libffi" ,libffi) - ("zlib" ,zlib) - ;; Require a bash with C plugin support to build. - ("bash" ,bash))) + (list elfutils + libelf + libffi + zlib + ;; Require a bash with C plugin support to build. + bash)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/taviso/ctypes.sh") (synopsis "Foreign function interface for Bash") (description "Bash-ctypes is a Bash plugin that provides a foreign diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm index 9cff05d949..2072dd467c 100644 --- a/gnu/packages/batik.scm +++ b/gnu/packages/batik.scm @@ -84,7 +84,7 @@ (define-public java-w3c-smil-3.0 "))) #t))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.w3.org/Style/CSS/SAC/") (synopsis "W3C SAC interface for CSS parsers in Java") (description "This package provides a SAC interface by the W3C. @@ -136,9 +136,9 @@ (define-public java-w3c-svg-1.0 "))) #t))))) (propagated-inputs - `(("java-w3c-smil" ,java-w3c-smil-3.0))) + (list java-w3c-smil-3.0)) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.w3.org/Style/CSS/SAC/") (synopsis "W3C SVG 1.0 interface") (description "This package provides a SVG 1.0 interface.") @@ -189,7 +189,7 @@ (define-public java-w3c-sac (lambda* (#:key source #:allow-other-keys) (invoke "unzip" source)))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.w3.org/Style/CSS/SAC/") (synopsis "W3C SAC interface for CSS parsers in Java") (description "This package provides a SAC interface by the W3C. @@ -248,8 +248,7 @@ (define-public java-xmlgraphics-commons ("java-mockito" ,java-mockito-1) ("java-objenesis" ,java-objenesis))) (propagated-inputs - `(("java-commons-io" ,java-commons-io) - ("java-commons-logging-minimal" ,java-commons-logging-minimal))) + (list java-commons-io java-commons-logging-minimal)) (home-page "https://xmlgraphics.apache.org/commons/") (synopsis "XMLGraphics constants") (description "This package provides XMLGraphics constants (originally diff --git a/gnu/packages/bdw-gc.scm b/gnu/packages/bdw-gc.scm index 5ced11bb64..2698d56da0 100644 --- a/gnu/packages/bdw-gc.scm +++ b/gnu/packages/bdw-gc.scm @@ -60,7 +60,7 @@ (define-public libgc (%current-target-system))) '("--disable-gcj-support") '())))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (propagated-inputs (if (%current-target-system) ;; The build system refuses to check for compiler intrinsics when @@ -109,7 +109,7 @@ (define-public libgc-7 (sha256 (base32 "10jhhi79d5brwlsyhwgpnrmc8nhlf7aan2lk9xhgihk5jc6srbvc")))) - (propagated-inputs `(("libatomic-ops" ,libatomic-ops))))) + (propagated-inputs (list libatomic-ops)))) (define-public libgc/back-pointers (package/inherit diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index fdb00ca538..b3be9bfed4 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -94,9 +94,7 @@ (define-public fio (find-files oldbin script?)))))))) (outputs '("out" "utils")) (inputs - `(("libaio" ,libaio) - ("python" ,python) - ("zlib" ,zlib))) + (list libaio python zlib)) (home-page "https://github.com/axboe/fio") (synopsis "Flexible I/O tester") (description @@ -132,7 +130,7 @@ (define-public intel-mpi-benchmarks/openmpi #t)))) (build-system gnu-build-system) (inputs - `(("openmpi" ,openmpi))) + (list openmpi)) (arguments `(#:phases (modify-phases %standard-phases @@ -241,7 +239,7 @@ (define-public bonnie++ "010bmlmi0nrlp3aq7p624sfaj5a65lswnyyxk3cnz1bqig0cn2vf")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + (list perl)) (arguments '(#:tests? #f)) ; there are no tests (home-page "https://doc.coker.com.au/projects/bonnie/") (synopsis "Hard drive and file system benchmark suite") @@ -298,20 +296,18 @@ (define-public python-locust "not test_custom_exit_code" "not test_webserver") " and "))))))) (propagated-inputs - `(("python-configargparse" ,python-configargparse) - ("python-flask" ,python-flask) - ("python-flask-basicauth" ,python-flask-basicauth) - ("python-gevent" ,python-gevent) - ("python-geventhttpclient" ,python-geventhttpclient) - ("python-msgpack" ,python-msgpack) - ("python-psutil" ,python-psutil) - ("python-pyzmq" ,python-pyzmq) - ("python-requests" ,python-requests) - ("python-werkzeug" ,python-werkzeug))) + (list python-configargparse + python-flask + python-flask-basicauth + python-gevent + python-geventhttpclient + python-msgpack + python-psutil + python-pyzmq + python-requests + python-werkzeug)) (native-inputs - `(("python-mock" ,python-mock) - ("python-pyquery" ,python-pyquery) - ("python-pytest" ,python-pytest))) ;for more easily skipping tests + (list python-mock python-pyquery python-pytest)) ;for more easily skipping tests (home-page "https://locust.io/") (synopsis "Distributed load testing framework") (description "Locust is a performance testing tool that aims to be easy to @@ -383,8 +379,7 @@ (define-public clpeak (build-system cmake-build-system) (home-page "https://github.com/krrishnarraj/clpeak") (inputs - `(("opencl-clhpp" ,opencl-clhpp) - ("opencl-icd-loader" ,opencl-icd-loader))) + (list opencl-clhpp opencl-icd-loader)) (synopsis "OpenCL benchmark tool") (description "A synthetic benchmarking tool to measure peak capabilities of OpenCL diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44bf5c7d24..17d15c06c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -73,7 +73,7 @@ (define-public r-org-eck12-eg-db `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description @@ -103,7 +103,7 @@ (define-public r-org-bt-eg-db (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.Bt.eg.db") (synopsis "Genome wide annotation for Bovine") (description @@ -125,7 +125,7 @@ (define-public r-reactome-db (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/reactome.db/") (synopsis "Annotation maps for reactome") (description @@ -148,7 +148,7 @@ (define-public r-bsgenome-btaurus-ucsc-bostau8 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") @@ -171,7 +171,7 @@ (define-public r-bsgenome-celegans-ucsc-ce6 `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") (synopsis "Full genome sequences for Worm") @@ -196,7 +196,7 @@ (define-public r-bsgenome-celegans-ucsc-ce10 `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") (synopsis "Full genome sequences for Worm") @@ -221,7 +221,7 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") (synopsis "Full genome sequences for Fly") @@ -246,7 +246,7 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") (synopsis "Full genome sequences for Fly") @@ -271,9 +271,7 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-dmelanogaster-ucsc-dm3" - ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") (synopsis "Full masked genome sequences for Fly") (description @@ -301,7 +299,7 @@ (define-public r-bsgenome-drerio-ucsc-danrer11 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11") (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)") (description @@ -324,7 +322,7 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") (synopsis "Full genome sequences for Homo sapiens") @@ -347,7 +345,7 @@ (define-public r-bsgenome-hsapiens-ncbi-grch38 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) (build-system r-build-system) - (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (propagated-inputs (list r-bsgenome)) (home-page "https://bioconductor.org/packages/release/data/annotation/html/\ BSgenome.Hsapiens.NCBI.GRCh38.html") @@ -372,9 +370,7 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19-masked `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" - ,r-bsgenome-hsapiens-ucsc-hg19))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19)) (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") (synopsis "Full masked genome sequences for Homo sapiens") (description @@ -403,7 +399,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") (synopsis "Full genome sequences for Mouse") @@ -427,9 +423,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9-masked `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-mmusculus-ucsc-mm9" - ,r-bsgenome-mmusculus-ucsc-mm9))) + (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9)) (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description @@ -458,7 +452,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") (synopsis "Full genome sequences for Mouse") @@ -501,7 +495,7 @@ (define-public r-go-db `((upstream-name . "GO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/GO.db") (synopsis "Annotation maps describing the entire Gene Ontology") (description @@ -523,12 +517,12 @@ (define-public r-homo-sapiens `((upstream-name . "Homo.sapiens"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures + r-go-db + r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene + r-organismdbi + r-annotationdbi)) (home-page "https://bioconductor.org/packages/Homo.sapiens/") (synopsis "Annotation package for the Homo.sapiens object") (description @@ -550,13 +544,12 @@ (define-public r-mus-musculus (properties `((upstream-name . "Mus.musculus"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) - ("r-organismdbi" ,r-organismdbi) - ("r-txdb-mmusculus-ucsc-mm10-knowngene" - ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (list r-annotationdbi + r-genomicfeatures + r-go-db + r-org-mm-eg-db + r-organismdbi + r-txdb-mmusculus-ucsc-mm10-knowngene)) (home-page "https://bioconductor.org/packages/Mus.musculus") (synopsis "Annotation package for the Mus.musculus object") (description @@ -578,7 +571,7 @@ (define-public r-org-ce-eg-db `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description @@ -600,7 +593,7 @@ (define-public r-org-dm-eg-db `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description @@ -622,7 +615,7 @@ (define-public r-org-dr-eg-db `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description @@ -644,7 +637,7 @@ (define-public r-org-hs-eg-db `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description @@ -666,7 +659,7 @@ (define-public r-org-mm-eg-db `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description @@ -689,7 +682,7 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") (synopsis "Full genome sequences for Homo sapiens") @@ -713,7 +706,7 @@ (define-public r-bsgenome-hsapiens-ucsc-hg38 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") @@ -737,7 +730,7 @@ (define-public r-ensdb-hsapiens-v75 `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs - `(("r-ensembldb" ,r-ensembldb))) + (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description @@ -760,8 +753,7 @@ (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") (synopsis "Annotation package for TxDb object(s)") @@ -785,7 +777,7 @@ (define-public r-txdb-hsapiens-ucsc-hg19-knowngene `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -810,7 +802,7 @@ (define-public r-txdb-hsapiens-ucsc-hg38-knowngene `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -835,8 +827,7 @@ (define-public r-txdb-mmusculus-ucsc-mm9-knowngene `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") @@ -861,9 +852,7 @@ (define-public r-txdb-mmusculus-ucsc-mm10-knowngene `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-bsgenome r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") @@ -890,8 +879,7 @@ (define-public r-txdb-celegans-ucsc-ce6-ensgene `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description @@ -914,11 +902,8 @@ (define-public r-fdb-infiniummethylation-hg19 `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description @@ -942,7 +927,7 @@ (define-public r-illuminahumanmethylationepicmanifest `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) (build-system r-build-system) (propagated-inputs - `(("r-minfi" ,r-minfi))) + (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") (synopsis "Manifest for Illumina's EPIC methylation arrays") (description @@ -963,7 +948,7 @@ (define-public r-do-db `((upstream-name . "DO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/DO.db/") (synopsis "Annotation maps describing the entire Disease Ontology") (description @@ -985,7 +970,7 @@ (define-public r-pfam-db (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/PFAM.db") (synopsis "Set of protein ID mappings for PFAM") (description @@ -1009,12 +994,12 @@ (define-public r-phastcons100way-ucsc-hg19 `((upstream-name . "phastCons100way.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors)) (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") (synopsis "UCSC phastCons conservation scores for hg19") (description @@ -1040,7 +1025,7 @@ (define-public r-abadata `((upstream-name . "ABAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/ABAData/") (synopsis "Gene expression in human brain regions from Allen Brain Atlas") (description @@ -1087,29 +1072,29 @@ (define-public r-aneufinder "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-aneufinderdata" ,r-aneufinderdata) - ("r-ecp" ,r-ecp) - ("r-foreach" ,r-foreach) - ("r-doparallel" ,r-doparallel) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-bamsignals" ,r-bamsignals) - ("r-dnacopy" ,r-dnacopy) - ("r-biostrings" ,r-biostrings) - ("r-genomicalignments" ,r-genomicalignments) - ("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2) - ("r-ggdendro" ,r-ggdendro) - ("r-ggrepel" ,r-ggrepel) - ("r-reordercluster" ,r-reordercluster) - ("r-mclust" ,r-mclust) - ("r-cowplot" ,r-cowplot))) + (list r-knitr)) + (propagated-inputs + (list r-genomicranges + r-aneufinderdata + r-ecp + r-foreach + r-doparallel + r-biocgenerics + r-s4vectors + r-genomeinfodb + r-iranges + r-rsamtools + r-bamsignals + r-dnacopy + r-biostrings + r-genomicalignments + r-ggplot2 + r-reshape2 + r-ggdendro + r-ggrepel + r-reordercluster + r-mclust + r-cowplot)) (home-page "https://bioconductor.org/packages/AneuFinder/") (synopsis "Copy number variation analysis in single-cell-sequencing data") (description "This package implements functions for copy number variant @@ -1152,10 +1137,8 @@ (define-public r-biscuiteerdata `((upstream-name . "biscuiteerData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-curl" ,r-curl) - ("r-experimenthub" ,r-experimenthub))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationhub r-curl r-experimenthub)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biscuiteerData") (synopsis "Data package for Biscuiteer") (description @@ -1222,8 +1205,7 @@ (define-public r-genelendatabase `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs - `(("r-rtracklayer" ,r-rtracklayer) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-rtracklayer r-genomicfeatures)) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description @@ -1248,7 +1230,7 @@ (define-public r-genomationdata ;; make sense to build substitutes. (arguments `(#:substitutable? #f)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description @@ -1271,10 +1253,7 @@ (define-public r-pasilla "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-dexseq" ,r-dexseq) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts @@ -1325,7 +1304,7 @@ (define-public r-all (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase))) + (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description @@ -1350,7 +1329,7 @@ (define-public r-affydata (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy))) + (list r-affy)) (home-page "https://bioconductor.org/packages/affydata/") (synopsis "Affymetrix data for demonstration purposes") (description @@ -1400,12 +1379,12 @@ (define-public r-curatedtcgadata `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-experimenthub" ,r-experimenthub) - ("r-hdf5array" ,r-hdf5array) - ("r-multiassayexperiment" ,r-multiassayexperiment) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-annotationhub + r-experimenthub + r-hdf5array + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -1473,12 +1452,12 @@ (define-public r-coverageview "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rsamtools" ,r-rsamtools))) + (list r-s4vectors + r-iranges + r-genomicranges + r-genomicalignments + r-rtracklayer + r-rsamtools)) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of @@ -1500,16 +1479,16 @@ (define-public r-cummerbund "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fastcluster" ,r-fastcluster) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-fastcluster + r-ggplot2 + r-gviz + r-plyr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/cummeRbund/") (synopsis "Analyze Cufflinks high-throughput sequencing data") (description "This package allows for persistent storage, access, @@ -1560,12 +1539,12 @@ (define-public r-decipher "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-dbi + r-iranges + r-rsqlite + r-s4vectors + r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing @@ -1585,15 +1564,15 @@ (define-public r-deepsnv (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-vgam" ,r-vgam))) + (list r-biostrings + r-genomicranges + r-iranges + r-rhtslib + r-summarizedexperiment + r-variantannotation + r-vgam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gerstung-lab/deepSNV/") (synopsis "Detection of subclonal SNVs in deep sequencing data") (description @@ -1622,13 +1601,10 @@ (define-public r-delayedarray `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) + (list r-biocgenerics r-s4vectors r-iranges r-matrix + r-matrixgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") (synopsis "Delayed operations on array-like objects") (description @@ -1654,11 +1630,9 @@ (define-public r-derfinderhelper (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs - `(("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-iranges r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/leekgroup/derfinderHelper") (synopsis "Helper for derfinder") (description @@ -1681,17 +1655,17 @@ (define-public r-drimseq (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-edger + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-mass + r-reshape2 + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description @@ -1716,15 +1690,15 @@ (define-public r-bluster (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs - `(("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-cluster" ,r-cluster) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocneighbors + r-biocparallel + r-cluster + r-igraph + r-matrix + r-rcpp + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily @@ -1745,12 +1719,12 @@ (define-public r-ideoviz "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb))) + (list r-biobase + r-iranges + r-genomicranges + r-rcolorbrewer + r-rtracklayer + r-genomeinfodb)) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with @@ -1771,8 +1745,7 @@ (define-public r-iranges `((upstream-name . "IRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (home-page "https://bioconductor.org/packages/IRanges") (synopsis "Infrastructure for manipulating intervals on sequences") (description @@ -1799,37 +1772,37 @@ (define-public r-isoformswitchanalyzer (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-dexseq" ,r-dexseq) - ("r-dplyr" ,r-dplyr) - ("r-drimseq" ,r-drimseq) - ("r-edger" ,r-edger) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tximeta" ,r-tximeta) - ("r-tximport" ,r-tximport) - ("r-venndiagram" ,r-venndiagram) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-dexseq + r-dplyr + r-drimseq + r-edger + r-futile-logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-rcurl + r-readr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-tximeta + r-tximport + r-venndiagram + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/") (synopsis "Analyze alternative splicing in RNA-seq data") (description @@ -1853,11 +1826,7 @@ (define-public r-absfiltergsea (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description @@ -1881,10 +1850,9 @@ (define-public r-bisquerna (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) + (list r-biobase r-limsolve)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type @@ -1911,10 +1879,8 @@ (define-public r-deconstructsigs `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-reshape2" ,r-reshape2))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb + r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the @@ -1938,25 +1904,25 @@ (define-public r-nmf (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-bigmemory" ,r-bigmemory) ; suggested - ("r-synchronicity" ,r-synchronicity) ; suggested - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-pkgmaker" ,r-pkgmaker) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-registry" ,r-registry) - ("r-reshape2" ,r-reshape2) - ("r-rngtools" ,r-rngtools) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cluster + r-biobase + r-biocmanager + r-bigmemory ; suggested + r-synchronicity ; suggested + r-colorspace + r-digest + r-doparallel + r-foreach + r-ggplot2 + r-gridbase + r-pkgmaker + r-rcolorbrewer + r-registry + r-reshape2 + r-rngtools + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -1981,14 +1947,14 @@ (define-public r-affy "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-preprocesscore + r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description @@ -2009,7 +1975,7 @@ (define-public r-affycomp "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/affycomp/") (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") (description @@ -2032,9 +1998,7 @@ (define-public r-affycompatible `((upstream-name . "AffyCompatible"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-biostrings r-rcurl r-xml)) (home-page "https://bioconductor.org/packages/AffyCompatible/") (synopsis "Work with Affymetrix GeneChip files") (description @@ -2059,9 +2023,7 @@ (define-public r-affycontam (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affydata" ,r-affydata) - ("r-biobase" ,r-biobase))) + (list r-affy r-affydata r-biobase)) (home-page "https://bioconductor.org/packages/affyContam/") (synopsis "Structured corruption of Affymetrix CEL file data") (description @@ -2084,27 +2046,27 @@ (define-public r-affycoretools (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-edger" ,r-edger) - ("r-gcrma" ,r-gcrma) - ("r-glimma" ,r-glimma) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gplots" ,r-gplots) - ("r-hwriter" ,r-hwriter) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-oligoclasses" ,r-oligoclasses) - ("r-reportingtools" ,r-reportingtools) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xtable" ,r-xtable))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-edger + r-gcrma + r-glimma + r-ggplot2 + r-gostats + r-gplots + r-hwriter + r-lattice + r-limma + r-oligoclasses + r-reportingtools + r-rsqlite + r-s4vectors + r-xtable)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -2125,9 +2087,9 @@ (define-public r-affyio "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + (list r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bmbolstad/affyio") (synopsis "Tools for parsing Affymetrix data files") (description @@ -2177,13 +2139,13 @@ (define-public r-annotate "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-httr" ,r-httr) - ("r-xml" ,r-xml) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-httr + r-xml + r-xtable)) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") @@ -2205,15 +2167,15 @@ (define-public r-annotationdbi `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-keggrest" ,r-keggrest) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-dbi + r-keggrest + r-iranges + r-rsqlite + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -2235,10 +2197,9 @@ (define-public r-annotationfilter `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) + (list r-genomicranges r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -2262,16 +2223,16 @@ (define-public r-annotationforge `((upstream-name . "AnnotationForge"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-rcurl + r-rsqlite + r-s4vectors + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -2293,21 +2254,21 @@ (define-public r-annotationhub (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biocversion + r-curl + r-dplyr + r-httr + r-interactivedisplaybase + r-rappdirs + r-rsqlite + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -2334,10 +2295,7 @@ (define-public r-aroma-light (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/aroma.light") (synopsis "Methods for normalization and visualization of microarray data") (description @@ -2360,14 +2318,14 @@ (define-public r-bamsignals "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -2391,7 +2349,7 @@ (define-public r-biobase `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description @@ -2413,17 +2371,17 @@ (define-public r-biomart `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) + (list r-annotationdbi + r-biocfilecache + r-digest + r-httr + r-progress + r-rappdirs + r-stringr + r-xml + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -2479,11 +2437,9 @@ (define-public r-biocparallel (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) + (list r-futile-logger r-snow r-bh)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -2506,12 +2462,12 @@ (define-public r-biostrings `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-crayon + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -2534,25 +2490,25 @@ (define-public r-biovizbase (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-annotationdbi + r-annotationfilter + r-biocgenerics + r-biostrings + r-dichromat + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-hmisc + r-iranges + r-rcolorbrewer + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/biovizBase") (synopsis "Basic graphic utilities for visualization of genomic data") (description @@ -2576,16 +2532,16 @@ (define-public r-bsgenome `((upstream-name . "BSgenome"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/BSgenome") (synopsis "Infrastructure for Biostrings-based genome data packages") (description @@ -2607,16 +2563,16 @@ (define-public r-category (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-genefilter + r-graph + r-gseabase + r-matrix + r-rbgl + r-dbi)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -2636,28 +2592,27 @@ (define-public r-chipseeker "1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-boot" ,r-boot) - ("r-enrichplot" ,r-enrichplot) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-dplyr" ,r-dplyr) - ("r-plotrix" ,r-plotrix) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" - ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-knitr)) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-boot + r-enrichplot + r-iranges + r-genomeinfodb + r-genomicranges + r-genomicfeatures + r-ggplot2 + r-gplots + r-gtools + r-dplyr + r-plotrix + r-dplyr + r-magrittr + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://www.bioconductor.org/packages/ChIPseeker/") (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") (description "This package implements functions to retrieve the nearest @@ -2684,12 +2639,12 @@ (define-public r-chipseq "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-lattice + r-s4vectors + r-shortread)) (home-page "https://bioconductor.org/packages/chipseq") (synopsis "Package for analyzing ChIPseq data") (description @@ -2712,20 +2667,20 @@ (define-public r-complexheatmap `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-clue + r-colorspace + r-digest + r-doparallel + r-foreach + r-getoptlong + r-globaloptions + r-iranges + r-matrixstats + r-png + r-rcolorbrewer)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -2750,20 +2705,20 @@ (define-public r-copywriter (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel + r-chipseq + r-copyhelper + r-data-table + r-dnacopy + r-futile-logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors)) (home-page "https://github.com/PeeperLab/CopywriteR") (synopsis "Copy number information from targeted sequencing") (description @@ -2790,14 +2745,14 @@ (define-public r-deseq (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-biocgenerics + r-genefilter + r-geneplotter + r-lattice + r-locfit + r-mass + r-rcolorbrewer)) (home-page "https://www-huber.embl.de/users/anders/DESeq/") (synopsis "Differential gene expression analysis") (description @@ -2821,21 +2776,21 @@ (define-public r-deseq2 (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-genefilter + r-geneplotter + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-rcpp + r-rcpparmadillo + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -2859,25 +2814,25 @@ (define-public r-dexseq (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-deseq2 + r-genefilter + r-geneplotter + r-genomicranges + r-hwriter + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -2905,11 +2860,9 @@ (define-public r-dirichletmultinomial `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/DirichletMultinomial") (synopsis "Dirichlet-Multinomial mixture models for microbiome data") (description @@ -2933,20 +2886,20 @@ (define-public r-edaseq (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-aroma-light + r-biobase + r-biocgenerics + r-biocmanager + r-biomart + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -2972,10 +2925,7 @@ (define-public r-edger (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp + (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -3000,24 +2950,24 @@ (define-public r-ensembldb "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-protgenerics + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -3045,11 +2995,8 @@ (define-public r-fastseg "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase r-biocgenerics r-genomicranges r-iranges + r-s4vectors)) (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description @@ -3075,10 +3022,7 @@ (define-public r-gage "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) + (list r-annotationdbi r-go-db r-graph r-keggrest)) (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" "articles/10.1186/1471-2105-10-161")) (synopsis "Generally applicable gene-set enrichment for pathway analysis") @@ -3106,14 +3050,10 @@ (define-public r-genefilter "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) + (list r-annotate r-annotationdbi r-biobase r-biocgenerics + r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -3133,8 +3073,7 @@ (define-public r-geneoverlap "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gplots" ,r-gplots))) + (list r-rcolorbrewer r-gplots)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -3153,28 +3092,28 @@ (define-public r-genomation "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridbase + r-impute + r-iranges + r-matrixstats + r-plotrix + r-plyr + r-rcpp + r-readr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqpattern)) + (native-inputs + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -3202,13 +3141,10 @@ (define-public r-genomeinfodb `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") (description @@ -3232,15 +3168,15 @@ (define-public r-genomicalignments `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GenomicAlignments") (synopsis "Representation and manipulation of short genomic alignments") (description @@ -3265,23 +3201,23 @@ (define-public r-genomicfeatures `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicranges + r-iranges + r-rcurl + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -3309,18 +3245,18 @@ (define-public r-genomicfiles (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixgenerics + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -3343,13 +3279,9 @@ (define-public r-genomicranges `((upstream-name . "GenomicRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -3374,15 +3306,15 @@ (define-public r-gostats (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) + (list r-annotate + r-annotationdbi + r-annotationforge + r-biobase + r-category + r-go-db + r-graph + r-rgraphviz + r-rbgl)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -3405,14 +3337,14 @@ (define-public r-gseabase (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-graph + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -3433,7 +3365,7 @@ (define-public r-hpar "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -3457,12 +3389,10 @@ (define-public r-rhtslib ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) + (list curl zlib ; packages using rhtslib need to link with zlib + r-zlibbioc)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -3482,7 +3412,7 @@ (define-public r-impute (base32 "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/impute") (synopsis "Imputation for microarray data") @@ -3506,11 +3436,9 @@ (define-public r-interactivedisplaybase `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) + (list r-biocgenerics r-dt r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -3532,11 +3460,9 @@ (define-public r-keggrest (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) + (list r-biostrings r-httr r-png)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -3576,27 +3502,27 @@ (define-public r-methylkit (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-data-table + r-emdbook + r-fastseg + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-kernsmooth + r-limma + r-mclust + r-mgcv + r-qvalue + r-r-utils + r-rcpp + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-zlibbioc)) + (native-inputs + (list r-knitr)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -3624,12 +3550,12 @@ (define-public r-motifrg (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-iranges + r-seqlogo + r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description @@ -3650,7 +3576,7 @@ (define-public r-mutationalpatterns "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) @@ -3697,30 +3623,30 @@ (define-public r-msnbase (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mscoreutils" ,r-mscoreutils) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-biobase + r-biocgenerics + r-biocparallel + r-digest + r-ggplot2 + r-impute + r-iranges + r-lattice + r-maldiquant + r-mass + r-mscoreutils + r-mzid + r-mzr + r-pcamethods + r-plyr + r-protgenerics + r-rcpp + r-s4vectors + r-scales + r-vsn + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -3747,32 +3673,32 @@ (define-public r-msnid (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biocstyle + r-biostrings + r-data-table + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-iterators + r-msnbase + r-msmstests + r-mzid + r-mzr + r-protgenerics + r-purrr + r-r-cache + r-rcpp + r-reshape2 + r-rlang + r-runit + r-stringr + r-tibble + r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -3799,14 +3725,14 @@ (define-public r-mzid (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) + (list r-doparallel + r-foreach + r-iterators + r-plyr + r-protgenerics + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -3848,20 +3774,20 @@ (define-public r-mzr -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.28.0. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list ;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.28.0. + boost-for-mysql ; use this instead of the bundled boost sources + zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-ncdf4 + r-protgenerics + r-rcpp + r-rhdf5lib + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -3887,17 +3813,17 @@ (define-public r-organismdbi (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-dbi + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -3919,10 +3845,7 @@ (define-public r-pcamethods (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description @@ -3969,8 +3892,7 @@ (define-public r-rbgl (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-graph" ,r-graph))) + (list r-bh r-graph)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -3991,35 +3913,35 @@ (define-public r-rcas (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-data-table + r-dt + r-genomation + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gprofiler2 + r-iranges + r-knitr + r-pbapply + r-pheatmap + r-plotly + r-plotrix + r-proxy + r-ranger + r-rsqlite + r-rtracklayer + r-rmarkdown + r-s4vectors + pandoc)) + (native-inputs + (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -4042,16 +3964,16 @@ (define-public r-regioner (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-memoise + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -4074,27 +3996,27 @@ (define-public r-reportingtools `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-category" ,r-category) - ("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gseabase" ,r-gseabase) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-pfam-db" ,r-pfam-db) - ("r-r-utils" ,r-r-utils) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-deseq2 + r-edger + r-ggbio + r-ggplot2 + r-gostats + r-gseabase + r-hwriter + r-iranges + r-knitr + r-lattice + r-limma + r-pfam-db + r-r-utils + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -4121,10 +4043,9 @@ (define-public r-rhdf5 "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5filters r-rhdf5lib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -4151,11 +4072,11 @@ (define-public r-rhdf5filters (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5lib)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -4186,16 +4107,16 @@ (define-public r-rsamtools (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bitops + r-genomeinfodb + r-genomicranges + r-iranges + r-rhtslib + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -4221,11 +4142,7 @@ (define-public r-restfulr (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description @@ -4253,24 +4170,24 @@ (define-public r-rtracklayer (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-restfulr" ,r-restfulr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-biocio + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcurl + r-restfulr + r-rsamtools + r-s4vectors + r-xml + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description @@ -4296,13 +4213,13 @@ (define-public r-samr (properties `((upstream-name . "samr"))) (build-system r-build-system) (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-gsa + r-impute + r-matrixstats + r-openxlsx + r-shiny + r-shinyfiles)) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/SAM/") (synopsis "Significance analysis of Microarrays") (description @@ -4324,23 +4241,23 @@ (define-public r-scdblfinder (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-xgboost" ,r-xgboost))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-igraph + r-mass + r-matrix + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) (home-page "https://github.com/plger/scDblFinder") (synopsis "Detect multiplets in single-cell RNA sequencing data") (description @@ -4365,7 +4282,7 @@ (define-public r-seqlogo (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -4388,11 +4305,7 @@ (define-public r-seqpattern `((upstream-name . "seqPattern"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) + (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix)) (home-page "https://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") (description @@ -4415,24 +4328,24 @@ (define-public r-shortread (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rhtslib + r-hwriter + r-iranges + r-lattice + r-latticeextra + r-rsamtools + r-s4vectors + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/ShortRead") (synopsis "FASTQ input and manipulation tools") (description @@ -4459,22 +4372,22 @@ (define-public r-simplifyenrichment `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-cluster" ,r-cluster) - ("r-complexheatmap" ,r-complexheatmap) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-matrix" ,r-matrix) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-proxyc" ,r-proxyc) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-circlize + r-clue + r-cluster + r-complexheatmap + r-digest + r-getoptlong + r-go-db + r-gosemsim + r-matrix + r-org-hs-eg-db + r-proxyc + r-slam + r-tm)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary @@ -4498,12 +4411,9 @@ (define-public r-trajectoryutils `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-igraph r-matrix r-s4vectors r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/TrajectoryUtils") (synopsis "Single-cell trajectory analysis utilities") (description @@ -4525,15 +4435,15 @@ (define-public r-slingshot "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrixstats" ,r-matrixstats) - ("r-princurve" ,r-princurve) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-trajectoryutils" ,r-trajectoryutils))) + (list r-igraph + r-matrixstats + r-princurve + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/slingshot") (synopsis "Tools for ordering single-cell sequencing") (description "This package provides functions for inferring continuous, @@ -4558,15 +4468,15 @@ (define-public r-stringdb (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-hash" ,r-hash) - ("r-igraph" ,r-igraph) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-sqldf" ,r-sqldf))) + (list r-gplots + r-hash + r-igraph + r-plotrix + r-plyr + r-png + r-rcolorbrewer + r-rcurl + r-sqldf)) (home-page "https://git.bioconductor.org/packages/STRINGdb") (synopsis "Search tool for the retrieval of interacting proteins database") (description @@ -4590,22 +4500,22 @@ (define-public r-structuralvariantannotation (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description @@ -4629,17 +4539,17 @@ (define-public r-summarizedexperiment `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-delayedarray + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-matrixgenerics + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -4662,12 +4572,12 @@ (define-public r-sva "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) + (list r-edger + r-genefilter + r-mgcv + r-biocparallel + r-matrixstats + r-limma)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -4694,21 +4604,21 @@ (define-public r-systempiper (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-crayon" ,r-crayon) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-magrittr + r-rsamtools + r-s4vectors + r-shortread + r-stringr + r-summarizedexperiment + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -4737,15 +4647,15 @@ (define-public r-topgo `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) + (list r-annotationdbi + r-dbi + r-biobase + r-biocgenerics + r-go-db + r-graph + r-lattice + r-matrixstats + r-sparsem)) (home-page "https://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") (description @@ -4768,7 +4678,7 @@ (define-public r-tximport "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description @@ -4793,24 +4703,24 @@ (define-public r-variantannotation (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixgenerics + r-summarizedexperiment + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector + r-zlibbioc)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") @@ -4831,13 +4741,9 @@ (define-public r-vsn "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) + (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -4867,14 +4773,14 @@ (define-public r-xina (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs - `(("r-alluvial" ,r-alluvial) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-mclust" ,r-mclust) - ("r-plyr" ,r-plyr) - ("r-stringdb" ,r-stringdb))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-alluvial + r-ggplot2 + r-gridextra + r-igraph + r-mclust + r-plyr + r-stringdb)) + (native-inputs (list r-knitr)) (home-page "https://git.bioconductor.org/packages/XINA") (synopsis "Identifying proteins that exhibit similar patterns") (description @@ -4941,11 +4847,9 @@ (define-public r-xvector (("import\\(zlibbioc\\)") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/XVector") (synopsis "Representation and manpulation of external sequences") (description @@ -4985,15 +4889,15 @@ (define-public r-zellkonverter (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk" ,r-basilisk) - ("r-cli" ,r-cli) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-reticulate" ,r-reticulate) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk + r-cli + r-delayedarray + r-matrix + r-reticulate + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://github.com/theislab/zellkonverter") (synopsis "Conversion between AnnData and single-cell experiments objects") (description @@ -5017,12 +4921,12 @@ (define-public r-geneplotter "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-lattice + r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description @@ -5043,19 +4947,19 @@ (define-public r-oligoclasses (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-biostrings + r-dbi + r-ff + r-foreach + r-genomicranges + r-iranges + r-rsqlite + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description @@ -5077,21 +4981,21 @@ (define-public r-oligo "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-affxparser" ,r-affxparser) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-affxparser + r-affyio + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-ff + r-oligoclasses + r-preprocesscore + r-rsqlite + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -5113,10 +5017,9 @@ (define-public r-qvalue "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -5168,13 +5071,13 @@ (define-public r-apeglm (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs - `(("r-emdbook" ,r-emdbook) - ("r-genomicranges" ,r-genomicranges) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -5195,14 +5098,14 @@ (define-public r-greylistchip (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-mass" ,r-mass) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-mass + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high @@ -5223,29 +5126,29 @@ (define-public r-diffbind (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apeglm" ,r-apeglm) - ("r-ashr" ,r-ashr) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gplots" ,r-gplots) - ("r-greylistchip" ,r-greylistchip) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" , r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-systempiper" ,r-systempiper))) + (list r-amap + r-apeglm + r-ashr + r-biocparallel + r-deseq2 + r-dplyr + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gplots + r-greylistchip + r-iranges + r-lattice + r-limma + r-locfit + r-rcolorbrewer + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-systempiper)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description @@ -5268,13 +5171,13 @@ (define-public r-ripseeker (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rsamtools" ,r-rsamtools) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-s4vectors + r-iranges + r-genomicranges + r-summarizedexperiment + r-rsamtools + r-genomicalignments + r-rtracklayer)) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") @@ -5299,20 +5202,20 @@ (define-public r-mbkmeans "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-benchmarkme" ,r-benchmarkme) - ("r-biocparallel" ,r-biocparallel) - ("r-clusterr" ,r-clusterr) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-knitr)) + (propagated-inputs + (list r-beachmat + r-benchmarkme + r-biocparallel + r-clusterr + r-delayedarray + r-matrix + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for @@ -5332,10 +5235,7 @@ (define-public r-multtest "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-survival r-biocgenerics r-biobase r-mass)) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description @@ -5369,7 +5269,7 @@ (define-public r-graph "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -5391,8 +5291,7 @@ (define-public r-ggm (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-igraph" ,r-igraph))) + (list r-graph r-igraph)) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description @@ -5415,9 +5314,7 @@ (define-public r-perfmeas (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-limma" ,r-limma) - ("r-rbgl" ,r-rbgl))) + (list r-graph r-limma r-rbgl)) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description @@ -5441,9 +5338,7 @@ (define-public r-codedepends (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-codetools r-graph r-xml)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -5469,33 +5364,33 @@ (define-public r-chippeakanno (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-matrixstats" ,r-matrixstats) - ("r-multtest" ,r-multtest) - ("r-rbgl" ,r-rbgl) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-dbi + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-graph + r-interactionset + r-iranges + r-keggrest + r-matrixstats + r-multtest + r-rbgl + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -5523,7 +5418,7 @@ (define-public r-matrixgenerics `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats))) + (list r-matrixstats)) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description @@ -5547,7 +5442,7 @@ (define-public r-marray (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma))) + (list r-limma)) (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted @@ -5567,8 +5462,7 @@ (define-public r-cghbase (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-marray" ,r-marray))) + (list r-biobase r-marray)) (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5587,11 +5481,7 @@ (define-public r-cghcall (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-impute" ,r-impute) - ("r-dnacopy" ,r-dnacopy) - ("r-snowfall" ,r-snowfall))) + (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall)) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5610,16 +5500,16 @@ (define-public r-qdnaseq (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-cghcall" ,r-cghcall) - ("r-dnacopy" ,r-dnacopy) - ("r-future-apply" ,r-future-apply) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils) - ("r-rsamtools" ,r-rsamtools))) + (list r-biobase + r-cghbase + r-cghcall + r-dnacopy + r-future-apply + r-genomicranges + r-iranges + r-matrixstats + r-r-utils + r-rsamtools)) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, @@ -5644,9 +5534,7 @@ (define-public r-bayseq (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges))) + (list r-abind r-edger r-genomicranges)) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description @@ -5670,16 +5558,16 @@ (define-public r-chipcomp (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics + r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-mmusculus-ucsc-mm9 + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description @@ -5704,24 +5592,24 @@ (define-public r-riboprofiling (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sqldf" ,r-sqldf))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -5745,13 +5633,13 @@ (define-public r-riboseqr (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bayseq" ,r-bayseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-seqlogo" ,r-seqlogo))) + (list r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-seqlogo)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description @@ -5774,16 +5662,16 @@ (define-public r-interactionset `((upstream-name . "InteractionSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -5808,24 +5696,24 @@ (define-public r-genomicinteractions `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gviz + r-igraph + r-interactionset + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description @@ -5846,7 +5734,7 @@ (define-public r-ctc (base32 "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) - (propagated-inputs `(("r-amap" ,r-amap))) + (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") (synopsis "Cluster and tree conversion") (description @@ -5867,12 +5755,12 @@ (define-public r-goseq "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biasedurn" ,r-biasedurn) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genelendatabase" ,r-genelendatabase) - ("r-go-db" ,r-go-db) - ("r-mgcv" ,r-mgcv))) + (list r-annotationdbi + r-biasedurn + r-biocgenerics + r-genelendatabase + r-go-db + r-mgcv)) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description @@ -5894,15 +5782,15 @@ (define-public r-glimma (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-deseq2 + r-edger + r-htmlwidgets + r-jsonlite + r-limma + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -5927,8 +5815,7 @@ (define-public r-rots (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-rcpp)) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description @@ -5950,8 +5837,7 @@ (define-public r-plgem "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-biobase r-mass)) (home-page "http://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description @@ -5976,30 +5862,29 @@ (define-public r-inspect (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-desolve" ,r-desolve) - ("r-gdata" ,r-gdata) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plgem" ,r-plgem) - ("r-proc" ,r-proc) - ("r-rootsolve" ,r-rootsolve) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-txdb-mmusculus-ucsc-mm9-knowngene" - ,r-txdb-mmusculus-ucsc-mm9-knowngene))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-deseq2 + r-desolve + r-gdata + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-kernsmooth + r-plgem + r-proc + r-rootsolve + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-txdb-mmusculus-ucsc-mm9-knowngene)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -6023,11 +5908,9 @@ (define-public r-dnabarcodes (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -6052,12 +5935,9 @@ (define-public r-ruvseq (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edaseq" ,r-edaseq) - ("r-edger" ,r-edger) - ("r-mass" ,r-mass))) + (list r-biobase r-edaseq r-edger r-mass)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -6080,13 +5960,9 @@ (define-public r-biocneighbors (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -6112,10 +5988,8 @@ (define-public r-scaledmatrix (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-delayedarray r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/LTLA/ScaledMatrix") (synopsis "Create a DelayedMatrix of scaled and centered values") (description @@ -6140,14 +6014,14 @@ (define-public r-treeio (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidytree" ,r-tidytree))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-jsonlite + r-magrittr + r-rlang + r-tibble + r-tidytree)) + (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") (description @@ -6172,20 +6046,20 @@ (define-public r-ggtree (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-aplot" ,r-aplot) - ("r-dplyr" ,r-dplyr) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr) - ("r-tidytree" ,r-tidytree) - ("r-treeio" ,r-treeio) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-aplot + r-dplyr + r-ggfun + r-ggplot2 + r-magrittr + r-purrr + r-rlang + r-scales + r-tidyr + r-tidytree + r-treeio + r-yulab-utils)) + (native-inputs (list r-knitr)) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") (description @@ -6209,9 +6083,9 @@ (define-public r-metapod (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/metapod") (synopsis "Meta-analyses on p-values of differential analyses") (description @@ -6238,18 +6112,18 @@ (define-public r-biocsingular (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-irlba + r-matrix + r-rcpp + r-rsvd + r-s4vectors + r-scaledmatrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -6272,30 +6146,30 @@ (define-public r-destiny "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ggplot-multistats" ,r-ggplot-multistats) - ("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-irlba" ,r-irlba) - ("r-knn-covertree" ,r-knn-covertree) - ("r-matrix" ,r-matrix) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-rspectra" ,r-rspectra) - ("r-scales" ,r-scales) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-smoother" ,r-smoother) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vim" ,r-vim))) - (native-inputs - `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes + (list r-biobase + r-biocgenerics + r-ggplot-multistats + r-ggplot2 + r-ggthemes + r-irlba + r-knn-covertree + r-matrix + r-pcamethods + r-proxy + r-rcpp + r-rcppeigen + r-rcpphnsw + r-rspectra + r-scales + r-scatterplot3d + r-singlecellexperiment + r-smoother + r-summarizedexperiment + r-tidyr + r-tidyselect + r-vim)) + (native-inputs + (list r-nbconvertr)) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -6317,11 +6191,7 @@ (define-public r-savr (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) + (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml)) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description @@ -6343,25 +6213,25 @@ (define-public r-chipexoqual (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biovizbase" ,r-biovizbase) - ("r-broom" ,r-broom) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-biovizbase + r-broom + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hexbin + r-iranges + r-rcolorbrewer + r-rmarkdown + r-rsamtools + r-s4vectors + r-scales + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -6381,10 +6251,7 @@ (define-public r-copynumber "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description @@ -6405,7 +6272,7 @@ (define-public r-dnacopy "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/DNAcopy") (synopsis "DNA copy number data analysis") (description @@ -6430,9 +6297,7 @@ (define-public r-htscluster (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs - `(("r-capushe" ,r-capushe) - ("r-edger" ,r-edger) - ("r-plotrix" ,r-plotrix))) + (list r-capushe r-edger r-plotrix)) (home-page "https://cran.r-project.org/web/packages/HTSCluster") (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") (description @@ -6484,7 +6349,7 @@ (define-public r-nbpseq (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-qvalue" ,r-qvalue))) + (list r-qvalue)) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description @@ -6506,9 +6371,7 @@ (define-public r-ebseq (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-blockmodeling" ,r-blockmodeling) - ("r-gplots" ,r-gplots) - ("r-testthat" ,r-testthat))) + (list r-blockmodeling r-gplots r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -6528,23 +6391,23 @@ (define-public r-karyoploter "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-bamsignals" ,r-bamsignals) - ("r-bezier" ,r-bezier) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-bamsignals + r-bezier + r-biovizbase + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-memoise + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -6567,10 +6430,9 @@ (define-public r-lpsymphony "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -6598,12 +6460,9 @@ (define-public r-ihw (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-fdrtool" ,r-fdrtool) - ("r-lpsymphony" ,r-lpsymphony) - ("r-slam" ,r-slam))) + (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -6630,19 +6489,19 @@ (define-public r-icobra (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-limma" ,r-limma) - ("r-reshape2" ,r-reshape2) - ("r-rocr" ,r-rocr) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-shinydashboard" ,r-shinydashboard) - ("r-upsetr" ,r-upsetr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-dt + r-ggplot2 + r-limma + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinybs + r-shinydashboard + r-upsetr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -6667,11 +6526,9 @@ (define-public r-residualmatrix `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-delayedarray r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/ResidualMatrix") (synopsis "Create a DelayedMatrix of regression residuals") (description @@ -6697,23 +6554,23 @@ (define-public r-batchelor (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-residualmatrix" ,r-residualmatrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-matrix + r-rcpp + r-residualmatrix + r-s4vectors + r-scaledmatrix + r-scuttle + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/batchelor") (synopsis "Single-Cell Batch Correction Methods") (description @@ -6740,20 +6597,20 @@ (define-public r-mast (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-abind + r-biobase + r-biocgenerics + r-data-table + r-ggplot2 + r-plyr + r-progress + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -6774,38 +6631,38 @@ (define-public r-monocle "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocviews" ,r-biocviews) - ("r-cluster" ,r-cluster) - ("r-combinat" ,r-combinat) - ("r-ddrtree" ,r-ddrtree) - ("r-densityclust" ,r-densityclust) - ("r-dplyr" ,r-dplyr) - ("r-fastica" ,r-fastica) - ("r-ggplot2" ,r-ggplot2) - ("r-hsmmsinglecell" ,r-hsmmsinglecell) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-proxy" ,r-proxy) - ("r-qlcmatrix" ,r-qlcmatrix) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vgam" ,r-vgam) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocviews + r-cluster + r-combinat + r-ddrtree + r-densityclust + r-dplyr + r-fastica + r-ggplot2 + r-hsmmsinglecell + r-igraph + r-irlba + r-limma + r-mass + r-matrix + r-matrixstats + r-pheatmap + r-plyr + r-proxy + r-qlcmatrix + r-rann + r-rcpp + r-reshape2 + r-rtsne + r-slam + r-stringr + r-tibble + r-vgam + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -6837,11 +6694,11 @@ (define-public r-leidenbase (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://github.com/cole-trapnell-lab/leidenbase") (synopsis "R and C wrappers to run the Leiden find_partition function") (description @@ -6870,11 +6727,7 @@ (define-public r-sanssouci "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) (build-system r-build-system) (propagated-inputs - `(("r-generics" ,r-generics) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://pneuvial.github.io/sanssouci") (synopsis "Post Hoc multiple testing inference") (description @@ -6899,50 +6752,50 @@ (define-public r-monocle3 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-batchelor" ,r-batchelor) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-grr" ,r-grr) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-leidenbase" ,r-leidenbase) - ("r-limma" ,r-limma) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrix-utils" ,r-matrix-utils) - ("r-pbapply" ,r-pbapply) - ("r-pbmcapply" ,r-pbmcapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-pryr" ,r-pryr) - ("r-proxy" ,r-proxy) - ("r-pscl" ,r-pscl) - ("r-purrr" ,r-purrr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-rsample" ,r-rsample) - ("r-rtsne" ,r-rtsne) - ("r-shiny" ,r-shiny) - ("r-slam" ,r-slam) - ("r-spdep" ,r-spdep) - ("r-speedglm" ,r-speedglm) - ("r-stringr" ,r-stringr) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-uwot" ,r-uwot) - ("r-viridis" ,r-viridis))) + (list r-assertthat + r-batchelor + r-biobase + r-biocgenerics + r-delayedmatrixstats + r-dplyr + r-ggplot2 + r-ggrepel + r-grr + r-htmlwidgets + r-igraph + r-irlba + r-leidenbase + r-limma + r-lmtest + r-mass + r-matrix + r-matrix-utils + r-pbapply + r-pbmcapply + r-pheatmap + r-plotly + r-pryr + r-proxy + r-pscl + r-purrr + r-rann + r-rcpp + r-rcppparallel + r-reshape2 + r-reticulate + r-rhpcblasctl + r-rsample + r-rtsne + r-shiny + r-slam + r-spdep + r-speedglm + r-stringr + r-singlecellexperiment + r-tibble + r-tidyr + r-uwot + r-viridis)) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description @@ -6963,8 +6816,7 @@ (define-public r-noiseq (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-matrix" ,r-matrix))) + (list r-biobase r-matrix)) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description @@ -6990,19 +6842,19 @@ (define-public r-scdd (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-biocparallel" ,r-biocparallel) - ("r-ebseq" ,r-ebseq) - ("r-fields" ,r-fields) - ("r-ggplot2" ,r-ggplot2) - ("r-mclust" ,r-mclust) - ("r-outliers" ,r-outliers) - ("r-s4vectors" ,r-s4vectors) - ("r-scran" ,r-scran) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-arm + r-biocparallel + r-ebseq + r-fields + r-ggplot2 + r-mclust + r-outliers + r-s4vectors + r-scran + r-singlecellexperiment + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -7027,29 +6879,29 @@ (define-public r-scone "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) (build-system r-build-system) (propagated-inputs - `(("r-aroma-light" ,r-aroma-light) - ("r-biocparallel" ,r-biocparallel) - ("r-boot" ,r-boot) - ("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-compositions" ,r-compositions) - ("r-diptest" ,r-diptest) - ("r-edger" ,r-edger) - ("r-fpc" ,r-fpc) - ("r-gplots" ,r-gplots) - ("r-hexbin" ,r-hexbin) - ("r-limma" ,r-limma) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-mixtools" ,r-mixtools) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-ruvseq" ,r-ruvseq) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aroma-light + r-biocparallel + r-boot + r-class + r-cluster + r-compositions + r-diptest + r-edger + r-fpc + r-gplots + r-hexbin + r-limma + r-matrixgenerics + r-matrixstats + r-mixtools + r-rarpack + r-rcolorbrewer + r-rhdf5 + r-ruvseq + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -7072,18 +6924,18 @@ (define-public r-geoquery (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) + (list r-biobase + r-data-table + r-dplyr + r-httr + r-limma + r-magrittr + r-r-utils + r-readr + r-tidyr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -7106,7 +6958,7 @@ (define-public r-illuminaio "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs - `(("r-base64" ,r-base64))) + (list r-base64)) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description @@ -7127,9 +6979,7 @@ (define-public r-siggenes "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multtest" ,r-multtest) - ("r-scrime" ,r-scrime))) + (list r-biobase r-multtest r-scrime)) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") @@ -7153,19 +7003,19 @@ (define-public r-bumphunter "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dorng" ,r-dorng) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biocgenerics + r-dorng + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-iterators + r-limma + r-locfit + r-matrixstats + r-s4vectors)) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description @@ -7187,37 +7037,37 @@ (define-public r-minfi "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bumphunter" ,r-bumphunter) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-geoquery" ,r-geoquery) - ("r-hdf5array" ,r-hdf5array) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-nlme" ,r-nlme) - ("r-nor1mix" ,r-nor1mix) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quadprog" ,r-quadprog) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-s4vectors" ,r-s4vectors) - ("r-siggenes" ,r-siggenes) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bumphunter + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genefilter + r-genomeinfodb + r-genomicranges + r-geoquery + r-hdf5array + r-illuminaio + r-iranges + r-lattice + r-limma + r-mass + r-mclust + r-nlme + r-nor1mix + r-preprocesscore + r-quadprog + r-rcolorbrewer + r-reshape + r-s4vectors + r-siggenes + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -7238,27 +7088,27 @@ (define-public r-methylumi "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-minfi" ,r-minfi) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-fdb-infiniummethylation-hg19 + r-genefilter + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-illuminaio + r-iranges + r-lattice + r-matrixstats + r-minfi + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -7285,21 +7135,21 @@ (define-public r-lumi "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-methylumi" ,r-methylumi) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite))) + (list r-affy + r-annotate + r-annotationdbi + r-biobase + r-dbi + r-genomicfeatures + r-genomicranges + r-kernsmooth + r-lattice + r-mass + r-methylumi + r-mgcv + r-nleqslv + r-preprocesscore + r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description @@ -7325,26 +7175,26 @@ (define-public r-linnorm (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apcluster" ,r-apcluster) - ("r-ellipse" ,r-ellipse) - ("r-fastcluster" ,r-fastcluster) - ("r-fpc" ,r-fpc) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rtsne" ,r-rtsne) - ("r-statmod" ,r-statmod) - ("r-vegan" ,r-vegan) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-amap + r-apcluster + r-ellipse + r-fastcluster + r-fpc + r-ggdendro + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-mass + r-mclust + r-rcpp + r-rcpparmadillo + r-rtsne + r-statmod + r-vegan + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -7386,21 +7236,21 @@ (define-public r-ioniser (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bit64" ,r-bit64) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-rhdf5" ,r-rhdf5) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bit64 + r-dplyr + r-ggplot2 + r-magrittr + r-rhdf5 + r-shortread + r-stringr + r-tibble + r-tidyr + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -7427,10 +7277,7 @@ (define-public r-mutoss (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs - `(("r-multcomp" ,r-multcomp) - ("r-multtest" ,r-multtest) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix))) + (list r-multcomp r-multtest r-mvtnorm r-plotrix)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description @@ -7455,10 +7302,7 @@ (define-public r-metap "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mutoss" ,r-mutoss) - ("r-rdpack" ,r-rdpack) - ("r-tfisher" ,r-tfisher))) + (list r-lattice r-mutoss r-rdpack r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -7481,28 +7325,28 @@ (define-public r-tradeseq "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-pbapply" ,r-pbapply) - ("r-princurve" ,r-princurve) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-slingshot" ,r-slingshot) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-trajectoryutils" ,r-trajectoryutils) - ("r-viridis" ,r-viridis))) + (list r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-igraph + r-magrittr + r-mass + r-matrix + r-matrixstats + r-mgcv + r-pbapply + r-princurve + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-tibble + r-trajectoryutils + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description @@ -7529,9 +7373,7 @@ (define-public r-triform "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-yaml" ,r-yaml))) + (list r-biocgenerics r-iranges r-yaml)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description @@ -7554,20 +7396,20 @@ (define-public r-varianttools (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description @@ -7594,7 +7436,7 @@ (define-public r-heatplus (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description @@ -7619,11 +7461,9 @@ (define-public r-gosemsim (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-rcpp" ,r-rcpp))) + (list r-annotationdbi r-go-db r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -7647,8 +7487,7 @@ (define-public r-anota "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs - `(("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue))) + (list r-multtest r-qvalue)) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description @@ -7700,15 +7539,15 @@ (define-public r-fcscan (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-doparallel + r-foreach + r-genomicranges + r-iranges + r-plyr + r-rtracklayer + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/fcScan") (synopsis "Detect clusters of coordinates with user defined options") (description @@ -7733,16 +7572,16 @@ (define-public r-fgsea "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh + r-biocparallel + r-data-table + r-fastmatch + r-ggplot2 + r-gridextra + r-matrix + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -7766,16 +7605,16 @@ (define-public r-dose (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocparallel" ,r-biocparallel) - ("r-do-db" ,r-do-db) - ("r-fgsea" ,r-fgsea) - ("r-ggplot2" ,r-ggplot2) - ("r-gosemsim" ,r-gosemsim) - ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2))) + (list r-annotationdbi + r-biocparallel + r-do-db + r-fgsea + r-ggplot2 + r-gosemsim + r-qvalue + r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description @@ -7800,23 +7639,23 @@ (define-public r-enrichplot "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-aplot" ,r-aplot) - ("r-dose" ,r-dose) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggtree" ,r-ggtree) - ("r-gosemsim" ,r-gosemsim) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aplot + r-dose + r-ggplot2 + r-ggraph + r-ggtree + r-gosemsim + r-igraph + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-reshape2 + r-scatterpie + r-shadowtext + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -7840,21 +7679,21 @@ (define-public r-clusterprofiler `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-downloader" ,r-downloader) - ("r-dplyr" ,r-dplyr) - ("r-enrichplot" ,r-enrichplot) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-qvalue" ,r-qvalue) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-dose + r-downloader + r-dplyr + r-enrichplot + r-go-db + r-gosemsim + r-magrittr + r-plyr + r-qvalue + r-rlang + r-tidyr + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -7874,33 +7713,33 @@ (define-public r-clusterexperiment "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocsingular" ,r-biocsingular) - ("r-cluster" ,r-cluster) - ("r-delayedarray" ,r-delayedarray) - ("r-edger" ,r-edger) - ("r-hdf5array" ,r-hdf5array) - ("r-howmany" ,r-howmany) - ("r-kernlab" ,r-kernlab) - ("r-limma" ,r-limma) - ("r-locfdr" ,r-locfdr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mbkmeans" ,r-mbkmeans) - ("r-nmf" ,r-nmf) - ("r-phylobase" ,r-phylobase) - ("r-pracma" ,r-pracma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-zinbwave" ,r-zinbwave))) + (list r-knitr)) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocsingular + r-cluster + r-delayedarray + r-edger + r-hdf5array + r-howmany + r-kernlab + r-limma + r-locfdr + r-matrix + r-matrixstats + r-mbkmeans + r-nmf + r-phylobase + r-pracma + r-rcolorbrewer + r-rcpp + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-zinbwave)) (home-page "https://bioconductor.org/packages/clusterExperiment/") (synopsis "Compare clusterings for single-cell sequencing") (description "This package provides functionality for running and comparing @@ -7922,26 +7761,26 @@ (define-public r-mlinterfaces (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fpc" ,r-fpc) - ("r-gbm" ,r-gbm) - ("r-gdata" ,r-gdata) - ("r-genefilter" ,r-genefilter) - ("r-ggvis" ,r-ggvis) - ("r-hwriter" ,r-hwriter) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mlbench" ,r-mlbench) - ("r-pls" ,r-pls) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rpart" ,r-rpart) - ("r-sfsmisc" ,r-sfsmisc) - ("r-shiny" ,r-shiny) - ("r-threejs" ,r-threejs))) + (list r-annotate + r-biobase + r-biocgenerics + r-cluster + r-fpc + r-gbm + r-gdata + r-genefilter + r-ggvis + r-hwriter + r-magrittr + r-mass + r-mlbench + r-pls + r-rcolorbrewer + r-rcpp + r-rpart + r-sfsmisc + r-shiny + r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -7970,11 +7809,7 @@ (define-public r-annaffy (substitute* "DESCRIPTION" ((", KEGG.db") ""))))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-go-db" ,r-go-db))) + (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db)) (home-page "https://bioconductor.org/packages/annaffy/") (synopsis "Annotation tools for Affymetrix biological metadata") (description @@ -8000,10 +7835,9 @@ (define-public r-a4core (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet))) + (list r-biobase r-glmnet)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description @@ -8025,15 +7859,15 @@ (define-public r-a4classif (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet) - ("r-pamr" ,r-pamr) - ("r-rocr" ,r-rocr) - ("r-varselrf" ,r-varselrf))) + (list r-a4core + r-a4preproc + r-biobase + r-glmnet + r-pamr + r-rocr + r-varselrf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description @@ -8055,10 +7889,9 @@ (define-public r-a4preproc (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-biobase r-biocgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description @@ -8080,9 +7913,9 @@ (define-public r-a4reporting (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs - `(("r-xtable" ,r-xtable))) + (list r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description @@ -8104,16 +7937,16 @@ (define-public r-a4base (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-genefilter" ,r-genefilter) - ("r-glmnet" ,r-glmnet) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-mpm" ,r-mpm) - ("r-multtest" ,r-multtest))) + (list r-a4core + r-a4preproc + r-annaffy + r-biobase + r-genefilter + r-glmnet + r-gplots + r-limma + r-mpm + r-multtest)) (home-page "https://bioconductor.org/packages/a4Base/") (synopsis "Automated Affymetrix array analysis base package") (description @@ -8134,11 +7967,7 @@ (define-public r-a4 "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs - `(("r-a4base" ,r-a4base) - ("r-a4classif" ,r-a4classif) - ("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-a4reporting" ,r-a4reporting))) + (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) (home-page "https://bioconductor.org/packages/a4/") (synopsis "Automated Affymetrix array analysis umbrella package") (description @@ -8160,28 +7989,28 @@ (define-public r-abseqr (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-circlize" ,r-circlize) - ("r-flexdashboard" ,r-flexdashboard) - ("r-ggcorrplot" ,r-ggcorrplot) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-vegan" ,r-vegan) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-biocparallel + r-biocstyle + r-circlize + r-flexdashboard + r-ggcorrplot + r-ggdendro + r-ggplot2 + r-gridextra + r-knitr + r-plotly + r-plyr + r-png + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-stringr + r-vegan + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -8207,11 +8036,9 @@ (define-public r-bacon "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-ellipse" ,r-ellipse) - ("r-ggplot2" ,r-ggplot2))) + (list r-biocparallel r-ellipse r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description @@ -8235,11 +8062,7 @@ (define-public r-rgadem (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo))) + (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo)) (home-page "https://bioconductor.org/packages/rGADEM/") (synopsis "De novo sequence motif discovery") (description @@ -8261,15 +8084,15 @@ (define-public r-motiv (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-rgadem" ,r-rgadem) - ("r-s4vectors" ,r-s4vectors))) + (list gsl)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-lattice + r-rgadem + r-s4vectors)) (home-page "https://bioconductor.org/packages/MotIV/") (synopsis "Motif identification and validation") (description @@ -8291,15 +8114,15 @@ (define-public r-motifdb (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-splitstackshape" ,r-splitstackshape))) + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-splitstackshape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -8318,26 +8141,26 @@ (define-public r-motifbreakr (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-grimport" ,r-grimport) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-motifdb" ,r-motifdb) - ("r-motifstack" ,r-motifstack) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-grimport + r-gviz + r-iranges + r-matrixstats + r-motifdb + r-motifstack + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tfmpvalue + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -8371,13 +8194,9 @@ (define-public r-motifstack (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-xml" ,r-xml))) + (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -8402,22 +8221,22 @@ (define-public r-genomicscores (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biobase + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biostrings + r-delayedarray + r-genomeinfodb + r-genomicranges + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -8439,26 +8258,26 @@ (define-public r-atacseqqc (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-chippeakanno" ,r-chippeakanno) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-motifstack" ,r-motifstack) - ("r-preseqr" ,r-preseqr) - ("r-randomforest" ,r-randomforest) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-chippeakanno + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-genomicscores + r-iranges + r-kernsmooth + r-limma + r-motifstack + r-preseqr + r-randomforest + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description @@ -8486,15 +8305,15 @@ (define-public r-gofuncr (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-mapplots" ,r-mapplots) - ("r-rcpp" ,r-rcpp) - ("r-vioplot" ,r-vioplot))) + (list r-annotationdbi + r-genomicranges + r-gtools + r-iranges + r-mapplots + r-rcpp + r-vioplot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description @@ -8535,14 +8354,14 @@ (define-public r-abaenrichment (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-abadata" ,r-abadata) - ("r-data-table" ,r-data-table) - ("r-gofuncr" ,r-gofuncr) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp))) + (list r-abadata + r-data-table + r-gofuncr + r-gplots + r-gtools + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -8568,8 +8387,7 @@ (define-public r-annotationfuncs `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi))) + (list r-annotationdbi r-dbi)) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description @@ -8592,7 +8410,7 @@ (define-public r-annotationtools (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description @@ -8618,27 +8436,27 @@ (define-public r-allelicimbalance `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-nlme" ,r-nlme) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridextra + r-gviz + r-iranges + r-lattice + r-latticeextra + r-nlme + r-rsamtools + r-s4vectors + r-seqinr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -8660,16 +8478,16 @@ (define-public r-aucell (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-gseabase" ,r-gseabase) - ("r-mixtools" ,r-mixtools) - ("r-r-utils" ,r-r-utils) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-gseabase + r-mixtools + r-r-utils + r-s4vectors + r-shiny + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -8699,18 +8517,18 @@ (define-public r-ebimage (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fftwtools" ,r-fftwtools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jpeg" ,r-jpeg) - ("r-locfit" ,r-locfit) - ("r-png" ,r-png) - ("r-rcurl" ,r-rcurl) - ("r-tiff" ,r-tiff))) + (list r-abind + r-biocgenerics + r-fftwtools + r-htmltools + r-htmlwidgets + r-jpeg + r-locfit + r-png + r-rcurl + r-tiff)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description @@ -8737,18 +8555,17 @@ (define-public r-yamss "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ebimage" ,r-ebimage) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-mzr" ,r-mzr) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" - ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-ebimage + r-iranges + r-limma + r-matrix + r-mzr + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -8771,12 +8588,9 @@ (define-public r-gtrellis "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges))) + (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -8802,21 +8616,21 @@ (define-public r-somaticsignatures `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-nmf" ,r-nmf) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-nmf + r-pcamethods + r-proxy + r-reshape2 + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -8840,31 +8654,31 @@ (define-public r-yapsa (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-corrplot" ,r-corrplot) - ("r-dendextend" ,r-dendextend) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtrellis" ,r-gtrellis) - ("r-keggrest" ,r-keggrest) - ("r-limsolve" ,r-limsolve) - ("r-magrittr" ,r-magrittr) - ("r-pmcmr" ,r-pmcmr) - ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-somaticsignatures" ,r-somaticsignatures) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-circlize + r-complexheatmap + r-corrplot + r-dendextend + r-doparallel + r-dplyr + r-genomeinfodb + r-genomicranges + r-getoptlong + r-ggbeeswarm + r-ggplot2 + r-gridextra + r-gtrellis + r-keggrest + r-limsolve + r-magrittr + r-pmcmr + r-pracma + r-reshape2 + r-somaticsignatures + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -8888,12 +8702,12 @@ (define-public r-gcrma "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-xvector" ,r-xvector))) + (list r-affy + r-affyio + r-biobase + r-biocmanager + r-biostrings + r-xvector)) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description @@ -8924,11 +8738,7 @@ (define-public r-simpleaffy "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gcrma" ,r-gcrma) - ("r-genefilter" ,r-genefilter))) + (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter)) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description @@ -8952,7 +8762,7 @@ (define-public r-yaqcaffy "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs - `(("r-simpleaffy" ,r-simpleaffy))) + (list r-simpleaffy)) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description @@ -8974,15 +8784,15 @@ (define-public r-quantro "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-minfi" ,r-minfi) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-doparallel + r-foreach + r-ggplot2 + r-iterators + r-minfi + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -9007,19 +8817,19 @@ (define-public r-yarn "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biomart" ,r-biomart) - ("r-downloader" ,r-downloader) - ("r-edger" ,r-edger) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quantro" ,r-quantro) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr))) + (list r-biobase + r-biomart + r-downloader + r-edger + r-gplots + r-limma + r-matrixstats + r-preprocesscore + r-quantro + r-rcolorbrewer + r-readr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -9044,14 +8854,14 @@ (define-public r-roar "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description @@ -9074,17 +8884,17 @@ (define-public r-xbseq (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-locfit" ,r-locfit) - ("r-magrittr" ,r-magrittr) - ("r-matrixstats" ,r-matrixstats) - ("r-pracma" ,r-pracma) - ("r-roar" ,r-roar))) + (list r-biobase + r-deseq2 + r-dplyr + r-ggplot2 + r-locfit + r-magrittr + r-matrixstats + r-pracma + r-roar)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -9114,7 +8924,7 @@ (define-public r-massspecwavelet `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (propagated-inputs - `(("r-waveslim" ,r-waveslim))) + (list r-waveslim)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -9136,25 +8946,25 @@ (define-public r-xcms "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-massspecwavelet" ,r-massspecwavelet) - ("r-mscoreutils" ,r-mscoreutils) - ("r-msfeatures" ,r-msfeatures) - ("r-msnbase" ,r-msnbase) - ("r-mzr" ,r-mzr) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-iranges + r-lattice + r-massspecwavelet + r-mscoreutils + r-msfeatures + r-msnbase + r-mzr + r-plyr + r-protgenerics + r-rann + r-rcolorbrewer + r-robustbase + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -9178,11 +8988,9 @@ (define-public r-wrench (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats))) + (list r-limma r-locfit r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -9203,18 +9011,18 @@ (define-public r-wiggleplotr "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-purrr" ,r-purrr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-assertthat + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-purrr + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -9258,17 +9066,16 @@ (define-public r-webbioc "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs - `(("netpbm" ,netpbm) - ("perl" ,perl))) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-gcrma" ,r-gcrma) - ("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue) - ("r-vsn" ,r-vsn))) + (list netpbm perl)) + (propagated-inputs + (list r-affy + r-annaffy + r-biobase + r-biocmanager + r-gcrma + r-multtest + r-qvalue + r-vsn)) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description @@ -9291,15 +9098,15 @@ (define-public r-zinbwave "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-matrix" ,r-matrix) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-softimpute" ,r-softimpute) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocparallel + r-edger + r-genefilter + r-matrix + r-singlecellexperiment + r-softimpute + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-inflated negative binomial model for RNA-seq data") (description "This package implements a general and flexible zero-inflated @@ -9325,13 +9132,9 @@ (define-public r-zfpkm (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -9354,13 +9157,11 @@ (define-public r-rbowtie2 (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools))) + (list r-magrittr r-rsamtools)) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))) + (list samtools zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -9382,14 +9183,14 @@ (define-public r-progeny "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -9413,7 +9214,7 @@ (define-public r-arrmnormalization (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) - (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (propagated-inputs (list r-arrmdata)) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description @@ -9436,16 +9237,16 @@ (define-public r-biocfilecache (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-filelock" ,r-filelock) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite))) + (list r-curl + r-dbi + r-dbplyr + r-dplyr + r-filelock + r-httr + r-rappdirs + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -9468,7 +9269,7 @@ (define-public r-iclusterplus "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description @@ -9499,7 +9300,7 @@ (define-public r-rbowtie (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -9522,22 +9323,22 @@ (define-public r-sgseq (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-igraph + r-iranges + r-rsamtools + r-rtracklayer + r-runit + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -9577,11 +9378,9 @@ (define-public r-rhisat2 (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-sgseq" ,r-sgseq))) + (list r-genomicfeatures r-genomicranges r-sgseq)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -9605,25 +9404,25 @@ (define-public r-quasr (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rbowtie" ,r-rbowtie) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-iranges + r-rbowtie + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -9647,26 +9446,26 @@ (define-public r-rqc (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biocstyle + r-biostrings + r-biovizbase + r-genomicalignments + r-genomicfiles + r-ggplot2 + r-iranges + r-knitr + r-markdown + r-plyr + r-rcpp + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -9690,10 +9489,7 @@ (define-public r-birewire (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-tsne" ,r-tsne))) + (list r-igraph r-matrix r-slam r-tsne)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9718,9 +9514,7 @@ (define-public r-birta "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass))) + (list r-biobase r-limma r-mass)) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description @@ -9748,18 +9542,18 @@ (define-public r-multidataset (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-qqman" ,r-qqman) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-qqman + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -9784,10 +9578,9 @@ (define-public r-ropls "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multidataset" ,r-multidataset))) + (list r-biobase r-multidataset)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description @@ -9822,13 +9615,9 @@ (define-public r-biosigner "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-multidataset" ,r-multidataset) - ("r-randomforest" ,r-randomforest) - ("r-ropls" ,r-ropls))) + (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -9855,21 +9644,21 @@ (define-public r-annotatr "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-regioner" ,r-regioner) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-readr + r-regioner + r-reshape2 + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -9896,9 +9685,9 @@ (define-public r-rsubread "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -9923,12 +9712,12 @@ (define-public r-flowutils (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-flowcore" ,r-flowcore) - ("r-graph" ,r-graph) - ("r-runit" ,r-runit) - ("r-xml" ,r-xml))) + (list r-biobase + r-corpcor + r-flowcore + r-graph + r-runit + r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description @@ -9950,9 +9739,7 @@ (define-public r-consensusclusterplus `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs - `(("r-all" ,r-all) - ("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster))) + (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description @@ -9974,14 +9761,14 @@ (define-public r-cytolib (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib))) + (list r-bh + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rhdf5lib + r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -10003,17 +9790,17 @@ (define-public r-flowcore (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors))) + (list r-bh + r-biobase + r-biocgenerics + r-cytolib + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rprotobuflib + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -10035,10 +9822,7 @@ (define-public r-flowmeans (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-feature" ,r-feature) - ("r-flowcore" ,r-flowcore) - ("r-rrcov" ,r-rrcov))) + (list r-biobase r-feature r-flowcore r-rrcov)) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description @@ -10061,16 +9845,16 @@ (define-public r-ncdfflow (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-flowcore" ,r-flowcore) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-bh + r-biobase + r-biocgenerics + r-flowcore + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -10092,19 +9876,19 @@ (define-public r-ggcyto (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-data-table + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-hexbin + r-ncdfflow + r-plyr + r-rcolorbrewer + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description @@ -10129,17 +9913,17 @@ (define-public r-flowviz (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-flowcore" ,r-flowcore) - ("r-hexbin" ,r-hexbin) - ("r-idpmisc" ,r-idpmisc) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-flowcore + r-hexbin + r-idpmisc + r-kernsmooth + r-lattice + r-latticeextra + r-mass + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -10163,20 +9947,19 @@ (define-public r-flowclust `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-corpcor" ,r-corpcor) - ("r-ellipse" ,r-ellipse) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-graph" ,r-graph) - ("r-mnormt" ,r-mnormt))) + (list r-biobase + r-biocgenerics + r-clue + r-corpcor + r-ellipse + r-flowcore + r-flowviz + r-graph + r-mnormt)) (inputs - `(("gsl" ,gsl))) + (list gsl)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -10207,7 +9990,7 @@ (define-public r-rprotobuflib (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -10229,35 +10012,35 @@ (define-public r-flowworkspace (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-s3" ,r-aws-s3) - ("r-aws-signature" ,r-aws-signature) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aws-s3 + r-aws-signature + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-data-table + r-delayedarray + r-digest + r-dplyr + r-flowcore + r-ggplot2 + r-graph + r-lattice + r-latticeextra + r-matrixstats + r-ncdfflow + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-s4vectors + r-scales + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -10283,20 +10066,20 @@ (define-public r-flowstats (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fda" ,r-fda) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rrcov" ,r-rrcov))) + (list r-biobase + r-biocgenerics + r-cluster + r-fda + r-flowcore + r-flowviz + r-flowworkspace + r-kernsmooth + r-ks + r-lattice + r-mass + r-ncdfflow + r-rcolorbrewer + r-rrcov)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description @@ -10319,29 +10102,29 @@ (define-public r-opencyto (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-data-table" ,r-data-table) - ("r-flowclust" ,r-flowclust) - ("r-flowcore" ,r-flowcore) - ("r-flowstats" ,r-flowstats) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-graph" ,r-graph) - ("r-gtools" ,r-gtools) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rbgl" ,r-rbgl) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-clue + r-data-table + r-flowclust + r-flowcore + r-flowstats + r-flowviz + r-flowworkspace + r-graph + r-gtools + r-ks + r-lattice + r-mass + r-ncdfflow + r-plyr + r-r-utils + r-rbgl + r-rcolorbrewer + r-rcpp + r-rrcov)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -10363,38 +10146,37 @@ (define-public r-cytoml (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggcyto" ,r-ggcyto) - ("r-graph" ,r-graph) - ("r-jsonlite" ,r-jsonlite) - ("r-lattice" ,r-lattice) - ("r-opencyto" ,r-opencyto) - ("r-plyr" ,r-plyr) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-runit" ,r-runit) - ("r-tibble" ,r-tibble) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list libxml2 zlib)) + (propagated-inputs + (list r-base64enc + r-bh + r-biobase + r-corpcor + r-cytolib + r-data-table + r-dplyr + r-flowcore + r-flowworkspace + r-ggcyto + r-graph + r-jsonlite + r-lattice + r-opencyto + r-plyr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-runit + r-tibble + r-xml + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description @@ -10416,28 +10198,28 @@ (define-public r-flowsom (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-colorramps" ,r-colorramps) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggforce" ,r-ggforce) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-scattermore" ,r-scattermore) - ("r-tidyr" ,r-tidyr) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-colorramps + r-consensusclusterplus + r-cytoml + r-dplyr + r-flowcore + r-flowworkspace + r-ggforce + r-ggnewscale + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggrepel + r-igraph + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rlang + r-rtsne + r-scattermore + r-tidyr + r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description @@ -10459,23 +10241,23 @@ (define-public r-mixomics (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) - ("r-ellipse" ,r-ellipse) - ("r-ggrepel" ,r-ggrepel) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-corpcor + r-dplyr + r-ellipse + r-ggrepel + r-ggplot2 + r-gridextra + r-igraph + r-lattice + r-mass + r-matrixstats + r-rarpack + r-rcolorbrewer + r-reshape2 + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description @@ -10505,25 +10287,25 @@ (define-public r-depecher (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-mixomics" ,r-mixomics) - ("r-moments" ,r-moments) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-robustbase" ,r-robustbase) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-gmodels + r-gplots + r-mass + r-matrixstats + r-mixomics + r-moments + r-rcpp + r-rcppeigen + r-reshape2 + r-robustbase + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description @@ -10551,20 +10333,20 @@ (define-public r-rcistarget (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-arrow" ,r-arrow) - ("r-aucell" ,r-aucell) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-feather" ,r-feather) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gseabase" ,r-gseabase) - ("r-r-utils" ,r-r-utils) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-arrow + r-aucell + r-biocgenerics + r-data-table + r-dplyr + r-feather + r-genomeinfodb + r-genomicranges + r-gseabase + r-r-utils + r-summarizedexperiment + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -10593,12 +10375,8 @@ (define-public r-chicago (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-delaporte" ,r-delaporte) - ("r-hmisc" ,r-hmisc) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description @@ -10618,30 +10396,30 @@ (define-public r-cicero "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-monocle" ,r-monocle) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vgam" ,r-vgam))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-fnn + r-genomicranges + r-ggplot2 + r-glasso + r-gviz + r-igraph + r-iranges + r-matrix + r-monocle + r-plyr + r-reshape2 + r-s4vectors + r-stringi + r-stringr + r-tibble + r-tidyr + r-vgam)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description @@ -10668,9 +10446,9 @@ (define-public r-cicero-monocle3 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs - `(("r-monocle3" ,r-monocle3) - ,@(alist-delete "r-monocle" - (package-propagated-inputs r-cicero))))))) + (modify-inputs (package-propagated-inputs r-cicero) + (delete "r-monocle") + (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package @@ -10687,31 +10465,31 @@ (define-public r-circrnaprofiler `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gwascat" ,r-gwascat) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-universalmotif" ,r-universalmotif))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-deseq2 + r-dplyr + r-edger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gwascat + r-iranges + r-magrittr + r-r-utils + r-readr + r-reshape2 + r-rlang + r-rtracklayer + r-s4vectors + r-seqinr + r-stringi + r-stringr + r-universalmotif)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis @@ -10740,22 +10518,22 @@ (define-public r-cistopic (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) - (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-dosnow" ,r-dosnow) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (propagated-inputs + (list r-aucell + r-data-table + r-dplyr + r-dosnow + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description @@ -10788,24 +10566,24 @@ (define-public r-cistopic-next "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . "cisTopic"))) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-text2vec" ,r-text2vec))) + (list r-aucell + r-data-table + r-dosnow + r-dplyr + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors + r-text2vec)) (native-inputs - `(("r-knitr" ,r-knitr)))))) + (list r-knitr))))) (define-public r-genie3 (package @@ -10821,10 +10599,9 @@ (define-public r-genie3 (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reshape2" ,r-reshape2))) + (list r-dplyr r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -10846,7 +10623,7 @@ (define-public r-roc (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -10871,7 +10648,7 @@ (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) (build-system r-build-system) - (propagated-inputs `(("r-minfi" ,r-minfi))) + (propagated-inputs (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") (synopsis "Annotation for Illumina's 450k methylation arrays") @@ -10894,17 +10671,16 @@ (define-public r-watermelon (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-illuminahumanmethylation450kanno-ilmn12-hg19" - ,r-illuminahumanmethylation450kanno-ilmn12-hg19) - ("r-illuminaio" ,r-illuminaio) - ("r-limma" ,r-limma) - ("r-lumi" ,r-lumi) - ("r-matrixstats" ,r-matrixstats) - ("r-methylumi" ,r-methylumi) - ("r-roc" ,r-roc))) + (list r-biobase + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminaio + r-limma + r-lumi + r-matrixstats + r-methylumi + r-roc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description @@ -10955,11 +10731,9 @@ (define-public r-gdsfmt (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs - `(("lz4" ,lz4) - ("xz" ,xz) - ("zlib" ,zlib))) + (list lz4 xz zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -10991,14 +10765,14 @@ (define-public r-bigmelon (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gdsfmt" ,r-gdsfmt) - ("r-geoquery" ,r-geoquery) - ("r-illuminaio" ,r-illuminaio) - ("r-methylumi" ,r-methylumi) - ("r-minfi" ,r-minfi) - ("r-watermelon" ,r-watermelon))) + (list r-biobase + r-biocgenerics + r-gdsfmt + r-geoquery + r-illuminaio + r-methylumi + r-minfi + r-watermelon)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -11020,9 +10794,7 @@ (define-public r-seqbias (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib))) + (list r-biostrings r-genomicranges r-rhtslib)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description @@ -11048,13 +10820,13 @@ (define-public r-snplocs-hsapiens-dbsnp144-grch37 ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-bsgenome" ,r-bsgenome) - ("r-biostrings" ,r-biostrings))) + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") @@ -11084,9 +10856,7 @@ (define-public r-reqon (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs - `(("r-rjava" ,r-rjava) - ("r-rsamtools" ,r-rsamtools) - ("r-seqbias" ,r-seqbias))) + (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description @@ -11109,22 +10879,22 @@ (define-public r-wavcluster (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-foreach" ,r-foreach) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-mclust" ,r-mclust) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-foreach + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-mclust + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqinr + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -11157,23 +10927,23 @@ (define-public r-timeseriesexperiment `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-proxy" ,r-proxy) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vegan" ,r-vegan) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-deseq2 + r-dplyr + r-dynamictreecut + r-edger + r-ggplot2 + r-hmisc + r-limma + r-magrittr + r-proxy + r-s4vectors + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -11198,30 +10968,30 @@ (define-public r-variantfiltering `((upstream-name . "VariantFiltering"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-graph" ,r-graph) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-shinytree" ,r-shinytree) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-xvector" ,r-xvector))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-graph + r-gviz + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-shinytree + r-summarizedexperiment + r-variantannotation + r-xvector)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description @@ -11244,7 +11014,7 @@ (define-public r-genomegraphs (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart))) + (list r-biomart)) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description @@ -11272,16 +11042,16 @@ (define-public r-wavetiling (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomegraphs" ,r-genomegraphs) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-oligo" ,r-oligo) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-waveslim" ,r-waveslim))) + (list r-affy + r-biobase + r-biostrings + r-genomegraphs + r-genomicranges + r-iranges + r-oligo + r-oligoclasses + r-preprocesscore + r-waveslim)) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description @@ -11304,25 +11074,25 @@ (define-public r-variancepartition `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-pbkrtest" ,r-pbkrtest) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocparallel + r-doparallel + r-foreach + r-ggplot2 + r-gplots + r-iterators + r-limma + r-lme4 + r-lmertest + r-mass + r-matrix + r-pbkrtest + r-progress + r-reshape2 + r-rlang + r-scales)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -11348,11 +11118,7 @@ (define-public r-htqpcr (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer)) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") @@ -11383,8 +11149,7 @@ (define-public r-unifiedwmwqpcr `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-htqpcr" ,r-htqpcr))) + (list r-biocgenerics r-htqpcr)) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description @@ -11415,18 +11180,18 @@ (define-public r-universalmotif (substitute* "src/Makevars" (("/usr/bin/strip") (which "strip")))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppthread" ,r-rcppthread) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-mass + r-rcpp + r-rcppthread + r-rlang + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/universalmotif/") (synopsis @@ -11458,15 +11223,15 @@ (define-public r-activedriverwgs `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -11493,10 +11258,9 @@ (define-public r-activepathways `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2))) + (list r-data-table r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description @@ -11521,7 +11285,7 @@ (define-public r-bgmix (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description @@ -11543,10 +11307,7 @@ (define-public r-bgx (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gcrma" ,r-gcrma) - ("r-rcpp" ,r-rcpp))) + (list r-affy r-biobase r-gcrma r-rcpp)) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description @@ -11594,9 +11355,7 @@ (define-public r-bicare (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-gseabase" ,r-gseabase) - ("r-multtest" ,r-multtest))) + (list r-biobase r-gseabase r-multtest)) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description @@ -11618,10 +11377,9 @@ (define-public r-bifet (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-poibin" ,r-poibin))) + (list r-genomicranges r-poibin)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -11648,12 +11406,11 @@ (define-public r-rsbml (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml))) + (list libsbml)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph))) + (list r-biocgenerics r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description @@ -11675,7 +11432,7 @@ (define-public r-hypergraph (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description @@ -11696,11 +11453,9 @@ (define-public r-hyperdraw "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) - (inputs `(("graphviz" ,graphviz))) + (inputs (list graphviz)) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-hypergraph" ,r-hypergraph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-graph r-hypergraph r-rgraphviz)) (home-page "https://bioconductor.org/packages/hyperdraw") (synopsis "Visualizing hypergraphs") (description @@ -11721,12 +11476,12 @@ (define-public r-biggr (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs - `(("r-hyperdraw" ,r-hyperdraw) - ("r-hypergraph" ,r-hypergraph) - ("r-lim" ,r-lim) - ("r-limsolve" ,r-limsolve) - ("r-rsbml" ,r-rsbml) - ("r-stringr" ,r-stringr))) + (list r-hyperdraw + r-hypergraph + r-lim + r-limsolve + r-rsbml + r-stringr)) (home-page "https://bioconductor.org/packages/BiGGR/") (synopsis "Constraint based modeling using metabolic reconstruction databases") (description @@ -11752,9 +11507,9 @@ (define-public r-bigmemoryextras `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory))) + (list r-bigmemory)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -11785,26 +11540,26 @@ (define-public r-bigpint (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-dplyr" ,r-dplyr) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-hmisc" ,r-hmisc) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-shiny" ,r-shiny) - ("r-shinycssloaders" ,r-shinycssloaders) - ("r-shinydashboard" ,r-shinydashboard) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-delayedarray + r-dplyr + r-ggally + r-ggplot2 + r-gridextra + r-hexbin + r-hmisc + r-htmlwidgets + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-shiny + r-shinycssloaders + r-shinydashboard + r-stringr + r-summarizedexperiment + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -11828,23 +11583,23 @@ (define-public r-chemminer (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-jsonlite" ,r-jsonlite) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg) - ("r-stringi" ,r-stringi))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-bh + r-biocgenerics + r-dbi + r-digest + r-dt + r-ggplot2 + r-gridextra + r-jsonlite + r-png + r-rcpp + r-rcurl + r-rjson + r-rsvg + r-stringi)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -11870,10 +11625,8 @@ (define-public r-fmcsr (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-runit" ,r-runit))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics r-chemminer r-runit)) + (native-inputs (list r-knitr)) (home-page "https://github.com/girke-lab/fmcsR") (synopsis "Mismatch tolerant maximum common substructure searching") (description @@ -11902,15 +11655,15 @@ (define-public r-bioassayr (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-dbi" ,r-dbi) - ("r-matrix" ,r-matrix) - ("r-rjson" ,r-rjson) - ("r-rsqlite" ,r-rsqlite) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-chemminer + r-dbi + r-matrix + r-rjson + r-rsqlite + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description @@ -11937,12 +11690,9 @@ (define-public r-biobroom (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr))) + (list r-biobase r-broom r-dplyr r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -11969,11 +11719,7 @@ (define-public r-graphite (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-checkmate" ,r-checkmate) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs))) + (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -11996,16 +11742,16 @@ (define-public r-reactomepa (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-graphite" ,r-graphite) - ("r-igraph" ,r-igraph) - ("r-reactome-db" ,r-reactome-db))) + (list r-annotationdbi + r-dose + r-enrichplot + r-ggplot2 + r-ggraph + r-graphite + r-igraph + r-reactome-db)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -12028,9 +11774,7 @@ (define-public r-ebarrays (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice))) + (list r-biobase r-cluster r-lattice)) (home-page "https://bioconductor.org/packages/EBarrays/") (synopsis "Gene clustering and differential expression identification") (description @@ -12052,7 +11796,7 @@ (define-public r-bioccasestudies (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/BiocCaseStudies") (synopsis "Support for the case studies monograph") (description @@ -12074,16 +11818,16 @@ (define-public r-bioccheck `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) + (list r-codetools + r-graph + r-httr + r-knitr + r-optparse + r-biocmanager + r-biocviews + r-stringdist)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -12104,10 +11848,7 @@ (define-public r-biocgraph (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-geneplotter" ,r-geneplotter) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biocgenerics r-geneplotter r-graph r-rgraphviz)) (home-page "https://bioconductor.org/packages/biocGraph/") (synopsis "Graph examples and use cases in Bioinformatics") (description @@ -12129,13 +11870,9 @@ (define-public r-biocstyle `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -12157,13 +11894,13 @@ (define-public r-biocviews `((upstream-name . "biocViews"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) + (list r-biobase + r-biocmanager + r-graph + r-rbgl + r-rcurl + r-xml + r-runit)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -12185,15 +11922,15 @@ (define-public r-experimenthub (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-curl" ,r-curl) - ("r-rappdirs" ,r-rappdirs) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocmanager + r-curl + r-rappdirs + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -12219,13 +11956,13 @@ (define-public r-grohmm (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-mass + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/Kraus-Lab/groHMM") (synopsis "GRO-seq analysis pipeline") (description @@ -12247,15 +11984,15 @@ (define-public r-multiassayexperiment `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -12281,30 +12018,30 @@ (define-public r-bioconcotk (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs - `(("r-bigrquery" ,r-bigrquery) - ("r-car" ,r-car) - ("r-complexheatmap" ,r-complexheatmap) - ("r-curatedtcgadata" ,r-curatedtcgadata) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bigrquery + r-car + r-complexheatmap + r-curatedtcgadata + r-dbi + r-dplyr + r-dt + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-graph + r-httr + r-iranges + r-magrittr + r-plyr + r-rgraphviz + r-rjson + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -12326,11 +12063,9 @@ (define-public r-biocor (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix))) + (list r-biocparallel r-gseabase r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -12355,30 +12090,30 @@ (define-public r-biocpkgtools (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-gh" ,r-gh) - ("r-graph" ,r-graph) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rbgl" ,r-rbgl) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-biocmanager + r-biocviews + r-dplyr + r-dt + r-gh + r-graph + r-htmltools + r-htmlwidgets + r-httr + r-igraph + r-jsonlite + r-magrittr + r-rbgl + r-readr + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -12403,18 +12138,18 @@ (define-public r-biocset (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocio" ,r-biocio) - ("r-dplyr" ,r-dplyr) - ("r-keggrest" ,r-keggrest) - ("r-ontologyindex" ,r-ontologyindex) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-annotationdbi + r-biocio + r-dplyr + r-keggrest + r-ontologyindex + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -12442,17 +12177,17 @@ (define-public r-biocworkflowtools `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-bookdown" ,r-bookdown) - ("r-git2r" ,r-git2r) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr) - ("r-usethis" ,r-usethis))) + (list r-biocstyle + r-bookdown + r-git2r + r-httr + r-knitr + r-rmarkdown + r-rstudioapi + r-stringr + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") (synopsis "Tools to aid the development of Bioconductor Workflow packages") (description @@ -12474,8 +12209,7 @@ (define-public r-biodist (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-biobase r-kernsmooth)) (home-page "https://bioconductor.org/packages/bioDist/") (synopsis "Different distance measures") (description @@ -12497,21 +12231,21 @@ (define-public r-pcatools (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-cowplot" ,r-cowplot) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocparallel + r-biocsingular + r-cowplot + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-ggplot2 + r-ggrepel + r-lattice + r-matrix + r-rcpp + r-reshape2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description @@ -12543,12 +12277,8 @@ (define-public r-rgreat (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description @@ -12571,17 +12301,17 @@ (define-public r-m3c (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-corpcor" ,r-corpcor) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-matrixcalc" ,r-matrixcalc) - ("r-rtsne" ,r-rtsne) - ("r-umap" ,r-umap))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cluster + r-corpcor + r-doparallel + r-dosnow + r-foreach + r-ggplot2 + r-matrix + r-matrixcalc + r-rtsne + r-umap)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/M3C") (synopsis "Monte Carlo reference-based consensus clustering") (description @@ -12604,7 +12334,7 @@ (define-public r-icens (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://bioconductor.org/packages/Icens") (synopsis "NPMLE for censored and truncated data") (description @@ -12629,10 +12359,7 @@ (define-public r-interval (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs - `(("r-icens" ,r-icens) - ("r-mlecens" ,r-mlecens) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-icens r-mlecens r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/interval/") (synopsis "Weighted Logrank tests and NPMLE for interval censored data") (description @@ -12656,11 +12383,7 @@ (define-public r-fhtest (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs - `(("r-interval" ,r-interval) - ("r-kmsurv" ,r-kmsurv) - ("r-mass" ,r-mass) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-interval r-kmsurv r-mass r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/FHtest/") (synopsis "Tests for survival data based on the Fleming-Harrington class") (description @@ -12689,23 +12412,23 @@ (define-public r-fourcseq (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-deseq2 + r-fda + r-genomicalignments + r-genomicranges + r-ggbio + r-ggplot2 + r-gtools + r-lsd + r-matrix + r-reshape2 + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") (synopsis "Analysis of multiplexed 4C sequencing data") @@ -12755,7 +12478,7 @@ (define-public r-s4vectors `((upstream-name . "S4Vectors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/S4Vectors") (synopsis "S4 implementation of vectors and lists") (description @@ -12784,18 +12507,18 @@ (define-public r-wgcna (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) + (list r-annotationdbi + r-doparallel + r-dynamictreecut + r-fastcluster + r-foreach + r-go-db + r-hmisc + r-impute + r-rcpp + r-survival + r-matrixstats + r-preprocesscore)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -12834,11 +12557,11 @@ (define-public r-rgraphviz ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description @@ -12859,11 +12582,9 @@ (define-public r-fithic (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) + (list r-data-table r-fdrtool r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -12885,13 +12606,13 @@ (define-public r-hitc (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcolorbrewer + r-rtracklayer)) (home-page "https://bioconductor.org/packages/HiTC") (synopsis "High throughput chromosome conformation capture analysis") (description @@ -12915,16 +12636,16 @@ (define-public r-hdf5array (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-delayedarray + r-iranges + r-matrix + r-rhdf5 + r-rhdf5filters + r-rhdf5lib + r-s4vectors)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient @@ -13004,8 +12725,7 @@ (define-public r-rhdf5lib (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10) - ("zlib" ,zlib))) + (list hdf5-1.10 zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) @@ -13028,12 +12748,9 @@ (define-public r-beachmat "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -13056,29 +12773,29 @@ (define-public r-cner (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-powerlaw" ,r-powerlaw) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-annotate + r-biocgenerics + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-go-db + r-iranges + r-keggrest + r-powerlaw + r-r-utils + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ge11232002/CNEr") (synopsis "CNE Detection and Visualization") (description @@ -13106,27 +12823,27 @@ (define-public r-tfbstools (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-catools" ,r-catools) - ("r-cner" ,r-cner) - ("r-dbi" ,r-dbi) - ("r-dirichletmultinomial" ,r-dirichletmultinomial) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqlogo" ,r-seqlogo) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-catools + r-cner + r-dbi + r-dirichletmultinomial + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-rsqlite + r-rtracklayer + r-s4vectors + r-seqlogo + r-tfmpvalue + r-xml + r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ge11232002/TFBSTools") (synopsis "Transcription factor binding site (TFBS) analysis") (description @@ -13152,19 +12869,19 @@ (define-public r-motifmatchr (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifmatchr") (synopsis "Fast motif matching in R") (description @@ -13185,29 +12902,29 @@ (define-public r-chromvar (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-nabor" ,r-nabor) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-matrix + r-miniui + r-nabor + r-plotly + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rsamtools + r-rtsne + r-s4vectors + r-shiny + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") (synopsis "Determine chromatin variation across regions") (description @@ -13234,13 +12951,10 @@ (define-public r-singlecellexperiment `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomicranges" ,r-genomicranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -13264,18 +12978,18 @@ (define-public r-scuttle (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomicranges" ,r-genomicranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-matrix + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description @@ -13297,28 +13011,28 @@ (define-public r-scater "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-ggbeeswarm + r-ggplot2 + r-ggrepel + r-gridextra + r-matrix + r-rcolorbrewer + r-rlang + r-rtsne + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -13339,28 +13053,28 @@ (define-public r-scran "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-metapod" ,r-metapod) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-igraph + r-limma + r-matrix + r-metapod + r-rcpp + r-s4vectors + r-scuttle + r-singlecellexperiment + r-statmod + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -13384,11 +13098,8 @@ (define-public r-sparsematrixstats `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-matrix r-matrixgenerics r-matrixstats r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description @@ -13412,15 +13123,15 @@ (define-public r-delayedmatrixstats `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors) - ("r-sparsematrixstats" ,r-sparsematrixstats))) + (list r-delayedarray + r-iranges + r-matrix + r-matrixgenerics + r-matrixstats + r-s4vectors + r-sparsematrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -13447,12 +13158,9 @@ (define-public r-mscoreutils (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-clue" ,r-clue) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-clue r-mass r-rcpp r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description @@ -13478,11 +13186,9 @@ (define-public r-msfeatures (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-mscoreutils" ,r-mscoreutils) - ("r-protgenerics" ,r-protgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-mscoreutils r-protgenerics r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsFeatures") (synopsis "Functionality for mass spectrometry features") (description @@ -13511,10 +13217,9 @@ (define-public r-biocio (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description @@ -13545,10 +13250,7 @@ (define-public r-msmseda (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-msnbase" ,r-msnbase) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-gplots r-mass r-msnbase r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/msmsEDA") (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") @@ -13571,10 +13273,7 @@ (define-public r-msmstests (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-msmseda" ,r-msmseda) - ("r-msnbase" ,r-msnbase) - ("r-qvalue" ,r-qvalue))) + (list r-edger r-msmseda r-msnbase r-qvalue)) (home-page "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") @@ -13603,34 +13302,34 @@ (define-public r-catalyst (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-drc" ,r-drc) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-nnls" ,r-nnls) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-data-table + r-dplyr + r-drc + r-flowcore + r-flowsom + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-magrittr + r-matrix + r-matrixstats + r-nnls + r-purrr + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") @@ -13660,22 +13359,22 @@ (define-public r-erma "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicfiles + r-genomicranges + r-ggplot2 + r-homo-sapiens + r-iranges + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -13710,35 +13409,35 @@ (define-public r-ggbio (("fechable") "fetchable")) #t))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-biovizbase + r-bsgenome + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-gtable + r-hmisc + r-iranges + r-organismdbi + r-reshape2 + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -13776,21 +13475,21 @@ (define-public r-gqtlbase (("importFrom\\(ff,.*") "import(ff)\n")) #t))))) (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-batchjobs + r-bbmisc + r-biocgenerics + r-bit + r-doparallel + r-ff + r-ffbase + r-foreach + r-genomicfiles + r-genomicranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -13813,38 +13512,38 @@ (define-public r-gqtlstats (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-batchjobs + r-bbmisc + r-beeswarm + r-biobase + r-biocgenerics + r-doparallel + r-dplyr + r-erma + r-ffbase + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-ggbeeswarm + r-ggplot2 + r-gqtlbase + r-hardyweinberg + r-homo-sapiens + r-iranges + r-limma + r-mgcv + r-plotly + r-reshape2 + r-s4vectors + r-shiny + r-snpstats + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -13869,30 +13568,30 @@ (define-public r-gviz (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-biovizbase + r-bsgenome + r-digest + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-lattice + r-latticeextra + r-matrixstats + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -13917,20 +13616,20 @@ (define-public r-gwascat "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-readr + r-s4vectors + r-snpstats + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -13951,10 +13650,7 @@ (define-public r-kegggraph (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-rcurl" ,r-rcurl) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-graph r-rcurl r-rgraphviz r-xml)) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description @@ -13978,18 +13674,18 @@ (define-public r-ldblock "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-ensdb-hsapiens-v75 + r-ensembldb + r-genomeinfodb + r-genomicfiles + r-httr + r-matrix + r-rsamtools + r-snpstats + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -14015,9 +13711,7 @@ (define-public r-ldheatmap (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) + (list r-genetics r-rcpp r-snpstats)) (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description @@ -14042,14 +13736,14 @@ (define-public r-abn "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjags" ,r-rjags))) + (list gsl)) + (propagated-inputs + (list r-lme4 + r-nnet + r-rcpp + r-rcpparmadillo + r-rgraphviz + r-rjags)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -14079,12 +13773,9 @@ (define-public r-spp "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) + (list r-bh r-catools r-rcpp r-rsamtools)) (home-page "https://cran.r-project.org/web/packages/spp/") (synopsis "ChIP-Seq processing pipeline") (description "This package provides tools for analysis of ChIP-seq and @@ -14104,14 +13795,14 @@ (define-public r-pathview (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-graph" ,r-graph) - ("r-kegggraph" ,r-kegggraph) - ("r-keggrest" ,r-keggrest) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-png" ,r-png) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-graph + r-kegggraph + r-keggrest + r-org-hs-eg-db + r-png + r-rgraphviz + r-xml)) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description @@ -14138,12 +13829,9 @@ (define-public r-snpstats "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics r-matrix r-survival r-zlibbioc)) (home-page "https://bioconductor.org/packages/snpStats") (synopsis "Methods for SNP association studies") (description @@ -14166,21 +13854,21 @@ (define-public r-chromstar (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs - `(("r-bamsignals" ,r-bamsignals) - ("r-biocgenerics" ,r-biocgenerics) - ("r-chromstardata" ,r-chromstardata) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bamsignals + r-biocgenerics + r-chromstardata + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-mvtnorm + r-reshape2 + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description @@ -14204,16 +13892,16 @@ (define-public r-guitar (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-annotationdbi + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-knitr + r-magrittr + r-rtracklayer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Guitar") (synopsis "Visualize genomic features") (description @@ -14235,8 +13923,7 @@ (define-public r-sushi (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) + (list r-biomart r-zoo)) (home-page "https://bioconductor.org/packages/Sushi") (synopsis "Tools for visualizing genomics data") (description @@ -14258,17 +13945,17 @@ (define-public r-ballgown (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sva" ,r-sva))) + (list r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-sva)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ballgown") (synopsis "Flexible, isoform-level differential expression analysis") (description @@ -14291,17 +13978,17 @@ (define-public r-megadepth "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) - (inputs `(("megadepth" ,megadepth))) + (inputs (list megadepth)) (propagated-inputs - `(("r-cmdfun" ,r-cmdfun) - ("r-dplyr" ,r-dplyr) - ("r-fs" ,r-fs) - ("r-genomicranges" ,r-genomicranges) - ("r-magrittr" ,r-magrittr) - ("r-readr" ,r-readr) - ("r-xfun" ,r-xfun))) + (list r-cmdfun + r-dplyr + r-fs + r-genomicranges + r-magrittr + r-readr + r-xfun)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LieberInstitute/megadepth") (synopsis "BigWig and BAM related utilities") (description @@ -14325,16 +14012,16 @@ (define-public r-beclear (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-futile-logger" ,r-futile-logger) - ("r-matrix" ,r-matrix) - ("r-outliers" ,r-outliers) - ("r-rcpp" ,r-rcpp) - ("r-rdpack" ,r-rdpack))) + (list r-abind + r-biocparallel + r-data-table + r-futile-logger + r-matrix + r-outliers + r-rcpp + r-rdpack)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/uds-helms/BEclear") (synopsis "Correction of batch effects in DNA methylation data") (description @@ -14358,19 +14045,19 @@ (define-public r-bgeecall (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs - `(("kallisto" ,kallisto) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-jsonlite" ,r-jsonlite) - ("r-rhdf5" ,r-rhdf5) - ("r-rslurm" ,r-rslurm) - ("r-rtracklayer" ,r-rtracklayer) - ("r-sjmisc" ,r-sjmisc) - ("r-tximport" ,r-tximport))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list kallisto + r-biomart + r-biostrings + r-data-table + r-dplyr + r-genomicfeatures + r-jsonlite + r-rhdf5 + r-rslurm + r-rtracklayer + r-sjmisc + r-tximport)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeCall") (synopsis "RNA-Seq present/absent gene expression calls generation") (description @@ -14394,18 +14081,18 @@ (define-public r-bgeedb (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-graph" ,r-graph) - ("r-r-utils" ,r-r-utils) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-tidyr" ,r-tidyr) - ("r-topgo" ,r-topgo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-curl + r-data-table + r-digest + r-dplyr + r-graph + r-r-utils + r-rcurl + r-rsqlite + r-tidyr + r-topgo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeDB_R") (synopsis "Annotation and gene expression data retrieval from Bgee database") (description @@ -14428,11 +14115,8 @@ (define-public r-biobtreer (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-stringi" ,r-stringi))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv r-httr r-jsonlite r-stringi)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tamerh/biobtreeR") (synopsis "Use biobtree tool from R") (description @@ -14455,7 +14139,7 @@ (define-public r-minet (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs - `(("r-infotheo" ,r-infotheo))) + (list r-infotheo)) (home-page "http://minet.meyerp.com") (synopsis "Mutual information networks") (description @@ -14478,10 +14162,7 @@ (define-public r-genetclassifier `((upstream-name . "geNetClassifier"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-ebarrays" ,r-ebarrays) - ("r-minet" ,r-minet))) + (list r-biobase r-e1071 r-ebarrays r-minet)) (home-page "https://www.cicancer.org") (synopsis "Classify diseases and build gene networks using expression profiles") (description @@ -14504,8 +14185,8 @@ (define-public r-dir-expiry "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) - (propagated-inputs `(("r-filelock" ,r-filelock))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-filelock)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/dir.expiry") (synopsis "Managing expiration for cache directories") (description @@ -14530,8 +14211,8 @@ (define-public r-basilisk-utils `((upstream-name . "basilisk.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-dir-expiry" ,r-dir-expiry))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dir-expiry)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk.utils") (synopsis "Basilisk installation utilities") (description @@ -14553,10 +14234,8 @@ (define-public r-basilisk (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk-utils" ,r-basilisk-utils) - ("r-dir-expiry" ,r-dir-expiry) - ("r-reticulate" ,r-reticulate))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk-utils r-dir-expiry r-reticulate)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk") (synopsis "Freeze Python dependencies inside Bioconductor packages") (description @@ -14586,13 +14265,13 @@ (define-public r-biocthis (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-styler" ,r-styler) - ("r-usethis" ,r-usethis))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocmanager + r-fs + r-glue + r-rlang + r-styler + r-usethis)) + (native-inputs (list r-knitr)) (home-page "https://github.com/lcolladotor/biocthis") (synopsis "Automate package and project setup for Bioconductor packages") (description @@ -14616,13 +14295,13 @@ (define-public r-biocdockermanager `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) (propagated-inputs - `(("docker" ,docker) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-memoise" ,r-memoise) - ("r-readr" ,r-readr) - ("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list docker + r-dplyr + r-httr + r-memoise + r-readr + r-whisker)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocDockerManager") (synopsis "Access and manage Bioconductor Docker images") (description @@ -14645,25 +14324,25 @@ (define-public r-biodb (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-chk" ,r-chk) - ("r-jsonlite" ,r-jsonlite) - ("r-lgr" ,r-lgr) - ("r-lifecycle" ,r-lifecycle) - ("r-openssl" ,r-openssl) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-stringr" ,r-stringr) - ("r-testthat" ,r-testthat) - ("r-withr" ,r-withr) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-chk + r-jsonlite + r-lgr + r-lifecycle + r-openssl + r-plyr + r-progress + r-r6 + r-rappdirs + r-rcpp + r-rcurl + r-rsqlite + r-stringr + r-testthat + r-withr + r-xml + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biodb") (synopsis "Library for connecting to chemical and biological databases") (description @@ -14690,11 +14369,8 @@ (define-public r-biomformat (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rhdf5" ,r-rhdf5))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-jsonlite r-matrix r-plyr r-rhdf5)) + (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/biomformat/") (synopsis "Interface package for the BIOM file format") (description @@ -14742,10 +14418,7 @@ (define-public r-biomvcclass (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-mvcclass" ,r-mvcclass) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biobase r-graph r-mvcclass r-rgraphviz)) (home-page "https://bioconductor.org/packages/BioMVCClass") (synopsis "Model-View-Controller (MVC) classes that use Biobase") (description @@ -14767,10 +14440,7 @@ (define-public r-biomvrcns (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-genomicranges r-gviz r-iranges r-mvtnorm)) (home-page "https://bioconductor.org/packages/biomvRCNS") (synopsis "Copy number study and segmentation for multivariate biological data") (description @@ -14795,28 +14465,28 @@ (define-public r-bionero (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-complexheatmap" ,r-complexheatmap) - ("r-deseq2" ,r-deseq2) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-genie3" ,r-genie3) - ("r-ggnetwork" ,r-ggnetwork) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-igraph" ,r-igraph) - ("r-intergraph" ,r-intergraph) - ("r-matrixstats" ,r-matrixstats) - ("r-minet" ,r-minet) - ("r-netrep" ,r-netrep) - ("r-networkd3" ,r-networkd3) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-sva" ,r-sva) - ("r-wgcna" ,r-wgcna))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-dynamictreecut + r-genie3 + r-ggnetwork + r-ggnewscale + r-ggplot2 + r-ggpubr + r-igraph + r-intergraph + r-matrixstats + r-minet + r-netrep + r-networkd3 + r-rcolorbrewer + r-reshape2 + r-summarizedexperiment + r-sva + r-wgcna)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description @@ -14851,11 +14521,7 @@ (define-public r-bionet (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-igraph" ,r-igraph) - ("r-rbgl" ,r-rbgl))) + (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl)) (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html") (synopsis "Functional analysis of biological networks") (description @@ -14884,26 +14550,26 @@ (define-public r-bionetstat (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-pathview" ,r-pathview) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rjsonio" ,r-rjsonio) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-dt + r-ggplot2 + r-hmisc + r-igraph + r-knitr + r-markdown + r-pathview + r-pheatmap + r-plyr + r-psych + r-rcolorbrewer + r-rjsonio + r-rmarkdown + r-shiny + r-shinybs + r-whisker + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jardimViniciusC/BioNetStat") (synopsis "Biological network analysis") (description @@ -14926,11 +14592,9 @@ (define-public r-bioqc (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edger" ,r-edger) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-edger r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://accio.github.io/BioQC/") (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") (description @@ -14954,15 +14618,15 @@ (define-public r-biotip (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-psych" ,r-psych) - ("r-stringr" ,r-stringr))) + (list r-cluster + r-genomicranges + r-hmisc + r-igraph + r-mass + r-psych + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/xyang2uchicago/BioTIP") (synopsis "R package for characterization of biological tipping-point") (description @@ -14984,20 +14648,20 @@ (define-public r-biotmle (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-dplyr" ,r-dplyr) - ("r-drtmle" ,r-drtmle) - ("r-ggplot2" ,r-ggplot2) - ("r-ggsci" ,r-ggsci) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-superheat" ,r-superheat) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biocparallel + r-dplyr + r-drtmle + r-ggplot2 + r-ggsci + r-limma + r-s4vectors + r-summarizedexperiment + r-superheat + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://code.nimahejazi.org/biotmle/") (synopsis "Targeted learning with moderated statistics for biomarker discovery") (description @@ -15026,31 +14690,31 @@ (define-public r-bsseq (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-permute" ,r-permute) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-iranges + r-limma + r-locfit + r-permute + r-r-utils + r-rcpp + r-rhdf5 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/bsseq") (synopsis "Analyze, manage and store bisulfite sequencing data") (description @@ -15072,25 +14736,25 @@ (define-public r-dmrseq (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-annotatr" ,r-annotatr) - ("r-biocparallel" ,r-biocparallel) - ("r-bsseq" ,r-bsseq) - ("r-bumphunter" ,r-bumphunter) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-nlme" ,r-nlme) - ("r-outliers" ,r-outliers) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-annotatr + r-biocparallel + r-bsseq + r-bumphunter + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-matrixstats + r-nlme + r-outliers + r-rcolorbrewer + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/dmrseq") (synopsis "Detection and inference of differentially methylated regions") (description @@ -15122,30 +14786,30 @@ (define-public r-omnipathr (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-crayon" ,r-crayon) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-logger" ,r-logger) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description @@ -15170,34 +14834,34 @@ (define-public r-biscuiteer (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biscuiteerdata" ,r-biscuiteerdata) - ("r-bsseq" ,r-bsseq) - ("r-data-table" ,r-data-table) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dmrseq" ,r-dmrseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-impute" ,r-impute) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mus-musculus" ,r-mus-musculus) - ("r-qdnaseq" ,r-qdnaseq) - ("r-qualv" ,r-qualv) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biscuiteerdata + r-bsseq + r-data-table + r-delayedmatrixstats + r-dmrseq + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-homo-sapiens + r-impute + r-matrix + r-matrixstats + r-mus-musculus + r-qdnaseq + r-qualv + r-r-utils + r-readr + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description @@ -15221,23 +14885,23 @@ (define-public r-tximeta (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tximport" ,r-tximport))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-matrix + r-s4vectors + r-summarizedexperiment + r-tibble + r-tximport)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description @@ -15261,24 +14925,24 @@ (define-public r-phyloseq (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomformat" ,r-biomformat) - ("r-biostrings" ,r-biostrings) - ("r-cluster" ,r-cluster) - ("r-data-table" ,r-data-table) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-multtest" ,r-multtest) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-vegan" ,r-vegan))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-ade4 + r-ape + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-cluster + r-data-table + r-foreach + r-ggplot2 + r-igraph + r-multtest + r-plyr + r-reshape2 + r-scales + r-vegan)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aad13317b8..8c3be14e65 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -265,21 +265,21 @@ (define-public bamm `("PATH" ":" prefix (,path)) `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("zlib" ,zlib) - ("python-nose" ,python2-nose) - ("python-pysam" ,python2-pysam))) - (inputs - `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. - ("samtools" ,samtools) - ("bwa" ,bwa) - ("grep" ,grep) - ("sed" ,sed) - ("coreutils" ,coreutils))) + (list autoconf + automake + libtool + zlib + python2-nose + python2-pysam)) + (inputs + (list htslib-1.3 ; At least one test fails on htslib-1.4+. + samtools + bwa + grep + sed + coreutils)) (propagated-inputs - `(("python-numpy" ,python2-numpy))) + (list python2-numpy)) (home-page "https://ecogenomics.github.io/BamM/") (synopsis "Metagenomics-focused BAM file manipulator") (description @@ -314,7 +314,7 @@ (define-public bamtools "-Wl,-rpath=" (assoc-ref outputs "out") "/lib/bamtools")) #t))))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") (description @@ -350,7 +350,7 @@ (define-public bamutils (copy-recursively (assoc-ref inputs "libstatgen") "../libStatGen")))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs `(("libstatgen" ,(origin @@ -399,11 +399,9 @@ (define-public bcftools (("/bin/bash") (which "bash"))) #t))))) (native-inputs - `(("htslib" ,htslib) - ("perl" ,perl))) + (list htslib perl)) (inputs - `(("gsl" ,gsl) - ("zlib" ,zlib))) + (list gsl zlib)) (home-page "https://samtools.github.io/bcftools/") (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") (description @@ -432,8 +430,7 @@ (define-public bcftools-1.10 #t)))) (build-system gnu-build-system) (native-inputs - `(("htslib" ,htslib-1.10) - ("perl" ,perl))))) + (list htslib-1.10 perl)))) (define-public bedops (package @@ -518,8 +515,7 @@ (define-public bedtools (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))) + (list samtools zlib)) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") (description @@ -567,8 +563,7 @@ (define-public bedtools-2.18 (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))))) + (list samtools zlib)))) (define-public pbcopper ;; This is the latest commit at the time of this writing. @@ -595,10 +590,9 @@ (define-public pbcopper (substitute* "meson.build" (("-msse4.1") ""))))))) (inputs - `(("boost" ,boost))) + (list boost)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (home-page "https://github.com/PacificBiosciences/pbcopper") (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications") (description @@ -639,12 +633,9 @@ (define-public pbbam (string-append "'" (which "sh") "'")))))))) ;; These libraries are listed as "Required" in the pkg-config file. (propagated-inputs - `(("htslib" ,htslib) - ("pbcopper" ,pbcopper) - ("zlib" ,zlib))) + (list htslib pbcopper zlib)) (inputs - `(("boost" ,boost) - ("samtools" ,samtools))) + (list boost samtools)) (native-inputs `(("googletest" ,googletest) ("pkg-config" ,pkg-config) @@ -676,10 +667,9 @@ (define-public pbgzip "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/nh13/pbgzip") (synopsis "Parallel Block GZIP") (description "This package implements parallel block gzip. For many @@ -741,14 +731,9 @@ (define-public blasr-libcpp #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs - `(("boost" ,boost) - ("hdf5" ,hdf5) - ("htslib" ,htslib) - ("pbbam" ,pbbam) - ("zlib" ,zlib))) + (list boost hdf5 htslib pbbam zlib)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (home-page "https://github.com/PacificBiosciences/blasr_libcpp") (synopsis "Library for analyzing PacBio genomic sequences") (description @@ -788,13 +773,9 @@ (define-public blasr #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs - `(("boost" ,boost) - ("blasr-libcpp" ,blasr-libcpp) - ("hdf5" ,hdf5) - ("pbbam" ,pbbam) - ("zlib" ,zlib))) + (list boost blasr-libcpp hdf5 pbbam zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/PacificBiosciences/blasr") (synopsis "PacBio long read aligner") (description @@ -830,14 +811,14 @@ (define-public ribotaper "Ribotaper.sh"))) #t))))) (inputs - `(("bedtools" ,bedtools-2.18) - ("samtools" ,samtools-0.1) - ("r-minimal" ,r-minimal) - ("r-foreach" ,r-foreach) - ("r-xnomial" ,r-xnomial) - ("r-domc" ,r-domc) - ("r-multitaper" ,r-multitaper) - ("r-seqinr" ,r-seqinr))) + (list bedtools-2.18 + samtools-0.1 + r-minimal + r-foreach + r-xnomial + r-domc + r-multitaper + r-seqinr)) (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") (synopsis "Define translated ORFs using ribosome profiling data") (description @@ -878,13 +859,10 @@ (define-public ribodiff (string-append line "\n" prefix "scripts=['scripts/TE.py'],\n")))))))) (inputs - `(("python-numpy" ,python2-numpy) - ("python-matplotlib" ,python2-matplotlib) - ("python-scipy" ,python2-scipy) - ("python-statsmodels" ,python2-statsmodels))) + (list python2-numpy python2-matplotlib python2-scipy + python2-statsmodels)) (native-inputs - `(("python-mock" ,python2-mock) - ("python-nose" ,python2-nose))) + (list python2-mock python2-nose)) (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein @@ -910,9 +888,9 @@ (define-public bioawk "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("bison" ,bison))) + (list bison)) (arguments `(#:tests? #f ; There are no tests to run. ;; Bison must generate files, before other targets can build. @@ -951,11 +929,9 @@ (define-public python-htsget "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (propagated-inputs - `(("python-humanize" ,python-humanize) - ("python-requests" ,python-requests) - ("python-six" ,python-six))) + (list python-humanize python-requests python-six)) (home-page "https://pypi.org/project/htsget/") (synopsis "Python API and command line interface for the GA4GH htsget API") (description "This package is a client implementation of the GA4GH htsget @@ -1018,20 +994,17 @@ (define (cythonized? c/c++-file) (with-directory-excursion "/tmp/test" (invoke "pytest" "-v" "--doctest-modules"))))))) (propagated-inputs - `(("bedtools" ,bedtools) - ("samtools" ,samtools) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-pyyaml" ,python-pyyaml))) - (native-inputs - `(("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-cython" ,python-cython) - ("kentutils" ,kentutils) ; for bedGraphToBigWig - ("python-six" ,python-six) - ;; For the test suite. - ("python-pytest" ,python-pytest) - ("python-psutil" ,python-psutil))) + (list bedtools samtools python-matplotlib python-pysam + python-pyyaml)) + (native-inputs + (list python-numpy + python-pandas + python-cython + kentutils ; for bedGraphToBigWig + python-six + ;; For the test suite. + python-pytest + python-psutil)) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -1046,8 +1019,8 @@ (define-public python2-pybedtools (package (inherit pybedtools) (native-inputs - `(("python2-pathlib" ,python2-pathlib) - ,@(package-native-inputs pybedtools)))))) + (modify-inputs (package-native-inputs pybedtools) + (prepend python2-pathlib)))))) (define-public python-biom-format (package @@ -1098,19 +1071,16 @@ (define-public python-biom-format (for-each (lambda (file) (chmod file #o644)) (find-files out "\\.gz")))))))) (propagated-inputs - `(("python-anndata" ,python-anndata) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-flake8" ,python-flake8) - ("python-future" ,python-future) - ("python-click" ,python-click) - ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-nose" ,python-nose))) + (list python-anndata + python-numpy + python-scipy + python-flake8 + python-future + python-click + python-h5py + python-pandas)) + (native-inputs + (list python-cython python-pytest python-pytest-cov python-nose)) (home-page "http://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description @@ -1149,17 +1119,15 @@ (define-public python-pairtools (with-directory-excursion "/tmp" (invoke "pytest" "-v"))))))) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-pytest" ,python-pytest))) + (list python-cython python-nose python-pytest)) (inputs `(("python" ,python-wrapper))) (propagated-inputs - `(("htslib" ,htslib) ; for bgzip, looked up in PATH - ("samtools" ,samtools) ; looked up in PATH - ("lz4" ,lz4) ; for lz4c - ("python-click" ,python-click) - ("python-numpy" ,python-numpy))) + (list htslib ; for bgzip, looked up in PATH + samtools ; looked up in PATH + lz4 ; for lz4c + python-click + python-numpy)) (home-page "https://github.com/mirnylab/pairtools") (synopsis "Process mapped Hi-C data") (description "Pairtools is a simple and fast command-line framework to @@ -1226,12 +1194,9 @@ (define-public bioperl-minimal (find-files bin "\\.pl$")) #t))))))) (inputs - `(("perl-module-build" ,perl-module-build) - ("perl-data-stag" ,perl-data-stag) - ("perl-libwww" ,perl-libwww) - ("perl-uri" ,perl-uri))) + (list perl-module-build perl-data-stag perl-libwww perl-uri)) (native-inputs - `(("perl-test-most" ,perl-test-most))) + (list perl-test-most)) (home-page "https://metacpan.org/release/BioPerl") (synopsis "Bioinformatics toolkit") (description @@ -1259,11 +1224,9 @@ (define-public perl-bio-db-hts "0hjg0igfkpvh27zdkdr6pa7cqm9n6r7cwz0np74cl4wmawgvr9hj")))) (build-system perl-build-system) (native-inputs - `(("perl-module-build" ,perl-module-build) - ("pkg-config" ,pkg-config))) + (list perl-module-build pkg-config)) (propagated-inputs - `(("bioperl-minimal" ,bioperl-minimal) - ("htslib" ,htslib-1.9))) + (list bioperl-minimal htslib-1.9)) (home-page "https://metacpan.org/release/Bio-DB-HTS") (synopsis "Perl interface to HTS library for DNA sequencing") (description "This is a Perl interface to the HTS library for DNA @@ -1289,7 +1252,7 @@ (define-public python-biopython ;; Some tests require a home directory to be set. (lambda _ (setenv "HOME" "/tmp") #t))))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description @@ -1363,7 +1326,7 @@ (define-public biosoup (when tests? (invoke "./bin/biosoup_test"))))))) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://github.com/rvaser/biosoup") (synopsis "C++ support library for bioinformatics tools") (description "Biosoup is a C++ collection of header-only data structures @@ -1394,11 +1357,11 @@ (define-public bioparser (when tests? (invoke "./bin/bioparser_test"))))))) (inputs - `(("biosoup" ,biosoup))) + (list biosoup)) (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://github.com/rvaser/bioparser") (synopsis "C++ library for parsing several formats in bioinformatics") (description "Bioparser is a C++ header only parsing library for several @@ -1448,12 +1411,9 @@ (define-public circtools ("rust-serde" ,rust-serde-1) ("rust-seq-io" ,rust-seq-io-0.3)))) (inputs - `(("bioparser" ,bioparser) - ("biosoup" ,biosoup))) + (list bioparser biosoup)) (native-inputs - `(("cmake" ,cmake) - ("pkg-config" ,pkg-config) - ("googletest" ,googletest))) + (list cmake pkg-config googletest)) (home-page "https://github.com/Kevinzjy/circtools") (synopsis "Accelerating functions in CIRI toolkit") (description "This package provides accelerated functions for the CIRI @@ -1501,21 +1461,19 @@ (define-public ciri-long (substitute* "CIRI_long/main.py" (("os.chmod\\(lib_path.*") ""))))))) (inputs - `(("circtools" ,circtools) - ("python-biopython" ,python-biopython) - ("python-bwapy" ,python-bwapy) - ("python-levenshtein" ,python-levenshtein) - ("python-mappy" ,python-mappy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-pyspoa" ,python-pyspoa) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-setuptools" ,python-setuptools))) + (list circtools + python-biopython + python-bwapy + python-levenshtein + python-mappy + python-numpy + python-pandas + python-pysam + python-pyspoa + python-scikit-learn + python-scipy)) + (native-inputs + (list python-cython python-nose python-setuptools)) (home-page "https://ciri-cookbook.readthedocs.io/") (synopsis "Circular RNA identification for Nanopore sequencing") (description "CIRI-long is a package for circular RNA identification using @@ -1583,14 +1541,14 @@ (define-public qtltools (mkdir-p bin) (install-file "bin/QTLtools" bin))))))) (inputs - `(("curl" ,curl) - ("gsl" ,gsl) - ("boost" ,boost) - ("rmath-standalone" ,rmath-standalone) - ("htslib" ,htslib-1.3) - ("openssl" ,openssl) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list curl + gsl + boost + rmath-standalone + htslib-1.3 + openssl + openblas + zlib)) (home-page "https://qtltools.github.io/qtltools/") (synopsis "Tool set for molecular QTL discovery and analysis") (description "QTLtools is a tool set for molecular QTL discovery @@ -1653,8 +1611,7 @@ (define-public bpp-phyl ;; so the tests fail. #:out-of-source? #f)) (inputs - `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq))) + (list bpp-core bpp-seq)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ phylogenetic Library") (description @@ -1685,8 +1642,7 @@ (define-public bpp-popgen `(#:parallel-build? #f #:tests? #f)) ; There are no tests. (inputs - `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq))) + (list bpp-core bpp-seq)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ population genetics library") (description @@ -1719,7 +1675,7 @@ (define-public bpp-seq ;; so the tests fail. #:out-of-source? #f)) (inputs - `(("bpp-core" ,bpp-core))) + (list bpp-core)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ sequence library") (description @@ -1750,9 +1706,7 @@ (define-public bppsuite `(#:parallel-build? #f #:tests? #f)) ; There are no tests. (native-inputs - `(("groff" ,groff) - ("man-db" ,man-db) - ("texinfo" ,texinfo))) + (list groff man-db texinfo)) (inputs `(("bpp-core" ,bpp-core) ("bpp-seq" ,bpp-seq) @@ -1891,7 +1845,7 @@ (define (which* cmd) ("perl" ,perl) ("python" ,python-wrapper))) (native-inputs - `(("cpio" ,cpio))) + (list cpio)) (home-page "https://blast.ncbi.nlm.nih.gov") (synopsis "Basic local alignment search tool") (description @@ -1977,13 +1931,9 @@ (define-public bless '("bless" "kmc/bin/kmc"))))) (delete 'configure)))) (native-inputs - `(("perl" ,perl))) + (list perl)) (inputs - `(("openmpi" ,openmpi) - ("boost" ,boost) - ("sparsehash" ,sparsehash) - ("pigz" ,pigz) - ("zlib" ,zlib))) + (list openmpi boost sparsehash pigz zlib)) (supported-systems '("x86_64-linux")) (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") (synopsis "Bloom-filter-based error correction tool for NGS reads") @@ -2042,10 +1992,7 @@ (define-public bowtie ("zlib" ,zlib) ("python" ,python-wrapper))) (native-inputs - `(("perl" ,perl) - ("perl-clone" ,perl-clone) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-simple" ,perl-test-simple))) + (list perl perl-clone perl-test-deep perl-test-simple)) (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description @@ -2086,9 +2033,7 @@ (define-public bowtie1 (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("python-wrapper" ,python-wrapper) - ("tbb" ,tbb-2020) - ("zlib" ,zlib))) + (list python-wrapper tbb-2020 zlib)) (supported-systems '("x86_64-linux")) (home-page "http://bowtie-bio.sourceforge.net/index.shtml") (synopsis "Fast aligner for short nucleotide sequence reads") @@ -2210,7 +2155,7 @@ (define-public bwa (install-file "bwa.1" man)))) ;; no "configure" script (delete 'configure)))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) @@ -2251,9 +2196,7 @@ (define-public bwa-pssm (substitute* "pssm.c" (("inline int map") "int map")))))))) (inputs - `(("gdsl" ,gdsl) - ("zlib" ,zlib) - ("perl" ,perl))) + (list gdsl zlib perl)) (home-page "http://bwa-pssm.binf.ku.dk/") (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") (description @@ -2292,9 +2235,9 @@ (define-public bwa-meth (("^checkX.*") "")) #t))))) (inputs - `(("bwa" ,bwa))) + (list bwa)) (native-inputs - `(("python-toolshed" ,python-toolshed))) + (list python-toolshed)) (home-page "https://github.com/brentp/bwa-meth") (synopsis "Fast and accurante alignment of BS-Seq reads") (description @@ -2322,13 +2265,11 @@ (define-public python-bx-python "0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc")))) (build-system python-build-system) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("python-lzo" ,python-lzo) - ("python-nose" ,python-nose) - ("python-cython" ,python-cython))) + (list python-lzo python-nose python-cython)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -2350,13 +2291,9 @@ (define-public python-pyega3 (arguments `(#:tests? #f)) ; The tests require network access. (native-inputs - `(("python-psutil" ,python-psutil) - ("python-htsget" ,python-htsget))) + (list python-psutil python-htsget)) (propagated-inputs - `(("python-requests" ,python-requests) - ("python-tqdm" ,python-tqdm) - ("python-urllib3" ,python-urllib3) - ("python-responses" ,python-responses))) + (list python-requests python-tqdm python-urllib3 python-responses)) (home-page "https://github.com/EGA-archive/ega-download-client") (synopsis "Python client for EGA") (description "This package is a python-based tool for viewing and @@ -2428,18 +2365,16 @@ (define-public python-pysam " and not TestHeaderCRAM" " and not test_text_processing"))))))))) (propagated-inputs - `(("htslib" ,htslib-1.10))) ; Included from installed header files. + (list htslib-1.10)) ; Included from installed header files. (inputs - `(("ncurses" ,ncurses) - ("curl" ,curl) - ("zlib" ,zlib))) + (list ncurses curl zlib)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ;; Dependencies below are are for tests only. - ("samtools" ,samtools-1.10) - ("bcftools" ,bcftools-1.10) - ("python-nose" ,python-nose))) + (list python-cython + python-pytest + ;; Dependencies below are are for tests only. + samtools-1.10 + bcftools-1.10 + python-nose)) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description @@ -2468,7 +2403,7 @@ (define-public python-twobitreader ;; Tests are not included (arguments '(#:tests? #f)) (native-inputs - `(("python-sphinx" ,python-sphinx))) + (list python-sphinx)) (home-page "https://github.com/benjschiller/twobitreader") (synopsis "Python library for reading .2bit files") (description @@ -2491,17 +2426,16 @@ (define-public python-plastid ;; Some test files are not included. `(#:tests? #f)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib) - ("python-biopython" ,python-biopython) - ("python-twobitreader" ,python-twobitreader) - ("python-termcolor" ,python-termcolor))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + (list python-numpy + python-scipy + python-pandas + python-pysam + python-matplotlib + python-biopython + python-twobitreader + python-termcolor)) + (native-inputs + (list python-cython python-nose)) (home-page "https://github.com/joshuagryphon/plastid") (synopsis "Python library for genomic analysis") (description @@ -2558,12 +2492,12 @@ (define-public tetoolkit "TEcount"))) #t))))) (inputs - `(("coreutils" ,coreutils) - ("bedtools" ,bedtools) - ("python-argparse" ,python2-argparse) - ("python-pysam" ,python2-pysam) - ("r-minimal" ,r-minimal) - ("r-deseq2" ,r-deseq2))) + (list coreutils + bedtools + python2-argparse + python2-pysam + r-minimal + r-deseq2)) (home-page "https://github.com/mhammell-laboratory/tetoolkit") (synopsis "Transposable elements in differential enrichment analysis") (description @@ -2615,7 +2549,7 @@ (define-public cd-hit (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("perl" ,perl))) + (list perl)) (home-page "http://weizhongli-lab.org/cd-hit/") (synopsis "Cluster and compare protein or nucleotide sequences") (description @@ -2680,20 +2614,20 @@ (define-public clipper ;; This is not a library (delete 'sanity-check)))) (inputs - `(("htseq" ,htseq) - ("python-pybedtools" ,python-pybedtools) - ("python-cython" ,python-cython) - ("python-scikit-learn" ,python-scikit-learn) - ("python-matplotlib" ,python-matplotlib) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy))) - (native-inputs - `(("python-setuptools-git" ,python-setuptools-git) - ("python-mock" ,python-mock) ; for tests - ("python-nose" ,python-nose) ; for tests - ("python-pytz" ,python-pytz))) ; for tests + (list htseq + python-pybedtools + python-cython + python-scikit-learn + python-matplotlib + python-pandas + python-pysam + python-numpy + python-scipy)) + (native-inputs + (list python-setuptools-git + python-mock ; for tests + python-nose ; for tests + python-pytz)) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description @@ -2729,7 +2663,7 @@ (define-public codingquarry (install-file "CodingQuarry" bin) (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) #t))))) - (inputs `(("openmpi" ,openmpi))) + (inputs (list openmpi)) (native-search-paths (list (search-path-specification (variable "QUARRY_PATH") @@ -2754,7 +2688,7 @@ (define-public clustal-omega "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) (build-system gnu-build-system) (inputs - `(("argtable" ,argtable))) + (list argtable)) (home-page "http://www.clustal.org/omega/") (synopsis "Multiple sequence aligner for protein and DNA/RNA") (description @@ -2782,14 +2716,10 @@ (define-public crossmap (delete-file-recursively ".eggs"))))) (build-system python-build-system) (inputs - `(("python-bx-python" ,python-bx-python) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("zlib" ,zlib))) + (list python-bx-python python-numpy python-pybigwig python-pysam + zlib)) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + (list python-cython python-nose)) (home-page "http://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description @@ -2811,9 +2741,7 @@ (define-public python-dnaio "14v5yyasq2bz34j38wi3xfcp06jj7l35ppibjcn95l2n73hz3zwi")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-xopen" ,python-xopen))) + (list python-cython python-pytest python-xopen)) (home-page "https://github.com/marcelm/dnaio/") (synopsis "Read FASTA and FASTQ files efficiently") (description @@ -2833,7 +2761,7 @@ (define-public python-deeptoolsintervals "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x")))) (build-system python-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/deeptools/deeptools_intervals") (synopsis "Create GTF-based interval trees with associated meta-data") (description @@ -2857,18 +2785,17 @@ (define-public python-deeptools "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + (list python-mock python-nose)) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy) - ("python-deeptoolsintervals" ,python-deeptoolsintervals) - ("python-plotly" ,python-plotly-2.4.1))) + (list python-matplotlib + python-numpy + python-numpydoc + python-py2bit + python-pybigwig + python-pysam + python-scipy + python-deeptoolsintervals + python-plotly-2.4.1)) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts @@ -2907,12 +2834,9 @@ (define-public cutadapt (("os.path.exists\\('PKG-INFO'\\):") "os.path.exists('totally-does-not-exist'):"))))))) (inputs - `(("python-dnaio" ,python-dnaio) - ("python-xopen" ,python-xopen))) + (list python-dnaio python-xopen)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + (list python-cython python-pytest python-setuptools-scm)) (home-page "https://cutadapt.readthedocs.io/en/stable/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description @@ -2944,8 +2868,7 @@ (define-public libbigwig (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("zlib" ,zlib) - ("curl" ,curl))) + (list zlib curl)) (native-inputs `(("doxygen" ,doxygen) ;; Need for tests @@ -2983,11 +2906,9 @@ (define-public python-pybigwig (("libs=\\[") "libs=[\"BigWig\", ")) #t))))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("libbigwig" ,libbigwig) - ("zlib" ,zlib) - ("curl" ,curl))) + (list libbigwig zlib curl)) (home-page "https://github.com/dpryan79/pyBigWig") (synopsis "Access bigWig files in Python using libBigWig") (description @@ -3022,18 +2943,16 @@ (define-public python-schema-salad "\"test requires network access\")\n" all)))))))) (propagated-inputs - `(("python-cachecontrol" ,python-cachecontrol) - ("python-lockfile" ,python-lockfile) - ("python-mistune" ,python-mistune) - ("python-rdflib" ,python-rdflib) - ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-typing-extensions" ,python-typing-extensions))) - (native-inputs - `(("python-black" ,python-black) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-cachecontrol + python-lockfile + python-mistune + python-rdflib + python-rdflib-jsonld + python-requests + python-ruamel.yaml + python-typing-extensions)) + (native-inputs + (list python-black python-pytest python-pytest-runner)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description @@ -3105,30 +3024,30 @@ (define-public cwltool (substitute* "tox.ini" (("-n auto") ""))))))) (propagated-inputs - `(("python-argcomplete" ,python-argcomplete) - ("python-bagit" ,python-bagit) - ("python-coloredlogs" ,python-coloredlogs) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-prov" ,python-prov) - ("python-pydot" ,python-pydot) - ("python-psutil" ,python-psutil) - ("python-rdflib" ,python-rdflib) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-schema-salad" ,python-schema-salad) - ("python-shellescape" ,python-shellescape) - ("python-typing-extensions" ,python-typing-extensions) - ;; Not listed as needed but still necessary: - ("node" ,node))) - (native-inputs - `(("python-arcp" ,python-arcp) - ("python-humanfriendly" ,python-humanfriendly) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-mock" ,python-pytest-mock) - ("python-pytest-runner" ,python-pytest-runner) - ("python-rdflib-jsonld" ,python-rdflib-jsonld))) + (list python-argcomplete + python-bagit + python-coloredlogs + python-mypy-extensions + python-prov + python-pydot + python-psutil + python-rdflib + python-requests + python-ruamel.yaml + python-schema-salad + python-shellescape + python-typing-extensions + ;; Not listed as needed but still necessary: + node)) + (native-inputs + (list python-arcp + python-humanfriendly + python-mock + python-pytest + python-pytest-cov + python-pytest-mock + python-pytest-runner + python-rdflib-jsonld)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation") @@ -3257,10 +3176,7 @@ (define-public delly (copy-recursively "excludeTemplates" templates) #t)))))) (inputs - `(("boost" ,boost) - ("bzip2" ,bzip2) - ("htslib" ,htslib) - ("zlib" ,zlib))) + (list boost bzip2 htslib zlib)) (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method @@ -3333,12 +3249,12 @@ (define-public repeat-masker (wrap-program (string-append bin "/RepeatMasker") `("PERL5LIB" ":" prefix (,path ,share))))))))) (inputs - `(("perl" ,perl) - ("perl-text-soundex" ,perl-text-soundex) - ("python" ,python) - ("python-h5py" ,python-h5py) - ("hmmer" ,hmmer) - ("trf" ,trf))) + (list perl + perl-text-soundex + python + python-h5py + hmmer + trf)) (home-page "https://github.com/Benson-Genomics-Lab/TRF") (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences") (description "A tandem repeat in DNA is two or more adjacent, approximate @@ -3373,7 +3289,7 @@ (define-public diamond (substitute* "CMakeLists.txt" (("-march=native") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bbuchfink/diamond") (synopsis "Accelerated BLAST compatible local sequence aligner") (description @@ -3428,9 +3344,7 @@ (define-public discrover (("#define FASTA_HPP" line) (string-append line "\n#include ")))))))) (inputs - `(("boost" ,boost) - ("cairo" ,cairo) - ("rmath-standalone" ,rmath-standalone))) + (list boost cairo rmath-standalone)) (native-inputs `(("texlive" ,(texlive-updmap.cfg (list texlive-cm texlive-amsfonts @@ -3491,11 +3405,8 @@ (define-public eigensoft (find-files "../bin" ".*")) #t)))))) (inputs - `(("gsl" ,gsl) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("perl" ,perl) - ("gfortran" ,gfortran "lib"))) + (list gsl lapack openblas perl + `(,gfortran "lib"))) (home-page "https://github.com/DReichLab/EIG") (synopsis "Tools for population genetics") (description "The EIGENSOFT package provides tools for population @@ -3585,23 +3496,23 @@ (define-public edirect "-filter" "-help") #t))))) (inputs - `(("edirect-go-programs" ,edirect-go-programs) - ("perl-html-parser" ,perl-html-parser) - ("perl-encode-locale" ,perl-encode-locale) - ("perl-file-listing" ,perl-file-listing) - ("perl-html-tagset" ,perl-html-tagset) - ("perl-html-tree" ,perl-html-tree) - ("perl-http-cookies" ,perl-http-cookies) - ("perl-http-date" ,perl-http-date) - ("perl-http-message" ,perl-http-message) - ("perl-http-negotiate" ,perl-http-negotiate) - ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) - ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) - ("perl-net-http" ,perl-net-http) - ("perl-uri" ,perl-uri) - ("perl-www-robotrules" ,perl-www-robotrules) - ("perl-xml-simple" ,perl-xml-simple) - ("perl" ,perl))) + (list edirect-go-programs + perl-html-parser + perl-encode-locale + perl-file-listing + perl-html-tagset + perl-html-tree + perl-http-cookies + perl-http-date + perl-http-message + perl-http-negotiate + perl-lwp-mediatypes + perl-lwp-protocol-https + perl-net-http + perl-uri + perl-www-robotrules + perl-xml-simple + perl)) (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") (description @@ -3658,16 +3569,16 @@ (define-public edirect-go-programs (native-inputs '()) (propagated-inputs '()) (inputs - `(("go-github-com-fatih-color" ,go-github-com-fatih-color) - ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg) - ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector) - ("go-github-com-golang-freetype" ,go-github-com-golang-freetype) - ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid) - ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory) - ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2) - ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode) - ("go-golang-org-x-image" ,go-golang-org-x-image) - ("go-golang-org-x-text" ,go-golang-org-x-text))))) + (list go-github-com-fatih-color + go-github-com-fogleman-gg + go-github-com-gedex-inflector + go-github-com-golang-freetype + go-github-com-klauspost-cpuid + go-github-com-pbnjay-memory + go-github-com-surgebase-porter2 + go-golang-org-rainycape-unidecode + go-golang-org-x-image + go-golang-org-x-text)))) (define-public exonerate (package @@ -3687,9 +3598,9 @@ (define-public exonerate (arguments `(#:parallel-build? #f)) ; Building in parallel fails on some machines. (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") (synopsis "Generic tool for biological sequence alignment") @@ -3736,10 +3647,7 @@ (define-public express (("check_version\\(PACKAGE_VERSION\\);") "")) #t))))) (inputs - `(("boost" ,boost) - ("bamtools" ,bamtools) - ("protobuf" ,protobuf) - ("zlib" ,zlib))) + (list boost bamtools protobuf zlib)) (home-page "http://bio.math.berkeley.edu/eXpress") (synopsis "Streaming quantification for high-throughput genomic sequencing") (description @@ -3859,10 +3767,10 @@ (define-public fastx-toolkit "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) (build-system gnu-build-system) (inputs - `(("libgtextutils" ,libgtextutils))) + (list libgtextutils)) (native-inputs - `(("gcc" ,gcc-6) ;; doesn't build with later versions - ("pkg-config" ,pkg-config))) + (list gcc-6 ;; doesn't build with later versions + pkg-config)) (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") (synopsis "Tools for FASTA/FASTQ file preprocessing") (description @@ -3909,11 +3817,9 @@ (define-public flexbar (bin (string-append out "/bin/"))) (install-file "flexbar" bin))))))) (inputs - `(("tbb" ,tbb-2020) - ("zlib" ,zlib))) + (list tbb-2020 zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("seqan" ,seqan-2))) + (list pkg-config seqan-2)) (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description @@ -4052,8 +3958,7 @@ (define-public fxtract (install-file "fxtract" bin) #t)))))) (inputs - `(("pcre" ,pcre) - ("zlib" ,zlib))) + (list pcre zlib)) (native-inputs ;; ctskennerton-util is licensed under GPL2. `(("ctskennerton-util" @@ -4100,9 +4005,7 @@ (define-public gemma #t)))) (build-system gnu-build-system) (inputs - `(("gsl" ,gsl) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list gsl openblas zlib)) (native-inputs `(("catch" ,catch-framework2-1) ("perl" ,perl) @@ -4166,12 +4069,9 @@ (define-public grit (("Cython.Setup") "Cython.Build")) #t))))) (inputs - `(("python-scipy" ,python2-scipy) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-networkx" ,python2-networkx))) + (list python2-scipy python2-numpy python2-pysam python2-networkx)) (native-inputs - `(("python-cython" ,python2-cython))) + (list python2-cython)) ;; The canonical home page times out as of 2020-01-21. (home-page "https://github.com/nboley/grit") (synopsis "Tool for integrative analysis of RNA-seq type assays") @@ -4234,11 +4134,9 @@ (define-public hisat "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))) (delete 'configure)))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (inputs - `(("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))) + (list perl python zlib)) ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) @@ -4297,8 +4195,7 @@ (define-public hisat2 (mkdir-p doc) (install-file "doc/manual.inc.html" doc))))))) (native-inputs - `(("perl" ,perl) - ("pandoc" ,pandoc))) ; for documentation + (list perl pandoc)) ; for documentation (inputs `(("python" ,python-wrapper))) (home-page "https://daehwankimlab.github.io/hisat2/") @@ -4329,8 +4226,7 @@ (define-public hmmer (base32 "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl) - ("python" ,python))) ; for tests + (native-inputs (list perl python)) ; for tests (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description @@ -4355,13 +4251,12 @@ (define-public htseq "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib))) + (list python-pysam python-matplotlib)) (home-page "https://htseq.readthedocs.io/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -4411,7 +4306,7 @@ (define-public java-htsjdk ("java-commons-jexl-2" ,java-commons-jexl-2) ("java-xz" ,java-xz))) (native-inputs - `(("java-testng" ,java-testng))) + (list java-testng)) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -4454,7 +4349,7 @@ (define-public java-htsjdk-latest ("java-commons-jexl-2" ,java-commons-jexl-2) ("java-xz" ,java-xz))) (native-inputs - `(("java-junit" ,java-junit))) + (list java-junit)) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -4557,10 +4452,9 @@ (define-public java-picard #t)) (replace 'install (install-jars "dist"))))) (inputs - `(("java-htsjdk" ,java-htsjdk) - ("java-guava" ,java-guava))) + (list java-htsjdk java-guava)) (native-inputs - `(("java-testng" ,java-testng))) + (list java-testng)) (home-page "http://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating @@ -4647,10 +4541,9 @@ (define-public java-picard-2.10.3 (rename-file "build.xml.new" "build.xml") #t))))) (propagated-inputs - `(("java-htsjdk" ,java-htsjdk-2.10.1))) + (list java-htsjdk-2.10.1)) (native-inputs - `(("java-testng" ,java-testng) - ("java-guava" ,java-guava))) + (list java-testng java-guava)) (home-page "http://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating @@ -4831,7 +4724,7 @@ (define-public fastqc ("java-picard-1.113" ,java-picard-1.113) ("java-jbzip2" ,java-jbzip2))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/") (synopsis "Quality control tool for high throughput sequence data") (description @@ -4880,7 +4773,7 @@ (define-public fastp (lambda* (#:key outputs #:allow-other-keys) (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/OpenGene/fastp/") (synopsis "All-in-one FastQ preprocessor") (description @@ -4910,13 +4803,12 @@ (define-public htslib "--enable-libcurl" "--enable-s3"))) (inputs - `(("curl" ,curl) - ("openssl" ,openssl))) + (list curl openssl)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "https://www.htslib.org") (synopsis "C library for reading/writing high-throughput sequencing data") (description @@ -5013,12 +4905,9 @@ (define-public idr ;; causes the tests to always fail. (arguments `(#:tests? #f)) (propagated-inputs - `(("python-scipy" ,python-scipy) - ("python-sympy" ,python-sympy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib))) + (list python-scipy python-sympy python-numpy python-matplotlib)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/nboley/idr") (synopsis "Tool to measure the irreproducible discovery rate (IDR)") (description @@ -5059,7 +4948,7 @@ (define-public jellyfish ("python" ,python-wrapper) ("pkg-config" ,pkg-config))) (inputs - `(("htslib" ,htslib))) + (list htslib)) (synopsis "Tool for fast counting of k-mers in DNA") (description "Jellyfish is a tool for fast, memory-efficient counting of k-mers in @@ -5140,15 +5029,9 @@ (define-public khmer (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v"))))))) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-cython python-pytest python-pytest-runner)) (inputs - `(("zlib" ,zlib) - ("bzip2" ,bzip2) - ("seqan" ,seqan-1) - ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file))) + (list zlib bzip2 seqan-1 python-screed python-bz2file)) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for @@ -5190,8 +5073,7 @@ (define-public kaiju (copy-recursively "bin" bin)) #t))))) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + (list perl zlib)) (home-page "http://kaiju.binf.ku.dk/") (synopsis "Fast and sensitive taxonomic classification for metagenomics") (description "Kaiju is a program for sensitive taxonomic classification @@ -5236,10 +5118,9 @@ (define-public macs (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v"))))))) (inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest))) + (list python-cython python-pytest)) (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description @@ -5319,11 +5200,7 @@ (define-public mafft `("PATH" ":" prefix (,path)))) (find-files bin)))))))) (inputs - `(("perl" ,perl) - ("ruby" ,ruby) - ("gawk" ,gawk) - ("grep" ,grep) - ("coreutils" ,coreutils))) + (list perl ruby gawk grep coreutils)) (home-page "https://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description @@ -5380,14 +5257,14 @@ (define-public mash (("c\\+\\+11") "c++14")) #t))))) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (inputs - `(;; Capnproto and htslib are statically embedded in the final - ;; application. Therefore we also list their licenses, below. - ("capnproto" ,capnproto) - ("htslib" ,htslib) - ("gsl" ,gsl) - ("zlib" ,zlib))) + (list ;; Capnproto and htslib are statically embedded in the final + ;; application. Therefore we also list their licenses, below. + capnproto + htslib + gsl + zlib)) (supported-systems '("x86_64-linux")) (home-page "https://mash.readthedocs.io") (synopsis "Fast genome and metagenome distance estimation using MinHash") @@ -5439,11 +5316,7 @@ (define-public metabat (("set\\(Boost.*") "") (("add_dependencies.*") ""))))))) (inputs - `(("zlib" ,zlib) - ("perl" ,perl) - ("samtools" ,samtools) - ("htslib" ,htslib) - ("boost" ,boost))) + (list zlib perl samtools htslib boost)) (home-page "https://bitbucket.org/berkeleylab/metabat") (synopsis "Reconstruction of single genomes from complex microbial communities") @@ -5547,14 +5420,11 @@ (define-public miso (inputs ;; Samtools must not be newer than 1.2. See ;; https://github.com/yarden/MISO/issues/135 - `(("samtools" ,samtools-1.2) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-scipy" ,python2-scipy) - ("python-matplotlib" ,python2-matplotlib))) + (list samtools-1.2 python2-numpy python2-pysam python2-scipy + python2-matplotlib)) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-pytz" ,python2-pytz))) ; for tests + (list python2-mock ; for tests + python2-pytz)) ; for tests (home-page "https://miso.readthedocs.io/en/fastmiso/") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (description @@ -5622,13 +5492,9 @@ (define-public newick-utils (inputs ;; XXX: TODO: Enable Lua and Guile bindings. ;; https://github.com/tjunier/newick_utils/issues/13 - `(("libxml2" ,libxml2) - ("flex" ,flex) - ("bison" ,bison))) + (list libxml2 flex bison)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (synopsis "Programs for working with newick format phylogenetic trees") (description "Newick-utils is a suite of utilities for processing phylogenetic trees @@ -5650,11 +5516,9 @@ (define-public orfm (base32 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) (build-system gnu-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (native-inputs - `(("ruby-bio-commandeer" ,ruby-bio-commandeer) - ("ruby-rspec" ,ruby-rspec) - ("ruby" ,ruby))) + (list ruby-bio-commandeer ruby-rspec ruby)) (synopsis "Simple and not slow open reading frame (ORF) caller") (description "An ORF caller finds stretches of DNA that, when translated, are not @@ -5685,13 +5549,9 @@ (define-public python2-pbcore (("^sphinx") "")) #t))))) (propagated-inputs - `(("python-cython" ,python2-cython) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-h5py" ,python2-h5py))) + (list python2-cython python2-numpy python2-pysam python2-h5py)) (native-inputs - `(("python-nose" ,python2-nose) - ("python-pyxb" ,python2-pyxb))) + (list python2-nose python2-pyxb)) (home-page "https://pacificbiosciences.github.io/pbcore/") (synopsis "Library for reading and writing PacBio data files") (description @@ -5723,17 +5583,15 @@ (define-public python2-warpedlmm "from scipy import linalg\nimport weave")) #t))))) (propagated-inputs - `(("python-scipy" ,python2-scipy) - ("python-numpy" ,python2-numpy) - ("python-matplotlib" ,python2-matplotlib) - ("python-fastlmm" ,python2-fastlmm) - ("python-pandas" ,python2-pandas) - ("python-pysnptools" ,python2-pysnptools) - ("python-weave" ,python2-weave))) - (native-inputs - `(("python-mock" ,python2-mock) - ("python-nose" ,python2-nose) - ("unzip" ,unzip))) + (list python2-scipy + python2-numpy + python2-matplotlib + python2-fastlmm + python2-pandas + python2-pysnptools + python2-weave)) + (native-inputs + (list python2-mock python2-nose unzip)) (home-page "https://github.com/PMBio/warpedLMM") (synopsis "Implementation of warped linear mixed models") (description @@ -5781,9 +5639,7 @@ (define-public prank `("PATH" ":" prefix (,path))) (install-file "prank.1" man))))))) (inputs - `(("mafft" ,mafft) - ("exonerate" ,exonerate) - ("bppsuite" ,bppsuite))) + (list mafft exonerate bppsuite)) (home-page "http://wasabiapp.org/software/prank/") (synopsis "Probabilistic multiple sequence alignment program") (description @@ -5855,7 +5711,7 @@ (define-public proteinortho ("lapack" ,lapack) ("openblas" ,openblas))) (native-inputs - `(("which" ,which))) + (list which)) (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") (synopsis "Detect orthologous genes across species") (description @@ -5884,7 +5740,7 @@ (define-public pyicoteo `(#:python ,python-2 ; does not work with Python 3 #:tests? #f)) ; there are no tests (inputs - `(("python2-matplotlib" ,python2-matplotlib))) + (list python2-matplotlib)) (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") (synopsis "Analyze high-throughput genetic sequencing data") (description @@ -6008,10 +5864,7 @@ (define-public roary (,(string-append coreutils-path ":" out "/bin")))))) #t))))) (native-inputs - `(("perl-env-path" ,perl-env-path) - ("perl-test-files" ,perl-test-files) - ("perl-test-most" ,perl-test-most) - ("perl-test-output" ,perl-test-output))) + (list perl-env-path perl-test-files perl-test-most perl-test-output)) (inputs `(("perl-array-utils" ,perl-array-utils) ("bioperl" ,bioperl-minimal) @@ -6084,7 +5937,7 @@ (define-public raxml (symlink (string-append bin "/" executable) "raxml")) #t))))) (inputs - `(("openmpi" ,openmpi))) + (list openmpi)) (home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html") (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") (description @@ -6172,11 +6025,7 @@ (define-public rsem "rsem-run-ebseq" "rsem-run-prsem-testing-procedure")))))))) (inputs - `(("boost" ,boost) - ("r-minimal" ,r-minimal) - ("perl" ,perl) - ("htslib" ,htslib-1.3) - ("zlib" ,zlib))) + (list boost r-minimal perl htslib-1.3 zlib)) (home-page "http://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") (description @@ -6204,14 +6053,14 @@ (define-public rseqc "0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m")))) (build-system python-build-system) (inputs - `(("python-cython" ,python-cython) - ("python-bx-python" ,python-bx-python) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-numpy" ,python-numpy) - ("zlib" ,zlib))) + (list python-cython + python-bx-python + python-pybigwig + python-pysam + python-numpy + zlib)) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (home-page "http://rseqc.sourceforge.net/") (synopsis "RNA-seq quality control package") (description @@ -6271,7 +6120,7 @@ (define-public seek ("python" ,python) ("readline" ,readline))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://seek.princeton.edu") (synopsis "Gene co-expression search engine") (description @@ -6329,13 +6178,9 @@ (define-public samtools (install-file file include)) (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (inputs - `(("htslib" ,htslib) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))) + (list htslib ncurses perl python zlib)) (home-page "http://samtools.sourceforge.net") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (description @@ -6364,11 +6209,7 @@ (define-public samtools-1.10 (delete-file-recursively "htslib-1.10") #t)))) (inputs - `(("htslib" ,htslib-1.10) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))))) + (list htslib-1.10 ncurses perl python zlib)))) (define-public samtools-1.2 (package (inherit samtools) @@ -6423,15 +6264,9 @@ (define-public samtools-1.2 (("P 52.out.*") "")))) (delete 'configure)))) (native-inputs - `(("grep" ,grep) - ("gawk" ,gawk) - ("pkg-config" ,pkg-config))) + (list grep gawk pkg-config)) (inputs - `(("htslib" ,htslib-for-samtools-1.2) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))))) + (list htslib-for-samtools-1.2 ncurses perl python zlib)))) (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input @@ -6543,8 +6378,7 @@ (define-public mosaicatcher (mkdir-p share) (copy-recursively "../R" share))))))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib))) + (list boost htslib)) (home-page "https://github.com/friendsofstrandseq/mosaicatcher") (synopsis "Count and classify Strand-seq reads") (description @@ -6586,7 +6420,7 @@ (define-public ngs-sdk #t))) (add-after 'unpack 'enter-dir (lambda _ (chdir "ngs-sdk") #t))))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) ;; According to the test ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) ;; in ngs-sdk/setup/konfigure.perl @@ -6724,7 +6558,7 @@ (define-public ncbi-vdb ("java-ngs" ,java-ngs) ("libmagic" ,file) ("hdf5" ,hdf5))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) ;; NCBI-VDB requires SSE capability. (supported-systems '("i686-linux" "x86_64-linux")) (home-page "https://github.com/ncbi/ncbi-vdb") @@ -6770,10 +6604,9 @@ (define-public plink "/bin/"))) (install-file "plink" bin))))))) (inputs - `(("zlib" ,zlib) - ("lapack" ,lapack))) + (list zlib lapack)) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") (synopsis "Whole genome association analysis toolset") (description @@ -6830,13 +6663,9 @@ (define-public plink-ng (invoke "bash" "test_setup.sh") (invoke "python3" "tests.py")))))))) (inputs - `(("lapack" ,lapack) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list lapack openblas zlib)) (native-inputs - `(("diffutils" ,diffutils) - ("plink" ,plink) - ("python" ,python))) ; for tests + (list diffutils plink python)) ; for tests (home-page "https://www.cog-genomics.org/plink/") (license license:gpl3+))) @@ -6883,8 +6712,7 @@ (define-public smithlab-cpp #t)) (delete 'configure)))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "https://github.com/smithlabcode/smithlab_cpp") (synopsis "C++ helper library for functions used in Smith lab projects") (description @@ -6924,10 +6752,7 @@ (define-public preseq "PROGS=preseq" "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs - `(("gsl" ,gsl) - ("samtools" ,samtools-0.1) - ("smithlab-cpp" ,smithlab-cpp) - ("zlib" ,zlib))) + (list gsl samtools-0.1 smithlab-cpp zlib)) (home-page "http://smithlabresearch.org/software/preseq/") (synopsis "Program for analyzing library complexity") (description @@ -6953,11 +6778,9 @@ (define-public python-screed "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-pytest python-pytest-cov python-pytest-runner)) (inputs - `(("python-bz2file" ,python-bz2file))) + (list python-bz2file)) (home-page "https://github.com/dib-lab/screed/") (synopsis "Short read sequence database utilities") (description "Screed parses FASTA and FASTQ files and generates databases. @@ -7055,7 +6878,7 @@ (define-public sra-tools (string-append "--with-hdf5-prefix=" (assoc-ref inputs "hdf5"))) #t))))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) (inputs `(("ngs-sdk" ,ngs-sdk) ("ncbi-vdb" ,ncbi-vdb) @@ -7093,9 +6916,7 @@ (define-public seqan (lambda _ (invoke "ctest" "test" "--output-on-failure")))))) (native-inputs - `(("bzip2" ,bzip2) - ("cereal" ,cereal) - ("zlib" ,zlib))) + (list bzip2 cereal zlib)) (home-page "https://www.seqan.de") (synopsis "Library for nucleotide sequence analysis") (description @@ -7188,9 +7009,9 @@ (define-public seqmagick "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) (build-system python-build-system) (inputs - `(("python-biopython" ,python-biopython))) + (list python-biopython)) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -7228,7 +7049,7 @@ (define-public seqtk (install-file "seqtk" bin) #t)))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/lh3/seqtk") (synopsis "Toolkit for processing biological sequences in FASTA/Q format") (description @@ -7265,7 +7086,7 @@ (define-public snap-aligner (install-file "snap-aligner" bin) (install-file "SNAPCommand" bin))))))) (native-inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://snap.cs.berkeley.edu/") (synopsis "Short read DNA sequence aligner") (description @@ -7313,7 +7134,7 @@ (define-public sortmerna (find-files "rRNA_databases" ".*fasta")) #t)))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/") (synopsis "Biological sequence analysis tool for NGS reads") (description @@ -7395,10 +7216,9 @@ (define-public star #t)) (delete 'configure)))) (native-inputs - `(("xxd" ,xxd))) + (list xxd)) (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (home-page "https://github.com/alexdobin/STAR") (synopsis "Universal RNA-seq aligner") (description @@ -7505,7 +7325,7 @@ (define-public subread (copy-recursively "../bin" bin)))) ;; no "configure" script (delete 'configure)))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "http://subread.sourceforge.net/") (synopsis "Tool kit for processing next-gen sequencing data") (description @@ -7562,8 +7382,7 @@ (define-public stringtie (install-file "stringtie" bin) #t)))))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "http://ccb.jhu.edu/software/stringtie/") (synopsis "Transcript assembly and quantification for RNA-Seq data") (description @@ -7617,16 +7436,16 @@ (define-public taxtastic ;; available. (delete 'sanity-check)))) (propagated-inputs - `(("python-sqlalchemy" ,python-sqlalchemy) - ("python-decorator" ,python-decorator) - ("python-biopython" ,python-biopython) - ("python-pandas" ,python-pandas) - ("python-psycopg2" ,python-psycopg2) - ("python-fastalite" ,python-fastalite) - ("python-pyyaml" ,python-pyyaml) - ("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-dendropy" ,python-dendropy))) + (list python-sqlalchemy + python-decorator + python-biopython + python-pandas + python-psycopg2 + python-fastalite + python-pyyaml + python-six + python-jinja2 + python-dendropy)) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description @@ -7656,10 +7475,9 @@ (define-public vcftools (string-append "PREFIX=" #$output) (string-append "MANDIR=" #$output "/share/man/man1")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + (list perl zlib)) (home-page "https://vcftools.github.io/") (synopsis "Tools for working with VCF files") (description @@ -7684,8 +7502,7 @@ (define-public infernal "1z4mgwqg1j4n5ika08ai8mg9yjyjhf4821jp83v2bgwzxrykqjgr")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl) - ("python" ,python))) ; for tests + (list perl python)) ; for tests (home-page "http://eddylab.org/infernal/") (synopsis "Inference of RNA alignments") (description "Infernal (\"INFERence of RNA ALignment\") is a tool for @@ -7718,15 +7535,15 @@ (define-public r-presto (properties `((upstream . "presto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-data-table + r-deseq2 + r-dplyr + r-matrix + r-rcpp + r-rcpparmadillo + r-reshape2 + r-rlang + r-tidyr)) (home-page "https://github.com/immunogenomics/presto") (synopsis "Fast Functions for Differential Expression using Wilcox and AUC") (description "This package performs a fast Wilcoxon rank sum test and @@ -7749,25 +7566,25 @@ (define-public r-snapatac (properties `((upstream-name . "SnapATAC"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-edger" ,r-edger) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-plot3d" ,r-plot3d) - ("r-rann" ,r-rann) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) + (list r-bigmemory + r-doparallel + r-dosnow + r-edger + r-foreach + r-genomicranges + r-igraph + r-iranges + r-irlba + r-matrix + r-plyr + r-plot3d + r-rann + r-raster + r-rcolorbrewer + r-rhdf5 + r-rtsne + r-scales + r-viridis)) (home-page "https://github.com/r3fang/SnapATAC") (synopsis "Single nucleus analysis package for ATAC-Seq") (description @@ -7812,12 +7629,10 @@ (define-public r-umi4cpackage (("\"perl") (string-append "\"" (which "perl"))))))))) (inputs - `(("perl" ,perl) - ("bowtie" ,bowtie))) + (list perl bowtie)) (propagated-inputs - `(("r-misha" ,r-misha) - ("r-zoo" ,r-zoo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-misha r-zoo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tanaylab/umi4cpackage") (synopsis "Processing and analysis of UMI-4C contact profiles") (description "This is a package that lets you process UMI-4C data from @@ -7844,16 +7659,16 @@ (define-public r-shinycell (properties `((upstream-name . "ShinyCell"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-hdf5r" ,r-hdf5r) - ("r-matrix" ,r-matrix) - ("r-r-utils" ,r-r-utils) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr) - ("r-reticulate" ,r-reticulate))) + (list r-data-table + r-ggplot2 + r-glue + r-gridextra + r-hdf5r + r-matrix + r-r-utils + r-rcolorbrewer + r-readr + r-reticulate)) (home-page "https://github.com/SGDDNB/ShinyCell") (synopsis "Shiny interactive web apps for single-cell data") (description @@ -7880,30 +7695,30 @@ (define-public r-archr (properties `((upstream-name . "ArchR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-chromvar" ,r-chromvar) - ("r-complexheatmap" ,r-complexheatmap) - ("r-data-table" ,r-data-table) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-gtools" ,r-gtools) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-motifmatchr" ,r-motifmatchr) - ("r-nabor" ,r-nabor) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-uwot" ,r-uwot))) + (list r-biocgenerics + r-biostrings + r-chromvar + r-complexheatmap + r-data-table + r-genomicranges + r-ggplot2 + r-ggrepel + r-gridextra + r-gtable + r-gtools + r-magrittr + r-matrix + r-matrixstats + r-motifmatchr + r-nabor + r-plyr + r-rcpp + r-rhdf5 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-uwot)) (home-page "https://github.com/GreenleafLab/ArchR") (synopsis "Analyze single-cell regulatory chromatin in R") (description @@ -7925,21 +7740,21 @@ (define-public r-scde "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-mgcv" ,r-mgcv) - ("r-rook" ,r-rook) - ("r-rjson" ,r-rjson) - ("r-cairo" ,r-cairo) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-edger" ,r-edger) - ("r-quantreg" ,r-quantreg) - ("r-nnet" ,r-nnet) - ("r-rmtstat" ,r-rmtstat) - ("r-extremes" ,r-extremes) - ("r-pcamethods" ,r-pcamethods) - ("r-biocparallel" ,r-biocparallel) - ("r-flexmix" ,r-flexmix))) + (list r-rcpp + r-rcpparmadillo + r-mgcv + r-rook + r-rjson + r-cairo + r-rcolorbrewer + r-edger + r-quantreg + r-nnet + r-rmtstat + r-extremes + r-pcamethods + r-biocparallel + r-flexmix)) (home-page "https://hms-dbmi.github.io/scde/") (synopsis "R package for analyzing single-cell RNA-seq data") (description "The SCDE package implements a set of statistical methods for @@ -7981,7 +7796,7 @@ (define-public r-misha (assoc-ref inputs "kentutils") "/bin/bigWigToWig")))))))) (inputs - `(("kentutils" ,kentutils))) + (list kentutils)) (home-page "https://github.com/tanaylab/misha") (synopsis "Toolkit for analysis of genomic data") (description "This package is intended to help users to efficiently @@ -8009,18 +7824,18 @@ (define-public r-shaman '(delete-file "inst/doc/shaman-package.R")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-domc" ,r-domc) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-misha" ,r-misha) - ("r-plyr" ,r-plyr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ;; For vignettes - ("r-rmarkdown" ,r-rmarkdown) - ("r-knitr" ,r-knitr))) + (list r-data-table + r-domc + r-ggplot2 + r-gviz + r-misha + r-plyr + r-rann + r-rcpp + r-reshape2 + ;; For vignettes + r-rmarkdown + r-knitr)) (home-page "https://github.com/tanaylab/shaman") (synopsis "Sampling HiC contact matrices for a-parametric normalization") (description "The Shaman package implements functions for @@ -8075,11 +7890,7 @@ (define-public r-demultiplex (properties `((upstream-name . "deMULTIplex"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-shortread" ,r-shortread) - ("r-stringdist" ,r-stringdist))) + (list r-kernsmooth r-reshape2 r-rtsne r-shortread r-stringdist)) (home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq") (synopsis "MULTI-seq pre-processing and classification tools") (description @@ -8118,17 +7929,17 @@ (define-public gdc-client (substitute* "requirements.txt" (("==") ">="))))))) (inputs - `(("python-cryptography" ,python-cryptography) - ("python-intervaltree" ,python-intervaltree) - ("python-jsonschema" ,python-jsonschema) - ("python-lxml" ,python-lxml) - ("python-ndg-httpsclient" ,python-ndg-httpsclient) - ("python-progressbar2" ,python-progressbar2) - ("python-pyasn1" ,python-pyasn1) - ("python-pyopenssl" ,python-pyopenssl) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-termcolor" ,python-termcolor))) + (list python-cryptography + python-intervaltree + python-jsonschema + python-lxml + python-ndg-httpsclient + python-progressbar2 + python-pyasn1 + python-pyopenssl + python-pyyaml + python-requests + python-termcolor)) (home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool") (synopsis "GDC data transfer tool") (description "The gdc-client provides several convenience functions over @@ -8160,12 +7971,9 @@ (define-public vsearch #t)))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib) - ("bzip2" ,bzip2) - ("cityhash" ,cityhash))) + (list zlib bzip2 cityhash)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (synopsis "Sequence search tools for metagenomics") (description "VSEARCH supports DNA sequence searching, clustering, chimera detection, @@ -8204,8 +8012,7 @@ (define-public pardre (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "ParDRe" bin))))))) (inputs - `(("openmpi-c++" ,openmpi-c++) - ("zlib" ,zlib))) + (list openmpi-c++ zlib)) (synopsis "Parallel tool to remove duplicate DNA reads") (description "ParDRe is a parallel tool to remove duplicate genetic sequence reads. @@ -8236,7 +8043,7 @@ (define-public ngshmmalign (build-system cmake-build-system) (arguments '(#:tests? #false)) ; there are none (inputs - `(("boost" ,boost))) + (list boost)) (home-page "https://github.com/cbg-ethz/ngshmmalign/") (synopsis "Profile HMM aligner for NGS reads") (description @@ -8282,14 +8089,14 @@ (define-public prinseq (,(getenv "PERL5LIB"))))) scripts))))))) (inputs - `(("guile" ,guile-3.0) ; for wrapper scripts - ("perl" ,perl) - ("perl-cairo" ,perl-cairo) - ("perl-data-dumper" ,perl-data-dumper) - ("perl-digest-md5" ,perl-digest-md5) - ("perl-getopt-long" ,perl-getopt-long) - ("perl-json" ,perl-json) - ("perl-statistics-pca" ,perl-statistics-pca))) + (list guile-3.0 ; for wrapper scripts + perl + perl-cairo + perl-data-dumper + perl-digest-md5 + perl-getopt-long + perl-json + perl-statistics-pca)) (home-page "http://prinseq.sourceforge.net/") (synopsis "Preprocess sequence data in FASTA or FASTQ formats") (description @@ -8340,14 +8147,14 @@ (define-public shorah (when tests? (invoke "make" "check"))))))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib) - ("python" ,python) - ("python-biopython" ,python-biopython) - ("python-numpy" ,python-numpy) - ("zlib" ,zlib))) + (list boost + htslib + python + python-biopython + python-numpy + zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "") (synopsis "Short reads assembly into haplotypes") (description @@ -8372,11 +8179,9 @@ (define-public ruby-bio-kseq (arguments `(#:test-target "spec")) (native-inputs - `(("bundler" ,bundler) - ("ruby-rspec" ,ruby-rspec) - ("ruby-rake-compiler" ,ruby-rake-compiler))) + (list bundler ruby-rspec ruby-rake-compiler)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") (description "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and @@ -8398,7 +8203,7 @@ (define-public bio-locus "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) (build-system ruby-build-system) (native-inputs - `(("ruby-rspec" ,ruby-rspec))) + (list ruby-rspec)) (synopsis "Tool for fast querying of genome locations") (description "Bio-locus is a tabix-like tool for fast querying of genome @@ -8421,10 +8226,9 @@ (define-public bio-blastxmlparser "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) (build-system ruby-build-system) (propagated-inputs - `(("ruby-bio-logger" ,ruby-bio-logger) - ("ruby-nokogiri" ,ruby-nokogiri))) + (list ruby-bio-logger ruby-nokogiri)) (inputs - `(("ruby-rspec" ,ruby-rspec))) + (list ruby-rspec)) (synopsis "Fast big data BLAST XML parser and library") (description "Very fast parallel big-data BLAST XML file parser which can be used as @@ -8446,9 +8250,9 @@ (define-public bioruby "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) (build-system ruby-build-system) (propagated-inputs - `(("ruby-libxml" ,ruby-libxml))) + (list ruby-libxml)) (native-inputs - `(("which" ,which))) ; required for test phase + (list which)) ; required for test phase (arguments `(#:phases (modify-phases %standard-phases @@ -8489,7 +8293,7 @@ (define-public bio-vcf "1glw5pn9s8z13spxk6yyfqaz80n9lga67f33w35nkpq9dwi2vg6g")))) (build-system ruby-build-system) (native-inputs - `(("ruby-cucumber" ,ruby-cucumber))) + (list ruby-cucumber)) (synopsis "Smart VCF parser DSL") (description "Bio-vcf provides a @acronym{DSL, domain specific language} for processing @@ -8532,16 +8336,16 @@ (define-public r-phantompeakqualtools (inputs `(("r" ,r-minimal))) (propagated-inputs - `(("r-catools" ,r-catools) - ("r-snow" ,r-snow) - ("r-snowfall" ,r-snowfall) - ("r-bitops" ,r-bitops) - ("r-rsamtools" ,r-rsamtools) - ("r-spp" ,r-spp) - ("gawk" ,gawk) - ("samtools" ,samtools) - ("boost" ,boost) - ("gzip" ,gzip))) + (list r-catools + r-snow + r-snowfall + r-bitops + r-rsamtools + r-spp + gawk + samtools + boost + gzip)) (home-page "https://github.com/kundajelab/phantompeakqualtools") (synopsis "Informative enrichment for ChIP-seq data") (description "This package computes informative enrichment and quality @@ -8564,8 +8368,7 @@ (define-public r-r4rna "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) (build-system r-build-system) (propagated-inputs - `(("r-optparse" ,r-optparse) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-optparse r-rcolorbrewer)) (home-page "https://www.e-rna.org/r-chie/index.cgi") (synopsis "Analysis framework for RNA secondary structure") (description @@ -8617,7 +8420,7 @@ (define-public rcas-web ("guile-json" ,guile-json-1) ("guile-redis" ,guile2.2-redis))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/BIMSBbioinfo/rcas-web") (synopsis "Web interface for RNA-centric annotation system (RCAS)") (description "This package provides a simple web interface for the @@ -8642,16 +8445,16 @@ (define-public r-chipkernels "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) (build-system r-build-system) (propagated-inputs - `(("r-iranges" ,r-iranges) - ("r-xvector" ,r-xvector) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-gtools" ,r-gtools) - ("r-genomicranges" ,r-genomicranges) - ("r-sfsmisc" ,r-sfsmisc) - ("r-kernlab" ,r-kernlab) - ("r-s4vectors" ,r-s4vectors) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-iranges + r-xvector + r-biostrings + r-bsgenome + r-gtools + r-genomicranges + r-sfsmisc + r-kernlab + r-s4vectors + r-biocgenerics)) (home-page "https://github.com/ManuSetty/ChIPKernels") (synopsis "Build string kernels for DNA Sequence analysis") (description "ChIPKernels is an R package for building different string @@ -8676,12 +8479,12 @@ (define-public r-seqgl "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-chipkernels" ,r-chipkernels) - ("r-genomicranges" ,r-genomicranges) - ("r-spams" ,r-spams) - ("r-wgcna" ,r-wgcna) - ("r-fastcluster" ,r-fastcluster))) + (list r-biostrings + r-chipkernels + r-genomicranges + r-spams + r-wgcna + r-fastcluster)) (home-page "https://github.com/ManuSetty/SeqGL") (synopsis "Group lasso for Dnase/ChIP-seq data") (description "SeqGL is a group lasso based algorithm to extract @@ -8731,17 +8534,14 @@ (define-public emboss (add-after 'disable-update-check 'autogen (lambda _ (invoke "autoreconf" "-vif") #t))))) (inputs - `(("perl" ,perl) - ("libpng" ,libpng) - ("gd" ,gd) - ("libx11" ,libx11) - ("libharu" ,libharu) - ("zlib" ,zlib))) + (list perl + libpng + gd + libx11 + libharu + zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "http://emboss.sourceforge.net") (synopsis "Molecular biology analysis suite") (description "EMBOSS is the \"European Molecular Biology Open Software @@ -8789,8 +8589,7 @@ (define-public bits "bin" (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("gsl" ,gsl) - ("zlib" ,zlib))) + (list gsl zlib)) (home-page "https://github.com/arq5x/bits") (synopsis "Implementation of binary interval search algorithm") (description "This package provides an implementation of the @@ -8880,9 +8679,7 @@ (define-public pepr `(#:python ,python-2 ; python2 only #:tests? #f)) ; no tests included (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pysam" ,python2-pysam))) + (list python2-numpy python2-scipy python2-pysam)) (home-page "https://github.com/shawnzhangyx/PePr") (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") (description @@ -8957,20 +8754,20 @@ (define-public multiqc ;; reasons. (delete 'sanity-check)))) (propagated-inputs - `(("python-click" ,python-click) - ("python-coloredlogs" ,python-coloredlogs) - ("python-future" ,python-future) - ("python-jinja2" ,python-jinja2) - ("python-lzstring" ,python-lzstring) - ("python-markdown" ,python-markdown) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-rich" ,python-rich) - ("python-simplejson" ,python-simplejson) - ("python-spectra" ,python-spectra))) + (list python-click + python-coloredlogs + python-future + python-jinja2 + python-lzstring + python-markdown + python-matplotlib + python-networkx + python-numpy + python-pyyaml + python-requests + python-rich + python-simplejson + python-spectra)) (native-inputs `(("python-pytest" ,python-pytest) ("tests" @@ -9009,19 +8806,16 @@ (define-public variant-tools "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g")))) (build-system python-build-system) (inputs - `(("boost" ,boost) - ("c-blosc" ,c-blosc) - ("gsl" ,gsl) - ("hdf5" ,hdf5) - ("hdf5-blosc" ,hdf5-blosc) - ("python-cython" ,python-cython) - ("zlib" ,zlib))) + (list boost + c-blosc + gsl + hdf5 + hdf5-blosc + python-cython + zlib)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-pycurl" ,python-pycurl) - ("python-pyzmq" ,python-pyzmq) - ("python-scipy" ,python-scipy) - ("python-tables" ,python-tables))) + (list python-numpy python-pycurl python-pyzmq python-scipy + python-tables)) (home-page "https://vatlab.github.io/vat-docs/") (synopsis "Analyze genetic variants from Next-Gen sequencing studies") (description @@ -9047,11 +8841,7 @@ (define-public r-raremetals2 (properties `((upstream-name . "RareMETALS2"))) (build-system r-build-system) (propagated-inputs - `(("r-seqminer" ,r-seqminer) - ("r-mvtnorm" ,r-mvtnorm) - ("r-mass" ,r-mass) - ("r-compquadform" ,r-compquadform) - ("r-getopt" ,r-getopt))) + (list r-seqminer r-mvtnorm r-mass r-compquadform r-getopt)) (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") (synopsis "Analyze gene-level association tests for binary trait") (description @@ -9082,11 +8872,7 @@ (define-public r-dropbead "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gridextra" ,r-gridextra) - ("r-gplots" ,r-gplots) - ("r-plyr" ,r-plyr))) + (list r-ggplot2 r-rcolorbrewer r-gridextra r-gplots r-plyr)) (home-page "https://github.com/rajewsky-lab/dropbead") (synopsis "Basic exploration and analysis of Drop-seq data") (description "This package offers a quick and straight-forward way to @@ -9118,41 +8904,41 @@ (define-public r-cellchat (properties `((upstream-name . "CellChat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-colorspace" ,r-colorspace) - ("r-complexheatmap" ,r-complexheatmap) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-expm" ,r-expm) - ("r-fnn" ,r-fnn) - ("r-forcats" ,r-forcats) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-gg-gap" ,r-gg-gap) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-nmf" ,r-nmf) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rspectra" ,r-rspectra) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-shape" ,r-shape) - ("r-sna" ,r-sna) - ("r-stringr" ,r-stringr) - ("r-svglite" ,r-svglite))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-circlize + r-colorspace + r-complexheatmap + r-cowplot + r-dplyr + r-expm + r-fnn + r-forcats + r-future + r-future-apply + r-gg-gap + r-ggalluvial + r-ggplot2 + r-ggrepel + r-igraph + r-irlba + r-magrittr + r-matrix + r-nmf + r-patchwork + r-pbapply + r-rcolorbrewer + r-rcpp + r-rcppeigen + r-reshape2 + r-reticulate + r-rspectra + r-rtsne + r-scales + r-shape + r-sna + r-stringr + r-svglite)) + (native-inputs (list r-knitr)) (home-page "https://github.com/sqjin/CellChat") (synopsis "Analysis of cell-cell communication from single-cell transcriptomics data") (description @@ -9198,11 +8984,9 @@ (define-public sambamba (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")))))))) (native-inputs - `(("python" ,python))) + (list python)) (inputs - `(("ldc" ,ldc) - ("lz4" ,lz4) - ("zlib" ,zlib))) + (list ldc lz4 zlib)) (home-page "https://github.com/biod/sambamba") (synopsis "Tools for working with SAM/BAM data") (description "Sambamba is a high performance modern robust and @@ -9245,10 +9029,7 @@ (define-public ritornello (install-file "bin/Ritornello" bin) #t)))))) (inputs - `(("samtools" ,samtools-0.1) - ("fftw" ,fftw) - ("boost" ,boost) - ("zlib" ,zlib))) + (list samtools-0.1 fftw boost zlib)) (home-page "https://github.com/KlugerLab/Ritornello") (synopsis "Control-free peak caller for ChIP-seq data") (description "Ritornello is a ChIP-seq peak calling algorithm based on @@ -9314,12 +9095,9 @@ (define-public trim-galore (install-file "trim_galore" bin) #t)))))) (inputs - `(("gzip" ,gzip) - ("perl" ,perl) - ("pigz" ,pigz) - ("cutadapt" ,cutadapt))) + (list gzip perl pigz cutadapt)) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") (synopsis "Wrapper around Cutadapt and FastQC") (description "Trim Galore! is a wrapper script to automate quality and @@ -9465,22 +9243,19 @@ (define-public imp `(("python" ,python-wrapper) ("swig" ,swig))) (inputs - `(("boost" ,boost) - ("cgal" ,cgal) - ("gsl" ,gsl) - ("hdf5" ,hdf5) - ("fftw" ,fftw) - ("eigen" ,eigen) - ;; Enabling MPI causes the build to use all the available memory and - ;; fail (tested on a machine with 32 GiB of RAM). - ;;("mpi" ,openmpi) - ("opencv" ,opencv))) + (list boost + cgal + gsl + hdf5 + fftw + eigen + ;; Enabling MPI causes the build to use all the available memory and + ;; fail (tested on a machine with 32 GiB of RAM). + ;;("mpi" ,openmpi) + opencv)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-pandas" ,python-pandas) - ("python-scikit-learn" ,python-scikit-learn) - ("python-networkx" ,python-networkx))) + (list python-numpy python-scipy python-pandas python-scikit-learn + python-networkx)) (home-page "https://integrativemodeling.org") (synopsis "Integrative modeling platform") (description "IMP's broad goal is to contribute to a comprehensive @@ -9538,18 +9313,18 @@ (define-public tadbit (add-installed-pythonpath inputs outputs) (invoke "python3" "test/test_all.py"))))))) (native-inputs - `(("glib" ,glib "bin") ;for gtester - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") ;for gtester + pkg-config)) (inputs ;; TODO: add Chimera for visualization - `(("imp" ,imp) - ("mcl" ,mcl) - ("python-future" ,python-future) - ("python-h5py" ,python-h5py) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam))) + (list imp + mcl + python-future + python-h5py + python-scipy + python-numpy + python-matplotlib + python-pysam)) (home-page "https://3dgenomes.github.io/TADbit/") (synopsis "Analyze, model, and explore 3C-based data") (description @@ -9728,8 +9503,7 @@ (define-public f-seq (install-file "build~/fseq.jar" lib) (copy-recursively "lib" lib))))))) (inputs - `(("perl" ,perl) - ("java-commons-cli" ,java-commons-cli))) + (list perl java-commons-cli)) (home-page "https://fureylab.web.unc.edu/software/fseq/") (synopsis "Feature density estimator for high-throughput sequence tags") (description @@ -9815,9 +9589,7 @@ (define-public bismark "/bin/gunzip -c"))) #t)))))) (inputs - `(("gzip" ,gzip) - ("perl-carp" ,perl-carp) - ("perl-getopt-long" ,perl-getopt-long))) + (list gzip perl-carp perl-getopt-long)) (native-inputs `(("plotly.js" ,(origin @@ -9926,11 +9698,9 @@ (define-public segemehl (install-file exe bin)) exes))))))) (inputs - `(("htslib" ,htslib) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) + (list htslib ncurses zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl") (synopsis "Map short sequencer reads to reference genomes") (description "Segemehl is software to map short sequencer reads to @@ -9979,9 +9749,7 @@ (define-public kallisto (("include_directories\\(\\.\\./ext/htslib\\)") "")) #t))))) (inputs - `(("hdf5" ,hdf5) - ("htslib" ,htslib-1.9) - ("zlib" ,zlib))) + (list hdf5 htslib-1.9 zlib)) (home-page "https://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") (description @@ -10147,7 +9915,7 @@ (define-public sailfish ("tbb" ,tbb-2020) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/") (synopsis "Mapping-based isoform quantification from RNA-Seq reads") (description "Sailfish is a tool for genomic transcript quantification @@ -10322,7 +10090,7 @@ (define-public salmon ("xz" ,xz) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/COMBINE-lab/salmon") (synopsis "Quantification from RNA-seq reads using lightweight alignments") (description "Salmon is a program to produce highly-accurate, @@ -10355,12 +10123,9 @@ (define-public python-loompy (lambda _ (invoke "pytest" "tests")))))) (propagated-inputs - `(("python-h5py" ,python-h5py) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + (list python-h5py python-numpy python-pandas python-scipy)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -10382,7 +10147,7 @@ (define-public python-biothings-client (base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4")))) (build-system python-build-system) (arguments `(#:tests? #false)) ; require internet access - (propagated-inputs `(("python-requests" ,python-requests))) + (propagated-inputs (list python-requests)) (home-page "https://github.com/biothings/biothings_client.py") (synopsis "Python client for BioThings API services") (description "This package provides a Python client for BioThings @@ -10401,7 +10166,7 @@ (define-public python-mygene (base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7")))) (build-system python-build-system) (propagated-inputs - `(("python-biothings-client" ,python-biothings-client))) + (list python-biothings-client)) (home-page "https://github.com/biothings/mygene.py") (synopsis "Python Client for MyGene.Info services.") (description "MyGene.Info provides simple-to-use REST web services @@ -10477,8 +10242,7 @@ (define-public java-forester ;; There is no install target (replace 'install (install-jars "."))))) (propagated-inputs - `(("java-commons-codec" ,java-commons-codec) - ("java-openchart2" ,java-openchart2))) + (list java-commons-codec java-openchart2)) (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") (synopsis "Phylogenomics libraries for Java") (description "Forester is a collection of Java libraries for @@ -10550,8 +10314,7 @@ (define-public java-forester-1.005 ;; There is no install target (replace 'install (install-jars "."))))) (propagated-inputs - `(("java-commons-codec" ,java-commons-codec) - ("java-openchart2" ,java-openchart2))) + (list java-commons-codec java-openchart2)) ;; The source archive does not contain the resources. (native-inputs `(("phyloxml.xsd" @@ -10619,13 +10382,10 @@ (define-public java-biojava-core "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple))) + (list java-log4j-api java-log4j-core java-slf4j-api + java-slf4j-simple)) (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Core libraries of Java framework for processing biological data") (description "BioJava is a project dedicated to providing a Java framework @@ -10660,15 +10420,14 @@ (define-public java-biojava-phylo "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core) - ("java-forester" ,java-forester))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core + java-forester)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the @@ -10696,16 +10455,15 @@ (define-public java-biojava-alignment "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core) - ("java-biojava-phylo" ,java-biojava-phylo) - ("java-forester" ,java-forester))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core + java-biojava-phylo + java-forester)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that @@ -10754,15 +10512,14 @@ (define-public java-biojava-phylo-4.0 "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core-4.0) - ("java-forester" ,java-forester-1.005))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core-4.0 + java-forester-1.005)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the @@ -10790,16 +10547,15 @@ (define-public java-biojava-alignment-4.0 "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core-4.0) - ("java-biojava-phylo" ,java-biojava-phylo-4.0) - ("java-forester" ,java-forester-1.005))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core-4.0 + java-biojava-phylo-4.0 + java-forester-1.005)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that @@ -10940,8 +10696,7 @@ (define-public dropseq-tools ("java-simple-xml" ,java-simple-xml) ("java-snakeyaml" ,java-snakeyaml))) (native-inputs - `(("unzip" ,unzip) - ("java-testng" ,java-testng))) + (list unzip java-testng)) (home-page "http://mccarrolllab.com/dropseq/") (synopsis "Tools for Drop-seq analyses") (description "Drop-seq is a technology to enable biologists to @@ -10985,44 +10740,42 @@ (define-public pigx-rnaseq (search-input-directory inputs "share/zoneinfo"))))))) (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("gzip" ,gzip) - ("snakemake" ,snakemake) - ("multiqc" ,multiqc) - ("star" ,star-for-pigx) - ("hisat2" ,hisat2) - ("fastp" ,fastp) - ("htseq" ,htseq) - ("samtools" ,samtools) - ("r-minimal" ,r-minimal) - ("r-rmarkdown" ,r-rmarkdown) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-gprofiler2" ,r-gprofiler2) - ("r-deseq2" ,r-deseq2) - ("r-dt" ,r-dt) - ("r-knitr" ,r-knitr) - ("r-pheatmap" ,r-pheatmap) - ("r-corrplot" ,r-corrplot) - ("r-reshape2" ,r-reshape2) - ("r-plotly" ,r-plotly) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-crosstalk" ,r-crosstalk) - ("r-tximport" ,r-tximport) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rjson" ,r-rjson) - ("salmon" ,salmon) - ("pandoc" ,pandoc) - ("python-wrapper" ,python-wrapper) - ("python-deeptools" ,python-deeptools) - ("python-pyyaml" ,python-pyyaml))) - (native-inputs - `(("tzdata" ,tzdata) - ("automake" ,automake) - ("autoconf" ,autoconf))) + (list coreutils + sed + gzip + snakemake + multiqc + star-for-pigx + hisat2 + fastp + htseq + samtools + r-minimal + r-rmarkdown + r-ggplot2 + r-ggpubr + r-ggrepel + r-gprofiler2 + r-deseq2 + r-dt + r-knitr + r-pheatmap + r-corrplot + r-reshape2 + r-plotly + r-scales + r-summarizedexperiment + r-crosstalk + r-tximport + r-rtracklayer + r-rjson + salmon + pandoc + python-wrapper + python-deeptools + python-pyyaml)) + (native-inputs + (list tzdata automake autoconf)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for RNA sequencing experiments") (description "PiGX RNAseq is an analysis pipeline for preprocessing and @@ -11055,58 +10808,56 @@ (define-public pigx-chipseq (lambda _ (invoke "autoreconf" "-vif")))))) (inputs - `(("grep" ,grep) - ("coreutils" ,coreutils) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-chipseq" ,r-chipseq) - ("r-corrplot" ,r-corrplot) - ("r-data-table" ,r-data-table) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gprofiler2" ,r-gprofiler2) - ("r-heatmaply" ,r-heatmaply) - ("r-hexbin" ,r-hexbin) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rsubread" ,r-rsubread) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-magic" ,python-magic) - ("python-xlrd" ,python-xlrd) - ("trim-galore" ,trim-galore) - ("macs" ,macs) - ("multiqc" ,multiqc) - ("perl" ,perl) - ("pandoc" ,pandoc) - ("fastqc" ,fastqc) - ("bowtie" ,bowtie) - ("idr" ,idr) - ("snakemake" ,snakemake) - ("samtools" ,samtools) - ("bedtools" ,bedtools) - ("kentutils" ,kentutils))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("python-pytest" ,python-pytest))) + (list grep + coreutils + r-minimal + r-argparser + r-biocparallel + r-biostrings + r-chipseq + r-corrplot + r-data-table + r-deseq2 + r-dplyr + r-dt + r-genomation + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gprofiler2 + r-heatmaply + r-hexbin + r-htmlwidgets + r-jsonlite + r-pheatmap + r-plotly + r-rmarkdown + r-rsamtools + r-rsubread + r-rtracklayer + r-s4vectors + r-stringr + r-tibble + r-tidyr + python-wrapper + python-pyyaml + python-magic + python-xlrd + trim-galore + macs + multiqc + perl + pandoc + fastqc + bowtie + idr + snakemake + samtools + bedtools + kentutils)) + (native-inputs + (list autoconf automake python-pytest)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak @@ -11149,41 +10900,39 @@ (define-public pigx-bsseq (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - `(("tzdata" ,tzdata) - ("automake" ,automake) - ("autoconf" ,autoconf))) - (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("grep" ,grep) - ("r-minimal" ,r-minimal) - ("r-annotationhub" ,r-annotationhub) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-ggbio" ,r-ggbio) - ("r-ggrepel" ,r-ggrepel) - ("r-matrixstats" ,r-matrixstats) - ("r-methylkit" ,r-methylkit) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-bookdown" ,r-bookdown) - ("r-ggplot2" ,r-ggplot2) - ("r-ggbio" ,r-ggbio) - ("pandoc" ,pandoc) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) - ("bismark" ,bismark) - ("bowtie" ,bowtie) - ("bwa-meth" ,bwa-meth) - ("fastqc" ,fastqc) - ("methyldackel" ,methyldackel) - ("multiqc" ,multiqc) - ("trim-galore" ,trim-galore) - ("cutadapt" ,cutadapt) - ("samblaster" ,samblaster) - ("samtools" ,samtools))) + (list tzdata automake autoconf)) + (inputs + (list coreutils + sed + grep + r-minimal + r-annotationhub + r-dt + r-genomation + r-ggbio + r-ggrepel + r-matrixstats + r-methylkit + r-reshape2 + r-rtracklayer + r-rmarkdown + r-bookdown + r-ggplot2 + r-ggbio + pandoc + python-wrapper + python-pyyaml + snakemake + bismark + bowtie + bwa-meth + fastqc + methyldackel + multiqc + trim-galore + cutadapt + samblaster + samtools)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") (description "PiGx BSseq is a data processing pipeline for raw fastq read @@ -11213,8 +10962,7 @@ (define-public pigx-scrnaseq (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf))) + (list automake autoconf)) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) @@ -11288,40 +11036,39 @@ (define-public pigx-sars-cov2-ww (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf))) - (inputs - `(("bash-minimal" ,bash-minimal) - ("bbmap" ,bbmap) - ("bedtools" ,bedtools) - ("bwa" ,bwa) - ("ensembl-vep" ,ensembl-vep) - ("fastp" ,fastp) - ("fastqc" ,fastqc) - ("ivar" ,ivar) - ("kraken2" ,kraken2) - ("krona-tools" ,krona-tools) - ("lofreq" ,lofreq) - ("multiqc" ,multiqc) - ("prinseq" ,prinseq) - ("python-pyyaml" ,python-pyyaml) - ("python-wrapper" ,python-wrapper) - ("r-base64url" ,r-base64url) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-minimal" ,r-minimal) - ("r-plotly" ,r-plotly) - ("r-qpcr" ,r-qpcr) - ("r-r-utils" ,r-r-utils) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("wget" ,wget))) + (list automake autoconf)) + (inputs + (list bash-minimal + bbmap + bedtools + bwa + ensembl-vep + fastp + fastqc + ivar + kraken2 + krona-tools + lofreq + multiqc + prinseq + python-pyyaml + python-wrapper + r-base64url + r-dplyr + r-dt + r-ggplot2 + r-magrittr + r-minimal + r-plotly + r-qpcr + r-r-utils + r-reshape2 + r-rmarkdown + r-stringr + r-tidyr + samtools + snakemake + wget)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for wastewater sequencing") (description "PiGx SARS-CoV-2 is a pipeline for analysing data from @@ -11345,11 +11092,7 @@ (define-public pigx "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7")))) (build-system gnu-build-system) (inputs - `(("python" ,python) - ("pigx-bsseq" ,pigx-bsseq) - ("pigx-chipseq" ,pigx-chipseq) - ("pigx-rnaseq" ,pigx-rnaseq) - ("pigx-scrnaseq" ,pigx-scrnaseq))) + (list python pigx-bsseq pigx-chipseq pigx-rnaseq pigx-scrnaseq)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipelines for genomics") (description "PiGx is a collection of genomics pipelines. It includes the @@ -11391,7 +11134,7 @@ (define-public genrich (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/jsh58/Genrich") (synopsis "Detecting sites of genomic enrichment") (description "Genrich is a peak-caller for genomic enrichment @@ -11421,11 +11164,9 @@ (define-public mantis '(#:tests? #f ; there are none #:configure-flags (list "-DNH=ON"))) ; do not use SSE4.2 instructions (inputs - `(("sdsl-lite" ,sdsl-lite) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list sdsl-lite openssl zlib)) (native-inputs - `(("gcc" ,gcc-7))) + (list gcc-7)) (home-page "https://github.com/splatlab/mantis") (synopsis "Large-scale sequence-search index data structure") (description "Mantis is a space-efficient data structure that can be @@ -11480,8 +11221,7 @@ (define-public sjcount "/bin"))) '("j_count" "b_count" "sjcount"))))))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "https://github.com/pervouchine/sjcount-full/") (synopsis "Annotation-agnostic splice junction counting pipeline") (description "Sjcount is a utility for fast quantification of splice @@ -11556,7 +11296,7 @@ (define-public minimap2 out ,version)))) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://lh3.github.io/minimap2/") (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences") (description "Minimap2 is a versatile sequence alignment program that @@ -11587,9 +11327,9 @@ (define-public python-mappy "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/lh3/minimap2") (synopsis "Python binding for minimap2") (description "This package provides a convenient interface to minimap2, @@ -11612,7 +11352,7 @@ (define-public miniasm "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (arguments `(#:tests? #f ; There are no tests. #:phases @@ -11670,10 +11410,9 @@ (define-public bandage (install-file "Bandage" (string-append out "/bin")) #t)))))) (inputs - `(("qtbase" ,qtbase-5) - ("qtsvg" ,qtsvg))) + (list qtbase-5 qtsvg)) (native-inputs - `(("imagemagick" ,imagemagick))) + (list imagemagick)) (home-page "https://rrwick.github.io/Bandage/") (synopsis "Bioinformatics Application for Navigating De novo Assembly Graphs Easily") @@ -11709,10 +11448,10 @@ (define-public libmaus2 ;; The test suite attempts to execute ../test-driver, which does not exist. (arguments '(#:tests? #false)) (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gcc" ,gcc-10) ;Code has C++17 requirements - ("pkg-config" ,pkg-config))) + (list gcc-10 ;Code has C++17 requirements + pkg-config)) (home-page "https://gitlab.com/german.tischler/libmaus2") (synopsis "Collection of data structures and algorithms useful for bioinformatics") (description "libmaus2 is a collection of data structures and @@ -11753,11 +11492,10 @@ (define-public biobambam2 ,#~(list (string-append "--with-libmaus2=" #$(this-package-input "libmaus2"))))) (inputs - `(("libmaus2" ,libmaus2) - ("xerces-c" ,xerces-c))) + (list libmaus2 xerces-c)) (native-inputs - `(("gcc" ,gcc-10) ;Code has C++17 requirements - ("pkg-config" ,pkg-config))) + (list gcc-10 ;Code has C++17 requirements + pkg-config)) (home-page "https://gitlab.com/german.tischler/biobambam2") (synopsis "Tools for processing BAM files") (description "This package contains some tools for processing BAM files @@ -11798,23 +11536,23 @@ (define-public r-circus "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biomart" ,r-biomart) - ("r-data-table" ,r-data-table) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hash" ,r-hash) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmysql" ,r-rmysql) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biomart + r-data-table + r-dbi + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hash + r-iranges + r-rcolorbrewer + r-rmysql + r-s4vectors + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/BIMSBbioinfo/ciRcus") (synopsis "Annotation, analysis and visualization of circRNA data") (description "Circus is an R package for annotation, analysis and @@ -11927,9 +11665,7 @@ (define-public find-circ "unmapped2anchors.py"))) #t))))) (inputs - `(("python2" ,python-2) - ("python2-pysam" ,python2-pysam) - ("python2-numpy" ,python2-numpy))) + (list python-2 python2-pysam python2-numpy)) (home-page "https://github.com/marvin-jens/find_circ") (synopsis "circRNA detection from RNA-seq reads") (description "This package provides tools to detect head-to-tail @@ -11980,7 +11716,7 @@ (define-public fit-sne (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n"))) (install-file "fast_tsne.R" share))))))) (inputs - `(("fftw" ,fftw))) + (list fftw)) (home-page "https://github.com/KlugerLab/FIt-SNE") (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE") (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a @@ -12078,28 +11814,28 @@ (define-public python-scanpy " and not test_pca_sparse" " and not test_pca_reproducible")))))))) (propagated-inputs - `(("python-anndata" ,python-anndata) - ("python-h5py" ,python-h5py) - ("python-igraph" ,python-igraph) - ("python-joblib" ,python-joblib) - ("python-legacy-api-wrap" ,python-legacy-api-wrap) - ("python-louvain" ,python-louvain-0.6) - ("python-matplotlib" ,python-matplotlib) - ("python-natsort" ,python-natsort) - ("python-networkx" ,python-networkx) - ("python-numba" ,python-numba) - ("python-packaging" ,python-packaging) - ("python-pandas" ,python-pandas) - ("python-patsy" ,python-patsy) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-seaborn" ,python-seaborn) - ("python-sinfo" ,python-sinfo) - ("python-statsmodels" ,python-statsmodels) - ("python-tables" ,python-tables) - ("python-pytoml" ,python-pytoml) - ("python-tqdm" ,python-tqdm) - ("python-umap-learn" ,python-umap-learn))) + (list python-anndata + python-h5py + python-igraph + python-joblib + python-legacy-api-wrap + python-louvain-0.6 + python-matplotlib + python-natsort + python-networkx + python-numba + python-packaging + python-pandas + python-patsy + python-scikit-learn + python-scipy + python-seaborn + python-sinfo + python-statsmodels + python-tables + python-pytoml + python-tqdm + python-umap-learn)) (native-inputs `(;; This package needs anndata.tests, which is not installed. ("python-anndata:source" ,(package-source python-anndata)) @@ -12138,12 +11874,12 @@ (define-public python-bbknn (substitute* "setup.py" (("'sklearn'") ""))))))) (propagated-inputs - `(("python-annoy" ,python-annoy) - ("python-cython" ,python-cython) - ("python-numpy" ,python-numpy) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-umap-learn" ,python-umap-learn))) + (list python-annoy + python-cython + python-numpy + python-scikit-learn + python-scipy + python-umap-learn)) (home-page "https://github.com/Teichlab/bbknn") (synopsis "Batch balanced KNN") (description "BBKNN is a batch effect removal tool that can be directly @@ -12171,14 +11907,14 @@ (define-public python-drep "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77")))) (build-system python-build-system) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pytest" ,python-pytest) - ("python-scikit-learn" ,python-scikit-learn) - ("python-seaborn" ,python-seaborn) - ("python-tqdm" ,python-tqdm))) + (list python-biopython + python-matplotlib + python-numpy + python-pandas + python-pytest + python-scikit-learn + python-seaborn + python-tqdm)) (home-page "https://github.com/MrOlm/drep") (synopsis "De-replication of microbial genomes assembled from multiple samples") (description @@ -12211,24 +11947,24 @@ (define-public instrain (("from job_utils") "from .job_utils"))))))) (inputs - `(("python-biopython" ,python-biopython-1.73) - ("python-boto3" ,python-boto3) - ("python-h5py" ,python-h5py) - ("python-lmfit" ,python-lmfit) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numba" ,python-numba) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-psutil" ,python-psutil) - ("python-pysam" ,python-pysam) - ("python-scikit-learn" ,python-scikit-learn) - ("python-seaborn" ,python-seaborn) - ("python-tqdm" ,python-tqdm) - ;; drep is needed for deprecated plot utilities - ("python-drep" ,python-drep))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-biopython-1.73 + python-boto3 + python-h5py + python-lmfit + python-matplotlib + python-networkx + python-numba + python-numpy + python-pandas + python-psutil + python-pysam + python-scikit-learn + python-seaborn + python-tqdm + ;; drep is needed for deprecated plot utilities + python-drep)) + (native-inputs + (list python-pytest)) (home-page "https://github.com/MrOlm/inStrain") (synopsis "Calculation of strain-level metrics") (description @@ -12359,9 +12095,9 @@ (define-public python-intervaltree (setenv "PY_IGNORE_IMPORTMISMATCH" "1") #t))))) (propagated-inputs - `(("python-sortedcontainers" ,python-sortedcontainers))) + (list python-sortedcontainers)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/chaimleib/intervaltree") (synopsis "Editable interval tree data structure") (description @@ -12401,7 +12137,7 @@ (define-public python-pypairix "/bin")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/4dn-dcic/pairix") (synopsis "Support for querying pairix-indexed bgzipped text files") (description @@ -12422,7 +12158,7 @@ (define-public python-pyfaidx "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q")))) (build-system python-build-system) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description @@ -12470,29 +12206,26 @@ (define-public python-cooler (when tests? (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs - `(("python-asciitree" ,python-asciitree) - ("python-biopython" ,python-biopython) - ("python-click" ,python-click) - ("python-cytoolz" ,python-cytoolz-for-cooler) - ("python-dask" ,python-dask) - ("python-h5py" ,python-h5py) - ("python-multiprocess" ,python-multiprocess) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pyfaidx" ,python-pyfaidx) - ("python-pypairix" ,python-pypairix) - ("python-pysam" ,python-pysam) - ("python-pyyaml" ,python-pyyaml) - ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson) - ("python-six" ,python-six) - ("python-sparse" ,python-sparse))) - (native-inputs - `(("python-codecov" ,python-codecov) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-flake8" ,python-pytest-flake8))) + (list python-asciitree + python-biopython + python-click + python-cytoolz-for-cooler + python-dask + python-h5py + python-multiprocess + python-numpy + python-pandas + python-pyfaidx + python-pypairix + python-pysam + python-pyyaml + python-scipy + python-simplejson + python-six + python-sparse)) + (native-inputs + (list python-codecov python-mock python-pytest python-pytest-cov + python-pytest-flake8)) ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") @@ -12526,14 +12259,14 @@ (define-public python-hicmatrix (when tests? (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-intervaltree" ,python-intervaltree) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy) - ("python-tables" ,python-tables))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-cooler + python-intervaltree + python-numpy + python-pandas + python-scipy + python-tables)) + (native-inputs + (list python-pytest)) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description @@ -12566,21 +12299,21 @@ (define-public python-hicexplorer (("==") ">=")) #t))))) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-configparser" ,python-configparser) - ("python-cooler" ,python-cooler) - ("python-future" ,python-future) - ("python-intervaltree" ,python-intervaltree) - ("python-jinja2" ,python-jinja2) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy) - ("python-six" ,python-six) - ("python-tables" ,python-tables) - ("python-unidecode" ,python-unidecode))) + (list python-biopython + python-configparser + python-cooler + python-future + python-intervaltree + python-jinja2 + python-matplotlib + python-numpy + python-pandas + python-pybigwig + python-pysam + python-scipy + python-six + python-tables + python-unidecode)) (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description @@ -12617,17 +12350,17 @@ (define-public python-pygenometracks "matplotlib >=3.1.1")) #t))))) (propagated-inputs - `(("python-future" ,python-future) - ("python-gffutils" ,python-gffutils) - ("python-hicmatrix" ,python-hicmatrix) - ("python-intervaltree" ,python-intervaltree) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-tqdm" ,python-tqdm))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-future + python-gffutils + python-hicmatrix + python-intervaltree + python-matplotlib + python-numpy + python-pybigwig + python-pysam + python-tqdm)) + (native-inputs + (list python-pytest)) (home-page "https://pygenometracks.readthedocs.io") (synopsis "Program and library to plot beautiful genome browser tracks") (description @@ -12651,10 +12384,7 @@ (define-public python-iced (build-system python-build-system) (arguments `(#:tests? #false)) ; there are none (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy) - ("python-scikit-learn" ,python-scikit-learn))) + (list python-numpy python-pandas python-scipy python-scikit-learn)) (home-page "https://github.com/hiclib/iced") (synopsis "ICE normalization") (description "This is a package for normalizing Hi-C contact counts @@ -12688,11 +12418,8 @@ (define-public python-hic2cool (list "test_data/hic2cool_0.4.2_single_res.cool" "test_data/hic2cool_0.7.0_multi_res.mcool"))))))) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-h5py" ,python-h5py) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + (list python-cooler python-h5py python-numpy python-pandas + python-scipy)) (home-page "https://github.com/4dn-dcic/hic2cool") (synopsis "Converter for .hic and .cool files") (description @@ -12717,11 +12444,7 @@ (define-public r-pore (properties `((upstream-name . "poRe"))) (build-system r-build-system) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-data-table" ,r-data-table) - ("r-rhdf5" ,r-rhdf5) - ("r-shiny" ,r-shiny) - ("r-svdialogs" ,r-svdialogs))) + (list r-bit64 r-data-table r-rhdf5 r-shiny r-svdialogs)) (home-page "https://sourceforge.net/projects/rpore/") (synopsis "Visualize Nanopore sequencing data") (description @@ -12748,15 +12471,15 @@ (define-public r-xbioc "0w8bsq5myiwkfhh83nm6is5ichiyvwa1axx2szvxnzq39x6knf66")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-digest" ,r-digest) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-stringr" ,r-stringr))) + (list r-annotationdbi + r-assertthat + r-biobase + r-biocmanager + r-digest + r-pkgmaker + r-plyr + r-reshape2 + r-stringr)) (home-page "https://github.com/renozao/xbioc/") (synopsis "Extra base functions for Bioconductor") (description "This package provides extra utility functions to perform @@ -12781,12 +12504,12 @@ (define-public r-cssam "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-ggplot2" ,r-ggplot2) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-rngtools" ,r-rngtools) - ("r-scales" ,r-scales))) + (list r-formula + r-ggplot2 + r-pkgmaker + r-plyr + r-rngtools + r-scales)) (home-page "https://github.com/shenorrLab/csSAM/") (synopsis "Cell type-specific statistical analysis of microarray") (description "This package implements the method csSAM that computes @@ -12812,23 +12535,23 @@ (define-public r-bseqsc "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-cssam" ,r-cssam) - ("r-dplyr" ,r-dplyr) - ("r-e1071" ,r-e1071) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-nmf" ,r-nmf) - ("r-openxlsx" ,r-openxlsx) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rngtools" ,r-rngtools) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-xbioc" ,r-xbioc))) + (list r-abind + r-annotationdbi + r-biobase + r-cssam + r-dplyr + r-e1071 + r-edger + r-ggplot2 + r-nmf + r-openxlsx + r-pkgmaker + r-plyr + r-preprocesscore + r-rngtools + r-scales + r-stringr + r-xbioc)) (home-page "https://github.com/shenorrLab/bseqsc") (synopsis "Deconvolution of bulk sequencing experiments using single cell data") (description "BSeq-sc is a bioinformatics analysis pipeline that @@ -12892,13 +12615,10 @@ (define-public poretools ;; requires python >=2.7, <3.0, and the same for python dependencies (arguments `(#:python ,python-2)) (inputs - `(("hdf5" ,hdf5))) + (list hdf5)) (propagated-inputs - `(("python-dateutil" ,python2-dateutil) - ("python-h5py" ,python2-h5py) - ("python-matplotlib" ,python2-matplotlib) - ("python-pandas" ,python2-pandas) - ("python-seaborn" ,python2-seaborn))) + (list python2-dateutil python2-h5py python2-matplotlib + python2-pandas python2-seaborn)) (home-page "https://poretools.readthedocs.io") (synopsis "Toolkit for working with nanopore sequencing data") (description @@ -12966,14 +12686,14 @@ (define-public jamm (list "JAMM.sh" "SignalGenerator.sh"))) #t))))) (inputs - `(("bash" ,bash) - ("coreutils" ,coreutils) - ("gawk" ,gawk) - ("perl" ,perl) - ("r-minimal" ,r-minimal) - ;;("r-parallel" ,r-parallel) - ("r-signal" ,r-signal) - ("r-mclust" ,r-mclust))) + (list bash + coreutils + gawk + perl + r-minimal + ;;("r-parallel" ,r-parallel) + r-signal + r-mclust)) (home-page "https://github.com/mahmoudibrahim/JAMM") (synopsis "Peak finder for NGS datasets") (description @@ -13038,63 +12758,59 @@ (define-public ngless (string-append bin "ngless-" ,version "-bwa")) #t)))))) (inputs - `(("prodigal" ,prodigal) - ("bwa" ,bwa) - ("samtools" ,samtools) - ("minimap2" ,minimap2) - ("ghc-aeson" ,ghc-aeson) - ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-async" ,ghc-async) - ("ghc-atomic-write" ,ghc-atomic-write) - ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) - ("ghc-conduit" ,ghc-conduit) - ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) - ("ghc-conduit-extra" ,ghc-conduit-extra) - ("ghc-configurator" ,ghc-configurator) - ("ghc-convertible" ,ghc-convertible) - ("ghc-data-default" ,ghc-data-default) - ("ghc-diagrams-core" ,ghc-diagrams-core) - ("ghc-diagrams-lib" ,ghc-diagrams-lib) - ("ghc-diagrams-svg" ,ghc-diagrams-svg) - ("ghc-double-conversion" ,ghc-double-conversion) - ("ghc-edit-distance" ,ghc-edit-distance) - ("ghc-either" ,ghc-either) - ("ghc-errors" ,ghc-errors) - ("ghc-extra" ,ghc-extra) - ("ghc-filemanip" ,ghc-filemanip) - ("ghc-file-embed" ,ghc-file-embed) - ("ghc-gitrev" ,ghc-gitrev) - ("ghc-hashtables" ,ghc-hashtables) - ("ghc-http-conduit" ,ghc-http-conduit) - ("ghc-inline-c" ,ghc-inline-c) - ("ghc-inline-c-cpp" ,ghc-inline-c-cpp) - ("ghc-int-interval-map" ,ghc-int-interval-map) - ("ghc-missingh" ,ghc-missingh) - ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-regex" ,ghc-regex) - ("ghc-safe" ,ghc-safe) - ("ghc-safeio" ,ghc-safeio) - ("ghc-strict" ,ghc-strict) - ("ghc-tar" ,ghc-tar) - ("ghc-tar-conduit" ,ghc-tar-conduit) - ("ghc-unliftio" ,ghc-unliftio) - ("ghc-unliftio-core" ,ghc-unliftio-core) - ("ghc-vector" ,ghc-vector) - ("ghc-yaml" ,ghc-yaml) - ("ghc-zlib" ,ghc-zlib))) + (list prodigal + bwa + samtools + minimap2 + ghc-aeson + ghc-ansi-terminal + ghc-async + ghc-atomic-write + ghc-bytestring-lexing + ghc-conduit + ghc-conduit-algorithms + ghc-conduit-extra + ghc-configurator + ghc-convertible + ghc-data-default + ghc-diagrams-core + ghc-diagrams-lib + ghc-diagrams-svg + ghc-double-conversion + ghc-edit-distance + ghc-either + ghc-errors + ghc-extra + ghc-filemanip + ghc-file-embed + ghc-gitrev + ghc-hashtables + ghc-http-conduit + ghc-inline-c + ghc-inline-c-cpp + ghc-int-interval-map + ghc-missingh + ghc-optparse-applicative + ghc-regex + ghc-safe + ghc-safeio + ghc-strict + ghc-tar + ghc-tar-conduit + ghc-unliftio + ghc-unliftio-core + ghc-vector + ghc-yaml + ghc-zlib)) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-hdf5r" ,r-hdf5r) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (native-inputs - `(("ghc-hpack" ,ghc-hpack) - ("ghc-quickcheck" ,ghc-quickcheck) - ("ghc-test-framework" ,ghc-test-framework) - ("ghc-test-framework-hunit",ghc-test-framework-hunit) - ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) - ("ghc-test-framework-th" ,ghc-test-framework-th))) + (list r-r6 r-hdf5r r-iterators r-itertools r-matrix)) + (native-inputs + (list ghc-hpack + ghc-quickcheck + ghc-test-framework + ghc-test-framework-hunit + ghc-test-framework-quickcheck2 + ghc-test-framework-th)) (home-page "https://ngless.embl.de/") (synopsis "DSL for processing next-generation sequencing data") (description "Ngless is a domain-specific language for @@ -13117,17 +12833,14 @@ (define-public ghc-int-interval-map (sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8")))) (build-system haskell-build-system) (inputs - `(("ghc-either" ,ghc-either) - ("ghc-primitive" ,ghc-primitive) - ("ghc-vector" ,ghc-vector) - ("ghc-vector-algorithms" ,ghc-vector-algorithms))) + (list ghc-either ghc-primitive ghc-vector ghc-vector-algorithms)) (native-inputs - `(("ghc-hedgehog" ,ghc-hedgehog) - ("ghc-tasty" ,ghc-tasty) - ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog) - ("ghc-tasty-hunit" ,ghc-tasty-hunit) - ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck) - ("ghc-tasty-th" ,ghc-tasty-th))) + (list ghc-hedgehog + ghc-tasty + ghc-tasty-hedgehog + ghc-tasty-hunit + ghc-tasty-quickcheck + ghc-tasty-th)) (home-page "https://github.com/luispedro/interval-to-int#readme") (synopsis "Interval map structure in Haskell") (description "An interval map structure that is optimized for low @@ -13300,17 +13013,17 @@ (define-public cnvkit (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) (build-system python-build-system) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-future" ,python-future) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-reportlab" ,python-reportlab) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-pyfaidx" ,python-pyfaidx) - ("python-scipy" ,python-scipy) - ;; R packages - ("r-dnacopy" ,r-dnacopy))) + (list python-biopython + python-future + python-matplotlib + python-numpy + python-reportlab + python-pandas + python-pysam + python-pyfaidx + python-scipy + ;; R packages + r-dnacopy)) (home-page "https://cnvkit.readthedocs.org/") (synopsis "Copy number variant detection from targeted DNA sequencing") (description @@ -13337,11 +13050,11 @@ (define-public python-pyfit-sne (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("fftw" ,fftw))) + (list fftw)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/KlugerLab/pyFIt-SNE") (synopsis "FFT-accelerated Interpolation-based t-SNE") (description @@ -13410,10 +13123,8 @@ (define-public bbmap #t))) #:jdk ,openjdk11)) (inputs - `(("gawk" ,gawk) - ("java-eclipse-jdt-core" ,java-eclipse-jdt-core) - ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt) - ("java-openmpi" ,java-openmpi))) + (list gawk java-eclipse-jdt-core java-eclipse-jdt-compiler-apt + java-openmpi)) (home-page "https://sourceforge.net/projects/bbmap/") (synopsis "Aligner and other tools for short sequencing reads") (description @@ -13468,8 +13179,7 @@ (define-public velvet (install-file "Manual.pdf" doc) (install-file "Columbus_manual.pdf" doc))))))) (inputs - `(("openmpi" ,openmpi) - ("zlib" ,zlib))) + (list openmpi zlib)) (native-inputs `(("texlive" ,(texlive-updmap.cfg (list texlive-latex-graphics texlive-fonts-ec @@ -13501,19 +13211,19 @@ (define-public python-velocyto '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (native-inputs - `(("python-joblib" ,python-joblib))) + (list python-joblib)) (propagated-inputs - `(("python-click" ,python-click) - ("python-cython" ,python-cython) - ("python-h5py" ,python-h5py) - ("python-loompy" ,python-loompy) - ("python-matplotlib" ,python-matplotlib) - ("python-numba" ,python-numba) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) + (list python-click + python-cython + python-h5py + python-loompy + python-matplotlib + python-numba + python-numpy + python-pandas + python-pysam + python-scikit-learn + python-scipy)) (home-page "https://github.com/velocyto-team/velocyto.py") (synopsis "RNA velocity analysis for single cell RNA-seq data") (description @@ -13565,14 +13275,14 @@ (define-public arriba `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("htslib" ,htslib) - ("r-minimal" ,r-minimal) - ("r-circlize" ,r-circlize) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("samtools" ,samtools) - ("star" ,star) - ("zlib" ,zlib))) + (list htslib + r-minimal + r-circlize + r-genomicalignments + r-genomicranges + samtools + star + zlib)) (home-page "https://github.com/suhrig/arriba") (synopsis "Gene fusion detection from RNA-Seq data ") (description @@ -13611,7 +13321,7 @@ (define-public adapterremoval (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://adapterremoval.readthedocs.io/") (synopsis "Rapid sequence adapter trimming, identification, and read merging") (description @@ -13730,7 +13440,7 @@ (define-public pplacer ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) ("pkg-config" ,pkg-config))) (propagated-inputs - `(("pplacer-scripts" ,pplacer-scripts))) + (list pplacer-scripts)) (synopsis "Phylogenetic placement of biological sequences") (description "Pplacer places query sequences on a fixed reference phylogenetic tree @@ -13800,11 +13510,8 @@ (define-public checkm (lambda _ (setenv "HOME" "/tmp")))))) (inputs - `(("python-dendropy" ,python-dendropy) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy))) + (list python-dendropy python-matplotlib python-numpy python-pysam + python-scipy)) (home-page "https://ecogenomics.github.io/CheckM/") (synopsis "Assess the quality of putative genome bins") (description @@ -13836,14 +13543,14 @@ (define-public umi-tools "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a")))) (build-system python-build-system) (inputs - `(("python-pandas" ,python-pandas) - ("python-future" ,python-future) - ("python-scipy" ,python-scipy) - ("python-matplotlib" ,python-matplotlib) - ("python-regex" ,python-regex) - ("python-pysam" ,python-pysam))) + (list python-pandas + python-future + python-scipy + python-matplotlib + python-regex + python-pysam)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/CGATOxford/UMI-tools") (synopsis "Tools for analyzing unique modular identifiers") (description "This package provides tools for dealing with @dfn{Unique @@ -13883,12 +13590,9 @@ (define-public ataqv (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) + (list boost htslib ncurses zlib)) (native-inputs - `(("lcov" ,lcov))) + (list lcov)) (home-page "https://github.com/ParkerLab/ataqv") (synopsis "Toolkit for quality control and visualization of ATAC-seq data") (description "This package provides a toolkit for measuring and comparing @@ -13912,13 +13616,13 @@ (define-public r-psiplot (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-magrittr" ,r-magrittr) - ("r-ggplot2" ,r-ggplot2))) + (list r-mass + r-dplyr + r-tidyr + r-purrr + r-readr + r-magrittr + r-ggplot2)) (home-page "https://github.com/kcha/psiplot") (synopsis "Plot percent spliced-in values of alternatively-spliced exons") (description @@ -13952,10 +13656,10 @@ (define-public vbz-compression ;; disable building them. "-DENABLE_PYTHON=OFF"))) (inputs - `(;("hdf5" ,hdf5-1.10) - ("zstd" ,zstd "lib"))) + (list ;("hdf5" ,hdf5-1.10) + `(,zstd "lib"))) (native-inputs - `(("googlebenchmark" ,googlebenchmark))) + (list googlebenchmark)) (home-page "https://github.com/nanoporetech/vbz_compression/") (synopsis "VBZ compression plugin for nanopore signal data") (description @@ -13994,12 +13698,9 @@ (define-public python-ont-fast5-api "/hdf5/lib/plugin/libvbz_hdf_plugin.so") "ont_fast5_api/vbz_plugin/")))))) (inputs - `(("vbz-compression" ,vbz-compression))) + (list vbz-compression)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-h5py" ,python-h5py) - ("python-packaging" ,python-packaging) - ("python-progressbar33" ,python-progressbar33))) + (list python-numpy python-h5py python-packaging python-progressbar33)) (home-page "https://github.com/nanoporetech/ont_fast5_api") (synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format") (description @@ -14035,13 +13736,13 @@ (define-public tbsp (substitute* "setup.py" ((", <3.0") ""))))))) ; matplotlib (inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-biopython" ,python-biopython-1.73) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) + (list python-matplotlib + python-networkx + python-numpy + python-pybigwig + python-biopython-1.73 + python-scikit-learn + python-scipy)) (home-page "https://github.com/phoenixding/tbsp/") (synopsis "SNP-based trajectory inference") (description @@ -14072,8 +13773,7 @@ (define-public tabixpp (delete-file-recursively "htslib") #t)))) (build-system gnu-build-system) (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (arguments `(#:tests? #f ; There are no tests to run. #:phases @@ -14249,7 +13949,7 @@ (define-public fsom (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "fsom" bin))))))) (native-inputs - `(("gcc" ,gcc-6))) + (list gcc-6)) (home-page "https://github.com/ekg/fsom") (synopsis "Manage SOM (Self-Organizing Maps) neural networks") (description "A tiny C library for managing SOM (Self-Organizing Maps) @@ -14360,15 +14060,15 @@ (define-public vcflib #t)))) (build-system cmake-build-system) (inputs - `(("bzip2" ,bzip2) - ("htslib" ,htslib) - ("fastahack" ,fastahack) - ("perl" ,perl) - ("python" ,python) - ("smithwaterman" ,smithwaterman) - ("tabixpp" ,tabixpp) - ("xz" ,xz) - ("zlib" ,zlib))) + (list bzip2 + htslib + fastahack + perl + python + smithwaterman + tabixpp + xz + zlib)) (native-inputs `(("pkg-config" ,pkg-config) ;; Submodules. @@ -14453,11 +14153,7 @@ (define-public freebayes #t)))) (build-system meson-build-system) (inputs - `(("fastahack" ,fastahack) - ("htslib" ,htslib) - ("smithwaterman" ,smithwaterman) - ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib))) + (list fastahack htslib smithwaterman tabixpp vcflib)) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -14574,24 +14270,24 @@ (define-public r-velocyto "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) (build-system r-build-system) (inputs - `(("boost" ,boost))) + (list boost)) (propagated-inputs - `(("r-hdf5r" ,r-hdf5r) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-pcamethods" ,r-pcamethods) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ;; Suggested packages - ("r-rtsne" ,r-rtsne) - ("r-cluster" ,r-cluster) - ("r-abind" ,r-abind) - ("r-h5" ,r-h5) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rsamtools" ,r-rsamtools) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph))) + (list r-hdf5r + r-mass + r-mgcv + r-pcamethods + r-rcpp + r-rcpparmadillo + ;; Suggested packages + r-rtsne + r-cluster + r-abind + r-h5 + r-biocgenerics + r-genomicalignments + r-rsamtools + r-edger + r-igraph)) (home-page "https://velocyto.org") (synopsis "RNA velocity estimation in R") (description @@ -14629,10 +14325,8 @@ (define-public methyldackel (("install MethylDackel \\$\\(prefix\\)" match) (string-append "install -d $(prefix); " match)))))))) (inputs - `(("curl" ,curl) ; XXX: needed by libbigwig - ("htslib" ,htslib-1.9) - ("libbigwig" ,libbigwig) - ("zlib" ,zlib))) + (list curl ; XXX: needed by libbigwig + htslib-1.9 libbigwig zlib)) ;; Needed for tests (native-inputs `(("python" ,python-wrapper))) @@ -14702,9 +14396,9 @@ (define-public phast ;; unknown reasons. (invoke "make" "-C" "test" "msa_view")))))) (inputs - `(("clapack" ,clapack))) + (list clapack)) (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "http://compgen.cshl.edu/phast/") (synopsis "Phylogenetic analysis with space/time models") (description @@ -14749,15 +14443,15 @@ (define-public python-gffutils (find-files "." "\\.gz")) #t))))) (propagated-inputs - `(("python-argcomplete" ,python-argcomplete) - ("python-argh" ,python-argh) - ("python-biopython" ,python-biopython) - ("python-pybedtools" ,python-pybedtools) - ("python-pyfaidx" ,python-pyfaidx) - ("python-simplejson" ,python-simplejson) - ("python-six" ,python-six))) + (list python-argcomplete + python-argh + python-biopython + python-pybedtools + python-pyfaidx + python-simplejson + python-six)) (native-inputs - `(("python-nose" , python-nose))) + (list python-nose)) (home-page "https://github.com/daler/gffutils") (synopsis "Tool for manipulation of GFF and GTF files") (description @@ -14790,7 +14484,7 @@ (define-public indelfixer `(("java-commons-lang2" ,java-commons-lang) ("java-args4j" ,java-args4j))) (native-inputs - `(("java-junit" ,java-junit))) + (list java-junit)) (home-page "https://github.com/cbg-ethz/InDelFixer/") (synopsis "Iterative and sensitive NGS sequence aligner") (description "InDelFixer is a sensitive aligner for 454, Illumina and @@ -14827,10 +14521,9 @@ (define-public libsbml #$(this-package-input "libxml2") "/include/libxml2")))) (propagated-inputs - `(("libxml2" ,libxml2))) + (list libxml2)) (native-inputs - `(("check" ,check-0.14) - ("swig" ,swig))) + (list check-0.14 swig)) (home-page "http://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") (description "LibSBML is a library to help you read, write, manipulate, @@ -14915,12 +14608,12 @@ (define-public kraken2 (install-file script bin)) scripts))))))))) (inputs - `(("gzip" ,gzip) - ("perl" ,perl) - ("rsync" ,rsync) - ("sed" ,sed) - ("wget" ,wget) - ("which" ,which))) + (list gzip + perl + rsync + sed + wget + which)) (home-page "https://github.com/DerrickWood/kraken2") (synopsis "Taxonomic sequence classification system") (description "Kraken is a taxonomic sequence classifier that assigns @@ -14952,9 +14645,7 @@ (define-public lofreq ("python" ,python-wrapper) ("zlib" ,zlib))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("which" ,which))) + (list autoconf automake which)) (home-page "https://csb5.github.io/lofreq/") (synopsis "Sensitive variant calling from sequencing data ") (description "LoFreq is a fast and sensitive variant-caller for inferring @@ -14980,11 +14671,9 @@ (define-public ivar (build-system gnu-build-system) (arguments `(#:parallel-tests? #false)) ; not supported (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (home-page "https://andersen-lab.github.io/ivar/html/") (synopsis "Tools for amplicon-based sequencing") (description "iVar is a computational package that contains functions @@ -15008,7 +14697,7 @@ (define-public python-pyliftover (build-system python-build-system) (arguments `(#:tests? #false)) ; the tests access the web (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/konstantint/pyliftover") (synopsis "Python implementation of UCSC liftOver genome coordinate conversion") (description @@ -15055,15 +14744,15 @@ (define-public python-cgatcore ("hostname" ,inetutils) ("openssl" ,openssl))) (inputs - `(("time" ,time))) + (list time)) (propagated-inputs - `(("python-apsw" ,python-apsw) - ("python-gevent" ,python-gevent) - ("python-pandas" ,python-pandas) - ("python-paramiko" ,python-paramiko) - ("python-pyyaml" ,python-pyyaml) - ("python-ruffus" ,python-ruffus) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-apsw + python-gevent + python-pandas + python-paramiko + python-pyyaml + python-ruffus + python-sqlalchemy)) (home-page "https://github.com/cgat-developers/cgat-core") (synopsis "Computational genomics analysis toolkit") (description @@ -15159,7 +14848,7 @@ (define-public perl-cworld-dekker ("python-scikit-learn" ,python-scikit-learn) ("r-minimal" ,r-minimal))) (native-inputs - `(("perl-module-build" ,perl-module-build))) + (list perl-module-build)) (home-page "https://github.com/dekkerlab/cworld-dekker") (synopsis "Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data") (description "This package is a collection of Perl, Python, and R @@ -15275,16 +14964,16 @@ (define-public ensembl-vep runtests(@test_files); ")))))))) (inputs - `(("bioperl-minimal" ,bioperl-minimal) - ("perl-bio-db-hts" ,perl-bio-db-hts) - ("perl-dbi" ,perl-dbi) - ("perl-dbd-mysql" ,perl-dbd-mysql) - ("perl-libwww" ,perl-libwww) - ("perl-http-tiny" ,perl-http-tiny) - ("perl-json" ,perl-json) - ("which" ,which))) + (list bioperl-minimal + perl-bio-db-hts + perl-dbi + perl-dbd-mysql + perl-libwww + perl-http-tiny + perl-json + which)) (propagated-inputs - `(("kentutils" ,kentutils))) + (list kentutils)) (native-inputs `(("unzip" ,unzip) ("perl" ,perl) @@ -15330,39 +15019,39 @@ (define-public r-signac "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fastmatch" ,r-fastmatch) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-iranges" ,r-iranges) - ("r-irlba" ,r-irlba) - ("r-lsa" ,r-lsa) - ("r-matrix" ,r-matrix) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-rcpp" ,r-rcpp) - ("r-rcpproll" ,r-rcpproll) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-seurat" ,r-seurat) - ("r-seuratobject" ,r-seuratobject) - ("r-stringi" ,r-stringi) - ("r-tidyr" ,r-tidyr))) + (list r-annotationfilter + r-biocgenerics + r-biostrings + r-biovizbase + r-data-table + r-dplyr + r-fastmatch + r-future + r-future-apply + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggforce + r-ggplot2 + r-ggrepel + r-ggseqlogo + r-iranges + r-irlba + r-lsa + r-matrix + r-patchwork + r-pbapply + r-rcpp + r-rcpproll + r-rsamtools + r-s4vectors + r-scales + r-seurat + r-seuratobject + r-stringi + r-tidyr)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description @@ -15386,18 +15075,17 @@ (define-public tombo "1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose2" ,python-nose2))) + (list python-cython python-nose2)) ;; The package mainly consists of a command-line tool, but also has a ;; Python-API. Thus these must be propagated. (propagated-inputs - `(("python-future" ,python-future) - ("python-h5py" ,python-h5py) - ("python-mappy" ,python-mappy) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-tqdm" ,python-tqdm) - ("python-rpy2" ,python-rpy2))) + (list python-future + python-h5py + python-mappy + python-numpy + python-scipy + python-tqdm + python-rpy2)) (home-page "https://github.com/nanoporetech/tombo") (synopsis "Analysis of raw nanopore sequencing data") (description "Tombo is a suite of tools primarily for the identification of @@ -15438,10 +15126,9 @@ (define-public python-pyvcf (delete-file-recursively (string-append (site-packages inputs outputs) "/vcf/test"))))))) - (native-inputs `(("python-cython" ,python-cython))) + (native-inputs (list python-cython)) (propagated-inputs - `(("python-pysam" ,python-pysam) - ("python-rpy2" ,python-rpy2))) + (list python-pysam python-rpy2)) (home-page "https://github.com/jamescasbon/PyVCF") (synopsis "Variant Call Format parser for Python") (description "This package provides a @acronym{VCF,Variant Call Format} @@ -15460,9 +15147,7 @@ (define-public nanosv "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) (build-system python-build-system) (inputs - `(("python-configparser" ,python-configparser) - ("python-pysam" ,python-pysam) - ("python-pyvcf" ,python-pyvcf))) + (list python-configparser python-pysam python-pyvcf)) (home-page "https://github.com/mroosmalen/nanosv") (synopsis "Structural variation detection tool for Oxford Nanopore data.") (description "NanoSV is a software package that can be used to identify @@ -15484,10 +15169,9 @@ (define-public python-strawc "1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6")))) (build-system python-build-system) (inputs - `(("curl" ,curl) - ("zlib" ,zlib))) + (list curl zlib)) (propagated-inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (home-page "https://github.com/aidenlab/straw") (synopsis "Stream data from .hic files") (description "Straw is library which allows rapid streaming of contact @@ -15520,18 +15204,11 @@ (define-public python-pybbi (with-directory-excursion "/tmp/tests" (invoke "python" "-m" "pytest" "-v")))))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-pkgconfig" ,python-pkgconfig) - ("python-pytest" ,python-pytest))) + (list pkg-config python-pkgconfig python-pytest)) (inputs - `(("libpng" ,libpng) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list libpng openssl zlib)) (propagated-inputs - `(("python-cython" ,python-cython) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-six" ,python-six))) + (list python-cython python-numpy python-pandas python-six)) (home-page "https://github.com/nvictus/pybbi") (synopsis "Python bindings to UCSC Big Binary file library") (description @@ -15555,8 +15232,7 @@ (define-public python-dna-features-viewer (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-matplotlib" ,python-matplotlib))) + (list python-biopython python-matplotlib)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") @@ -15579,28 +15255,28 @@ (define-public python-coolbox (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-dna-features-viewer" ,python-dna-features-viewer) - ("python-fire" ,python-fire) - ("python-h5py" ,python-h5py) - ("python-intervaltree" ,python-intervaltree) - ("python-ipywidgets" ,python-ipywidgets) - ("jupyter" ,jupyter) - ("python-matplotlib" ,python-matplotlib) - ("python-nbformat" ,python-nbformat) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-pandas" ,python-pandas) - ("python-pybbi" ,python-pybbi) - ("python-pytest" ,python-pytest) - ("python-scipy" ,python-scipy) - ("python-statsmodels" ,python-statsmodels) - ("python-strawc" ,python-strawc) - ("python-svgutils" ,python-svgutils) - ("python-termcolor" ,python-termcolor) - ("python-voila" ,python-voila))) + (list python-cooler + python-dna-features-viewer + python-fire + python-h5py + python-intervaltree + python-ipywidgets + jupyter + python-matplotlib + python-nbformat + python-numpy + python-numpydoc + python-pandas + python-pybbi + python-pytest + python-scipy + python-statsmodels + python-strawc + python-svgutils + python-termcolor + python-voila)) (home-page "https://github.com/GangCaoLab/CoolBox") (synopsis "Genomic data visualization toolkit") (description @@ -15648,7 +15324,7 @@ (define-public python-pyspoa (add-installed-pythonpath inputs outputs) (invoke "python" "tests/test_pyspoa.py"))))))) (propagated-inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (native-inputs `(("cmake" ,cmake-minimal))) (home-page "https://github.com/nanoporetech/pyspoa") @@ -15685,11 +15361,9 @@ (define-public python-bwapy ;; problem with the C sources. (delete 'sanity-check)))) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-setuptools" ,python-setuptools) - ("python-wheel" ,python-wheel))) + (list python-cffi python-setuptools python-wheel)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/ACEnglish/bwapy") (synopsis "Python bindings to bwa alinger") (description "This package provides Python bindings to the bwa mem @@ -15722,21 +15396,21 @@ (define-public scregseg (substitute* "setup.py" (("'sklearn',") ""))))))) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (propagated-inputs - `(("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-hmmlearn" ,python-hmmlearn) - ("python-pandas" ,python-pandas) - ("python-numba" ,python-numba) - ("python-anndata" ,python-anndata) - ("python-scanpy" ,python-scanpy) - ("python-pybedtools" ,python-pybedtools) - ("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib) - ("python-seaborn" ,python-seaborn) - ("python-coolbox" ,python-coolbox))) + (list python-scikit-learn + python-scipy + python-numpy + python-hmmlearn + python-pandas + python-numba + python-anndata + python-scanpy + python-pybedtools + python-pysam + python-matplotlib + python-seaborn + python-coolbox)) (home-page "https://github.com/BIMSBbioinfo/scregseg") (synopsis "Single-cell regulatory landscape segmentation") (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a @@ -15795,15 +15469,9 @@ (define-public megadepth (copy-file "megadepth_dynamic" (string-append bin "/megadepth")))))))) (native-inputs - `(("diffutils" ,diffutils) - ("perl" ,perl) - ("grep" ,grep))) + (list diffutils perl grep)) (inputs - `(("curl" ,curl) - ("htslib" ,htslib) - ("libdeflate" ,libdeflate) - ("libbigwig" ,libbigwig) - ("zlib" ,zlib))) + (list curl htslib libdeflate libbigwig zlib)) (home-page "https://github.com/ChristopherWilks/megadepth") (synopsis "BigWig and BAM/CRAM related utilities") (description "Megadepth is an efficient tool for extracting coverage @@ -15834,7 +15502,7 @@ (define-public r-ascat (lambda _ (chdir "ASCAT")))))) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/VanLoo-lab/ascat/") (synopsis "Allele-Specific Copy Number Analysis of Tumors in R") (description "This package provides the @acronym{ASCAT,Allele-Specific Copy @@ -15857,14 +15525,14 @@ (define-public r-battenberg "0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h")))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-readr" ,r-readr) - ("r-doparallel" ,r-doparallel) - ("r-ggplot2" ,r-ggplot2) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-ascat" ,r-ascat))) + (list r-devtools + r-readr + r-doparallel + r-ggplot2 + r-rcolorbrewer + r-gridextra + r-gtools + r-ascat)) (home-page "https://github.com/Wedge-lab/battenberg") (synopsis "Subclonal copy number estimation in R") (description "This package contains the Battenberg R package for subclonal @@ -15919,51 +15587,51 @@ (define-public r-spectre (properties `((upstream-name . "Spectre"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-caret" ,r-caret) - ("r-class" ,r-class) - ("r-colorramps" ,r-colorramps) - ("r-data-table" ,r-data-table) - ("r-devtools" ,r-devtools) - ("r-dplyr" ,r-dplyr) - ("r-exactextractr" ,r-exactextractr) - ("r-factoextra" ,r-factoextra) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-flowviz" ,r-flowviz) - ("r-fnn" ,r-fnn) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggraph" ,r-ggraph) - ("r-ggthemes" ,r-ggthemes) - ("r-gridextra" ,r-gridextra) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-irlba" ,r-irlba) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-qs" ,r-qs) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rgeos" ,r-rgeos) - ("r-rhdf5" ,r-rhdf5) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-s2" ,r-s2) - ("r-scales" ,r-scales) - ("r-sf" ,r-sf) - ("r-sp" ,r-sp) - ("r-stars" ,r-stars) - ("r-stringr" ,r-stringr) - ("r-tidygraph" ,r-tidygraph) - ("r-tidyr" ,r-tidyr) - ("r-tidyr" ,r-tidyr) - ("r-tiff" ,r-tiff) - ("r-umap" ,r-umap))) + (list r-biobase + r-biocmanager + r-caret + r-class + r-colorramps + r-data-table + r-devtools + r-dplyr + r-exactextractr + r-factoextra + r-flowcore + r-flowsom + r-flowviz + r-fnn + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggraph + r-ggthemes + r-gridextra + r-gridextra + r-gtools + r-hdf5array + r-irlba + r-pheatmap + r-plyr + r-qs + r-raster + r-rcolorbrewer + r-rgeos + r-rhdf5 + r-rstudioapi + r-rsvd + r-rtsne + r-s2 + r-scales + r-sf + r-sp + r-stars + r-stringr + r-tidygraph + r-tidyr + r-tidyr + r-tiff + r-umap)) (home-page "https://github.com/ImmuneDynamics/Spectre") (synopsis "High-dimensional cytometry and imaging analysis") (description @@ -15991,16 +15659,16 @@ (define-public r-cytonorm (properties `((upstream-name . "CytoNorm"))) (build-system r-build-system) (propagated-inputs - `(("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-emdist" ,r-emdist) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-pheatmap" ,r-pheatmap) - ("r-stringr" ,r-stringr))) + (list r-cytoml + r-dplyr + r-emdist + r-flowcore + r-flowsom + r-flowworkspace + r-ggplot2 + r-gridextra + r-pheatmap + r-stringr)) (home-page "https://github.com/saeyslab/CytoNorm") (synopsis "Normalize cytometry data measured across multiple batches") (description @@ -16049,12 +15717,12 @@ (define-public ccwl ("guile" ,guile-3.0) ("guile-libyaml" ,guile-libyaml))) (native-inputs - `(("pkg-config" ,pkg-config) - ("lzip" ,lzip) - ;; To build documentation - ("cwltool" ,cwltool) - ("graphviz" ,graphviz) - ("skribilo" ,skribilo))) + (list pkg-config + lzip + ;; To build documentation + cwltool + graphviz + skribilo)) (home-page "https://ccwl.systemreboot.net") (synopsis "Concise common workflow language") (description "The @acronym{ccwl, Concise Common Workflow Language} is a diff --git a/gnu/packages/bison.scm b/gnu/packages/bison.scm index 252cd56c15..5fd25452ff 100644 --- a/gnu/packages/bison.scm +++ b/gnu/packages/bison.scm @@ -52,11 +52,11 @@ (define-public bison ;; "./examples/c/reccalc/scan.l:13:10: fatal error: parse.h: No such file ;; or directory". Full log in . #:parallel-tests? #f)) - (native-inputs `(("perl" ,perl) - ;; m4 is not present in PATH when cross-building. - ("m4" ,m4))) - (inputs `(("flex" ,flex))) - (propagated-inputs `(("m4" ,m4))) + (native-inputs (list perl + ;; m4 is not present in PATH when cross-building. + m4)) + (inputs (list flex)) + (propagated-inputs (list m4)) (home-page "https://www.gnu.org/software/bison/") (synopsis "Yacc-compatible parser generator") (description diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index 3f69d7e8d2..0dcb1ee991 100644 --- a/gnu/packages/bittorrent.scm +++ b/gnu/packages/bittorrent.scm @@ -122,14 +122,9 @@ (define-public transmission (string-append gui "/share/man/man1/transmission-gtk.1")) #t)))))) (inputs - `(("libevent" ,libevent) - ("curl" ,curl) - ("openssl" ,openssl) - ("zlib" ,zlib) - ("gtk+" ,gtk+))) + (list libevent curl openssl zlib gtk+)) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (home-page "https://transmissionbt.com/") (synopsis "Fast and easy BitTorrent client") (description @@ -163,13 +158,9 @@ (define-public transmission-remote-gtk (base32 "0qz9wi70qc6vgnaymivc3xz6y86c9hglk6wjv3snnqxpxmp9saay")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gnu-gettext) - ("pkg-config" ,pkg-config))) + (list gnu-gettext pkg-config)) (inputs - `(("appstream-glib" ,appstream-glib) - ("curl" ,curl) - ("gtk+" ,gtk+) - ("json-glib" ,json-glib))) + (list appstream-glib curl gtk+ json-glib)) (synopsis "Gtk frontend to the Transmission daemon") (description "transmission-remote-gtk is a GTK client for remote management of the Transmission BitTorrent client, using its HTTP RPC protocol.") @@ -189,10 +180,8 @@ (define-public libtorrent (base32 "10z9i1rc41cmmi7nx8k7k1agsx6afv09g9cl7g9zr35fyhl5l4gd")))) (build-system gnu-build-system) - (inputs `(("openssl" ,openssl) - ("zlib" ,zlib))) - (native-inputs `(("pkg-config" ,pkg-config) - ("cppunit" ,cppunit))) + (inputs (list openssl zlib)) + (native-inputs (list pkg-config cppunit)) (synopsis "BitTorrent library of rtorrent") (description "LibTorrent is a BitTorrent library used by and developed in parallel @@ -214,14 +203,13 @@ (define-public rtorrent (base32 "1bs2fnf4q7mlhkhzp3i1v052v9xn8qa7g845pk9ia8hlpw207pwy")))) (build-system gnu-build-system) - (inputs `(("libtorrent" ,libtorrent) - ("ncurses" ,ncurses) - ("curl" ,curl) - ("cyrus-sasl" ,cyrus-sasl) - ("openssl" ,openssl) - ("zlib" ,zlib))) - (native-inputs `(("pkg-config" ,pkg-config) - ("cppunit" ,cppunit))) + (inputs (list libtorrent + ncurses + curl + cyrus-sasl + openssl + zlib)) + (native-inputs (list pkg-config cppunit)) (synopsis "BitTorrent client with ncurses interface") (description "rTorrent is a BitTorrent client with an ncurses interface. It supports @@ -255,7 +243,7 @@ (define-public tremc (delete 'configure) (delete 'build)))) (inputs - `(("python" ,python))) + (list python)) (synopsis "Console client for the Transmission BitTorrent daemon") (description "Tremc is a console client, with a curses interface, for the Transmission BitTorrent daemon.") @@ -334,17 +322,17 @@ (define-public aria2 (string-append "// " text))) #t))))) (native-inputs - `(("cppunit" ,cppunit) ; for the tests - ("pkg-config" ,pkg-config))) + (list cppunit ; for the tests + pkg-config)) (inputs - `(("c-ares" ,c-ares) - ("gnutls" ,gnutls) - ("gmp" ,gmp) - ("libssh2" ,libssh2) - ("libxml2" ,libxml2) - ("nettle" ,nettle) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list c-ares + gnutls + gmp + libssh2 + libxml2 + nettle + sqlite + zlib)) (home-page "https://aria2.github.io/") (synopsis "Utility for parallel downloading files") (description @@ -369,17 +357,16 @@ (define-public uget (arguments `(#:configure-flags '("CFLAGS=-fcommon"))) (inputs - `(("curl" ,curl) - ("gtk+" ,gtk+) - ("glib" ,glib) - ("gnutls" ,gnutls) - ("gstreamer" ,gstreamer) - ("libgcrypt" ,libgcrypt) - ("libnotify" ,libnotify) - ("openssl" ,openssl))) + (list curl + gtk+ + glib + gnutls + gstreamer + libgcrypt + libnotify + openssl)) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (home-page "https://ugetdm.com/") (synopsis "Universal download manager with GTK+ interface") (description @@ -459,8 +446,7 @@ (define-public libtorrent-rasterbar "-j" (if parallel-tests? (number->string (parallel-job-count)) "1"))))))))) - (inputs `(("boost" ,boost) - ("openssl" ,openssl))) + (inputs (list boost openssl)) (native-inputs `(("libfaketime" ,libfaketime) ("python" ,python-wrapper) ("pkg-config" ,pkg-config))) @@ -506,8 +492,7 @@ (define-public qbittorrent (wrap-qt-program "qbittorrent" #:output out #:inputs inputs)) #t))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list pkg-config qttools)) (inputs `(("boost" ,boost) ("libtorrent-rasterbar" ,libtorrent-rasterbar) @@ -560,8 +545,7 @@ (define-public deluge ("python-twisted" ,python-twisted) ("python-zope-interface" ,python-zope-interface))) (native-inputs - `(("intltool" ,intltool) - ("python-wheel" ,python-wheel))) + (list intltool python-wheel)) ;; TODO: Enable tests. ;; After "pytest-twisted" is packaged, HOME is set, and an X server is ;; started, some of the tests still fail. There are likely some tests diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index 440728caea..53815c0268 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -77,8 +77,7 @@ (define-public boost (base32 "0m08hhk3l7zvzajyk39qlw566q3fhixayhc2j11328qf0gy8b7zw")))) (build-system gnu-build-system) - (inputs `(("icu4c" ,icu4c) - ("zlib" ,zlib))) + (inputs (list icu4c zlib)) (native-inputs `(("perl" ,perl) ,@(if (%current-target-system) @@ -216,9 +215,7 @@ (define-public boost-for-irods ("libcxxabi" ,libcxxabi-6) ("zlib" ,zlib))) (native-inputs - `(("clang" ,clang-6) - ("perl" ,perl) - ("tcsh" ,tcsh))) + (list clang-6 perl tcsh)) (arguments `(#:tests? #f #:make-flags @@ -462,7 +459,7 @@ (define-public mdds "03b8i43pw4m767mm0cnbi77x7qhpkzpi9b1f6dpp4cmyszmnsk8l")))) (build-system gnu-build-system) (propagated-inputs - `(("boost" ,boost))) ; inclusion of header files + (list boost)) ; inclusion of header files (home-page "https://gitlab.com/mdds/mdds") (synopsis "Multi-dimensional C++ data structures and indexing algorithms") (description "Mdds (multi-dimensional data structure) provides a diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index c3c3ec14b9..be6cb8f22a 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -263,11 +263,11 @@ (define-public grub-minimal (inherit grub) (name "grub-minimal") (inputs - (fold alist-delete (package-inputs grub) - '("lvm2" "mdadm" "fuse" "console-setup"))) + (modify-inputs (package-inputs grub) + (delete "lvm2" "mdadm" "fuse" "console-setup"))) (native-inputs - (fold alist-delete (package-native-inputs grub) - '("help2man" "texinfo" "parted" "qemu" "xorriso"))) + (modify-inputs (package-native-inputs grub) + (delete "help2man" "texinfo" "parted" "qemu" "xorriso"))) (arguments (substitute-keyword-arguments (package-arguments grub) ((#:configure-flags _ ''()) @@ -295,9 +295,8 @@ (define-public grub-efi (name "grub-efi") (synopsis "GRand Unified Boot loader (UEFI version)") (inputs - `(("efibootmgr" ,efibootmgr) - ("mtools" ,mtools) - ,@(package-inputs grub))) + (modify-inputs (package-inputs grub) + (prepend efibootmgr mtools))) (arguments `(;; TODO: Tests need a UEFI firmware for qemu. There is one at ;; https://github.com/tianocore/edk2/tree/master/OvmfPkg . @@ -344,8 +343,8 @@ (define-public grub-hybrid (name "grub-hybrid") (synopsis "GRand Unified Boot loader (hybrid version)") (inputs - `(("grub" ,grub) - ,@(package-inputs grub-efi))) + (modify-inputs (package-inputs grub-efi) + (prepend grub))) (arguments (substitute-keyword-arguments (package-arguments grub-efi) ((#:modules modules `((guix build utils) (guix build gnu-build-system))) @@ -455,14 +454,14 @@ (define-public dtc "0wrl43rvd8nnm1v1wyfdr17vk8q7ymib62vli6da8n9ni4lwbkk5")))) (build-system gnu-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("libyaml" ,libyaml) - ("pkg-config" ,pkg-config) - ("swig" ,swig) - ("valgrind" ,valgrind))) + (list bison + flex + libyaml + pkg-config + swig + valgrind)) (inputs - `(("python" ,python))) + (list python)) (arguments `(#:make-flags (list (string-append "CC=" ,(cc-for-target)) @@ -556,8 +555,8 @@ (define-public u-boot-tools (inherit u-boot) (name "u-boot-tools") (native-inputs - `(("sdl2" ,sdl2) - ,@(package-native-inputs u-boot))) + (modify-inputs (package-native-inputs u-boot) + (prepend sdl2))) (arguments `(#:make-flags '("HOSTCC=gcc") #:test-target "tcheck" @@ -1263,9 +1262,7 @@ (define-public ipxe (lambda _ (chdir "..") #t))) #:tests? #f)) ; no test suite (native-inputs - `(("perl" ,perl) - ("syslinux" ,syslinux) - ("xorriso" ,xorriso))) + (list perl syslinux xorriso)) (home-page "https://ipxe.org") (synopsis "PXE-compliant network boot firmware") (description "iPXE is a network boot firmware. It provides a full PXE diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 249d8bc45b..6750446d77 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -91,7 +91,7 @@ (define-public bam (native-inputs `(("python" ,python-2))) (inputs - `(("lua" ,lua))) + (list lua)) (home-page "https://matricks.github.io/bam/") (synopsis "Fast and flexible build system") (description "Bam is a fast and flexible build system. Bam uses Lua to @@ -166,7 +166,7 @@ (define-public bmake (inputs `(("bash" ,bash-minimal))) (native-inputs - `(("coreutils" ,coreutils))) + (list coreutils)) (arguments `(#:tests? #f ; test during build #:phases @@ -284,12 +284,12 @@ (define-public meson ;; Meson calls the various executables in out/bin through the ;; Python interpreter, so we cannot use the shell wrapper. (delete 'wrap)))) - (inputs `(("ninja" ,ninja))) + (inputs (list ninja)) ;; XXX: Python is propagated just to 'GUIX_PYTHONPATH' is set (!). ;; MESON-WRAPPED below fixes that by wrapping the 'meson' executable. ;; TODO: Make MESON-WRAPPED the new MESON on the next core update cycle. - (propagated-inputs `(("python" ,python))) + (propagated-inputs (list python)) (home-page "https://mesonbuild.com/") (properties '((hidden? . #t))) @@ -358,7 +358,7 @@ (define-public premake4 "1017rd0wsjfyq2jvpjjhpszaa7kmig6q1nimw76qx3cjz2868lrn")))) (build-system gnu-build-system) (native-inputs - `(("unzip" ,unzip))) ; for unpacking the source + (list unzip)) ; for unpacking the source (arguments `(#:make-flags (list (string-append "CC=" ,(cc-for-target))) #:tests? #f ; No test suite @@ -465,12 +465,11 @@ (define-public tup (display "au BufNewFile,BufRead Tupfile,*.tup setf tup"))) #t)))))) (inputs - `(("fuse" ,fuse) - ("pcre" ,pcre) - ("pcre" ,pcre "bin") ; pcre-config - ("sqlite" ,sqlite))) + (list fuse pcre + `(,pcre "bin") ; pcre-config + sqlite)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://gittup.org/tup/") (synopsis "Fast build system that's hard to get wrong") (description "Tup is a generic build system based on a directed acyclic @@ -507,11 +506,9 @@ (define-public osc (string-append bin "osc")) #t)))))) (native-inputs - `(("python-chardet" ,python-chardet))) + (list python-chardet)) (inputs - `(("python-m2crypto" ,python-m2crypto) - ("python-pycurl" ,python-pycurl) - ("rpm" ,rpm))) ; for python-rpm + (list python-m2crypto python-pycurl rpm)) ; for python-rpm (home-page "https://github.com/openSUSE/osc") (synopsis "Open Build Service command line tool") (description "@command{osc} is a command line interface to the Open Build @@ -540,10 +537,9 @@ (define-public compiledb (substitute* "setup.py" (("^ *'shutilwhich'\n") "")) (substitute* "compiledb/compiler.py" (("shutilwhich") "shutil"))))))) (propagated-inputs - `(("python-bashlex" ,python-bashlex) - ("python-click" ,python-click))) + (list python-bashlex python-click)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/nickdiego/compiledb") (synopsis diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm index f3652813ed..17b91da59f 100644 --- a/gnu/packages/busybox.scm +++ b/gnu/packages/busybox.scm @@ -106,11 +106,11 @@ (define-public busybox (apply invoke "make" (string-append "CONFIG_PREFIX=" out) "install" make-flags))))))) - (native-inputs `(("perl" ,perl) ; needed to generate the man pages (pod2man) - ;; The following are needed by the tests. - ("inetutils" ,inetutils) - ("which" ,(@ (gnu packages base) which)) - ("zip" ,zip))) + (native-inputs (list perl ; needed to generate the man pages (pod2man) + ;; The following are needed by the tests. + inetutils + (@ (gnu packages base) which) + zip)) (synopsis "Many common UNIX utilities in a single executable") (description "BusyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides a fairly complete environment for @@ -162,7 +162,7 @@ (define-public toybox (let ((out (assoc-ref outputs "out"))) (delete-file-recursively (string-append out "/usr")))))) #:test-target "tests")) - (native-inputs `(("bc" ,bc))) + (native-inputs (list bc)) (synopsis "Many common UNIX utilities in a single executable") (description "ToyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides a fairly complete environment for diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index e37c173fc0..5c28ea9fb8 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -69,8 +69,7 @@ (define-public tcc (base32 "177bdhwzrnqgyrdv1dwvpd04fcxj68s5pm1dzwny6359ziway8yy")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl) - ("texinfo" ,texinfo))) + (native-inputs (list perl texinfo)) (arguments `(#:configure-flags (list (string-append "--elfinterp=" (assoc-ref %build-inputs "libc") @@ -130,8 +129,7 @@ (define-public pcc (replace 'check (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t))))) (native-inputs - `(("bison" ,bison) - ("flex" ,flex))) + (list bison flex)) (synopsis "Portable C compiler") (description "PCC is a portable C compiler. The project goal is to write a C99 @@ -162,8 +160,7 @@ (define-public libbytesize ("pkg-config" ,pkg-config) ("python" ,python))) (inputs - `(("mpfr" ,mpfr) - ("pcre2" ,pcre2))) + (list mpfr pcre2)) (home-page "https://github.com/storaged-project/libbytesize") (synopsis "Tiny C library for working with arbitrary big sizes in bytes") (description @@ -205,7 +202,7 @@ (define-public udunits `(#:configure-flags (list "--disable-static"))) (inputs - `(("expat" ,expat))) + (list expat)) (home-page "https://www.unidata.ucar.edu/software/udunits/") (synopsis "C library for units of physical quantities and value-conversion utils") (description @@ -238,11 +235,7 @@ (define-public libfixposix "1x4q6yspi5g2s98vq4qszw4z3zjgk9l5zs8471w4d4cs6l97w08j")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("check" ,check))) + (list autoconf automake libtool pkg-config check)) (synopsis "Thin wrapper over POSIX syscalls") (description "The purpose of libfixposix is to offer replacements for parts of POSIX @@ -317,7 +310,7 @@ (define-public libwuya headers) (install-file "libwuya.a" (string-append out "/lib")) #t)))))) - (inputs `(("lua" ,lua))) + (inputs (list lua)) (home-page "https://github.com/WuBingzheng/libwuya/") (synopsis "C library implementing various data structures") (description "The @code{libwuya} library implements data structures such @@ -368,7 +361,7 @@ (define-public packcc (string-append out "/share/doc/packcc")) #t)))))) (native-inputs - `(("bats" ,bats))) + (list bats)) (synopsis "Packrat parser generator for C") (description "PackCC is a packrat parser generator for the C programming language. @@ -398,7 +391,7 @@ (define-public sparse (base32 "0z1qds52144nvsdnl82r3zs3vax618v920jmffyyssmwj54qpcka")))) (build-system gnu-build-system) - (inputs `(("perl" ,perl))) + (inputs (list perl)) (arguments '(#:make-flags `(,(string-append "PREFIX=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases @@ -441,10 +434,7 @@ (define-public libestr (replace 'bootstrap (lambda _ (invoke "autoreconf" "-vfi")))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("libtool" ,libtool))) + (list autoconf automake pkg-config libtool)) (home-page "https://github.com/rsyslog/libestr") (synopsis "Helper functions for handling strings") (description @@ -467,9 +457,7 @@ (define-public libfastjson (base32 "12rqcdqxazw8czzxbivdapdgj19pcswpw1jp2915sxbljis83g6q")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (home-page "https://github.com/rsyslog/libfastjson") (synopsis "Fast JSON library for C") (description @@ -500,12 +488,12 @@ (define-public liblogging (replace 'bootstrap (lambda _ (invoke "autoreconf" "-vfi")))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("libtool" ,libtool) - ;; For rst2man.py - ("python-docutils" ,python-docutils))) + (list autoconf + automake + pkg-config + libtool + ;; For rst2man.py + python-docutils)) (home-page "https://github.com/rsyslog/liblogging") (synopsis "Easy to use and lightweight signal-safe logging library") (description @@ -538,7 +526,7 @@ (define-public unifdef (string-append "prefix=" %output)) #:tests? #f)) ;no test suite (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "https://dotat.at/prog/unifdef/") (synopsis "Utility to selectively processes conditional C preprocessor") (description "The @command{unifdef} utility selectively processes @@ -596,7 +584,7 @@ (define-public aws-checksums (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (inputs - `(("aws-c-common" ,aws-c-common))) + (list aws-c-common)) (synopsis "Amazon Web Services checksum library") (description "This library provides cross-Platform hardware accelerated CRC32c and CRC32 @@ -625,12 +613,9 @@ (define-public aws-c-event-stream (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (propagated-inputs - `(("aws-c-common" ,aws-c-common) - ("aws-c-io" ,aws-c-io) - ("aws-checksums" ,aws-checksums))) + (list aws-c-common aws-c-io aws-checksums)) (inputs - `(("aws-c-cal" ,aws-c-cal) - ("s2n" ,s2n))) + (list aws-c-cal s2n)) (synopsis "Amazon Web Services client-server message format library") (description "This library is a C99 implementation for @acronym{AWS,Amazon Web Services} @@ -661,9 +646,7 @@ (define-public aws-c-io (assoc-ref %build-inputs "aws-c-common")) "-DENABLE_NET_TESTS=OFF"))) (propagated-inputs - `(("aws-c-cal" ,aws-c-cal) - ("aws-c-common" ,aws-c-common) - ("s2n" ,s2n))) + (list aws-c-cal aws-c-common s2n)) (synopsis "Event driven framework for implementing application protocols") (description "This library provides a C99 framework for constructing event-driven, asynchronous network application protocols.") @@ -691,7 +674,7 @@ (define-public aws-c-cal (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (propagated-inputs - `(("aws-c-common" ,aws-c-common))) + (list aws-c-common)) (inputs `(("openssl" ,openssl) ("openssl:static" ,openssl "static"))) @@ -742,8 +725,7 @@ (define-public aws-c-http (assoc-ref %build-inputs "aws-c-common")) "-DENABLE_NET_TESTS=OFF"))) (propagated-inputs - `(("aws-c-compression" ,aws-c-compression) - ("aws-c-io" ,aws-c-io))) + (list aws-c-compression aws-c-io)) (synopsis "Amazon Web Services HTTP library") (description "This library provides a C99 implementation of the HTTP/1.1 and HTTP/2 @@ -772,7 +754,7 @@ (define-public aws-c-compression (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (propagated-inputs - `(("aws-c-common" ,aws-c-common))) + (list aws-c-common)) (synopsis "Amazon Web Services compression library") (description "This library provides a C99 implementation of compression algorithms, @@ -805,10 +787,7 @@ (define-public aws-c-auth (assoc-ref %build-inputs "aws-c-common")) "-DENABLE_NET_TESTS=OFF"))) (propagated-inputs - `(("aws-c-cal" ,aws-c-cal) - ("aws-c-common" ,aws-c-common) - ("aws-c-http" ,aws-c-http) - ("aws-c-io" ,aws-c-io))) + (list aws-c-cal aws-c-common aws-c-http aws-c-io)) (synopsis "Amazon Web Services client-side authentication library") (description "This library provides a C99 implementation for AWS client-side @@ -838,8 +817,7 @@ (define-public aws-c-s3 (assoc-ref %build-inputs "aws-c-common")) "-DENABLE_NET_TESTS=OFF"))) (propagated-inputs - `(("aws-c-auth" ,aws-c-auth) - ("aws-c-http" ,aws-c-http))) + (list aws-c-auth aws-c-http)) (synopsis "Amazon Web Services client library for Amazon S3") (description "This library provides a C99 client implementation of the Simple Storage @@ -868,8 +846,7 @@ (define-public aws-c-mqtt (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (propagated-inputs - `(("aws-c-http" ,aws-c-http) - ("aws-c-io" ,aws-c-io))) + (list aws-c-http aws-c-io)) (synopsis "Amazon Web Services MQTT library") (description "This library provides a C99 implementation of the Message Queuing diff --git a/gnu/packages/calcurse.scm b/gnu/packages/calcurse.scm index b44f88fea9..5da701492b 100644 --- a/gnu/packages/calcurse.scm +++ b/gnu/packages/calcurse.scm @@ -39,8 +39,8 @@ (define-public calcurse (sha256 (base32 "0cgkd285x5pk62lmdx9fjxl46c5lj8wj2cqbxq7d99yb4il5fdjk")))) (build-system gnu-build-system) - (inputs `(("ncurses" ,ncurses))) - (native-inputs `(("tzdata" ,tzdata-for-tests))) + (inputs (list ncurses)) + (native-inputs (list tzdata-for-tests)) (arguments ;; The ical tests all want to create a ".calcurse" directory, and may ;; fail with "cannot create directory '.calcurse': File exists" if run diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 6c815daf7d..129eb58aa0 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -80,7 +80,7 @@ (define-public date ;; Install pkg-config files ;; https://github.com/HowardHinnant/date/pull/538 (search-patches "date-output-pkg-config-files.patch")))) - (inputs `(("tzdata" ,tzdata))) + (inputs (list tzdata)) (build-system cmake-build-system) (arguments '(#:configure-flags (list "-DUSE_SYSTEM_TZ_DB=ON" @@ -158,19 +158,17 @@ (define-public libical (("\\\"/usr/share/lib/zoneinfo\\\"") ""))) #t))))) (native-inputs - `(("docbook-xml" ,docbook-xml-4.3) - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("vala" ,vala))) + (list docbook-xml-4.3 + gobject-introspection + gtk-doc/stable + perl + pkg-config + vala)) (inputs - `(("glib" ,glib) - ("libxml2" ,libxml2) - ("tzdata" ,tzdata))) + (list glib libxml2 tzdata)) (propagated-inputs ;; In Requires.private of libical.pc. - `(("icu4c" ,icu4c))) + (list icu4c)) (home-page "https://libical.github.io/libical/") (synopsis "iCalendar protocols and data formats implementation") (description @@ -204,23 +202,22 @@ (define-public khal (string-append (assoc-ref outputs "out") "/share/man/man1")) #t))))) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm) - ;; Required to build manpage - ("python-sphinxcontrib-newsfeed" ,python-sphinxcontrib-newsfeed) - ("python-sphinx" ,python-sphinx))) + (list python-setuptools-scm + ;; Required to build manpage + python-sphinxcontrib-newsfeed python-sphinx)) (inputs - `(("sqlite" ,sqlite) - ("python-configobj" ,python-configobj) - ("python-dateutil" ,python-dateutil) - ("python-icalendar" ,python-icalendar) - ("python-tzlocal" ,python-tzlocal) - ("python-urwid" ,python-urwid) - ("python-pytz" ,python-pytz) - ("python-setproctitle" ,python-setproctitle) - ("python-atomicwrites" ,python-atomicwrites) - ("python-click" ,python-click) - ("python-click-log" ,python-click-log) - ("python-pyxdg" ,python-pyxdg))) + (list sqlite + python-configobj + python-dateutil + python-icalendar + python-tzlocal + python-urwid + python-pytz + python-setproctitle + python-atomicwrites + python-click + python-click-log + python-pyxdg)) (synopsis "Console calendar program") (description "Khal is a standards based console calendar program, able to synchronize with CalDAV servers through vdirsyncer.") @@ -275,10 +272,7 @@ (define-public remind (list "bin/cm2rem.tcl" "bin/tkremind")))))))) (inputs - `(("inetutils" ,inetutils) - ("tcl" ,tcl) - ("tcllib" ,tcllib) - ("tk" ,tk))) + (list inetutils tcl tcllib tk)) (home-page "https://dianne.skoll.ca/projects/remind/") (synopsis "Sophisticated calendar and alarm program") (description @@ -347,9 +341,9 @@ (define-public confclerk #t)))) #:tests? #f)) ; no tests (native-inputs - `(("perl" ,perl))) ; pod2man + (list perl)) ; pod2man (inputs - `(("qtbase" ,qtbase-5))) + (list qtbase-5)) (home-page "https://www.toastfreeware.priv.at/confclerk") (synopsis "Offline conference schedule application") (description @@ -423,11 +417,9 @@ (define-public gsimplecal "1qyf65l088dqsz25hm6s1cv18j52yaias0llqvpqwjfnvssa5cxg")) (modules '((guix build utils))))) (build-system gnu-build-system) - (inputs `(("gtk+" ,gtk+))) + (inputs (list gtk+)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config))) + (list autoconf automake pkg-config)) (home-page "https://dmedvinsky.github.io/gsimplecal/") (synopsis "Lightweight calendar applet") (description "@command{gsimplecal} is a lightweight calendar application diff --git a/gnu/packages/ccache.scm b/gnu/packages/ccache.scm index 44b0ef606a..bffbff5715 100644 --- a/gnu/packages/ccache.scm +++ b/gnu/packages/ccache.scm @@ -40,10 +40,10 @@ (define-public ccache (sha256 (base32 "186b5lfbdd48cvbxqv2yh93pgr8lhahl1jzw00k2rmjzmbxwl04j")))) (build-system cmake-build-system) - (native-inputs `(("perl" ,perl) ; for test/run - ("which" ,(@ (gnu packages base) which)))) - (inputs `(("zlib" ,zlib) - ("zstd" ,zstd "lib"))) + (native-inputs (list perl ; for test/run + (@ (gnu packages base) which))) + (inputs (list zlib + `(,zstd "lib"))) (arguments '( ;; The Redis backend must be explicitly disabled to build without Redis. #:configure-flags diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 1ad4829dc4..42571531e5 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -118,11 +118,9 @@ (define-public libcdio "0avi6apv5ydjy6b9c3z9a46rvp5i57qyr09vr7x4nndxkmcfjl45")))) (build-system gnu-build-system) (inputs - `(("ncurses" ,ncurses) - ("libcddb" ,libcddb))) + (list ncurses libcddb)) (native-inputs - `(("help2man" ,help2man) - ("pkg-config" ,pkg-config))) + (list help2man pkg-config)) (home-page "https://www.gnu.org/software/libcdio/") (synopsis "CD Input and Control library") (description @@ -147,8 +145,8 @@ (define-public libcdio-paranoia (base32 "12hfnrq7amv9qjzc92cr265m7kh0a1hpasck8cxx1gygbhqczc9k")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (propagated-inputs `(("libcdio" ,libcdio))) + (native-inputs (list pkg-config)) + (propagated-inputs (list libcdio)) (home-page "https://www.gnu.org/software/libcdio/") (synopsis "Jitter- and error-tolerant CD audio extraction") (description @@ -198,10 +196,7 @@ (define-public xorriso `("PATH" ":" prefix (,(string-append out "/bin")))) #t)))))) (inputs - `(("acl" ,acl) - ("readline" ,readline) - ("tk" ,tk) - ("zlib" ,zlib))) + (list acl readline tk zlib)) (home-page "https://www.gnu.org/software/xorriso/") (synopsis "Create, manipulate, burn ISO-9660 file systems") (description @@ -283,14 +278,9 @@ (define-public cdrdao (substitute* "configure.ac" (("^AM_GCONF_SOURCE_2.*") "")) #t))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config))) + (list autoconf automake pkg-config)) (inputs - `(("ao" ,ao) - ("lame" ,lame) - ("libmad" ,libmad) - ("libvorbis" ,libvorbis))) + (list ao lame libmad libvorbis)) (home-page "http://cdrdao.sourceforge.net") (synopsis "Read and write CDs in disk-at-once mode") (description "cdrdao records audio or data CDs in disk-at-once (DAO) mode, @@ -382,9 +372,9 @@ (define-public dvd+rw-tools (patches (search-patches "dvd+rw-tools-add-include.patch")))) (build-system gnu-build-system) (inputs - `(("cdrtools" ,cdrtools))) + (list cdrtools)) (native-inputs - `(("m4" ,m4))) + (list m4)) (arguments `(#:tests? #f ; No tests. #:phases @@ -430,7 +420,7 @@ (define-public dvdisaster (base32 "1hz3fvqfdrwb7dn6ggqkpcgyjag37ivm1layw27ncjz9glklxjbr")))) (build-system gnu-build-system) (inputs - `(("gtk+" ,gtk+-2))) + (list gtk+-2)) (native-inputs `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config) @@ -572,8 +562,7 @@ (define-public libcue (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) (native-inputs - `(("bison" ,bison) - ("flex" ,flex))) + (list bison flex)) (home-page "https://github.com/lipnitsk/libcue") (synopsis "C library to parse cue sheets") (description "Libcue is a C library to parse so-called @dfn{cue sheets} @@ -684,20 +673,18 @@ (define (wrap file) #t))) #:tests? #f)) ; no test target - (inputs `(("wget" ,wget) - ("which" ,which) - ("cdparanoia" ,cdparanoia) - ("cd-discid" ,cd-discid) - ("vorbis-tools" ,vorbis-tools) - ("flac" ,flac) - - ("perl-musicbrainz-discid" ,perl-musicbrainz-discid) - ("perl-webservice-musicbrainz" ,perl-webservice-musicbrainz) - ("perl-mojolicious" ,perl-mojolicious) ;indirect dependency - - ;; A couple of Python and Perl scripts are included. - ("python" ,python) - ("perl" ,perl))) + (inputs (list wget + which + cdparanoia + cd-discid + vorbis-tools + flac + perl-musicbrainz-discid + perl-webservice-musicbrainz + perl-mojolicious ;indirect dependency + ;; A couple of Python and Perl scripts are included. + python + perl)) (synopsis "Command-line audio CD ripper") (description @@ -730,7 +717,7 @@ (define-public geteltorito (let ((out (assoc-ref outputs "out"))) (install-file "geteltorito" (string-append out "/bin")))))))) - (inputs `(("perl" ,perl))) + (inputs (list perl)) (synopsis "Extract the boot image from a CD-ROM") (description "@command{geteltorito} can extract the initial/default boot @@ -771,8 +758,7 @@ (define (bin-directory input-name) "flac" "opus-tools" "wavpack")))))))))) - (native-inputs `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (native-inputs (list intltool pkg-config)) ;; TODO: Add the necessary packages for Musepack encoding. (inputs `(("gtk+-2" ,gtk+-2) ("glib" ,glib) @@ -823,15 +809,11 @@ (define-public ripit (("\\$\\(DESTDIR\\)/usr/local") (assoc-ref outputs "out")) (("../../etc") "etc"))))))) (native-inputs - `(("coreutils" ,coreutils))) + (list coreutils)) (inputs - `(("perl" ,perl))) + (list perl)) (propagated-inputs - `(("cdparanoia" ,cdparanoia) - ("flac" ,flac) - ("vorbis-tools" ,vorbis-tools) - ("wavpack" ,wavpack) - ("perl-cddb-get" ,perl-cddb-get))) + (list cdparanoia flac vorbis-tools wavpack perl-cddb-get)) (home-page (string-append "https://web.archive.org/web/20170119092156/" "http://www.suwald.com/ripit/about.php")) (synopsis "Command-line program to extract audio CDs") @@ -875,7 +857,7 @@ (define-public libburn "0m1vyry6pi115nysfgb0cg313qqhnlxqdg7f920wpiar0z8mjl2j")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://dev.lovelyhq.com/libburnia/libburn") (synopsis "Library for reading and writing optical discs") (description @@ -897,10 +879,9 @@ (define-public libisofs "13m82l13cb5d7ca53dv3akma1jr9gw0hnnshdwqpj6ahly0fv85a")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib) - ("acl" ,acl))) + (list zlib acl)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://dev.lovelyhq.com/libburnia/libisofs") (synopsis "Library to create ISO 9660 images") (description @@ -939,10 +920,7 @@ (define-public cdrkit-libre "extern char\t*outfile")))))) (build-system cmake-build-system) (inputs - `(("bzip2" ,bzip2) - ("libcap" ,libcap) - ("perl" ,perl) - ("zlib" ,zlib))) + (list bzip2 libcap perl zlib)) (arguments `(#:tests? #f ;no tests #:phases @@ -975,10 +953,9 @@ (define-public libmirage "0f8i2ha44rykkk3ac2q8zsw3y1zckw6qnf6zvkyrj3qqbzhrf3fm")))) (build-system cmake-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool))) + (list pkg-config intltool)) (inputs - `(("glib" ,glib))) + (list glib)) (arguments ;; No tests. '(#:tests? #f)) @@ -1004,12 +981,9 @@ (define-public cdemu-daemon "16g6fv1lxkdmbsy6zh5sj54dvgwvm900fd18aq609yg8jnqm644d")))) (build-system cmake-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool))) + (list pkg-config intltool)) (inputs - `(("libmirage" ,libmirage) - ("glib" ,glib) - ("ao" ,ao))) + (list libmirage glib ao)) (arguments ;; No tests. '(#:tests? #f)) @@ -1033,12 +1007,9 @@ (define-public cdemu-client "1prrdhv0ia0axc6b73crszqzh802wlkihz6d100yvg7wbgmqabd7")))) (build-system cmake-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool))) + (list pkg-config intltool)) (inputs - `(("python" ,python) - ("python-pygobject" ,python-pygobject) - ("cdemu-daemon" ,cdemu-daemon))) + (list python python-pygobject cdemu-daemon)) (arguments ;; No tests. `(#:tests? #f diff --git a/gnu/packages/cedille.scm b/gnu/packages/cedille.scm index decaf25605..1f00e8f698 100644 --- a/gnu/packages/cedille.scm +++ b/gnu/packages/cedille.scm @@ -42,11 +42,7 @@ (define-public cedille (base32 "1h5s6ayh3s76z184jai3jidcs4cjk8s4nvkkv2am8dg4gfsybq22")))) (inputs - `(("agda" ,agda) - ("agda-ial" ,agda-ial) - ("ghc" ,ghc) - ("ghc-alex" ,ghc-alex) - ("ghc-happy" ,ghc-happy))) + (list agda agda-ial ghc ghc-alex ghc-happy)) (build-system emacs-build-system) (arguments `(#:phases diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm index d09778f6da..fc4f4f2686 100644 --- a/gnu/packages/certs.scm +++ b/gnu/packages/certs.scm @@ -76,7 +76,7 @@ (define-public desec-certbot-hook #:install-plan '(("." "etc/desec" #:include ("hook.sh"))))) (inputs - `(("curl" ,curl))) + (list curl)) (synopsis "Certbot DNS challenge automatization for deSEC") (description "The deSEC can be used to obtain certificates with certbot DNS ownership verification. With the help of this hook script, you can obtain @@ -133,8 +133,7 @@ (define-public nss-certs (build-system gnu-build-system) (outputs '("out")) (native-inputs - `(("certdata2pem" ,certdata2pem) - ("openssl" ,openssl))) + (list certdata2pem openssl)) (inputs '()) (propagated-inputs '()) (arguments @@ -201,8 +200,7 @@ (define-public le-certs (string-append openssl "/bin/c_rehash") "."))))) (native-inputs - `(("openssl" ,openssl) - ("perl" ,perl))) ;for 'c_rehash' + (list openssl perl)) ;for 'c_rehash' (inputs `(; The Let's Encrypt root certificate, "ISRG Root X1". ("isrgrootx1.pem" diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 50a00e5a90..5368de3356 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -107,7 +107,7 @@ (define-public pedansee ("pkg-config" ,pkg-config) ("python" ,python-wrapper))) (inputs - `(("glib" ,glib))) + (list glib)) (synopsis "Code checker for C") (description "Pedansee checks C source files for compliance with a particular programming style. The style is currently defined by the pedansee source code @@ -248,7 +248,7 @@ (define-public clitest (string-append out "/share/doc/clitest-" ,version)) #t)))))) (native-inputs - `(("perl" ,perl))) ;for tests + (list perl)) ;for tests (synopsis "Command line test tool") (description "@command{clitest} is a portable shell script that performs automatic @@ -276,9 +276,7 @@ (define-public cunit (replace 'bootstrap (lambda _ (invoke "autoreconf" "-vfi")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf) - ("libtool" ,libtool))) + (list automake autoconf libtool)) (home-page "http://cunit.sourceforge.net/") (synopsis "Automated testing framework for C") (description @@ -460,12 +458,9 @@ (define-public cmdtest (build-system python-build-system) (arguments `(#:tests? #f)) ;requires Python 2! (native-inputs - `(("python-coverage-test-runner" ,python-coverage-test-runner) - ("python" ,python))) + (list python-coverage-test-runner python)) (inputs - `(("python-cliapp" ,python-cliapp) - ("python-markdown" ,python-markdown) - ("python-ttystatus" ,python-ttystatus))) + (list python-cliapp python-markdown python-ttystatus)) (home-page "https://liw.fi/cmdtest/") (synopsis "Black box Unix program tester") (description @@ -559,7 +554,7 @@ (define-public cxxtest (copy-recursively "../sample" (string-append doc-dir "/sample")) #t)))))) (propagated-inputs - `(("python-ply" ,python-ply))) + (list python-ply)) (home-page "https://cxxtest.com/") (synopsis "Unit testing framework for C++") (description "CxxTest is a unit testing framework for C++ that is similar @@ -634,7 +629,7 @@ (define-public go-github.com-smartystreets-assertions (arguments '(#:import-path "github.com/smartystreets/assertions")) (native-inputs - `(("go-github.com-smartystreets-gunit" ,go-github.com-smartystreets-gunit))) + (list go-github.com-smartystreets-gunit)) (synopsis "Assertions for testing with Go") (description "The @code{assertions} package provides convenient assertion functions @@ -659,8 +654,7 @@ (define-public go-github.com-smartystreets-goconvey (arguments '(#:import-path "github.com/smartystreets/goconvey")) (propagated-inputs - `(("go-github.com-jtolds-gls" ,go-github.com-jtolds-gls) - ("go-github.com-smartystreets-assertions" ,go-github.com-smartystreets-assertions))) + (list go-github.com-jtolds-gls go-github.com-smartystreets-assertions)) (synopsis "Go testing tool with both a web and terminal user interface") (description "GoConvey is a testing tool for Go. It integrates with go test, can show @@ -748,7 +742,7 @@ (define-public cpputest "1xslavlb1974y5xvs8n1j9zkk05dlw8imy4saasrjlmibl895ii1")))) (build-system gnu-build-system) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://cpputest.github.io/") (synopsis "Unit testing and mocking framework for C/C++") (description @@ -777,8 +771,7 @@ (define-public python-parameterized (format #t "test suite not run~%")) #t))))) (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + (list python-mock python-nose)) (home-page "https://github.com/wolever/parameterized") (synopsis "Parameterized testing with any Python test framework") (description @@ -830,7 +823,7 @@ (define-public python-mock (base32 "1hrp6j0yrx2xzylfv02qa8kph661m6yq4p0mc8fnimch9j4psrc3")))) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (build-system python-build-system) (arguments ;; FIXME: Tests require "pytest", which depends on this package. @@ -891,9 +884,7 @@ (define-public python-nose2 (build-system python-build-system) (arguments `(#:tests? #f)) ; 'module' object has no attribute 'collector' (propagated-inputs - `(("python-cov-core" ,python-cov-core) - ("python-pytest-cov" ,python-pytest-cov) - ("python-six" ,python-six))) + (list python-cov-core python-pytest-cov python-six)) (home-page "https://github.com/nose-devs/nose2") (synopsis "Next generation of nicer testing for Python") (description @@ -928,8 +919,7 @@ (define-public python-unittest2 (lambda _ (zero? (system* "python" "-m" "unittest2" "discover" "--verbose"))))))) (propagated-inputs - `(("python-six" ,python-six) - ("python-traceback2" ,python-traceback2))) + (list python-six python-traceback2)) (home-page "https://pypi.org/project/unittest2/") (synopsis "Python unit testing library") (description @@ -1056,9 +1046,8 @@ (define-public python-pytest-bootstrap (package (inherit (strip-python2-variant python-pytest)) (name "python-pytest-bootstrap") - (native-inputs `(("python-iniconfig" ,python-iniconfig) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-toml" ,python-toml))) + (native-inputs (list python-iniconfig python-setuptools-scm + python-toml)) (arguments `(#:tests? #f)) (properties `((python2-variant . ,(delay python2-pytest-bootstrap)))))) @@ -1102,8 +1091,7 @@ (define-public python-pytest-assume (when tests? (invoke "pytest"))))))) (propagated-inputs - `(("python-pytest" ,python-pytest) - ("python-six" ,python-six))) + (list python-pytest python-six)) (home-page "https://github.com/astraw38/pytest-assume") (synopsis "Pytest plugin that allows multiple failures per test") @@ -1139,8 +1127,7 @@ (define-public python-pytest-cov (invoke "python" "./setup.py" "check" "--strict" "--metadata")))))) (propagated-inputs - `(("python-coverage" ,python-coverage) - ("python-pytest" ,python-pytest))) + (list python-coverage python-pytest)) (home-page "https://github.com/pytest-dev/pytest-cov") (synopsis "Pytest plugin for measuring coverage") (description @@ -1164,9 +1151,9 @@ (define-public python-pytest-httpserver "0vbls0j570l5my83j4jnk5blmnir44i0w511azlh41nl6k8rac5f")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (propagated-inputs - `(("python-werkzeug" ,python-werkzeug))) + (list python-werkzeug)) (arguments '(#:phases (modify-phases %standard-phases @@ -1201,7 +1188,7 @@ (define-public python-pytest-random-order (when tests? (invoke "python" "-m" "pytest" "--random-order"))))))) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/jbasko/pytest-random-order") (synopsis "Pytest plugin to randomize the order of tests") (description "@code{pytest-random-order} is a Pytest plugin that @@ -1237,7 +1224,7 @@ (define-public python-pytest-runner (format #t "test suite not run~%")) #t))))) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (home-page "https://github.com/pytest-dev/pytest-runner") (synopsis "Invoke py.test as a distutils command") (description @@ -1284,7 +1271,7 @@ (define-public python-pytest-lazy-fixture (add-installed-pythonpath inputs outputs) (invoke "pytest" "-vv")))))) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/tvorog/pytest-lazy-fixture") (synopsis "Use fixtures in @code{pytest.mark.parametrize}") (description "This plugin helps to use fixtures in @@ -1317,10 +1304,9 @@ (define-public python-pytest-mock (invoke "pytest" "--assert=plain" "-k" "not test_standalone_mock"))))))) (native-inputs - `(("python-pytest-asyncio" ,python-pytest-asyncio) - ("python-setuptools-scm" ,python-setuptools-scm))) + (list python-pytest-asyncio python-setuptools-scm)) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/pytest-dev/pytest-mock/") (synopsis "Thin-wrapper around the mock package for easier use with py.test") (description @@ -1388,12 +1374,9 @@ (define-public python-pytest-xdist (invoke "pytest" "-vv" "-n" (number->string (parallel-job-count))))))))) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (propagated-inputs - `(("python-execnet" ,python-execnet) - ("python-pytest" ,python-pytest) - ("python-py" ,python-py) - ("python-pytest-forked" ,python-pytest-forked))) + (list python-execnet python-pytest python-py python-pytest-forked)) (home-page "https://github.com/pytest-dev/pytest-xdist") (synopsis @@ -1446,10 +1429,9 @@ (define-public python-pytest-timeout (add-installed-pythonpath inputs outputs) (invoke "pytest" "-vv")))))) (propagated-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-pytest python-pytest-cov)) (native-inputs - `(("python-pexpect" ,python-pexpect))) + (list python-pexpect)) (home-page "https://github.com/pytest-dev/pytest-timeout") (synopsis "Plugin for py.test to abort hanging tests") (description @@ -1514,7 +1496,7 @@ (define-public python-scripttest "0f4w84k8ck82syys7yg9maz93mqzc8p5ymis941x034v44jzq74m")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page (string-append "https://web.archive.org/web/20161029233413/" "http://pythonpaste.org/scripttest/")) (synopsis "Python library to test command-line scripts") @@ -1560,9 +1542,7 @@ (define-public python-testtools (invoke "python" "-m" "testtools.run" "testtools.tests.test_suite"))))))) (propagated-inputs - `(("python-extras" ,python-extras) - ("python-fixtures" ,python-fixtures) - ("python-pbr" ,python-pbr))) + (list python-extras python-fixtures python-pbr)) (native-inputs `(("python-testscenarios" ,python-testscenarios-bootstrap))) (description @@ -1602,8 +1582,7 @@ (define-public python-testscenarios (inherit python-testscenarios-bootstrap) (name "python-testscenarios") (propagated-inputs - `(("python-pbr" ,python-pbr) - ("python-testtools" ,python-testtools))) + (list python-pbr python-testtools)) (description "Testscenarios provides clean dependency injection for Python unittest style tests."))) @@ -1637,7 +1616,7 @@ (define-public python-testresources (inherit python-testresources-bootstrap) (name "python-testresources") (propagated-inputs - `(("python-pbr" ,python-pbr))) + (list python-pbr)) (arguments '()) (native-inputs `(("python-fixtures" ,python-fixtures) @@ -1677,12 +1656,9 @@ (define-public python-subunit (inherit python-subunit-bootstrap) (name "python-subunit") (propagated-inputs - `(("python-extras" ,python-extras) - ("python-testtools" ,python-testtools))) + (list python-extras python-testtools)) (native-inputs - `(("python-fixtures" ,python-fixtures) - ("python-hypothesis" ,python-hypothesis) - ("python-testscenarios" ,python-testscenarios))) + (list python-fixtures python-hypothesis python-testscenarios)) (description "Python-subunit is a Python implementation of the subunit test streaming protocol."))) @@ -1709,8 +1685,7 @@ (define-public python-fixtures-bootstrap ;; Package is not loadable on its own at this stage. (delete 'sanity-check)))) (propagated-inputs - `(("python-pbr-minimal" ,python-pbr-minimal) - ("python-six" ,python-six))) + (list python-pbr-minimal python-six)) (home-page "https://launchpad.net/python-fixtures") (synopsis "Python test fixture library") (description @@ -1732,8 +1707,7 @@ (define-public python-fixtures "fixtures.test_suite"))))))) (propagated-inputs ;; Fixtures uses pbr at runtime to check versions, etc. - `(("python-pbr" ,python-pbr) - ("python-six" ,python-six))) + (list python-pbr python-six)) (native-inputs `(("python-mock" ,python-mock) ("python-testtools" ,python-testtools-bootstrap))) @@ -1759,7 +1733,7 @@ (define-public python-testrepository-bootstrap ("python-subunit" ,python-subunit-bootstrap) ("python-testtools" ,python-testtools-bootstrap))) (native-inputs - `(("python-mimeparse" ,python-mimeparse))) + (list python-mimeparse)) (home-page "https://launchpad.net/testrepository") (synopsis "Database for Python test results") (description @@ -1774,11 +1748,9 @@ (define-public python-testrepository ;; FIXME: Many tests are failing. '(#:tests? #f)) (propagated-inputs - `(("python-fixtures" ,python-fixtures) - ("python-subunit" ,python-subunit) - ("python-testtools" ,python-testtools))) + (list python-fixtures python-subunit python-testtools)) (native-inputs - `(("python-mimeparse" ,python-mimeparse))) + (list python-mimeparse)) (description "Testrepository provides a database of test results which can be used as part of a developer's workflow to check things such as what tests have failed since the last commit or what tests are currently failing."))) @@ -1825,10 +1797,8 @@ (define-public python-pytest-asyncio (base32 "03drs4myv1ik79148xyhli37q6mp931jb14cz65n8qvls2zvvwgx")))) (build-system python-build-system) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-async-generator" ,python-async-generator) - ("python-hypothesis" ,python-hypothesis) - ("python-pytest" ,python-pytest))) + (list python-coverage python-async-generator python-hypothesis + python-pytest)) (home-page "https://github.com/pytest-dev/pytest-asyncio") (synopsis "Pytest support for asyncio") (description "Python asyncio code is usually written in the form of @@ -1850,7 +1820,7 @@ (define-public python-cov-core "0k3np9ymh06yv1ib96sb6wfsxjkqhmik8qfsn119vnhga9ywc52a")))) (build-system python-build-system) (propagated-inputs - `(("python-coverage" ,python-coverage))) + (list python-coverage)) (home-page "https://github.com/schlamar/cov-core") (synopsis "Coverage plugin core for pytest-cov, nose-cov and nose2-cov") (description @@ -1875,10 +1845,9 @@ (define-public python-codecov "1217c0vqf7ii65635gvl27a5pfhv0r7zhrpdp9cx640hg73bgn4f")))) (build-system python-build-system) (native-inputs - `(("python-unittest2" ,python-unittest2))) + (list python-unittest2)) (propagated-inputs - `(("python-coverage" ,python-coverage) - ("python-requests" ,python-requests))) + (list python-coverage python-requests)) (home-page "https://github.com/codecov/codecov-python") (synopsis "Upload code coverage reports to @code{codecov.io}") (description @@ -1926,7 +1895,7 @@ (define-public python-testpath wheel (string-append "--prefix=" out))) (find-files "dist" "\\.whl$")))))))) (native-inputs - `(("python-flit" ,python-flit))) + (list python-flit)) (home-page "https://github.com/takluyver/testpath") (synopsis "Test utilities for code working with files and commands") (description @@ -1947,7 +1916,7 @@ (define-public python-testlib (base32 "1mz26cxn4x8bbgv0rn0mvj2z05y31rkc8009nvdlb3lam5b4mj3y")))) (build-system python-build-system) (native-inputs - `(("unzip" ,unzip))) ; for unpacking the source + (list unzip)) ; for unpacking the source (synopsis "Python micro test suite harness") (description "A micro unittest suite harness for Python.") (home-page "https://github.com/trentm/testlib") @@ -1969,10 +1938,7 @@ (define-public python-pytest-cache "1a873fihw4rhshc722j4h6j7g3nj7xpgsna9hhg3zn6ksknnhx5y")))) (build-system python-build-system) (propagated-inputs - `(("python-apipkg" ,python-apipkg) - ("python-execnet" ,python-execnet) - ("python-py" ,python-py) - ("python-pytest" ,python-pytest))) + (list python-apipkg python-execnet python-py python-pytest)) (synopsis "Py.test plugin with mechanisms for caching across test runs") (description "The pytest-cache plugin provides tools to rerun failures from the last py.test invocation.") @@ -2000,11 +1966,9 @@ (define-public python-pytest-localserver (lambda _ (invoke "py.test" "-v")))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-requests" ,python-requests) - ("python-six" ,python-six))) + (list python-pytest python-requests python-six)) (propagated-inputs - `(("python-werkzeug" ,python-werkzeug))) + (list python-werkzeug)) (synopsis "Py.test plugin to test server connections locally") (description "Pytest-localserver is a plugin for the pytest testing framework which enables you to test server connections locally.") @@ -2023,10 +1987,9 @@ (define-public python-pytest-xprocess "0rm2rchrr63imn44xk5slwydxf8gvy579524qcxq7dc42pnk17zx")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (propagated-inputs - `(("python-pytest" ,python-pytest) - ("python-psutil" ,python-psutil))) + (list python-pytest python-psutil)) (synopsis "Pytest plugin to manage external processes across test runs") (description "Pytest-xprocess is an experimental py.test plugin for managing processes across test runs.") @@ -2045,7 +2008,7 @@ (define-public python-pytest-subtesthack "15kzcr5pchf3id4ikdvlv752rc0j4d912n589l4rifp8qsj19l1x")))) (build-system python-build-system) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (synopsis "Set-up and tear-down fixtures for unit tests") (description "This plugin allows you to set up and tear down fixtures within unit test functions that use @code{py.test}. This is useful for using @@ -2070,9 +2033,7 @@ (define-public python-pytest-sugar (base32 "1i0hv3h49zvl62jbiyjag84carbrp3zprqzxffdr291nxavvac0n")))) (build-system python-build-system) (propagated-inputs - `(("python-packaging" ,python-packaging) - ("python-pytest" ,python-pytest) - ("python-termcolor" ,python-termcolor))) + (list python-packaging python-pytest python-termcolor)) (home-page "https://pivotfinland.com/pytest-sugar/") (synopsis "Plugin for pytest that changes the default look and feel") (description @@ -2131,8 +2092,8 @@ (define-public python2-hypothesis (base32 "183gpxbfcdhdqzlahkji5a71n6lmvgqsbkcb0ihqad51n2j6jhrw")))) (propagated-inputs - `(("python2-enum34" ,python2-enum34) - ,@(package-propagated-inputs hypothesis)))))) + (modify-inputs (package-propagated-inputs hypothesis) + (prepend python2-enum34)))))) (define-public python-hypothesmith (package @@ -2176,7 +2137,7 @@ (define-public python-lit (lambda _ (invoke "python" "lit.py" "tests")))))) (native-inputs - `(("llvm" ,llvm))) + (list llvm)) (home-page "https://llvm.org/") (synopsis "LLVM Software Testing Tool") (description "@code{lit} is a portable tool for executing LLVM and Clang @@ -2209,9 +2170,9 @@ (define-public python-pytest-pep8 (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v"))))))) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (propagated-inputs - `(("python-pep8" ,python-pep8))) + (list python-pep8)) (home-page "https://bitbucket.org/pytest-dev/pytest-pep8") (synopsis "Py.test plugin to check PEP8 requirements") (description "Pytest plugin for checking PEP8 compliance.") @@ -2242,12 +2203,10 @@ (define-public python-pytest-flakes (add-installed-pythonpath inputs outputs) (invoke "py.test" "-vv" "-k" "not test_syntax_error")))))) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-pytest" ,python-pytest) - ("python-pytest-cache" ,python-pytest-cache) - ("python-pytest-pep8" ,python-pytest-pep8))) + (list python-coverage python-pytest python-pytest-cache + python-pytest-pep8)) (propagated-inputs - `(("python-pyflakes" ,python-pyflakes))) + (list python-pyflakes)) (home-page "https://github.com/fschulze/pytest-flakes") (synopsis "Py.test plugin to check source code with pyflakes") (description "Pytest plugin for checking Python source code with pyflakes.") @@ -2278,7 +2237,7 @@ (define-public python-coverage-test-runner (lambda _ (invoke "./testrun")))))) (propagated-inputs - `(("python-coverage" ,python-coverage))) + (list python-coverage)) (home-page "https://liw.fi/coverage-test-runner/") (synopsis "Python module for running unit tests") (description "@code{CoverageTestRunner} is a python module for running @@ -2304,14 +2263,9 @@ (define-public python-pylint (base32 "15yw69v1cj6zkndk60c2g0dgl0khh8bfm1lrwhjffpdjfc7nkc9a")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-benchmark" ,python-pytest-benchmark) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-pytest python-pytest-benchmark python-pytest-runner)) (propagated-inputs - `(("python-astroid" ,python-astroid) - ("python-isort" ,python-isort) - ("python-mccabe" ,python-mccabe) - ("python-toml" ,python-toml))) + (list python-astroid python-isort python-mccabe python-toml)) (home-page "https://github.com/PyCQA/pylint") (synopsis "Python source code analyzer which looks for coding standard errors") @@ -2416,7 +2370,7 @@ (define-public python-pytest-catchlog "1w7wxh27sbqwm4jgwrjr9c2gy384aca5jzw9c0wzhl0pmk2mvqab")))) (build-system python-build-system) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (propagated-inputs `(("pytest" ,python-pytest))) (home-page "https://github.com/eisensheng/pytest-catchlog") @@ -2441,8 +2395,7 @@ (define-public python-nosexcover "10xqr12qv62k2flxwqhh8cr00cjhn7sfjrm6p35gd1x5bmjkr319")))) (build-system python-build-system) (propagated-inputs - `(("python-coverage" ,python-coverage) - ("python-nose" ,python-nose))) + (list python-coverage python-nose)) (home-page "https://github.com/cmheisel/nose-xcover") (synopsis "Extends nose.plugins.cover to add Cobertura-style XML reports") (description "Nose-xcover is a companion to the built-in @@ -2493,14 +2446,10 @@ (define-public behave "behave-skip-a-couple-of-tests.patch")))) (build-system python-build-system) (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-pathpy" ,python-pathpy) - ("python-pyhamcrest" ,python-pyhamcrest) - ("python-pytest" ,python-pytest))) + (list python-mock python-nose python-pathpy python-pyhamcrest + python-pytest)) (propagated-inputs - `(("python-parse" ,python-parse) - ("python-parse-type" ,python-parse-type))) + (list python-parse python-parse-type)) (arguments '(#:test-target "behave_test")) (home-page "https://github.com/behave/behave") @@ -2535,8 +2484,7 @@ (define-public python-behave-web-api (("'ordereddict==1.1'") "")) ; Python >= 2.7 has it built-in. #t))))) (propagated-inputs - `(("behave" ,behave) - ("python-requests" ,python-requests))) + (list behave python-requests)) (home-page "https://github.com/jefersondaniel/behave-web-api") (synopsis "Provides testing for JSON APIs with Behave for Python") (description "This package provides testing utility modules for testing @@ -2565,11 +2513,9 @@ (define-public python-rednose (("six==1.10.0") "six")) #t))))) (propagated-inputs - `(("python-colorama" ,python-colorama) - ("python-termstyle" ,python-termstyle))) + (list python-colorama python-termstyle)) (native-inputs - `(("python-six" ,python-six) - ("python-nose" ,python-nose))) + (list python-six python-nose)) (home-page "https://github.com/JBKahn/rednose") (synopsis "Colored output for Python nosetests") (description "This package provides colored output for the @@ -2595,7 +2541,7 @@ (define-public python-nose-random "1dvip61r2frjv35mv6mmfjc07402z73pjbndfp3mhxyjn2zhksw2")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (home-page "https://github.com/fzumstein/nose-random") (synopsis "Nose plugin to facilitate randomized unit testing with Python") @@ -2617,8 +2563,7 @@ (define-public python-nose-randomly (base32 "0z662rqhfk4bjmg806mn4frb8nz4gbh7mrddsrhfffp1g4yklj3y")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose) - ("python-numpy" ,python-numpy))) + (list python-nose python-numpy)) (home-page "https://github.com/adamchainz/nose-randomly") (synopsis "Nose plugin to randomly order tests and control random.seed") @@ -2645,8 +2590,7 @@ (define-public python-nose-timer (base32 "05wzkc88vbzw62pqkvhl33211b90kns0lny70b7qw62rcg4flzk4")))) (build-system python-build-system) (propagated-inputs - `(("python-nose" ,python-nose) - ("python-termcolor" ,python-termcolor))) + (list python-nose python-termcolor)) (home-page "https://github.com/mahmoudimus/nose-timer") (synopsis "Timer plugin for nosetests") (description "Shows how much time was needed to run individual tests.") @@ -2667,11 +2611,9 @@ (define-public python-freezegun (base32 "0al75mk829j1izxi760b7yjnknjihyfhp2mvi5qiyrxb9cpxwqk2")))) (build-system python-build-system) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + (list python-mock python-pytest)) (propagated-inputs - `(("python-six" ,python-six) - ("python-dateutil" ,python-dateutil))) + (list python-six python-dateutil)) (arguments `(#:phases (modify-phases %standard-phases @@ -2754,10 +2696,7 @@ (define-public python-pyhamcrest (base32 "05kdzlhs2kvj82pfca13qszszcj6dyrk4b9pbr46x06sq2s4qyls")))) (native-inputs ;all native inputs are for tests - `(("python-pytest-cov" ,python-pytest-cov) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-hypothesis" ,python-hypothesis))) + (list python-pytest-cov python-mock python-pytest python-hypothesis)) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -2840,9 +2779,9 @@ (define-public libfaketime (("/bin/bash") (which "bash")))))) #:test-target "test")) (native-inputs - `(("perl" ,perl))) ;for tests + (list perl)) ;for tests (inputs - `(("coreutils" ,coreutils))) + (list coreutils)) (synopsis "Fake the system time for single applications") (description "The libfaketime library allows users to modify the system time that an @@ -2873,18 +2812,15 @@ (define-public umockdev (("/run") "/tmp")) #t))))) (native-inputs - `(("vala" ,vala) - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("pkg-config" ,pkg-config) - - ;; For tests. - ("python" ,python) - ("which" ,which))) + (list vala + gobject-introspection + gtk-doc/stable + pkg-config + ;; For tests. + python + which)) (inputs - `(("glib" ,glib) - ("eudev" ,eudev) - ("libgudev" ,libgudev))) + (list glib eudev libgudev)) (home-page "https://github.com/martinpitt/umockdev/") (synopsis "Mock hardware devices for creating unit tests") (description "umockdev mocks hardware devices for creating integration @@ -2961,7 +2897,7 @@ (define-public python-pyfakefs "python" "-m" "pytest" "pyfakefs/pytest_tests/pytest_plugin_test.py")))))) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (build-system python-build-system) ;; Guix lint doesn't like that this is a permanent redirect to the GitHub ;; page, but the pyfakefs documentation asks us to use this specific URL @@ -3016,10 +2952,9 @@ (define-public python-aiounittest (invoke "nosetests" "-v") (format #t "test suite not run~%")) #t))))) - (propagated-inputs `(("python-wrapt" ,python-wrapt))) + (propagated-inputs (list python-wrapt)) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-nose" ,python-nose))) + (list python-coverage python-nose)) (home-page "https://github.com/kwarunek/aiounittest") (synopsis "Test asyncio code more easily") @@ -3040,7 +2975,7 @@ (define-public python-pytest-dependency "0swl3mxca7nnjbb5grfzrm3fa2750h9vjsha0f2kyrljc6895a62")))) (build-system python-build-system) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/RKrahl/pytest-dependency") (synopsis "Manage dependencies of tests") @@ -3062,10 +2997,9 @@ (define-public python-pytest-datadir "066bg6wlzgq2pqnjp73dfrcmk8951xw3aqcxa3p1axgqimrixbyk")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (propagated-inputs - `(("python-pytest" ,python-pytest) - ("python-wheel" ,python-wheel))) + (list python-pytest python-wheel)) (home-page "https://github.com/gabrielcnr/pytest-datadir") (synopsis "Pytest plugin for manipulating test data directories and files") (description @@ -3086,19 +3020,17 @@ (define-public python-pytest-regressions "05jpsvv8rj8i4x24fphpnar5dl4s6d6bw6ikjk5d8v96rdviz9qm")))) (build-system python-build-system) (propagated-inputs - `(("python-pytest-datadir" ,python-pytest-datadir) - ("python-pyyaml" ,python-pyyaml))) + (list python-pytest-datadir python-pyyaml)) (native-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pillow" ,python-pillow) - ("python-pre-commit" ,python-pre-commit) - ("python-restructuredtext-lint" - ,python-restructuredtext-lint) - ("python-tox" ,python-tox) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-pytest" ,python-pytest))) + (list python-matplotlib + python-numpy + python-pandas + python-pillow + python-pre-commit + python-restructuredtext-lint + python-tox + python-setuptools-scm + python-pytest)) (home-page "https://github.com/ESSS/pytest-regressions") (synopsis "Easy to use fixtures to write regression tests") (description diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 61b213cd1f..94803719ac 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -70,20 +70,20 @@ (define-public avogadrolibs (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("eigen" ,eigen) - ("mmtf-cpp" ,mmtf-cpp) - ("msgpack" ,msgpack) - ("googletest" ,googletest) - ("pkg-config" ,pkg-config) - ("pybind11" ,pybind11))) + (list eigen + mmtf-cpp + msgpack + googletest + pkg-config + pybind11)) (inputs - `(("glew" ,glew) - ("libarchive" ,libarchive) - ("libmsym" ,libmsym) - ("molequeue" ,molequeue) - ("python" ,python) - ("spglib" ,spglib) - ("qtbase" ,qtbase-5))) + (list glew + libarchive + libmsym + molequeue + python + spglib + qtbase-5)) (arguments '(#:configure-flags (list "-DENABLE_TESTING=ON" (string-append "-DSPGLIB_INCLUDE_DIR=" @@ -113,13 +113,9 @@ (define-public avogadro2 (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("eigen" ,eigen) - ("pkg-config" ,pkg-config))) + (list eigen pkg-config)) (inputs - `(("avogadrolibs" ,avogadrolibs) - ("hdf5" ,hdf5) - ("molequeue" ,molequeue) - ("qtbase" ,qtbase-5))) + (list avogadrolibs hdf5 molequeue qtbase-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments '(#:tests? #f)) @@ -147,7 +143,7 @@ (define-public domainfinder "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr")))) (build-system python-build-system) (inputs - `(("python-mmtk" ,python2-mmtk))) + (list python2-mmtk)) (arguments `(#:python ,python-2 ;; No test suite @@ -303,7 +299,7 @@ (define-public molequeue "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998")))) (build-system cmake-build-system) (inputs - `(("qtbase" ,qtbase-5))) + (list qtbase-5)) (arguments '(#:configure-flags '("-DENABLE_TESTING=ON") #:phases @@ -355,12 +351,10 @@ (define-public nmoldyn "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r")))) (build-system python-build-system) (inputs - `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib)) - ("python-scientific" ,python2-scientific) - ("netcdf" ,netcdf) - ("gv" ,gv))) + (list (with-numpy-1.8 python2-matplotlib) python2-scientific netcdf + gv)) (propagated-inputs - `(("python-mmtk" ,python2-mmtk))) + (list python2-mmtk)) (arguments `(#:python ,python-2 #:tests? #f ; No test suite @@ -416,7 +410,7 @@ (define-public tng "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) (build-system cmake-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (arguments `(#:phases (modify-phases %standard-phases @@ -502,13 +496,13 @@ (define-public gromacs ("python-pygments" ,python-pygments) ("python-sphinx" ,python-sphinx))) (inputs - `(("fftwf" ,fftwf) - ("hwloc" ,hwloc-2 "lib") - ("lmfit" ,lmfit) - ("openblas" ,openblas) - ("perl" ,perl) - ("tinyxml2" ,tinyxml2) - ("tng" ,tng))) + (list fftwf + `(,hwloc-2 "lib") + lmfit + openblas + perl + tinyxml2 + tng)) (home-page "http://www.gromacs.org/") (synopsis "Molecular dynamics software package") (description "GROMACS is a versatile package to perform molecular dynamics, @@ -549,12 +543,9 @@ (define-public openbabel (assoc-ref %build-inputs "inchi") "/include/inchi")) #:test-target "test")) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("eigen" ,eigen) - ("inchi" ,inchi) - ("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list eigen inchi libxml2 zlib)) (home-page "http://openbabel.org/wiki/Main_Page") (synopsis "Chemistry data manipulation toolbox") (description @@ -649,19 +640,18 @@ (define-public python-pymol (string-append "--prefix=" (assoc-ref outputs "out")) "--root=/")))))) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("freeglut" ,freeglut) - ("glew" ,glew) - ("libxml2" ,libxml2) - ("mmtf-cpp" ,mmtf-cpp) - ("msgpack" ,msgpack) - ("python-pyqt" ,python-pyqt) - ("glm" ,glm) - ("netcdf" ,netcdf))) + (list freetype + libpng + freeglut + glew + libxml2 + mmtf-cpp + msgpack + python-pyqt + glm + netcdf)) (native-inputs - `(("catch2" ,catch-framework2) - ("python-setuptools" ,python-setuptools))) + (list catch-framework2 python-setuptools)) (home-page "https://pymol.org") (synopsis "Molecular visualization system") (description "PyMOL is a capable molecular viewer and renderer. It can be diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm index c1591a83ce..aaef513538 100644 --- a/gnu/packages/chez.scm +++ b/gnu/packages/chez.scm @@ -284,7 +284,7 @@ (define-public chez-srfi (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (arguments `(#:make-flags (let ((out (assoc-ref %outputs "out"))) (list (string-append "PREFIX=" out) @@ -481,9 +481,9 @@ (define-public chez-matchable (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("chez-srfi" ,chez-srfi))) ; for tests + (list chez-srfi)) ; for tests (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (arguments `(#:make-flags ,(chez-make-flags name version) #:test-target "test" @@ -510,11 +510,11 @@ (define-public chez-irregex (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("chez-matchable" ,chez-matchable))) ; for tests + (list chez-matchable)) ; for tests (propagated-inputs - `(("chez-srfi" ,chez-srfi))) ; for irregex-utils + (list chez-srfi)) ; for irregex-utils (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (arguments `(#:make-flags ,(chez-make-flags name version) #:test-target "test" @@ -542,9 +542,9 @@ (define-public chez-fmt (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) (propagated-inputs - `(("chez-srfi" ,chez-srfi))) ; for irregex-utils + (list chez-srfi)) ; for irregex-utils (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (arguments `(#:make-flags ,(chez-make-flags name version) #:test-target "chez-check" @@ -582,9 +582,9 @@ (define-public chez-mit (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("chez-srfi" ,chez-srfi))) ; for tests + (list chez-srfi)) ; for tests (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (arguments `(#:make-flags ,(chez-make-flags name version) #:test-target "test" @@ -612,12 +612,11 @@ (define-public chez-scmutils (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("chez-srfi" ,chez-srfi))) ; for tests + (list chez-srfi)) ; for tests (native-inputs - `(("chez-scheme" ,chez-scheme))) + (list chez-scheme)) (propagated-inputs - `(("chez-mit" ,chez-mit) - ("chez-srfi" ,chez-srfi))) + (list chez-mit chez-srfi)) (arguments `(#:make-flags ,(chez-make-flags name version) #:tests? #f ; no test suite diff --git a/gnu/packages/chicken.scm b/gnu/packages/chicken.scm index 866ba8a062..d611c1762e 100644 --- a/gnu/packages/chicken.scm +++ b/gnu/packages/chicken.scm @@ -68,7 +68,7 @@ (define-public chicken (variable "CHICKEN_REPOSITORY_PATH") ;; TODO extract binary version into a module level definition. (files (list "var/lib/chicken/11"))))) - (propagated-inputs `(("gcc-toolchain" ,gcc-toolchain))) + (propagated-inputs (list gcc-toolchain)) (home-page "https://www.call-cc.org/") (synopsis "R5RS Scheme implementation that compiles native code via C") (description @@ -99,7 +99,7 @@ (define-public chicken-srfi-1 (build-system chicken-build-system) (arguments '(#:egg-name "srfi-1")) (inputs - `(("chicken-test" ,chicken-test))) + (list chicken-test)) (home-page "https://wiki.call-cc.org/eggref/5/srfi-1") (synopsis "SRFI-1 list library") (description @@ -182,11 +182,9 @@ (define-public chicken-agrep ;; TODO do we really have to make these propagated? ;; I don't know Chicken's module system well enough to tell (propagated-inputs - `(("chicken-datatype" ,chicken-datatype) - ("chicken-srfi-1" ,chicken-srfi-1) - ("chicken-srfi-14" ,chicken-srfi-14))) + (list chicken-datatype chicken-srfi-1 chicken-srfi-14)) (inputs - `(("chicken-test" ,chicken-test))) + (list chicken-test)) (build-system chicken-build-system) (arguments '(#:egg-name "agrep")) (synopsis "Approximate string matching library") @@ -217,8 +215,7 @@ (define-public chicken-datatype (build-system chicken-build-system) (arguments '(#:egg-name "datatype")) (inputs - `(("chicken-srfi-1" ,chicken-srfi-1) - ("chicken-test" ,chicken-test))) + (list chicken-srfi-1 chicken-test)) (home-page "https://wiki.call-cc.org/eggref/5/datatype") (synopsis "Facility for creating and using variant records") (description @@ -245,7 +242,7 @@ (define-public chicken-iset (base32 "0gz50n5i561n5sk9prry0lrxz6bfrq9if5bclaq6a0f7lzinhnzb")))) (inputs - `(("chicken-test" ,chicken-test))) + (list chicken-test)) (build-system chicken-build-system) (arguments '(#:egg-name "iset")) (synopsis "Integer set library") diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 652722c74a..2fa7260b7f 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -168,28 +168,24 @@ (define-public cuirass `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,objs))) #t)))))) (inputs - `(("guile" ,guile-3.0-latest) - ("guile-avahi" ,guile-avahi) - ("guile-fibers" ,guile-fibers) - ("guile-gcrypt" ,guile-gcrypt) - ("guile-json" ,guile-json-4) - ("guile-simple-zmq" ,guile-simple-zmq) - ("guile-squee" ,guile-squee-dev) - ("guile-git" ,guile-git) - ("guile-zlib" ,guile-zlib) - ("guile-mastodon" ,guile-mastodon) - ("gnutls" ,gnutls) - ("mailutils" ,mailutils) - ;; FIXME: this is propagated by "guile-git", but it needs to be among - ;; the inputs to add it to GUILE_LOAD_PATH. - ("guile-bytestructures" ,guile-bytestructures) - ("guix" ,guix))) + (list guile-3.0-latest + guile-avahi + guile-fibers + guile-gcrypt + guile-json-4 + guile-simple-zmq + guile-squee-dev + guile-git + guile-zlib + guile-mastodon + gnutls + mailutils + ;; FIXME: this is propagated by "guile-git", but it needs to be among + ;; the inputs to add it to GUILE_LOAD_PATH. + guile-bytestructures + guix)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) - ("ephemeralpg" ,ephemeralpg))) + (list autoconf automake pkg-config texinfo ephemeralpg)) (native-search-paths ;; For HTTPS access, Cuirass itself honors these variables, with the ;; same semantics as Git and OpenSSL (respectively). @@ -275,11 +271,7 @@ (define-public laminar #t))))) (inputs - `(("capnproto" ,capnproto) - ("rapidjson" ,rapidjson) - ("sqlite" ,sqlite) - ("boost" ,boost) - ("zlib" ,zlib))) + (list capnproto rapidjson sqlite boost zlib)) (native-inputs `(("googletest" ,googletest) ("uglifyjs" ,node-uglify-js) diff --git a/gnu/packages/clojure.scm b/gnu/packages/clojure.scm index 5b238ab996..f48101079e 100644 --- a/gnu/packages/clojure.scm +++ b/gnu/packages/clojure.scm @@ -207,7 +207,7 @@ (define-public clojure-algo-monads #:test-dirs '("src/test/clojure/") #:doc-dirs '())) (native-inputs - `(("clojure-tools-macro" ,clojure-tools-macro))) + (list clojure-tools-macro)) (synopsis "Monad Macros and Definitions") (description diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 3043760830..d27544e992 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -165,13 +165,9 @@ (define-public keepalived (string-append infodir "/keepalived-figures")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-sphinx" ,python-sphinx) - ("texinfo" ,texinfo))) + (list pkg-config python-sphinx texinfo)) (inputs - `(("openssl" ,openssl) - ("libnfnetlink" ,libnfnetlink) - ("libnl" ,libnl))) + (list openssl libnfnetlink libnl)) (home-page "https://www.keepalived.org/") (synopsis "Load balancing and high-availability frameworks") (description @@ -204,8 +200,7 @@ (define-public libraft ((".*test_uv_append.c.*") "")) #t))))) (inputs - `(("libuv" ,libuv) - ("lz4" ,lz4))) + (list libuv lz4)) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -245,15 +240,11 @@ (define-public libdqlite ;; race condition when tearing down the test server. ((".*test_client.c.*") ""))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("libraft" ,libraft) - ("libuv" ,libuv))) + (list libraft libuv)) (propagated-inputs - `(("sqlite" ,sqlite))) ; dqlite.h includes sqlite3.h + (list sqlite)) ; dqlite.h includes sqlite3.h (build-system gnu-build-system) (synopsis "Distributed SQLite") (description "dqlite is a C library that implements an embeddable and replicated diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm index 3adda91fd3..36f8dcf8ff 100644 --- a/gnu/packages/cmake.scm +++ b/gnu/packages/cmake.scm @@ -83,7 +83,7 @@ (define-public cmake-shared (arguments `(#:tests? #f)) ; No target (native-inputs - `(("extra-cmake-modules" ,extra-cmake-modules))) + (list extra-cmake-modules)) (synopsis "Shared CMake functions and macros") (description "CMake-Shared are shared functions and macros for projects using the CMake build system.") @@ -291,8 +291,8 @@ (define preserved-files ',%preserved-third-party-files) lstat) #t)))) (inputs - `(("jsoncpp" ,jsoncpp) - ,@(package-inputs cmake-bootstrap))) + (modify-inputs (package-inputs cmake-bootstrap) + (prepend jsoncpp))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -373,8 +373,9 @@ (define-public cmake (string-append doc html)) (delete-file-recursively (string-append out html))))))))) (inputs - `(("ncurses" ,ncurses) ;required for ccmake - ,@(package-inputs cmake-minimal))) + (modify-inputs (package-inputs cmake-minimal) + (prepend ncurses ;required for ccmake + ))) ;; Extra inputs required to build the documentation. (native-inputs `(,@(package-native-inputs cmake-minimal) diff --git a/gnu/packages/cobol.scm b/gnu/packages/cobol.scm index 60af9f6a53..9386f3fca2 100644 --- a/gnu/packages/cobol.scm +++ b/gnu/packages/cobol.scm @@ -68,11 +68,7 @@ (define-public gnucobol (base32 "1yb1plmv4firfnbb119r2vh1hay221w1ya34nyz0qwsxppfr56hy")))))) (inputs - `(("bdb" ,bdb) - ("gmp" ,gmp) - ("json-c" ,json-c) - ("libxml2" ,libxml2) - ("ncurses" ,ncurses))) + (list bdb gmp json-c libxml2 ncurses)) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/gnucobol/") (synopsis "A modern COBOL compiler") diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 3720383664..d3ff6ae7c8 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -116,8 +116,7 @@ (define-public complexity "0lr0l9kj2w3jilz9h9y4np9pf9i9ccpy6331lanki2fnz4z8ldvd")))) (build-system gnu-build-system) (native-inputs - `(("texinfo" ,texinfo) - ("autogen" ,autogen))) + (list texinfo autogen)) (home-page "https://www.gnu.org/software/complexity/") (synopsis "Analyze complexity of C functions") (description @@ -256,7 +255,7 @@ (define ref #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))))) - (inputs `(("perl" ,perl))) + (inputs (list perl)) (home-page "https://dwheeler.com/sloccount/") (synopsis "Count physical source lines of code (SLOC)") (description @@ -282,12 +281,12 @@ (define-public cloc (base32 "0ic9q6qqw5f1wafp9lpmhr0miasbdb9zr59c0jlymnzffdmnliyc")))) (build-system gnu-build-system) (inputs - `(("coreutils" ,coreutils) - ("perl" ,perl) - ("perl-algorithm-diff" ,perl-algorithm-diff) - ("perl-digest-md5" ,perl-digest-md5) - ("perl-parallel-forkmanager" ,perl-parallel-forkmanager) - ("perl-regexp-common" ,perl-regexp-common))) + (list coreutils + perl + perl-algorithm-diff + perl-digest-md5 + perl-parallel-forkmanager + perl-regexp-common)) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) ; nothing to configure @@ -340,11 +339,9 @@ (define-public the-silver-searcher ;; https://gcc.gnu.org/gcc-10/porting_to.html. `(#:configure-flags (list "CFLAGS=-fcommon"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("pcre" ,pcre) - ("xz" ,xz) - ("zlib" ,zlib))) + (list pcre xz zlib)) (home-page "https://geoff.greer.fm/ag/") (synopsis "Fast code searching tool") (description @@ -426,16 +423,9 @@ (define-public universal-ctags (substitute* "Tmain/utils.sh" (("/bin/echo") (which "echo")))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("packcc" ,packcc) - ("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list autoconf automake packcc perl pkg-config)) (inputs - `(("jansson" ,jansson) - ("libseccomp" ,libseccomp) - ("libxml2" ,libxml2) - ("libyaml" ,libyaml))) + (list jansson libseccomp libxml2 libyaml)) (home-page "https://ctags.io/") (synopsis "Generate tag files for source code") (description @@ -491,9 +481,8 @@ (define-public withershins #t))))) (home-page "https://github.com/cameronwhite/withershins") (inputs - `(("libiberty" ,libiberty) - ("binutils" ,binutils) ;for libbfd - ("zlib" ,zlib))) + (list libiberty binutils ;for libbfd + zlib)) (synopsis "C++11 library for generating stack traces") (description "Withershins is a simple cross-platform C++11 library for generating @@ -538,9 +527,7 @@ (define-public lcov (wrap-program (string-append out "/bin/geninfo") `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))) #t))))) - (inputs `(("perl" ,perl) - ("perl-io-compress" ,perl-io-compress) - ("perl-json" ,perl-json))) + (inputs (list perl perl-io-compress perl-json)) (home-page "http://ltp.sourceforge.net/coverage/lcov.php") (synopsis "Code coverage tool that enhances GNU gcov") (description "LCOV is an extension of @command{gcov}, a tool part of the @@ -598,13 +585,9 @@ (define-public kcov (("/bin/(bash|sh)" shell) (string-append (assoc-ref inputs "bash") shell))))))))) (inputs - `(("curl" ,curl) - ("elfutils" ,elfutils) - ("libelf" ,libelf) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl elfutils libelf openssl zlib)) (native-inputs - `(("python" ,python))) + (list python)) (home-page "https://github.com/SimonKagstrom/kcov") (synopsis "Code coverage tester for compiled languages, Python and Bash") (description "Kcov is a FreeBSD/Linux/OSX code coverage tester for compiled @@ -649,14 +632,14 @@ (define-public rtags "-DBUILD_TESTING=FALSE") #:tests? #f)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("bash-completion" ,bash-completion) - ("clang" ,clang) - ("llvm" ,llvm) - ("lua" ,lua) - ("rct" ,rct) - ("selene" ,selene))) + (list bash-completion + clang + llvm + lua + rct + selene)) (home-page "https://github.com/Andersbakken/rtags") (synopsis "Indexer for the C language family with Emacs integration") (description @@ -682,8 +665,7 @@ (define-public colormake (base32 "1f9v5s0viq4yc9iv6701h3pv7j21zz1ckl37lpp9hsnliiizv03p")))) (build-system trivial-build-system) (native-inputs - `(("bash" ,bash) - ("perl" ,perl))) + (list bash perl)) (arguments `(#:modules ((guix build utils)) #:builder @@ -738,7 +720,7 @@ (define-public makefile2graph (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("graphviz" ,graphviz))) + (list graphviz)) (home-page "https://github.com/lindenb/makefile2graph") (synopsis "Creates a graph of dependencies from GNU Make") (description @@ -885,8 +867,7 @@ (define-public indent '("config.sub" "config.guess"))) #t))))) (native-inputs - `(("texinfo" ,texinfo) - ("automake" ,automake))) ; For up to date 'config.guess' and 'config.sub'. + (list texinfo automake)) ; For up to date 'config.guess' and 'config.sub'. (synopsis "Code reformatter") (description "Indent is a program that makes source code easier to read by @@ -955,7 +936,7 @@ (define-public cscope (sha256 (base32 "0ngiv4aj3rr35k3q3wjx0y19gh7i1ydqa0cqip6sjwd8fph5ll65")))) (build-system gnu-build-system) - (inputs `(("ncurses" ,ncurses))) + (inputs (list ncurses)) (arguments `(#:configure-flags ;; Specify the correct ncurses directory to prevent incorrect fallback diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 5fe559e294..17f6c276b4 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -169,10 +169,8 @@ (define-public minizip (delete-file (string-append out "/include/minizip/crypt.h")) #t)))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - (propagated-inputs `(("zlib" ,zlib))) + (list autoconf automake libtool)) + (propagated-inputs (list zlib)) (home-page (package-home-page zlib)) (synopsis "Zip Compression library") (description @@ -193,7 +191,7 @@ (define-public fastjar (base32 "0iginbz2m15hcsa3x4y7v3mhk54gr1r7m3ghx0pg4n46vv2snmpi")))) (build-system gnu-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://savannah.nongnu.org/projects/fastjar") (synopsis "Replacement for Sun's 'jar' utility") (description @@ -221,11 +219,9 @@ (define-public libtar (build-system gnu-build-system) (arguments `(#:tests? #f)) ; no "check" target (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (synopsis "C library for manipulating POSIX tar files") (description "libtar is a C library for manipulating POSIX tar files. It handles @@ -466,7 +462,7 @@ (define-public pbzip2 "1rnvgcdixjzbrmcr1nv9b6ccrjfrhryaj7jwz28yxxv6lam3xlcg")))) (build-system gnu-build-system) (inputs - `(("bzip2" ,bzip2))) + (list bzip2)) (arguments `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases @@ -550,7 +546,7 @@ (define-public lhasa (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - `(("tzdata" ,tzdata-for-tests))) + (list tzdata-for-tests)) (home-page "https://fragglet.github.com/lhasa/") (synopsis "LHA archive decompressor") (description "Lhasa is a replacement for the Unix LHA tool, for @@ -600,7 +596,7 @@ (define-public lzop (base32 "0h9gb8q7y54m9mvy3jvsmxf21yx8fc3ylzh418hgbbv0i8mbcwky")))) (build-system gnu-build-system) - (inputs `(("lzo" ,lzo))) + (inputs (list lzo)) (home-page "https://www.lzop.org/") (synopsis "Compress or expand files") (description @@ -696,7 +692,7 @@ (define-public sharutils (string-append "extern " all))))))) (build-system gnu-build-system) (native-inputs - `(("which" ,which))) + (list which)) (arguments `(#:phases (modify-phases %standard-phases @@ -739,7 +735,7 @@ (define-public sfarklib (("/usr/local") (assoc-ref outputs "out"))) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/raboof/sfArkLib") (synopsis "Library for SoundFont decompression") (description @@ -775,8 +771,7 @@ (define-public sfarkxtc (("/usr/local") (assoc-ref outputs "out"))) #t))))) (inputs - `(("zlib" ,zlib) - ("sfarklib" ,sfarklib))) + (list zlib sfarklib)) (home-page "https://github.com/raboof/sfarkxtc") (synopsis "Basic sfArk decompressor") (description "SfArk extractor converts SoundFonts in the compressed legacy @@ -818,9 +813,8 @@ (define-public lz4 (build-system gnu-build-system) (outputs (list "out" "static")) (native-inputs - `(;; For tests. - ("python" ,python) - ("valgrind" ,valgrind))) + (list ;; For tests. + python valgrind)) (arguments `(;; Not designed for parallel testing. ;; See https://github.com/lz4/lz4/issues/957#issuecomment-737419821 @@ -936,10 +930,7 @@ (define-public squashfs-tools-ng `(#:configure-flags (list "--disable-static"))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs `(("libselinux" ,libselinux) @@ -1009,7 +1000,7 @@ (define-public pigz #:make-flags (list ,(string-append "CC=" (cc-for-target))) #:test-target "tests")) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://zlib.net/pigz/") (synopsis "Parallel implementation of gzip") (description @@ -1034,8 +1025,7 @@ (define-public pixz "1ifxr18f2h75gkcrkx8033kwmwmrcgxshpaawyc2n4dzn1p2rqz5")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("libarchive" ,libarchive))) + (list pkg-config libarchive)) (home-page "https://github.com/vasi/pixz") (synopsis "Parallel indexing implementation of LZMA") (description @@ -1081,7 +1071,7 @@ (define-public cabextract (delete-file-recursively dir-name) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("libmspack" ,libmspack) ("libmspack-source" ,(package-source libmspack)))) @@ -1106,17 +1096,15 @@ (define-public libjcat (base32 "18qkyg19r7fxzv93kar5n808n3582ygjmqwa7rnyg5y4b6hnwihl")))) (build-system meson-build-system) (native-inputs - `(("gobject-introspection" ,gobject-introspection) - ("help2man" ,help2man) - ("pkg-config" ,pkg-config))) + (list gobject-introspection help2man pkg-config)) (inputs - `(("git" ,git) - ("glib" ,glib) - ("gnupg" ,gnupg) - ("gnutls" ,gnutls) - ("gpgme" ,gpgme) - ("json-glib" ,json-glib) - ("vala" ,vala))) + (list git + glib + gnupg + gnutls + gpgme + json-glib + vala)) (home-page "https://github.com/hughsie/libjcat") (synopsis "Library for reading and writing Jcat files") (description @@ -1146,8 +1134,7 @@ (define-public xdelta #t)))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (arguments `(#:phases (modify-phases %standard-phases @@ -1182,10 +1169,7 @@ (define-public lrzip '()) ("perl" ,perl))) (inputs - `(("bzip2" ,bzip2) - ("lz4" ,lz4) - ("lzo" ,lzo) - ("zlib" ,zlib))) + (list bzip2 lz4 lzo zlib)) (home-page "http://ck.kolivas.org/apps/lrzip/") (synopsis "Large file compressor with a very high compression ratio") (description "lrzip is a compression utility that uses long-range @@ -1295,8 +1279,7 @@ (define-public snappy-with-clang6 (native-inputs `(("clang" ,clang-toolchain-6))) (inputs - `(("libcxx+libcxxabi" ,libcxx+libcxxabi-6) - ("libcxxabi" ,libcxxabi-6))))) + (list libcxx+libcxxabi-6 libcxxabi-6)))) (define-public p7zip (package @@ -1404,7 +1387,7 @@ (define-public gzstream (install-file "libgzstream.a" lib) (install-file "gzstream.h" include) #t)))))) - (propagated-inputs `(("zlib" ,zlib))) + (propagated-inputs (list zlib)) (home-page "http://www.cs.unc.edu/Research/compgeom/gzstream/") (synopsis "Compressed C++ iostream") (description "gzstream is a small library for providing zlib @@ -1454,7 +1437,7 @@ (define-public zpaq (string-append "PREFIX=" (assoc-ref %outputs "out"))))) (native-inputs - `(("perl" ,perl))) ; for pod2man + (list perl)) ; for pod2man (home-page "http://mattmahoney.net/dc/zpaq.html") (synopsis "Incremental journaling archiver") (description "ZPAQ is a command-line archiver for realistic situations with @@ -1518,7 +1501,7 @@ (define-public unshield (base32 "1k5cw6vnpja8yjlnhx5124xrw9i8s1l539hfdqqrqz3l5gn0bnyd")) (file-name "unshield-the-feeble-files-spanish.zip"))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (arguments `(#:out-of-source? #f #:phases @@ -1710,7 +1693,7 @@ (define-public zip (base32 "0sb3h3067pzf3a7mlxn1hikpcjrsvycjcnj9hl9b1c3ykcgvps7h")))) (build-system gnu-build-system) - (inputs `(("bzip2" ,bzip2))) + (inputs (list bzip2)) (arguments `(#:tests? #f ; no test target #:make-flags (let ((out (assoc-ref %outputs "out"))) @@ -1889,11 +1872,9 @@ (define-public zziplib "0i6bpa2b13z19alm6ig80364dnin1w28cvif18k6wkkb0w3dzp8y")))) (build-system cmake-build-system) (inputs - `(("zlib" ,zlib))) - (native-inputs `(("perl" ,perl) ; for the documentation - ("pkg-config" ,pkg-config) - ("python" ,python) - ("zip" ,zip))) ; to create test files + (list zlib)) + (native-inputs (list perl ; for the documentation + pkg-config python zip)) ; to create test files (synopsis "Library for accessing zip files") (description "ZZipLib is a library based on zlib for accessing zip files.") @@ -1913,8 +1894,7 @@ (define-public libzip (base32 "0zn9vaiwy2izj8cnm8i7c2mbdn38n328grqb8f07x55s4kd3nxph")))) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list perl pkg-config)) (inputs `(("gnutls" ,gnutls) ("liblzma" ,xz) @@ -1954,8 +1934,7 @@ (define-public atool "/bin/file'"))) #t))))) (inputs - `(("perl" ,perl) - ("file" ,file))) + (list perl file)) (home-page "https://www.nongnu.org/atool/") (synopsis "Universal tool to manage file archives of various types") (description "The main command is @command{aunpack} which extracts files @@ -2059,7 +2038,7 @@ (define-public plzip (base32 "19zinpx7hssl6r3vilpvq2s7wha3545xan8b0vcvsxnyipdx3n0l")))) (build-system gnu-build-system) (inputs - `(("lzlib" ,lzlib))) + (list lzlib)) (home-page "https://www.nongnu.org/lzip/plzip.html") (synopsis "Parallel lossless data compressor for the lzip format") (description @@ -2091,10 +2070,8 @@ (define-public innoextract (build-system cmake-build-system) (arguments `(#:tests? #f)) - (inputs `(("boost" ,boost) - ("libiconv" ,libiconv) - ("xz" ,xz))) - (native-inputs `(("pkg-config" ,pkg-config))) + (inputs (list boost libiconv xz)) + (native-inputs (list pkg-config)) (home-page "https://constexpr.org/innoextract/") (synopsis "Tool for extracting Inno Setup installers") (description "innoextract allows extracting Inno Setup installers under @@ -2210,10 +2187,9 @@ (define-public upx (patches (search-patches "upx-CVE-2021-20285.patch")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + (list perl)) (inputs - `(("ucl" ,ucl) - ("zlib" ,zlib))) + (list ucl zlib)) (arguments `(#:make-flags (list "all") @@ -2260,10 +2236,9 @@ (define-public quazip-0 (arguments `(#:tests? #f)) ;no test (native-inputs - `(("doxygen" ,doxygen))) + (list doxygen)) (inputs - `(("qtbase" ,qtbase-5) - ("zlib" ,zlib))) + (list qtbase-5 zlib)) (home-page "https://stachenov.github.io/quazip/index.html") (synopsis "Qt/C++ wrapper for Minizip") (description "QuaZIP is a simple C++ wrapper over Gilles Vollant's @@ -2318,10 +2293,9 @@ (define-public zchunk (string-append (assoc-ref inputs "zstd") "/bin/zstd")))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("zstd" ,zstd))) + (list curl zstd)) (propagated-inputs `(("zstd:lib" ,zstd "lib"))) ;in Requires.private of zck.pc (home-page "https://github.com/zchunk/zchunk") @@ -2378,7 +2352,7 @@ (define-public zutils make-flags)))))) (native-inputs ;; Needed to extract the source tarball and run the test suite. - `(("lzip" ,lzip))) + (list lzip)) (home-page "https://www.nongnu.org/zutils/zutils.html") (synopsis "Utilities that transparently operate on compressed files") (description @@ -2494,8 +2468,8 @@ (define-public xarchiver ("libxslt" ,libxslt) ("pkg-config" ,pkg-config))) (inputs - `(("adwaita-icon-theme" ,adwaita-icon-theme) ; hard-coded theme - ("gtk+" ,gtk+))) + (list adwaita-icon-theme ; hard-coded theme + gtk+)) (home-page "https://github.com/ib/xarchiver") (synopsis "Graphical front-end for archive operations") (description "Xarchiver is a front-end to various command line archiving @@ -2633,7 +2607,7 @@ (define-public libdeflate (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/ebiggers/libdeflate") (synopsis "Library for DEFLATE/zlib/gzip compression and decompression") (description "Libdeflate is a library for fast, whole-buffer DEFLATE-based @@ -2660,9 +2634,9 @@ (define-public tarlz (base32 "1x5dw03lcwfigcv97cg70gkbkfycjmv1012s9lwnl4izvl9235qg")))) (build-system gnu-build-system) (native-inputs - `(("lzip" ,lzip))) + (list lzip)) (inputs - `(("lzlib" ,lzlib))) + (list lzlib)) (home-page "https://www.nongnu.org/lzip/tarlz.html") (synopsis "Combination of the tar archiver and the lzip compressor") (description diff --git a/gnu/packages/compton.scm b/gnu/packages/compton.scm index 2a5f3bff27..290e06478b 100644 --- a/gnu/packages/compton.scm +++ b/gnu/packages/compton.scm @@ -58,25 +58,21 @@ (define-public compton (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("dbus" ,dbus) - ("libconfig" ,libconfig) - ("libx11" ,libx11) - ("libxcomposite" ,libxcomposite) - ("libxdamage" ,libxdamage) - ("libxext" ,libxext) - ("libxfixes" ,libxfixes) - ("libxinerama" ,libxinerama) - ("libxrandr" ,libxrandr) - ("libxrender" ,libxrender) - ("mesa" ,mesa) - ("xprop" ,xprop) - ("xwininfo" ,xwininfo))) + (list dbus + libconfig + libx11 + libxcomposite + libxdamage + libxext + libxfixes + libxinerama + libxrandr + libxrender + mesa + xprop + xwininfo)) (native-inputs - `(("asciidoc" ,asciidoc) - ("libdrm" ,libdrm) - ("pkg-config" ,pkg-config) - ("python" ,python) - ("xorgproto" ,xorgproto))) + (list asciidoc libdrm pkg-config python xorgproto)) (arguments `(#:make-flags (list "CC=gcc" @@ -127,23 +123,21 @@ (define-public picom (file-name (string-append "picom-" version)))) (build-system meson-build-system) (inputs - `(("dbus" ,dbus) - ("libconfig" ,libconfig) - ("libx11" ,libx11) - ("libxext" ,libxext) - ("libev" ,libev) - ("mesa" ,mesa) - ("xprop" ,xprop) - ("xcb-util-renderutil" ,xcb-util-renderutil) - ("xcb-util-image" ,xcb-util-image) - ("pixman" ,pixman) - ("uthash" ,uthash) - ("libxdg-basedir" ,libxdg-basedir) - ("pcre" ,pcre))) + (list dbus + libconfig + libx11 + libxext + libev + mesa + xprop + xcb-util-renderutil + xcb-util-image + pixman + uthash + libxdg-basedir + pcre)) (native-inputs - `(("asciidoc" ,asciidoc) - ("pkg-config" ,pkg-config) - ("xorgproto" ,xorgproto))) + (list asciidoc pkg-config xorgproto)) (arguments `(#:build-type "release" #:configure-flags '("-Dwith_docs=true"))) diff --git a/gnu/packages/configuration-management.scm b/gnu/packages/configuration-management.scm index 9aee13a172..c64b937fe5 100644 --- a/gnu/packages/configuration-management.scm +++ b/gnu/packages/configuration-management.scm @@ -48,56 +48,56 @@ (define-public chezmoi ;; We don't need to install the source code for end-user applications. #:install-source? #f)) (native-inputs - `(("go-github-com-masterminds-sprig" ,go-github-com-masterminds-sprig) - ("go-github-com-masterminds-goutils" ,go-github-com-masterminds-goutils) - ("go-github-com-masterminds-semver" ,go-github-com-masterminds-semver) - ("go-github-com-google-uuid" ,go-github-com-google-uuid) - ("go-github-com-huandu-xstrings" ,go-github-com-huandu-xstrings) - ("go-github-com-imdario-mergo" ,go-github-com-imdario-mergo) - ("go-github-com-mitchellh-reflectwalk" ,go-github-com-mitchellh-reflectwalk) - ("go-github-com-mitchellh-copystructure" ,go-github-com-mitchellh-copystructure) - ("go-github-com-bmatcuk-doublestar" ,go-github-com-bmatcuk-doublestar) - ("go-github-com-charmbracelet-glamour" ,go-github-com-charmbracelet-glamour) - ("go-github-com-alecthomas-chroma" ,go-github-com-alecthomas-chroma) - ("go-github-com-coreos-go-semver" ,go-github-com-coreos-go-semver) - ("go-github-com-danwakefield-fnmatch" ,go-github-com-danwakefield-fnmatch) - ("go-github-com-dlclark-regexp2" ,go-github-com-dlclark-regexp2) - ("go-github-go-git" ,go-github-go-git) - ("go-github-com-google-go-github" ,go-github-com-google-go-github) - ("go-github-com-google-go-querystring" ,go-github-com-google-go-querystring) - ("go-github-com-google-renameio" ,go-github-com-google-renameio) - ("go-github-com-microcosm-cc-bluemonday",go-github-com-microcosm-cc-bluemonday) - ("go-github-com-aymerick-douceur" ,go-github-com-aymerick-douceur) - ("go-github-com-chris-ramon-douceur" ,go-github-com-chris-ramon-douceur) - ("go-github-com-gorilla-css" ,go-github-com-gorilla-css) - ("go-github-com-muesli-reflow-ansi" ,go-github-com-muesli-reflow-ansi) - ("go-github-com-muesli-reflow-wordwrap" ,go-github-com-muesli-reflow-wordwrap) - ("go-github-com-muesli-reflow-indent" ,go-github-com-muesli-reflow-indent) - ("go-github-com-muesli-reflow-padding" ,go-github-com-muesli-reflow-padding) - ("go-github-com-muesli-termenv" ,go-github-com-muesli-termenv) - ("go-github-com-google-goterm" ,go-github-com-google-goterm) - ("go-golang-org-colorful" ,go-golang-org-colorful) - ("go-github-com-mattn-go-isatty" ,go-github-com-mattn-go-isatty) - ("go-github.com-mattn-go-runewidth" ,go-github.com-mattn-go-runewidth) - ("go-github-com-olekukonko-tablewriter" ,go-github-com-olekukonko-tablewriter) - ("go-github-com-pelletier-go-toml" ,go-github-com-pelletier-go-toml) - ("go-github-com-pkg-diff" ,go-github-com-pkg-diff) - ("go-github-com-sergi-go-diff" ,go-github-com-sergi-go-diff) - ("go-github-com-spf13-cobra" ,go-github-com-spf13-cobra) - ("go-github-com-spf13-viper" ,go-github-com-spf13-viper) - ("go-github-com-twpayne-go-shell" ,go-github-com-twpayne-go-shell) - ("go-github-com-twpayne-go-vfs" ,go-github-com-twpayne-go-vfs) - ("go-github-com-twpayne-go-vfsafero" ,go-github-com-twpayne-go-vfsafero) - ("go-github-com-twpayne-go-xdg" ,go-github-com-twpayne-go-xdg) - ("go-github-com-yuin-goldmark" ,go-github-com-yuin-goldmark) - ("go-github-com-zalando-go-keyring" ,go-github-com-zalando-go-keyring) - ("go-github-com-godbus-dbus" ,go-github-com-godbus-dbus) - ("go-etcd-io-bbolt" ,go-etcd-io-bbolt) - ("go-golang-org-x-crypto" ,go-golang-org-x-crypto) - ("go-golang-org-x-net" ,go-golang-org-x-net) - ("go-golang-org-x-oauth2" ,go-golang-org-x-oauth2) - ("go-github-com-rogpeppe-go-internal" ,go-github-com-rogpeppe-go-internal) - ("gopkg-in-errgo-fmt-errors" ,gopkg-in-errgo-fmt-errors))) + (list go-github-com-masterminds-sprig + go-github-com-masterminds-goutils + go-github-com-masterminds-semver + go-github-com-google-uuid + go-github-com-huandu-xstrings + go-github-com-imdario-mergo + go-github-com-mitchellh-reflectwalk + go-github-com-mitchellh-copystructure + go-github-com-bmatcuk-doublestar + go-github-com-charmbracelet-glamour + go-github-com-alecthomas-chroma + go-github-com-coreos-go-semver + go-github-com-danwakefield-fnmatch + go-github-com-dlclark-regexp2 + go-github-go-git + go-github-com-google-go-github + go-github-com-google-go-querystring + go-github-com-google-renameio + go-github-com-microcosm-cc-bluemonday + go-github-com-aymerick-douceur + go-github-com-chris-ramon-douceur + go-github-com-gorilla-css + go-github-com-muesli-reflow-ansi + go-github-com-muesli-reflow-wordwrap + go-github-com-muesli-reflow-indent + go-github-com-muesli-reflow-padding + go-github-com-muesli-termenv + go-github-com-google-goterm + go-golang-org-colorful + go-github-com-mattn-go-isatty + go-github.com-mattn-go-runewidth + go-github-com-olekukonko-tablewriter + go-github-com-pelletier-go-toml + go-github-com-pkg-diff + go-github-com-sergi-go-diff + go-github-com-spf13-cobra + go-github-com-spf13-viper + go-github-com-twpayne-go-shell + go-github-com-twpayne-go-vfs + go-github-com-twpayne-go-vfsafero + go-github-com-twpayne-go-xdg + go-github-com-yuin-goldmark + go-github-com-zalando-go-keyring + go-github-com-godbus-dbus + go-etcd-io-bbolt + go-golang-org-x-crypto + go-golang-org-x-net + go-golang-org-x-oauth2 + go-github-com-rogpeppe-go-internal + gopkg-in-errgo-fmt-errors)) (home-page "https://www.chezmoi.io/") (synopsis "Personal configuration files manager") (description "This package helps to manage personal configuration files diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index ad4d396289..9843cbe3c0 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -74,20 +74,20 @@ (define-public conky (install-file "src/conky" bin)) #t))))) (inputs - `(("freetype" ,freetype) - ("imlib2" ,imlib2) - ("libx11" ,libx11) - ("libxdamage" ,libxdamage) - ("libxext" ,libxext) - ("libxft" ,libxft) - ("libxinerama" ,libxinerama) - ("pulseaudio" ,pulseaudio) - ("lua" ,lua) - ("ncurses" ,ncurses) - ("curl" ,curl) - ("wireless-tools" ,wireless-tools))) + (list freetype + imlib2 + libx11 + libxdamage + libxext + libxft + libxinerama + pulseaudio + lua + ncurses + curl + wireless-tools)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Lightweight system monitor for X") (description "Conky is a lightweight system monitor for X that displays operating diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm index 85536f933b..f2ebfc95eb 100644 --- a/gnu/packages/connman.scm +++ b/gnu/packages/connman.scm @@ -71,22 +71,22 @@ (define-public connman `(("pkg-config" ,pkg-config) ("python" ,python-wrapper))) (inputs - `(("dbus" ,dbus) - ("glib" ,glib) - ("gnutls" ,gnutls) - ("iptables" ,iptables) - ("libmnl" ,libmnl) - ("lz4" ,lz4) ; required by openconnect.pc - ("readline" ,readline) - ;; These inputs are needed for connman to include the interface to - ;; these technologies so IF they are installed they can be used. - ;; TODO: add neard, ofono - ("openconnect" ,openconnect) - ("openvpn" ,openvpn) - ("ppp" ,ppp) - ("vpnc" ,vpnc) - ("wpa-supplicant" ,wpa-supplicant) - ("xl2tpd" ,xl2tpd))) + (list dbus + glib + gnutls + iptables + libmnl + lz4 ; required by openconnect.pc + readline + ;; These inputs are needed for connman to include the interface to + ;; these technologies so IF they are installed they can be used. + ;; TODO: add neard, ofono + openconnect + openvpn + ppp + vpnc + wpa-supplicant + xl2tpd)) (home-page "https://01.org/connman") (synopsis "Connection management daemon") (description "Connman provides a daemon for managing Internet connections. @@ -125,7 +125,7 @@ (define-public econnman (wrap-program bin `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))) #t)))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (inputs `(("efl" ,efl) ("python" ,python-wrapper) @@ -150,9 +150,9 @@ (define-public cmst (sha256 (base32 "0jn12wxwjznady6aniwmvahg1dj25p902sdwj0070biv6vx5c7dq")))) (inputs - `(("qtbase" ,qtbase-5))) + (list qtbase-5)) (native-inputs - `(("qttools" ,qttools))) + (list qttools)) (build-system gnu-build-system) (arguments '(#:phases diff --git a/gnu/packages/convmv.scm b/gnu/packages/convmv.scm index 9e6f141818..a7a5129566 100644 --- a/gnu/packages/convmv.scm +++ b/gnu/packages/convmv.scm @@ -50,7 +50,7 @@ (define-public convmv (patch-shebang "suite/parsable_tester.pl") #t))))) (inputs - `(("perl" ,perl))) + (list perl)) (synopsis "Convert filenames between character sets") (description "convmv is a file renamer, that converts between different encodings, diff --git a/gnu/packages/cook.scm b/gnu/packages/cook.scm index ba13709eda..7a064480d4 100644 --- a/gnu/packages/cook.scm +++ b/gnu/packages/cook.scm @@ -70,17 +70,17 @@ (define-public cook (setenv "SH" (which "sh")) #t))))) - (native-inputs `(("bison" ,bison) - ;; For building the documentation: - ("groff" ,groff) - ;; For the tests: - ("sharutils" ,sharutils) - ;; One test wants rsh. However there is no rsh server - ;; running in the build environment and so far as I'm - ;; aware, it cannot be started without root. - ;; This test is therefore just skipped. - ;; ("inetutils" ,inetutils) - ("ed" ,ed))) + (native-inputs (list bison + ;; For building the documentation: + groff + ;; For the tests: + sharutils + ;; One test wants rsh. However there is no rsh server + ;; running in the build environment and so far as I'm + ;; aware, it cannot be started without root. + ;; This test is therefore just skipped. + ;; ("inetutils" ,inetutils) + ed)) (home-page (string-append "https://web.archive.org/web/20140727122520/" "http://miller.emu.id.au/pmiller/software/cook/")) (synopsis "Tool for constructing files") diff --git a/gnu/packages/coq.scm b/gnu/packages/coq.scm index cf0c67f214..5173726ec2 100644 --- a/gnu/packages/coq.scm +++ b/gnu/packages/coq.scm @@ -78,11 +78,9 @@ (define-public coq-core (separator #f)))) (build-system dune-build-system) (inputs - `(("gmp" ,gmp) - ("ocaml-zarith" ,ocaml-zarith))) + (list gmp ocaml-zarith)) (native-inputs - `(("ocaml-ounit2" ,ocaml-ounit2) - ("which" ,which))) + (list ocaml-ounit2 which)) (arguments `(#:package "coq-core" #:test-target ".")) @@ -105,9 +103,7 @@ (define-public coq-stdlib `(#:package "coq-stdlib" #:test-target ".")) (inputs - `(("coq-core" ,coq-core) - ("gmp" ,gmp) - ("ocaml-zarith" ,ocaml-zarith))) + (list coq-core gmp ocaml-zarith)) (native-inputs '()))) (define-public coq @@ -118,8 +114,7 @@ (define-public coq `(#:package "coq" #:test-target ".")) (propagated-inputs - `(("coq-core" ,coq-core) - ("coq-stdlib" ,coq-stdlib))) + (list coq-core coq-stdlib)) (native-inputs '()))) (define-public coq-ide-server @@ -130,9 +125,7 @@ (define-public coq-ide-server `(#:tests? #f #:package "coqide-server")) (inputs - `(("coq" ,coq) - ("gmp" ,gmp) - ("ocaml-zarith" ,ocaml-zarith))))) + (list coq gmp ocaml-zarith)))) (define-public coq-ide (package @@ -142,8 +135,7 @@ (define-public coq-ide `(#:tests? #f #:package "coqide")) (propagated-inputs - `(("coq" ,coq) - ("coq-ide-server" ,coq-ide-server))) + (list coq coq-ide-server)) (inputs `(("lablgtk3" ,lablgtk3))))) @@ -170,7 +162,7 @@ (define-public proof-general `(("emacs" ,emacs-minimal) ("texinfo" ,texinfo))) (inputs - `(("perl" ,perl))) + (list perl)) (arguments (let ((base-directory "/share/emacs/site-lisp/ProofGeneral")) `(#:tests? #f ; no check target @@ -250,11 +242,7 @@ (define-public coq-flocq "0j7vq7ifqcdaj2x881aha2rl51l2p72y1cn7r2xya0fjgsssfigy")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("ocaml" ,ocaml) - ("which" ,which) - ("coq" ,coq))) + (list autoconf automake ocaml which coq)) (arguments `(#:configure-flags (list (string-append "COQUSERCONTRIB=" (assoc-ref %outputs "out") @@ -301,21 +289,18 @@ (define-public coq-gappa "1ivh8xm1c8191rm4riamjzya2x6ls96qax5byir1fywf9hbxr1vg")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("ocaml" ,ocaml) - ("which" ,which) - ("coq" ,coq) - ("camlp5" ,camlp5) - ("bison" ,bison) - ("flex" ,flex))) + (list autoconf + automake + ocaml + which + coq + camlp5 + bison + flex)) (inputs - `(("gmp" ,gmp) - ("mpfr" ,mpfr) - ("ocaml-zarith" ,ocaml-zarith) - ("boost" ,boost))) + (list gmp mpfr ocaml-zarith boost)) (propagated-inputs - `(("coq-flocq" ,coq-flocq))) + (list coq-flocq)) (arguments `(#:configure-flags (list (string-append "COQUSERCONTRIB=" (assoc-ref %outputs "out") @@ -361,9 +346,7 @@ (define-public coq-mathcomp (base32 "0aj8hsdzzds5w0p1858s2b6k9zssjcxa6kgpi0q1nvaml4zfpkcc")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) - ("which" ,which) - ("coq" ,coq))) + (list ocaml which coq)) (arguments `(#:tests? #f ; No tests. #:make-flags (list (string-append "COQLIBINSTALL=" @@ -401,11 +384,7 @@ (define-public coq-coquelicot "146s5y2xsc7wb43m1pq1n4p14hw99gqbzx0ic3a4naxq16v7cv4w")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("ocaml" ,ocaml) - ("which" ,which) - ("coq" ,coq))) + (list autoconf automake ocaml which coq)) (propagated-inputs `(("mathcomp" ,coq-mathcomp))) (arguments @@ -453,11 +432,9 @@ (define-public coq-bignums "0jsgdvj0ddhkls32krprp34r64y1rb5mwxl34fgaxk2k4664yq06")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) - ("coq" ,coq))) + (list ocaml coq)) (inputs - `(("camlp5" ,camlp5) - ("ocaml-zarith" ,ocaml-zarith))) + (list camlp5 ocaml-zarith)) (arguments `(#:tests? #f ; No test target. #:make-flags @@ -488,11 +465,7 @@ (define-public coq-interval "0sr9psildc0sda07r2r47rfgyry49yklk38bg04yyvry5j5pryb6")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("ocaml" ,ocaml) - ("which" ,which) - ("coq" ,coq))) + (list autoconf automake ocaml which coq)) (propagated-inputs `(("flocq" ,coq-flocq) ("bignums" ,coq-bignums) @@ -549,7 +522,7 @@ (define-public coq-autosubst (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("coq" ,coq))) + (list coq)) (home-page "https://www.ps.uni-saarland.de/autosubst/") (synopsis "Coq library for parallel de Bruijn substitutions") (description "Formalizing syntactic theories with variable binders is @@ -580,11 +553,9 @@ (define-public coq-equations "19bj9nncd1r9g4273h5qx35gs3i4bw5z9bhjni24b413hyj55hkv")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) - ("coq" ,coq) - ("camlp5" ,camlp5))) + (list ocaml coq camlp5)) (inputs - `(("ocaml-zarith" ,ocaml-zarith))) + (list ocaml-zarith)) (arguments `(#:test-target "test-suite" #:make-flags (list (string-append "COQLIBINSTALL=" @@ -625,12 +596,9 @@ (define-public coq-semantics "0ldrp86bfcjpzsb08p45sgs3aczjzr1gksy5dsf7pxapg05pc7ac")))) (build-system gnu-build-system) (native-inputs - `(("coq" ,coq) - ("ocaml" ,ocaml) - ("ocamlbuild" ,ocamlbuild) - ("ocaml-findlib" ,ocaml-findlib))) + (list coq ocaml ocamlbuild ocaml-findlib)) (inputs - `(("ocaml-num" ,ocaml-num))) + (list ocaml-num)) (arguments `(#:tests? #f ;included in Makefile #:make-flags (list (string-append "COQLIBINSTALL=" @@ -670,7 +638,7 @@ (define-public coq-stdpp "1l1w6srzydjg0h3f4krrfgvz455h56shyy2lbcnwdbzjkahibl7v")))) (build-system gnu-build-system) (inputs - `(("coq" ,coq))) + (list coq)) (arguments `(#:tests? #f ; Tests are executed during build phase. #:make-flags (list (string-append "COQLIBINSTALL=" diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 87bf66d1d1..1b6779a036 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -95,11 +95,9 @@ (define-public range-v3 (base32 "18230bg4rq9pmm5f8f65j444jpq56rld4fhmpham8q3vr1c1bdjh")))) (build-system cmake-build-system) (native-inputs - `(("doxygen" ,doxygen) - ("gcc" ,gcc-9) - ("perl" ,perl))) + (list doxygen gcc-9 perl)) (inputs - `(("boost" ,boost))) + (list boost)) (synopsis "Range library for C++14/17/20") (description "Range-v3 is an extension of the Standard Template Library that makes its iterators and algorithms more powerful by making them composable. @@ -140,8 +138,7 @@ (define-public c++-gsl (base32 "0gbvr48f03830g3154bjhw92b8ggmg6wwh5xyb8nppk9v6w752l0")))) (build-system cmake-build-system) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (synopsis "Guidelines Support Library") (description "c++-gsl contains functions and types that are suggested for use by the C++ Core Guidelines maintained by the Standard C++ Foundation.") @@ -164,9 +161,7 @@ (define-public libzen (base32 "1rwaxmid9iv65n0y6xlcyxxydsvihjni9ldxpg6pbqz43amp49xx")))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (build-system gnu-build-system) (arguments '(#:phases @@ -209,7 +204,7 @@ (define-public rttr (substitute* "src/unit_tests/unit_tests.cmake" (("misc/library_test.cpp") "")) #t))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (home-page "https://github.com/rttrorg/rttr/") (synopsis "C++ Reflection Library") (description @@ -240,11 +235,9 @@ (define-public rct '("-DWITH_TESTS=ON" ; To run the test suite "-DRCT_RTTI_ENABLED=ON"))) (native-inputs - `(("cppunit" ,cppunit) - ("pkg-config" ,pkg-config))) + (list cppunit pkg-config)) (inputs - `(("openssl" ,openssl) - ("zlib" ,zlib))) + (list openssl zlib)) (home-page "https://github.com/Andersbakken/rct") (synopsis "C++ library providing Qt-like APIs on top of the STL") (description "Rct is a set of C++ tools that provide nicer (more Qt-like) @@ -267,7 +260,7 @@ (define-public dashel (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (home-page "https://github.com/aseba-community/dashel") (synopsis "Data stream helper encapsulation library") (description @@ -295,7 +288,7 @@ (define-public xsimd `(#:configure-flags (list "-DBUILD_TESTS=ON") #:test-target "xtest")) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://github.com/QuantStack/xsimd") (synopsis "C++ wrappers for SIMD intrinsics and math implementations") (description @@ -359,7 +352,7 @@ (define-public fifo-map (modules '((guix build utils))) (snippet '(delete-file-recursively "./test/thirdparty")))) (native-inputs - `(("catch2" ,catch-framework2-1))) + (list catch-framework2-1)) (build-system cmake-build-system) (arguments `(#:phases @@ -447,7 +440,7 @@ (define-public json-modern-cxx (base32 "0nzsjzlvk14dazwh7k2jb1dinb0pv9jbx5jsyn264wvva0y7daiv"))))))) (inputs - `(("fifo-map" ,fifo-map))) + (list fifo-map)) (synopsis "JSON parser and printer library for C++") (description "JSON for Modern C++ is a C++ JSON library that provides intuitive syntax and trivial integration.") @@ -468,8 +461,7 @@ (define-public xtl "1kd9zl4h6nrsg29hq13vwp4zhfj8sa90vj40726lpw6vxz48k4di")) (file-name (git-file-name name version)))) (native-inputs - `(("googletest" ,googletest) - ("json-modern-cxx" ,json-modern-cxx))) + (list googletest json-modern-cxx)) (arguments `(#:configure-flags '("-DBUILD_TESTS=ON") @@ -504,10 +496,9 @@ (define-public ccls (arguments '(#:tests? #f)) ; no check target (inputs - `(("rapidjson" ,rapidjson))) + (list rapidjson)) (native-inputs - `(("clang" ,clang) - ("llvm" ,llvm))) + (list clang llvm)) (home-page "https://github.com/MaskRay/ccls") (synopsis "C/C++/Objective-C language server") (description @@ -558,11 +549,9 @@ (define-public gperftools ;; https://bugs.gnu.org/46562 '(#:parallel-tests? #f)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ;; For tests. - ("perl" ,perl))) + (list autoconf automake libtool + ;; For tests. + perl)) (home-page "https://github.com/gperftools/gperftools") (synopsis "Multi-threaded malloc() and performance analysis tools for C++") (description @@ -626,11 +615,9 @@ (define-public cpp-httplib (invoke "make")))))))) (native-inputs ;; required to build shared lib - `(("python" ,python))) + (list python)) (inputs - `(("brotli" ,brotli) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list brotli openssl zlib)) (home-page "https://github.com/yhirose/cpp-httplib") (synopsis "C++ HTTP/HTTPS server and client library") (description "cpp-httplib is a C++11 single-file cross platform blocking @@ -663,9 +650,7 @@ (define-public cpplint #t))))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-pytest python-pytest-cov python-pytest-runner)) (home-page "https://github.com/cpplint/cpplint") (synopsis "Static code checker for C++") (description "@code{cpplint} is a command-line tool to check C/C++ files @@ -695,7 +680,7 @@ (define-public reproc ;; Enable building of shared library. #:configure-flags `("-DBUILD_SHARED_LIBS=1"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (synopsis "Process IO library") (description "reproc (Redirected Process) is a C/C++ library that simplifies starting, stopping and communicating with external programs. The @@ -803,7 +788,7 @@ (define-public abseil-cpp-20200923.3 (("check_target\\(gtest_main\\)") "") (("check_target\\(gmock\\)") ""))))))) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://abseil.io") (synopsis "Augmented C++ standard library") (description "Abseil is a collection of C++ library code designed to @@ -893,26 +878,23 @@ (define-public folly ;; Leave tests disabled; see https://github.com/facebook/folly/issues/1456 #:tests? #f)) (propagated-inputs - `(("boost" ,boost) - ("gflags" ,gflags) - ("glog" ,glog) - ("liburing" ,liburing))) + (list boost gflags glog liburing)) (inputs - `(("bzip2" ,bzip2) - ("double-conversion" ,double-conversion) - ("fmt" ,fmt) - ("libaio" ,libaio) - ("libevent" ,libevent) - ("libiberty" ,libiberty) - ("libsodium" ,libsodium) - ("libunwind" ,libunwind) - ("lz4" ,lz4) - ("openssl" ,openssl) - ("snappy" ,snappy) - ("zlib" ,zlib) - ("zstd" ,zstd "lib"))) + (list bzip2 + double-conversion + fmt + libaio + libevent + libiberty + libsodium + libunwind + lz4 + openssl + snappy + zlib + `(,zstd "lib"))) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (synopsis "Collection of C++ components complementing the standard library") (description "Folly (acronymed loosely after Facebook Open Source Library) is a library @@ -949,12 +931,12 @@ (define-public aws-crt-cpp (assoc-ref %build-inputs "aws-c-common")) "-DENABLE_NET_TESTS=OFF"))) (propagated-inputs - `(("aws-c-auth" ,aws-c-auth) - ("aws-c-cal" ,aws-c-cal) - ("aws-c-event-stream" ,aws-c-event-stream) - ("aws-c-http" ,aws-c-http) - ("aws-c-mqtt" ,aws-c-mqtt) - ("aws-c-s3" ,aws-c-s3))) + (list aws-c-auth + aws-c-cal + aws-c-event-stream + aws-c-http + aws-c-mqtt + aws-c-s3)) (synopsis "C++ wrapper for Amazon Web Services C libraries") (description "The AWS Common Runtime (CRT) library provides a C++ wrapper implementation for the following @acronym{AWS,Amazon Web Services} C libraries: @@ -988,12 +970,9 @@ (define-public aws-sdk-cpp (string-append "-DCMAKE_PREFIX_PATH=" (assoc-ref %build-inputs "aws-c-common"))))) (propagated-inputs - `(("aws-crt-cpp" ,aws-crt-cpp))) + (list aws-crt-cpp)) (inputs - `(("curl" ,curl) - ("openssl" ,openssl) - ("pulseaudio" ,pulseaudio) - ("zlib" ,zlib))) + (list curl openssl pulseaudio zlib)) (synopsis "Amazon Web Services SDK for C++") (description "The AWS SDK for C++ provides a C++11 interface to the @acronym{AWS,Amazon @@ -1029,7 +1008,7 @@ (define-public libexpected (lambda _ (invoke "./tests")))))) (native-inputs - `(("catch2" ,catch-framework2))) + (list catch-framework2)) (synopsis "C++11/14/17 std::expected with functional-style extensions") (description "@code{std::expected} is proposed as the preferred way to represent objects which will either have an expected value, or an unexpected @@ -1056,7 +1035,7 @@ (define-public magic-enum "1x47radgsifgz3vn2561mlvf4cq46ii33cpyqf01znm56iirwq89")))) (build-system cmake-build-system) (native-inputs - `(("gcc" ,gcc-9))) + (list gcc-9)) (synopsis "C++17 header only library for compile time reflection of enums") (description "Magic Enum offers static reflection of enums, with conversions to and from strings, iteration and related functionality.") @@ -1102,8 +1081,7 @@ (define-public cli11 (("^ PROPERTIES FOLDER \"Extern\"\\)") "")) #t))))) (native-inputs - `(("doxygen" ,doxygen) - ("googletest" ,googletest))) + (list doxygen googletest)) (synopsis "Command line parser for C++11") (description "CLI11 is a command line parser for C++11 and beyond that provides a rich @@ -1129,7 +1107,7 @@ (define-public caf '(#:configure-flags '("-DCAF_ENABLE_EXAMPLES=OFF"))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (synopsis "C++ implementation of the actor model") (description "The C++ Actor Framework (CAF) offers a high-level C++17 programming environment using the actor model for concurrent, distributed @@ -1186,9 +1164,7 @@ (define-public libconfini (replace 'bootstrap (lambda _ (invoke "sh" "bootstrap" "--noconfigure")))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (home-page "https://madmurphy.github.io/libconfini/html/index.html") (synopsis "INI file parser") (description "@code{libconfini} is an INI file parser library written in @@ -1225,8 +1201,8 @@ (define-public libcutl ;;"--with-external-boost" "--with-external-expat"))) (inputs - `(;;("boost ,boost) - ("expat" ,expat))) + (list ;;("boost ,boost) + expat)) (home-page "https://www.codesynthesis.com/projects/libcutl/") (synopsis "C++ utility library with generic and independent components") (description "libcutl is a C++ utility library. It contains a collection @@ -1271,7 +1247,7 @@ (define-public libxsd-frontend #:include-regexp ("\\.so$"))) args)))))) (native-inputs - `(("build" ,build))) + (list build)) (inputs `(("libcutl" ,libcutl) ("libxerces-c" ,xerces-c))) @@ -1319,9 +1295,9 @@ (define-public cli (string-append "edge_dispatcher::" all))))) (delete 'configure)))) (native-inputs - `(("build" ,build))) + (list build)) (inputs - `(("libcutl" ,libcutl))) + (list libcutl)) (synopsis "C++ Command Line Interface (CLI) definition language") (description "@code{cli} is a domain-specific language (DSL) for defining command line interfaces of C++ programs. It allows you to describe the @@ -1362,16 +1338,13 @@ (define-public xsd ,version))))) (delete 'configure)))) (native-inputs - `(("build" ,build) - ("cli" ,cli))) + (list build cli)) (inputs - `(("libcutl" ,libcutl) - ("libnsl" ,libnsl) - ("libxsd-frontend" ,libxsd-frontend))) + (list libcutl libnsl libxsd-frontend)) (propagated-inputs ;; The code XSD generates requires the following library at run time; ;; propagate it for convenience. - `(("xerces-c" ,xerces-c))) + (list xerces-c)) (synopsis "XML Data Binding for C++") (description "CodeSynthesis XSD (also known as libxsd or xsdcxx) is an XML Schema to C++ data binding compiler. Provided with an XML instance @@ -1415,10 +1388,9 @@ (define-public jsonnet `(#:configure-flags '("-DUSE_SYSTEM_GTEST=ON" "-DUSE_SYSTEM_JSON=ON" "-DBUILD_STATIC_LIBS=OFF"))) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (inputs - `(("json-modern-cxx" ,json-modern-cxx))) + (list json-modern-cxx)) (home-page "https://jsonnet.org/") (synopsis "Data templating language") (description "Jsonnet is a templating language extending JSON diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5efc49f079..0c224379b1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -146,8 +146,7 @@ (define-public r-cachem (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs - `(("r-fastmap" ,r-fastmap) - ("r-rlang" ,r-rlang))) + (list r-fastmap r-rlang)) (home-page "https://cachem.r-lib.org/") (synopsis "Cache R objects with automatic pruning") (description @@ -199,9 +198,9 @@ (define-public r-datawizard (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight))) + (list r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://easystats.github.io/datawizard/") (synopsis "Easy data wrangling") (description @@ -223,8 +222,8 @@ (define-public r-diffobj "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) - (propagated-inputs `(("r-crayon" ,r-crayon))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-crayon)) + (native-inputs (list r-knitr)) (home-page "https://github.com/brodieG/diffobj") (synopsis "Diffs for R objects") (description @@ -266,22 +265,22 @@ (define-public r-googledrive (properties `((upstream-name . "googledrive"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-uuid" ,r-uuid) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cli + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-magrittr + r-pillar + r-purrr + r-rlang + r-tibble + r-uuid + r-vctrs + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://googledrive.tidyverse.org") (synopsis "Interface to Google Drive") (description "This package lets you manage Google Drive files from R.") @@ -301,9 +300,8 @@ (define-public r-ids (properties `((upstream-name . "ids"))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-uuid" ,r-uuid))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-openssl r-uuid)) + (native-inputs (list r-knitr)) (home-page "https://github.com/richfitz/ids") (synopsis "Generate random identifiers") (description @@ -325,20 +323,20 @@ (define-public r-googlesheets4 (properties `((upstream-name . "googlesheets4"))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-cli" ,r-cli) - ("r-curl" ,r-curl) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-googledrive" ,r-googledrive) - ("r-httr" ,r-httr) - ("r-ids" ,r-ids) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-cellranger + r-cli + r-curl + r-gargle + r-glue + r-googledrive + r-httr + r-ids + r-magrittr + r-purrr + r-rematch2 + r-rlang + r-tibble + r-vctrs)) (home-page "https://github.com/tidyverse/googlesheets4") (synopsis "Access Google Sheets using the Sheets API V4") (description @@ -361,13 +359,13 @@ (define-public r-waldo (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-diffobj" ,r-diffobj) - ("r-fansi" ,r-fansi) - ("r-glue" ,r-glue) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-cli + r-diffobj + r-fansi + r-glue + r-rematch2 + r-rlang + r-tibble)) (home-page "https://github.com/r-lib/waldo") (synopsis "Find differences between R objects") (description @@ -391,11 +389,7 @@ (define-public r-rticles (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tinytex" ,r-tinytex) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml))) + (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml)) (home-page "https://github.com/rstudio/rticles") (synopsis "Article formats for R Markdown") (description @@ -415,8 +409,7 @@ (define-public r-benchmarkmedata "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-tibble" ,r-tibble))) + (list r-dplyr r-tibble)) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") (description "This package contains the data set for the crowd-sourced @@ -435,15 +428,15 @@ (define-public r-benchmarkme "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-benchmarkmedata" ,r-benchmarkmedata) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-tibble" ,r-tibble))) + (list r-benchmarkmedata + r-doparallel + r-dplyr + r-foreach + r-httr + r-matrix + r-tibble)) (home-page "https://csgillespie.github.io/benchmarkme/") (synopsis "Crowd-sourced system benchmarks") (description "This package provides functionality to benchmark your CPU @@ -505,11 +498,9 @@ (define-public r-v8 `(("node" ,libnode) ("zlib" ,zlib))) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp))) + (list r-curl r-jsonlite r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://jeroen.cran.dev/V8") (synopsis "Embedded JavaScript and WebAssembly engine for R") (description @@ -531,7 +522,7 @@ (define-public r-dot (properties `((upstream-name . "DOT"))) (build-system r-build-system) (propagated-inputs - `(("r-v8" ,r-v8))) + (list r-v8)) (home-page "http://haghish.com/dot") (synopsis "Render and Export DOT Graphs in R") (description @@ -554,7 +545,7 @@ (define-public r-clipr "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description @@ -574,7 +565,7 @@ (define-public r-zoo "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "http://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally @@ -595,8 +586,7 @@ (define-public r-fontawesome (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-rlang" ,r-rlang))) + (list r-htmltools r-rlang)) (home-page "https://github.com/rstudio/fontawesome") (synopsis "Easily work with Font Awesome icons") (description @@ -645,7 +635,7 @@ (define-public r-fpeek (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii")))) (properties `((upstream-name . "fpeek"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/davidgohel/fpeek") (synopsis "Check text files content at a glance") (description @@ -668,14 +658,14 @@ (define-public r-ggalluvial (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lazyeval" ,r-lazyeval) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + (list r-dplyr + r-ggplot2 + r-lazyeval + r-rlang + r-tidyr + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. @@ -698,22 +688,22 @@ (define-public r-ggpp (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-polynom" ,r-polynom) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-ggplot2 + r-glue + r-gridextra + r-lubridate + r-magrittr + r-mass + r-polynom + r-rlang + r-scales + r-stringr + r-tibble + r-xts + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "https://docs.r4photobiology.info/ggpp/") (synopsis "Grammar extensions to ggplot2") (description @@ -763,22 +753,22 @@ (define-public r-ggpmisc "01dnr2a33zmgi0gjsxlcz4hp68b18xsi8z1lkhgcla5im59qf9xi")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpp" ,r-ggpp) - ("r-lmodel2" ,r-lmodel2) - ("r-lubridate" ,r-lubridate) - ("r-mass" ,r-mass) - ("r-plyr" ,r-plyr) - ("r-polynom" ,r-polynom) - ("r-quantreg" ,r-quantreg) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-splus2r" ,r-splus2r) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-ggplot2 + r-ggpp + r-lmodel2 + r-lubridate + r-mass + r-plyr + r-polynom + r-quantreg + r-rlang + r-scales + r-splus2r + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://www.r4photobiology.info/") (synopsis "Miscellaneous Extensions to @code{ggplot2}") (description "This package provides extensions to @code{ggplot2}, @@ -799,8 +789,7 @@ (define-public r-gprofiler (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcurl" ,r-rcurl))) + (list r-plyr r-rcurl)) (home-page "https://cran.r-project.org/web/packages/gProfileR/") (synopsis "Interface to the g:Profiler toolkit") (description @@ -823,16 +812,16 @@ (define-public r-gprofiler2 (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs - `(("r-crosstalk" ,r-crosstalk) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-jsonlite" ,r-jsonlite) - ("r-plotly" ,r-plotly) - ("r-rcurl" ,r-rcurl) - ("r-tidyr" ,r-tidyr) - ("r-viridislite" ,r-viridislite))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-crosstalk + r-dplyr + r-ggplot2 + r-gridextra + r-jsonlite + r-plotly + r-rcurl + r-tidyr + r-viridislite)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gprofiler2/") (synopsis "Interface to the g:Profiler toolset") (description @@ -870,9 +859,8 @@ (define-public r-oenb (properties `((upstream-name . "oenb"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-xml" ,r-xml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr r-xml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/franzmohr/oenb") (synopsis "Tools for the OeNB Data Web Service") (description @@ -893,13 +881,13 @@ (define-public r-scales (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0")))) (build-system r-build-system) (propagated-inputs - `(("r-farver" ,r-farver) - ("r-labeling" ,r-labeling) - ("r-lifecycle" ,r-lifecycle) - ("r-munsell" ,r-munsell) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-r6" ,r-r6) - ("r-viridislite" ,r-viridislite))) + (list r-farver + r-labeling + r-lifecycle + r-munsell + r-rcolorbrewer + r-r6 + r-viridislite)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description @@ -920,7 +908,7 @@ (define-public r-pacman "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) (build-system r-build-system) (propagated-inputs - `(("r-remotes" ,r-remotes))) + (list r-remotes)) (home-page "https://github.com/trinker/pacman") (synopsis "Package Management Tool") (description "This package provides tools to more conveniently perform @@ -943,9 +931,7 @@ (define-public r-pheatmap "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs - `(("r-gtable" ,r-gtable) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-scales" ,r-scales))) + (list r-gtable r-rcolorbrewer r-scales)) (home-page "https://cran.r-project.org/web/packages/pheatmap") (synopsis "Pretty heatmaps") (description @@ -986,7 +972,7 @@ (define-public r-ecp "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ecp/") (synopsis "Multiple change-point analysis of multivariate data") (description @@ -1011,7 +997,7 @@ (define-public r-ellipsis "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9")))) (build-system r-build-system) (propagated-inputs - `(("r-rlang" ,r-rlang))) + (list r-rlang)) (home-page "https://github.com/hadley/ellipsis") (synopsis "Tools for working with additional arguments") (description @@ -1056,8 +1042,7 @@ (define-public r-matrix-utils (properties `((upstream-name . "Matrix.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-grr" ,r-grr) - ("r-matrix" ,r-matrix))) + (list r-grr r-matrix)) (home-page "https://github.com/cvarrichio/Matrix.utils") (synopsis "Data.frame-Like Operations on Sparse and Dense Matrix Objects") @@ -1079,13 +1064,13 @@ (define-public r-mboost "0yg07fdd1sbjfhhxn1dqgph2vzqyq7l52cdk5iq2a2zy1vh176yg")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-nnls" ,r-nnls) - ("r-partykit" ,r-partykit) - ("r-quadprog" ,r-quadprog) - ("r-stabs" ,r-stabs) - ("r-survival" ,r-survival))) + (list r-lattice + r-matrix + r-nnls + r-partykit + r-quadprog + r-stabs + r-survival)) (home-page "https://github.com/boost-R/mboost") (synopsis "Model-based boosting") (description @@ -1109,10 +1094,9 @@ (define-public r-shadowtext (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/shadowtext/") (synopsis "Shadow text grob and layer") (description "This package implements @code{shadowtextGrob()} for @@ -1158,15 +1142,15 @@ (define-public r-ashr (properties `((upstream-name . "ashr"))) (build-system r-build-system) (propagated-inputs - `(("r-etrunct" ,r-etrunct) - ("r-invgamma" ,r-invgamma) - ("r-matrix" ,r-matrix) - ("r-mixsqp" ,r-mixsqp) - ("r-rcpp" ,r-rcpp) - ("r-squarem" ,r-squarem) - ("r-truncnorm" ,r-truncnorm))) + (list r-etrunct + r-invgamma + r-matrix + r-mixsqp + r-rcpp + r-squarem + r-truncnorm)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stephens999/ashr") (synopsis "Methods for adaptive shrinkage, using empirical bayes") (description "This package implements an empirical Bayes approach for @@ -1185,7 +1169,7 @@ (define-public r-askpass (base32 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) (build-system r-build-system) - (propagated-inputs `(("r-sys" ,r-sys))) + (propagated-inputs (list r-sys)) (home-page "https://github.com/jeroen/askpass") (synopsis "Safe password entry for R") (description @@ -1230,14 +1214,10 @@ (define-public r-vegan "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) ; needed for vignettes - ("gfortran" ,gfortran))) + (list r-knitr ; needed for vignettes + gfortran)) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-permute" ,r-permute))) + (list r-cluster r-lattice r-mass r-mgcv r-permute)) (home-page "https://cran.r-project.org/web/packages/vegan") (synopsis "Functions for community ecology") (description @@ -1260,37 +1240,37 @@ (define-public r-tidyverse "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-dtplyr" ,r-dtplyr) - ("r-forcats" ,r-forcats) - ("r-ggplot2" ,r-ggplot2) - ("r-googledrive" ,r-googledrive) - ("r-googlesheets4" ,r-googlesheets4) - ("r-haven" ,r-haven) - ("r-hms" ,r-hms) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-modelr" ,r-modelr) - ("r-pillar" ,r-pillar) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-reprex" ,r-reprex) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-broom + r-cli + r-crayon + r-dbplyr + r-dplyr + r-dtplyr + r-forcats + r-ggplot2 + r-googledrive + r-googlesheets4 + r-haven + r-hms + r-httr + r-jsonlite + r-lubridate + r-magrittr + r-modelr + r-pillar + r-purrr + r-readr + r-readxl + r-reprex + r-rlang + r-rstudioapi + r-rvest + r-stringr + r-tibble + r-tidyr + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://tidyverse.tidyverse.org") (synopsis "Install and load packages from the \"Tidyverse\"") (description @@ -1312,15 +1292,15 @@ (define-public r-rvest (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9")))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-selectr" ,r-selectr) - ("r-tibble" ,r-tibble) - ("r-xml2" ,r-xml2))) + (list r-httr + r-lifecycle + r-magrittr + r-rlang + r-selectr + r-tibble + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/rvest") (synopsis "Simple web scraping for R") (description @@ -1341,8 +1321,7 @@ (define-public r-selectr (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-r6" ,r-r6))) + (list r-stringr r-r6)) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description @@ -1366,18 +1345,18 @@ (define-public r-reprex "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-clipr" ,r-clipr) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-knitr" ,r-knitr) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-callr + r-cli + r-clipr + r-fs + r-glue + r-knitr + r-rlang + r-rmarkdown + r-rstudioapi + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description @@ -1401,8 +1380,7 @@ (define-public r-reordercluster "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58")))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-rcpp" ,r-rcpp))) + (list r-gplots r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ReorderCluster") (synopsis "Reordering the dendrogram according to the class labels") (description "This package provides tools for performing the leaf reordering @@ -1423,8 +1401,7 @@ (define-public r-callr "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-processx" ,r-processx))) + (list r-r6 r-processx)) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description @@ -1444,10 +1421,7 @@ (define-public r-depmixs4 (base32 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) (propagated-inputs - `(("r-nnet" ,r-nnet) - ("r-nlme" ,r-nlme) - ("r-mass" ,r-mass) - ("r-rsolnp" ,r-rsolnp))) + (list r-nnet r-nlme r-mass r-rsolnp)) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/depmixS4/") (synopsis "Dependent Mixture Models") @@ -1469,10 +1443,7 @@ (define-public r-readxl "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-cellranger r-progress r-rcpp r-tibble)) (home-page "https://readxl.tidyverse.org") (synopsis "Read Excel files") (description @@ -1495,12 +1466,12 @@ (define-public r-model4you "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-partykit" ,r-partykit) - ("r-sandwich" ,r-sandwich) - ("r-survival" ,r-survival))) + (list r-formula + r-ggplot2 + r-gridextra + r-partykit + r-sandwich + r-survival)) (home-page "https://cran.r-project.org/web/packages/model4you/") (synopsis "Stratified and personalised models based on trees and forests") (description @@ -1526,14 +1497,14 @@ (define-public r-modelr "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-broom + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description @@ -1572,7 +1543,7 @@ (define-public r-hiddenmarkov "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") (synopsis "Hidden markov models for R") (description "This package contains functions for the analysis of Discrete @@ -1614,13 +1585,9 @@ (define-public r-httpuv (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))))))) (inputs - `(("libuv" ,libuv) - ("zlib" ,zlib))) + (list libuv zlib)) (propagated-inputs - `(("r-later" ,r-later) - ("r-promises" ,r-promises) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp))) + (list r-later r-promises r-r6 r-rcpp)) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description @@ -1645,7 +1612,7 @@ (define-public r-jsonlite "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description @@ -1671,10 +1638,7 @@ (define-public r-servr "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr")))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-xfun" ,r-xfun))) + (list r-httpuv r-jsonlite r-mime r-xfun)) (home-page "https://github.com/yihui/servr") (synopsis "Simple HTTP server to serve static files or dynamic documents") (description @@ -1718,10 +1682,7 @@ (define-public r-htmltools "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest) - ("r-fastmap" ,r-fastmap) - ("r-rlang" ,r-rlang))) + (list r-base64enc r-digest r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description @@ -1740,11 +1701,9 @@ (define-public r-htmlwidgets "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-yaml" ,r-yaml))) + (list r-htmltools r-jsonlite r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") (synopsis "HTML Widgets for R") (description @@ -1766,15 +1725,15 @@ (define-public r-htmltable (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr))) + (list r-checkmate + r-htmltools + r-htmlwidgets + r-knitr + r-magrittr + r-rstudioapi + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description @@ -1819,8 +1778,7 @@ (define-public r-curl `(("libcurl" ,curl) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description @@ -1909,7 +1867,7 @@ (define-public r-fastghquad (properties `((upstream-name . "fastGHQuad"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/awblocker/fastGHQuad") (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature") (description @@ -1931,16 +1889,16 @@ (define-public r-rstpm2 (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs - `(("r-bbmle" ,r-bbmle) - ("r-bh" ,r-bh) - ("r-desolve" ,r-desolve) - ("r-fastghquad" ,r-fastghquad) - ("r-mgcv" ,r-mgcv) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-bbmle + r-bh + r-desolve + r-fastghquad + r-mgcv + r-rcpp + r-rcpparmadillo + r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://github.com/mclements/rstpm2") (synopsis "Link-based survival models") (description @@ -1996,9 +1954,9 @@ (define-public r-jquerylib (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools))) + (list r-htmltools)) (native-inputs - `(("esbuild" ,esbuild))) + (list esbuild)) (home-page "https://cran.r-project.org/package=jquerylib") (synopsis "Obtain jQuery as an HTML dependency object") (description @@ -2023,12 +1981,8 @@ (define-public r-sass (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) - ("r-htmltools" ,r-htmltools) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-fs r-htmltools r-r6 r-rappdirs r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/sass") (synopsis "Syntactically Awesome Style Sheets (SASS)") (description @@ -2090,11 +2044,7 @@ (define-public r-bslib (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jquerylib" ,r-jquerylib) - ("r-jsonlite" ,r-jsonlite) - ("r-rlang" ,r-rlang) - ("r-sass" ,r-sass))) + (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass)) (native-inputs `(("esbuild" ,esbuild) ("js-bootstrap4-bundle" @@ -2207,31 +2157,28 @@ (define-public r-shiny ("showdown/src/showdown.js" . "showdown/compressed/showdown.js")))))))))) (propagated-inputs - `(("r-bslib" ,r-bslib) - ("r-cachem" ,r-cachem) - ("r-commonmark" ,r-commonmark) - ("r-crayon" ,r-crayon) - ("r-ellipsis" ,r-ellipsis) - ("r-fastmap" ,r-fastmap) - ("r-fontawesome" ,r-fontawesome) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-lifecycle" ,r-lifecycle) - ("r-mime" ,r-mime) - ("r-promises" ,r-promises) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-sourcetools" ,r-sourcetools) - ("r-withr" ,r-withr) - ("r-xtable" ,r-xtable))) + (list r-bslib + r-cachem + r-commonmark + r-crayon + r-ellipsis + r-fastmap + r-fontawesome + r-glue + r-htmltools + r-httpuv + r-jsonlite + r-later + r-lifecycle + r-mime + r-promises + r-r6 + r-rlang + r-sourcetools + r-withr + r-xtable)) (inputs - `(("js-datatables" ,js-datatables) - ("js-selectize" ,js-selectize) - ("js-strftime" ,js-strftime) - ("js-highlight" ,js-highlight))) + (list js-datatables js-selectize js-strftime js-highlight)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("gfortran" ,gfortran) @@ -2307,13 +2254,9 @@ (define-public r-shinytree sources targets)))) #t))))) (propagated-inputs - `(("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-promises" ,r-promises) - ("r-shiny" ,r-shiny) - ("r-stringr" ,r-stringr))) + (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr)) (inputs - `(("js-requirejs" ,js-requirejs))) + (list js-requirejs)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" @@ -2357,11 +2300,9 @@ (define-public r-shinydashboard (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-promises" ,r-promises) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-promises r-shiny)) (native-inputs - `(("esbuild" ,esbuild))) + (list esbuild)) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web @@ -2384,11 +2325,7 @@ (define-public r-shinyfiles (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny) - ("r-tibble" ,r-tibble))) + (list r-fs r-htmltools r-jsonlite r-shiny r-tibble)) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description @@ -2412,7 +2349,7 @@ (define-public r-shinythemes "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) - (propagated-inputs `(("r-shiny" ,r-shiny))) + (propagated-inputs (list r-shiny)) (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description @@ -2469,10 +2406,7 @@ (define-public r-d3r (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-htmltools r-rlang r-tidyr)) (native-inputs `(("esbuild" ,esbuild) ("d3.v3.js" @@ -2540,10 +2474,7 @@ (define-public r-sankeyd3 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs - `(("r-d3r" ,r-d3r) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-shiny" ,r-shiny) - ("r-magrittr" ,r-magrittr))) + (list r-d3r r-htmlwidgets r-shiny r-magrittr)) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description @@ -2588,8 +2519,7 @@ (define-public r-gg-gap (properties `((upstream-name . "gg.gap"))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-ggplot2" ,r-ggplot2))) + (list r-cowplot r-ggplot2)) (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") (synopsis "Define segments on the y-axis for ggplot2") (description @@ -2642,9 +2572,7 @@ (define-public r-tablerdash sources targets)))) #t))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-knitr r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-requirejs" @@ -2686,10 +2614,7 @@ (define-public r-spelling (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs - `(("r-commonmark" ,r-commonmark) - ("r-hunspell" ,r-hunspell) - ("r-knitr" ,r-knitr) - ("r-xml2" ,r-xml2))) + (list r-commonmark r-hunspell r-knitr r-xml2)) (home-page "https://docs.ropensci.org/spelling/") (synopsis "Tools for spell checking in R") (description @@ -2715,10 +2640,7 @@ (define-public r-crosstalk "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) - ("r-r6" ,r-r6))) + (list r-htmltools r-jsonlite r-lazyeval r-r6)) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description @@ -2740,7 +2662,7 @@ (define-public r-rook "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) - (propagated-inputs `(("r-brew" ,r-brew))) + (propagated-inputs (list r-brew)) (home-page "https://cran.r-project.org/web/packages/Rook") (synopsis "Web server interface for R") (description @@ -2765,8 +2687,7 @@ (define-public r-miniui (properties `((upstream-name . "miniUI"))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-shiny)) (home-page "https://cran.r-project.org/web/packages/miniUI/") (synopsis "Shiny UI widgets for small screens") (description @@ -2787,9 +2708,7 @@ (define-public r-feather "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) (build-system r-build-system) (propagated-inputs - `(("r-hms" ,r-hms) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-hms r-rcpp r-tibble)) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar @@ -2827,7 +2746,7 @@ (define-public r-mapproj (base32 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h")))) (build-system r-build-system) - (propagated-inputs `(("r-maps" ,r-maps))) + (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") (synopsis "Map projection in R") (description "This package converts latitude/longitude into projected @@ -2851,8 +2770,7 @@ (define-public r-rgooglemaps (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs - `(("r-png" ,r-png) - ("r-sp" ,r-sp))) + (list r-png r-sp)) (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") (synopsis "Use Google Maps in R") (description "This package serves two purposes: @@ -2876,7 +2794,7 @@ (define-public r-geosphere (base32 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj")))) (build-system r-build-system) - (propagated-inputs `(("r-sp" ,r-sp))) + (propagated-inputs (list r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic @@ -2917,23 +2835,23 @@ (define-public r-ggmap "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) (build-system r-build-system) (propagated-inputs - `(("r-bitops" ,r-bitops) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jpeg" ,r-jpeg) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-purrr" ,r-purrr) - ("r-rgooglemaps" ,r-rgooglemaps) - ("r-rjson" ,r-rjson) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-bitops + r-digest + r-dplyr + r-ggplot2 + r-glue + r-httr + r-jpeg + r-magrittr + r-plyr + r-png + r-purrr + r-rgooglemaps + r-rjson + r-scales + r-stringr + r-tibble + r-tidyr)) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize @@ -2967,18 +2885,18 @@ (define-public r-haven (substitute* "src/Makevars" (("-lz") "-lreadstat"))))))) (inputs - `(("readstat" ,readstat))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-forcats" ,r-forcats) - ("r-hms" ,r-hms) - ("r-rlang" ,r-rlang) - ("r-readr" ,r-readr) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list readstat)) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-cpp11 + r-forcats + r-hms + r-rlang + r-readr + r-tibble + r-tidyselect + r-vctrs)) (home-page "https://haven.tidyverse.org") (synopsis "Import and export SPSS, Stata and SAS files") (description @@ -2998,7 +2916,7 @@ (define-public r-amap "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") (synopsis "Another multidimensional analysis package") (description "This package provides tools for clustering and principal @@ -3018,9 +2936,7 @@ (define-public r-ape "16i9sny7j90zi0k3znfff5lpnj5naxcy1142v73zxslr9g3h3am3")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp))) + (list r-lattice r-nlme r-rcpp)) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -3045,12 +2961,12 @@ (define-public r-abbyyr (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-readr" ,r-readr) - ("r-xml" ,r-xml))) + (list r-curl + r-httr + r-plyr + r-progress + r-readr + r-xml)) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description @@ -3073,7 +2989,7 @@ (define-public r-colorspace (base32 "0fhq2aykdkxh3r90i8aqjyb37p5api3mjd19ch8mzv99q4pcv4dq")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description @@ -3144,7 +3060,7 @@ (define-public r-pastecs "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot))) + (list r-boot)) (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description @@ -3165,12 +3081,12 @@ (define-public r-partykit "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-inum" ,r-inum) - ("r-libcoin" ,r-libcoin) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rpart" ,r-rpart) - ("r-survival" ,r-survival))) + (list r-formula + r-inum + r-libcoin + r-mvtnorm + r-rpart + r-survival)) (home-page "http://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description @@ -3263,14 +3179,14 @@ (define-public r-pkgbuild (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6) - ("r-rprojroot" ,r-rprojroot) - ("r-withr" ,r-withr))) + (list r-callr + r-cli + r-crayon + r-desc + r-prettyunits + r-r6 + r-rprojroot + r-withr)) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description @@ -3292,13 +3208,13 @@ (define-public r-pkgload "0jdkaj5cl0viy0i0hkcm4n2wlg1mfv3camr7f385njfararfanhh")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-cli + r-crayon + r-desc + r-rlang + r-rprojroot + r-rstudioapi + r-withr)) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") (description @@ -3384,8 +3300,7 @@ (define-public r-rcppnumerical "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-rcpp r-rcppeigen)) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis"Numerical computing libraries integration with @code{Rcpp}") (description "This package provides a collection of libraries for numerical @@ -3425,9 +3340,7 @@ (define-public r-bindrcpp "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs - `(("r-bindr" ,r-bindr) - ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp))) + (list r-bindr r-plogr r-rcpp)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description @@ -3471,7 +3384,7 @@ (define-public r-calibrate (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description @@ -3511,7 +3424,7 @@ (define-public r-globaloptions (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description @@ -3532,11 +3445,9 @@ (define-public r-circlize "16rnqlkgzhnm69y70k9fiz8vvwlm5dyng04hlxqvvaxix3wdpfkc")))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-globaloptions" ,r-globaloptions) - ("r-shape" ,r-shape))) + (list r-colorspace r-globaloptions r-shape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/circlize") (synopsis "Circular visualization") (description @@ -3564,9 +3475,9 @@ (define-public r-powerlaw (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs - `(("r-pracma" ,r-pracma))) + (list r-pracma)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description @@ -3611,11 +3522,9 @@ (define-public r-dendextend "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-viridis" ,r-viridis))) + (list r-ggplot2 r-magrittr r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description @@ -3641,13 +3550,11 @@ (define-public r-getoptlong (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs - `(("perl" ,perl))) + (list perl)) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-globaloptions" ,r-globaloptions) - ("r-rjson" ,r-rjson))) + (list r-crayon r-globaloptions r-rjson)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description @@ -3689,7 +3596,7 @@ (define-public r-ff (base32 "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls")))) (build-system r-build-system) - (propagated-inputs `(("r-bit" ,r-bit))) + (propagated-inputs (list r-bit)) (home-page "http://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description @@ -3713,9 +3620,7 @@ (define-public r-ffbase "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (propagated-inputs - `(("r-bit" ,r-bit) - ("r-fastmatch" ,r-fastmatch) - ("r-ff" ,r-ff))) + (list r-bit r-fastmatch r-ff)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description @@ -3754,7 +3659,7 @@ (define-public r-princurve "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/rcannood/princurve") (synopsis "Fit a principal curve in arbitrary dimension") (description "This package provides procedures for fitting a principal @@ -3774,8 +3679,7 @@ (define-public r-reshape "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp))) + (list r-plyr r-rcpp)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description @@ -3795,15 +3699,15 @@ (define-public r-restrserve (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rserve" ,r-rserve) - ("r-uuid" ,r-uuid))) + (list r-checkmate + r-jsonlite + r-mime + r-r6 + r-rcpp + r-rserve + r-uuid)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://restrserve.org") (synopsis "R web API framework") (description @@ -3826,10 +3730,7 @@ (define-public r-progress "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-hms" ,r-hms) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6))) + (list r-crayon r-hms r-prettyunits r-r6)) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description @@ -3853,20 +3754,20 @@ (define-public r-ggally (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs - `(("openssl" ,openssl))) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-forcats" ,r-forcats) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-lifecycle" ,r-lifecycle) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr))) + (list openssl)) + (propagated-inputs + (list r-dplyr + r-forcats + r-ggplot2 + r-gtable + r-lifecycle + r-plyr + r-progress + r-rcolorbrewer + r-reshape + r-rlang + r-scales + r-tidyr)) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -3910,9 +3811,9 @@ (define-public r-sp (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description @@ -3981,9 +3882,9 @@ (define-public r-rmpi (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs - `(("openmpi" ,openmpi))) + (list openmpi)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description @@ -4005,8 +3906,7 @@ (define-public r-lmoments (properties `((upstream-name . "Lmoments"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "http://www.tilastotiede.fi/juha_karvanen.html") (synopsis "L-moments and quantile mixtures") (description @@ -4070,8 +3970,7 @@ (define-public r-extremes (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs - `(("r-distillery" ,r-distillery) - ("r-lmoments" ,r-lmoments))) + (list r-distillery r-lmoments)) (home-page "https://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") (description @@ -4093,9 +3992,9 @@ (define-public r-lmtest "126l0y7j2iy6g1w4zii1qkfcjq6wrnc3w2li0bz376smpryddy3i")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/lmtest") (synopsis "Testing linear regression models") (description @@ -4157,7 +4056,7 @@ (define-public r-inum "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) (build-system r-build-system) (propagated-inputs - `(("r-libcoin" ,r-libcoin))) + (list r-libcoin)) (home-page "https://cran.r-project.org/web/packages/inum/") (synopsis "Interval and enum-type representation of vectors") (description @@ -4217,14 +4116,14 @@ (define-public r-bbmle "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81")))) (build-system r-build-system) (propagated-inputs - `(("r-bdsmatrix" ,r-bdsmatrix) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv))) + (list r-bdsmatrix + r-lattice + r-mass + r-matrix + r-mvtnorm + r-numderiv)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description @@ -4247,11 +4146,7 @@ (define-public r-emdbook "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) (build-system r-build-system) (propagated-inputs - `(("r-bbmle" ,r-bbmle) - ("r-coda" ,r-coda) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-plyr" ,r-plyr))) + (list r-bbmle r-coda r-lattice r-mass r-plyr)) (home-page "http://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description @@ -4297,10 +4192,8 @@ (define-public r-limsolve (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-mass" ,r-mass) - ("r-quadprog" ,r-quadprog))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-lpsolve r-mass r-quadprog)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description @@ -4330,10 +4223,9 @@ (define-public r-fitdistrplus "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-survival" ,r-survival))) + (list r-mass r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description @@ -4360,9 +4252,7 @@ (define-public r-energy "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-gsl" ,r-gsl) - ("r-rcpp" ,r-rcpp))) + (list r-boot r-gsl r-rcpp)) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description @@ -4415,7 +4305,7 @@ (define-public r-ksamples (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs - `(("r-suppdists" ,r-suppdists))) + (list r-suppdists)) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description @@ -4443,8 +4333,7 @@ (define-public r-cvst (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs - `(("r-kernlab" ,r-kernlab) - ("r-matrix" ,r-matrix))) + (list r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description @@ -4496,7 +4385,7 @@ (define-public r-progressr (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest))) + (list r-digest)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description @@ -4521,13 +4410,9 @@ (define-public r-lava "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) (build-system r-build-system) (propagated-inputs - `(("r-future-apply" ,r-future-apply) - ("r-numderiv" ,r-numderiv) - ("r-progressr" ,r-progressr) - ("r-squarem" ,r-squarem) - ("r-survival" ,r-survival))) + (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description @@ -4549,9 +4434,7 @@ (define-public r-drr (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs - `(("r-cvst" ,r-cvst) - ("r-kernlab" ,r-kernlab) - ("r-matrix" ,r-matrix))) + (list r-cvst r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/DRR") (synopsis "Dimensionality reduction via regression") (description @@ -4572,10 +4455,7 @@ (define-public r-prodlim "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-lava" ,r-lava) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival))) + (list r-kernsmooth r-lava r-rcpp r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description @@ -4598,8 +4478,7 @@ (define-public r-dimred (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs - `(("r-drr" ,r-drr) - ("r-magrittr" ,r-magrittr))) + (list r-drr r-magrittr)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -4642,7 +4521,7 @@ (define-public r-magic "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind))) + (list r-abind)) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description @@ -4669,7 +4548,7 @@ (define-public r-rmysql `(("mariadb-dev" ,mariadb "dev") ("zlib" ,zlib))) (propagated-inputs - `(("r-dbi" ,r-dbi))) + (list r-dbi)) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description @@ -4693,9 +4572,9 @@ (define-public r-rpostgresql (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs - `(("postgresql" ,postgresql))) + (list postgresql)) (propagated-inputs - `(("r-dbi" ,r-dbi))) + (list r-dbi)) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description @@ -4717,7 +4596,7 @@ (define-public r-linprog (base32 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) (build-system r-build-system) - (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) + (propagated-inputs (list r-lpsolve)) (home-page "http://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description @@ -4738,11 +4617,7 @@ (define-public r-geometry "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) (build-system r-build-system) (propagated-inputs - `(("r-magic" ,r-magic) - ("r-linprog" ,r-linprog) - ("r-lpsolve" ,r-lpsolve) - ("r-rcpp" ,r-rcpp) - ("r-rcppprogress" ,r-rcppprogress))) + (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description @@ -4773,15 +4648,15 @@ (define-public r-ddalpha "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-class" ,r-class) - ("r-geometry" ,r-geometry) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-robustbase" ,r-robustbase) - ("r-sfsmisc" ,r-sfsmisc))) + (list r-bh + r-class + r-geometry + r-mass + r-rcpp + r-robustbase + r-sfsmisc)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ddalpha") (synopsis "Depth-Based classification and calculation of data depth") (description @@ -4828,7 +4703,7 @@ (define-public r-rcpproll (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description @@ -4851,12 +4726,12 @@ (define-public r-ipred "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn")))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-prodlim" ,r-prodlim) - ("r-rpart" ,r-rpart) - ("r-survival" ,r-survival))) + (list r-class + r-mass + r-nnet + r-prodlim + r-rpart + r-survival)) (home-page "https://cran.r-project.org/web/packages/ipred") (synopsis "Improved predictors") (description @@ -4878,11 +4753,9 @@ (define-public r-psych "032h33i2qlwsw2iq82nri5y8hs7d593w40aghcvnibpi2wxf0x8l")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mnormt" ,r-mnormt) - ("r-nlme" ,r-nlme))) + (list r-lattice r-mnormt r-nlme)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description @@ -4933,19 +4806,19 @@ (define-public r-broom "0ks64xwkaqh5cinq8j56d89rn9kipm7cdipsgqmz9xxy7ajxb7qj")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-backports + r-dplyr + r-ellipsis + r-generics + r-ggplot2 + r-glue + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description @@ -4972,26 +4845,26 @@ (define-public r-recipes "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-gower" ,r-gower) - ("r-ipred" ,r-ipred) - ("r-lifecycle" ,r-lifecycle) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-timedate" ,r-timedate) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-ellipsis + r-generics + r-glue + r-gower + r-ipred + r-lifecycle + r-lubridate + r-magrittr + r-matrix + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-timedate + r-vctrs + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description @@ -5040,12 +4913,9 @@ (define-public r-ggrepel "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-rcpp r-rlang r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description @@ -5067,7 +4937,7 @@ (define-public r-corrplot "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description @@ -5113,7 +4983,7 @@ (define-public r-ucminf (base32 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description @@ -5138,14 +5008,14 @@ (define-public r-useful (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-scales" ,r-scales))) + (list r-assertthat + r-dplyr + r-ggplot2 + r-magrittr + r-matrix + r-plyr + r-purrr + r-scales)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been @@ -5168,10 +5038,7 @@ (define-public r-ordinal "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-numderiv" ,r-numderiv) - ("r-ucminf" ,r-ucminf))) + (list r-mass r-matrix r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description @@ -5195,10 +5062,7 @@ (define-public r-jomo "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir")))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-ordinal" ,r-ordinal) - ("r-survival" ,r-survival))) + (list r-lme4 r-mass r-ordinal r-survival)) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description @@ -5222,7 +5086,7 @@ (define-public r-pan (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description @@ -5243,11 +5107,9 @@ (define-public r-mitml "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) (build-system r-build-system) (propagated-inputs - `(("r-haven" ,r-haven) - ("r-jomo" ,r-jomo) - ("r-pan" ,r-pan))) + (list r-haven r-jomo r-pan)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description @@ -5270,14 +5132,14 @@ (define-public r-mice "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cpp11" ,r-cpp11) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-lattice" ,r-lattice) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-cpp11 + r-dplyr + r-generics + r-lattice + r-rcpp + r-rlang + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description @@ -5329,7 +5191,7 @@ (define-public r-rsolnp (properties `((upstream-name . "Rsolnp"))) (build-system r-build-system) (propagated-inputs - `(("r-truncnorm" ,r-truncnorm))) + (list r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented @@ -5352,9 +5214,7 @@ (define-public r-hardyweinberg (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs - `(("r-mice" ,r-mice) - ("r-rcpp" ,r-rcpp) - ("r-rsolnp" ,r-rsolnp))) + (list r-mice r-rcpp r-rsolnp)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description @@ -5382,7 +5242,7 @@ (define-public r-sm (base32 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description @@ -5405,7 +5265,7 @@ (define-public r-venndiagram (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger))) + (list r-futile-logger)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description @@ -5428,10 +5288,9 @@ (define-public r-vioplot "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) (build-system r-build-system) (propagated-inputs - `(("r-sm" ,r-sm) - ("r-zoo" ,r-zoo))) + (list r-sm r-zoo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description @@ -5456,7 +5315,7 @@ (define-public r-rsofia (properties `((upstream-name . "RSofia"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a @@ -5476,7 +5335,7 @@ (define-public r-xts (base32 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) - (propagated-inputs `(("r-zoo" ,r-zoo))) + (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description @@ -5501,9 +5360,7 @@ (define-public r-performanceanalytics `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-quadprog r-xts r-zoo)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for @@ -5529,8 +5386,7 @@ (define-public r-laeken "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mass" ,r-mass))) + (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators @@ -5551,9 +5407,7 @@ (define-public r-vcd "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55")))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass))) + (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, @@ -5576,20 +5430,20 @@ (define-public r-vcfr "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-memuse" ,r-memuse) - ("r-pinfsc50" ,r-pinfsc50) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vegan" ,r-vegan) - ("r-viridislite" ,r-viridislite))) + (list r-ape + r-dplyr + r-magrittr + r-memuse + r-pinfsc50 + r-rcpp + r-stringr + r-tibble + r-vegan + r-viridislite)) (home-page "https://github.com/knausb/vcfR") (synopsis "Manipulate and visualize VCF data") (description "This package facilitates easy manipulation of variant call @@ -5634,7 +5488,7 @@ (define-public r-dtw (base32 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z")))) (build-system r-build-system) - (propagated-inputs `(("r-proxy" ,r-proxy))) + (propagated-inputs (list r-proxy)) (home-page "http://dtw.r-forge.r-project.org/") (synopsis "Dynamic Time Warping Algorithms") (description "This package provides a comprehensive implementation of @@ -5658,7 +5512,7 @@ (define-public r-sdmtools "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) - (propagated-inputs `(("r-r-utils" ,r-r-utils))) + (propagated-inputs (list r-r-utils)) (home-page "https://www.rforge.net/SDMTools/") (synopsis "Species distribution modelling tools") (description "This package provides a set of tools for post processing @@ -5700,12 +5554,9 @@ (define-public r-ggridges "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales) - ("r-withr" ,r-withr))) + (list r-ggplot2 r-plyr r-scales r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -5727,8 +5578,7 @@ (define-public r-ggjoy "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges))) + (list r-ggplot2 r-ggridges)) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in @@ -5749,7 +5599,7 @@ (define-public r-cli "04ff3bgsahi736s8l6a26zlwwil8jw4shx7bb56ah1pp1f1n22n7")))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue))) + (list r-glue)) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build @@ -5790,7 +5640,7 @@ (define-public r-debugme (base32 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) (build-system r-build-system) - (propagated-inputs `(("r-crayon" ,r-crayon))) + (propagated-inputs (list r-crayon)) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description @@ -5810,8 +5660,7 @@ (define-public r-processx (base32 "0azw8sx6nv6pp8m8jrwq01b9na2swrnznn7dwrhn07268w82svzd")))) (build-system r-build-system) (propagated-inputs - `(("r-ps" ,r-ps) - ("r-r6" ,r-r6))) + (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -5837,7 +5686,7 @@ (define-public r-tsp "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) - (propagated-inputs `(("r-foreach" ,r-foreach))) + (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some @@ -5857,7 +5706,7 @@ (define-public r-qap (base32 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic @@ -5877,7 +5726,7 @@ (define-public r-gclus (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) - (propagated-inputs `(("r-cluster" ,r-cluster))) + (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and @@ -5899,9 +5748,7 @@ (define-public r-webshot "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr))) + (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description @@ -5924,14 +5771,14 @@ (define-public r-seriation "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-colorspace" ,r-colorspace) - ("r-gclus" ,r-gclus) - ("r-mass" ,r-mass) - ("r-qap" ,r-qap) - ("r-registry" ,r-registry) - ("r-tsp" ,r-tsp))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster + r-colorspace + r-gclus + r-mass + r-qap + r-registry + r-tsp)) + (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description @@ -5978,8 +5825,7 @@ (define-public r-utf8 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) ; for vignettes + (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -6022,11 +5868,9 @@ (define-public r-vctrs "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang))) + (list r-ellipsis r-glue r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description @@ -6060,16 +5904,16 @@ (define-public r-pillar "17m13rzgwdddwa0n3gpmax6wmfaphbg71l13ffhw5vnxf6i94fh3")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-ellipsis" ,r-ellipsis) - ("r-fansi" ,r-fansi) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-utf8" ,r-utf8) - ("r-vctrs" ,r-vctrs))) + (list r-cli + r-crayon + r-ellipsis + r-fansi + r-lifecycle + r-rlang + r-utf8 + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description @@ -6129,7 +5973,7 @@ (define-public r-tinytex "04ng34kfds2isz4j9ch1xlii0dfclqay9fsc6wvr6sfifzv9fqyk")))) (build-system r-build-system) (propagated-inputs - `(("r-xfun" ,r-xfun))) + (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description @@ -6188,9 +6032,7 @@ (define-public r-network "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w")))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-statnet-common" ,r-statnet-common) - ("r-tibble" ,r-tibble))) + (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description @@ -6212,7 +6054,7 @@ (define-public r-stabs "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description @@ -6261,7 +6103,7 @@ (define-public r-statnet-common `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda))) + (list r-coda)) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the @@ -6281,9 +6123,7 @@ (define-public r-statcheck "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-ggplot2 r-plyr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical @@ -6305,8 +6145,7 @@ (define-public r-sna "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s")))) (build-system r-build-system) (propagated-inputs - `(("r-network" ,r-network) - ("r-statnet-common" ,r-statnet-common))) + (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description @@ -6330,9 +6169,7 @@ (define-public r-tfisher (properties `((upstream-name . "TFisher"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sn" ,r-sn))) + (list r-matrix r-mvtnorm r-sn)) (home-page "https://cran.r-project.org/web/packages/TFisher/") (synopsis "Optimal thresholding Fisher's p-value combination method") (description @@ -6359,9 +6196,7 @@ (define-public r-ttr (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-curl r-xts r-zoo)) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description @@ -6381,7 +6216,7 @@ (define-public r-leaps (base32 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description @@ -6423,8 +6258,7 @@ (define-public r-ifultools "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-splus2r" ,r-splus2r))) + (list r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and @@ -6444,8 +6278,7 @@ (define-public r-sapa "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-splus2r" ,r-splus2r))) + (list r-ifultools r-splus2r)) (home-page "https://cran.r-project.org/web/packages/sapa/") (synopsis "Spectral analysis for physical applications") (description "This package provides software for the book Spectral @@ -6486,10 +6319,7 @@ (define-public r-quantmod "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-ttr" ,r-ttr) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-curl r-ttr r-xts r-zoo)) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling @@ -6510,11 +6340,9 @@ (define-public r-tseries "1fhldj95d16cwygw8xg0kvr4xk569mpzprdvahlsf4hzykc2dgs5")))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog) - ("r-quantmod" ,r-quantmod) - ("r-zoo" ,r-zoo))) + (list r-quadprog r-quantmod r-zoo)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description @@ -6535,9 +6363,7 @@ (define-public r-wmtsa "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-mass" ,r-mass) - ("r-splus2r" ,r-splus2r))) + (list r-ifultools r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description @@ -6560,10 +6386,7 @@ (define-public r-tsa (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs - `(("r-leaps" ,r-leaps) - ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv) - ("r-tseries" ,r-tseries))) + (list r-leaps r-locfit r-mgcv r-tseries)) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description @@ -6586,7 +6409,7 @@ (define-public r-extradistr (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description @@ -6608,12 +6431,12 @@ (define-public r-fractal "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-mass" ,r-mass) - ("r-sapa" ,r-sapa) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-splus2r" ,r-splus2r) - ("r-wmtsa" ,r-wmtsa))) + (list r-ifultools + r-mass + r-sapa + r-scatterplot3d + r-splus2r + r-wmtsa)) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description @@ -6633,8 +6456,8 @@ (define-public r-urca (base32 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) (build-system r-build-system) - (propagated-inputs `(("r-nlme" ,r-nlme))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-nlme)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description @@ -6655,9 +6478,9 @@ (define-public r-cubature "0kk9lw3s66h0sayza3in8rdj7bmgqn4v5lfckhslarpvj2fxsnv0")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description @@ -6682,9 +6505,9 @@ (define-public r-trend "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs")))) (build-system r-build-system) (propagated-inputs - `(("r-extradistr" ,r-extradistr))) + (list r-extradistr)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description @@ -6712,8 +6535,8 @@ (define-public r-expm (base32 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) (build-system r-build-system) - (propagated-inputs `(("r-matrix" ,r-matrix))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-matrix)) + (native-inputs (list gfortran)) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description @@ -6734,8 +6557,7 @@ (define-public r-complexplus "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs - `(("r-expm" ,r-expm) - ("r-matrix" ,r-matrix))) + (list r-expm r-matrix)) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description @@ -6778,10 +6600,7 @@ (define-public r-np "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-cubature" ,r-cubature) - ("r-quadprog" ,r-quadprog) - ("r-quantreg" ,r-quantreg))) + (list r-boot r-cubature r-quadprog r-quantreg)) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) @@ -6803,11 +6622,7 @@ (define-public r-powerplus "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs - `(("r-complexplus" ,r-complexplus) - ("r-expm" ,r-expm) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-phontools" ,r-phontools))) + (list r-complexplus r-expm r-mass r-matrix r-phontools)) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description @@ -6829,9 +6644,7 @@ (define-public r-egg (properties `((upstream-name . "egg"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable))) + (list r-ggplot2 r-gridextra r-gtable)) (home-page "https://cran.r-project.org/web/packages/egg") (synopsis "Extensions for ggplot2") (description @@ -6855,9 +6668,9 @@ (define-public r-heatmap3 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) (build-system r-build-system) (propagated-inputs - `(("r-fastcluster" ,r-fastcluster))) + (list r-fastcluster)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/heatmap3/") (synopsis "Improved heatmap package") (description @@ -6879,22 +6692,22 @@ (define-public r-heatmaply "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-colorspace" ,r-colorspace) - ("r-dendextend" ,r-dendextend) - ("r-egg" ,r-egg) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-seriation" ,r-seriation) - ("r-viridis" ,r-viridis) - ("r-webshot" ,r-webshot))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-colorspace + r-dendextend + r-egg + r-ggplot2 + r-htmlwidgets + r-magrittr + r-plotly + r-rcolorbrewer + r-reshape2 + r-scales + r-seriation + r-viridis + r-webshot)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description @@ -6922,12 +6735,11 @@ (define-public r-h5 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib) - ("hdf5" ,hdf5))) + (list zlib hdf5)) (native-inputs - `(("which" ,which))) + (list which)) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description @@ -6952,9 +6764,7 @@ (define-public r-cgdsr "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo))) + (list r-httr r-r-methodss3 r-r-oo)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description @@ -6976,7 +6786,7 @@ (define-public r-import "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description @@ -7003,8 +6813,7 @@ (define-public r-shinyace (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny) - ("r-jsonlite" ,r-jsonlite))) + (list r-shiny r-jsonlite)) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description @@ -7026,7 +6835,7 @@ (define-public r-randomizr (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description @@ -7047,7 +6856,7 @@ (define-public r-base64url "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports))) + (list r-backports)) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description @@ -7081,38 +6890,38 @@ (define-public r-radiant-data (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-broom" ,r-broom) - ("r-car" ,r-car) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-glue" ,r-glue) - ("r-ggplot2" ,r-ggplot2) - ("r-import" ,r-import) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-markdown" ,r-markdown) - ("r-mass" ,r-mass) - ("r-patchwork" ,r-patchwork) - ("r-plotly" ,r-plotly) - ("r-psych" ,r-psych) - ("r-randomizr" ,r-randomizr) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles) - ("r-shinyace" ,r-shinyace) - ("r-stringi" ,r-stringi) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-writexl" ,r-writexl))) + (list r-base64enc + r-broom + r-car + r-curl + r-dplyr + r-dt + r-glue + r-ggplot2 + r-import + r-jsonlite + r-knitr + r-lubridate + r-magrittr + r-markdown + r-mass + r-patchwork + r-plotly + r-psych + r-randomizr + r-readr + r-readxl + r-rlang + r-rmarkdown + r-rstudioapi + r-scales + r-shiny + r-shinyfiles + r-shinyace + r-stringi + r-tibble + r-tidyr + r-writexl)) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description @@ -7156,7 +6965,7 @@ (define-public r-alluvial (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) (properties `((upstream-name . "alluvial"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/mbojan/alluvial") (synopsis "Create parallel sets plots (Alluvial Diagrams)") (description @@ -7176,8 +6985,8 @@ (define-public r-signal (base32 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-mass)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description @@ -7199,7 +7008,7 @@ (define-public r-gsubfn (base32 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) - (propagated-inputs `(("r-proto" ,r-proto))) + (propagated-inputs (list r-proto)) (home-page "https://code.google.com/archive/p/gsubfn/") (synopsis "Utilities for strings and function arguments.") (description @@ -7226,11 +7035,7 @@ (define-public r-sqldf "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) (build-system r-build-system) (propagated-inputs - `(("r-chron" ,r-chron) - ("r-dbi" ,r-dbi) - ("r-gsubfn" ,r-gsubfn) - ("r-proto" ,r-proto) - ("r-rsqlite" ,r-rsqlite))) + (list r-chron r-dbi r-gsubfn r-proto r-rsqlite)) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description @@ -7304,21 +7109,21 @@ (define-public r-vim (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-colorspace" ,r-colorspace) - ("r-data-table" ,r-data-table) - ("r-e1071" ,r-e1071) - ("r-laeken" ,r-laeken) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-ranger" ,r-ranger) - ("r-rcpp" ,r-rcpp) - ("r-robustbase" ,r-robustbase) - ("r-sp" ,r-sp) - ("r-vcd" ,r-vcd))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-car + r-colorspace + r-data-table + r-e1071 + r-laeken + r-magrittr + r-mass + r-nnet + r-ranger + r-rcpp + r-robustbase + r-sp + r-vcd)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/alexkowa/VIM") (synopsis "Visualization and imputation of missing values") (description @@ -7368,7 +7173,7 @@ (define-public r-smoother "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) (build-system r-build-system) (propagated-inputs - `(("r-ttr" ,r-ttr))) + (list r-ttr)) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description @@ -7391,9 +7196,9 @@ (define-public r-riverplot "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description @@ -7417,7 +7222,7 @@ (define-public r-dyn "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/dyn") (synopsis "Time series regression") (description @@ -7444,7 +7249,7 @@ (define-public r-catdap "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/catdap/") (synopsis "Tools for categorical data analysis") (description @@ -7467,8 +7272,7 @@ (define-public r-arules "0zzwr1mg92ha5l6razdb04da8ik3z3k74rm0rah44l1j2a6d30sk")))) (build-system r-build-system) (propagated-inputs - `(("r-generics" ,r-generics) - ("r-matrix" ,r-matrix))) + (list r-generics r-matrix)) (home-page "https://github.com/mhahsler/arules") (synopsis "Mining association rules and frequent itemsets") (description @@ -7491,7 +7295,7 @@ (define-public r-parsedate "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb")))) (build-system r-build-system) (propagated-inputs - `(("r-rematch2" ,r-rematch2))) + (list r-rematch2)) (home-page "https://github.com/gaborcsardi/parsedate") (synopsis "Recognize and parse dates in various formats") @@ -7537,11 +7341,7 @@ (define-public r-abc "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) (build-system r-build-system) (propagated-inputs - `(("r-abc-data" ,r-abc-data) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-quantreg" ,r-quantreg))) + (list r-abc-data r-locfit r-mass r-nnet r-quantreg)) (home-page "https://cran.r-project.org/web/packages/abc/") (synopsis "Tools for Approximate Bayesian Computation (ABC)") (description @@ -7585,11 +7385,9 @@ (define-public r-openxlsx "0vn8ifxb7ccip6b1ijf5lpa6c0n5y5ll8fbabybsb8nfc0y1nmxg")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-stringi" ,r-stringi) - ("r-zip" ,r-zip))) + (list r-rcpp r-stringi r-zip)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description @@ -7613,15 +7411,15 @@ (define-public r-rio "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-foreign" ,r-foreign) - ("r-haven" ,r-haven) - ("r-openxlsx" ,r-openxlsx) - ("r-readxl" ,r-readxl) - ("r-tibble" ,r-tibble))) + (list r-curl + r-data-table + r-foreign + r-haven + r-openxlsx + r-readxl + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description @@ -7649,9 +7447,7 @@ (define-public r-maptools "0fa4a43zax8gn3jdp4ngqav61x4g6l33bg9wzqbngkbjhipck59r")))) (build-system r-build-system) (propagated-inputs - `(("r-foreign" ,r-foreign) - ("r-lattice" ,r-lattice) - ("r-sp" ,r-sp))) + (list r-foreign r-lattice r-sp)) (home-page "https://r-forge.r-project.org/projects/maptools/") (synopsis "Tools for reading and handling spatial objects") (description @@ -7677,10 +7473,9 @@ (define-public r-later "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-rcpp r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/later") (synopsis "Utilities for delaying function execution") (description @@ -7701,13 +7496,9 @@ (define-public r-promises "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld")))) (build-system r-build-system) (propagated-inputs - `(("r-later" ,r-later) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-later r-magrittr r-r6 r-rcpp r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rstudio.github.io/promises") (synopsis "Abstractions for promise-based asynchronous programming") (description @@ -7732,9 +7523,7 @@ (define-public r-dosnow (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-snow" ,r-snow))) + (list r-foreach r-iterators r-snow)) (home-page "https://cran.r-project.org/web/packages/doSNOW") (synopsis "Foreach parallel adaptor for the snow package") (description @@ -7755,7 +7544,7 @@ (define-public r-fst "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr")))) (properties `((upstream-name . "fst"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "http://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description @@ -7778,7 +7567,7 @@ (define-public r-snowfall (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) (build-system r-build-system) (propagated-inputs - `(("r-snow" ,r-snow))) + (list r-snow)) (home-page "https://cran.r-project.org/web/packages/snowfall/") (synopsis "Easier cluster computing") (description "This package is a usability wrapper around snow for easier @@ -7836,9 +7625,7 @@ (define-public r-rgexf (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-servr" ,r-servr) - ("r-xml" ,r-xml))) + (list r-igraph r-servr r-xml)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) @@ -7891,10 +7678,9 @@ (define-public r-data-tree (properties `((upstream-name . "data.tree"))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-stringi" ,r-stringi))) + (list r-r6 r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description @@ -7918,18 +7704,18 @@ (define-public r-dtplyr (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-crayon + r-data-table + r-dplyr + r-ellipsis + r-glue + r-lifecycle + r-rlang + r-tibble + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/dtplyr") (synopsis "Data Table back-end for dplyr") (description @@ -7971,8 +7757,7 @@ (define-public r-collapsibletree (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-data-tree" ,r-data-tree) - ("r-htmlwidgets" ,r-htmlwidgets))) + (list r-data-tree r-htmlwidgets)) (native-inputs `(("esbuild" ,esbuild) ("d3.v4.js" @@ -8025,15 +7810,15 @@ (define-public r-rastervis (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs - `(("r-hexbin" ,r-hexbin) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sp" ,r-sp) - ("r-terra" ,r-terra) - ("r-viridislite" ,r-viridislite) - ("r-zoo" ,r-zoo))) + (list r-hexbin + r-lattice + r-latticeextra + r-raster + r-rcolorbrewer + r-sp + r-terra + r-viridislite + r-zoo)) (home-page "https://oscarperpinan.github.io/rastervis/") (synopsis "Visualization methods for raster data") (description @@ -8057,11 +7842,9 @@ (define-public r-rentrez (properties `((upstream-name . "rentrez"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-xml" ,r-xml))) + (list r-httr r-jsonlite r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description @@ -8084,7 +7867,7 @@ (define-public r-renv (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description @@ -8108,20 +7891,20 @@ (define-public r-learnr "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-ellipsis" ,r-ellipsis) - ("r-evaluate" ,r-evaluate) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-rappdirs" ,r-rappdirs) - ("r-renv" ,r-renv) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rprojroot" ,r-rprojroot) - ("r-shiny" ,r-shiny) - ("r-withr" ,r-withr))) + (list r-checkmate + r-ellipsis + r-evaluate + r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-markdown + r-rappdirs + r-renv + r-rmarkdown + r-rprojroot + r-shiny + r-withr)) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description @@ -8143,18 +7926,18 @@ (define-public r-analytics "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-cluster" ,r-cluster) - ("r-fractal" ,r-fractal) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-np" ,r-np) - ("r-powerplus" ,r-powerplus) - ("r-robust" ,r-robust) - ("r-trend" ,r-trend) - ("r-tsa" ,r-tsa) - ("r-urca" ,r-urca) - ("r-vim" ,r-vim))) + (list r-car + r-cluster + r-fractal + r-lmtest + r-mass + r-np + r-powerplus + r-robust + r-trend + r-tsa + r-urca + r-vim)) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description @@ -8177,8 +7960,8 @@ (define-public r-here (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) (properties `((upstream-name . "here"))) (build-system r-build-system) - (propagated-inputs `(("r-rprojroot" ,r-rprojroot))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-rprojroot)) + (native-inputs (list r-knitr)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description @@ -8199,17 +7982,17 @@ (define-public r-reticulate (base32 "0v7m2pv94lfqiw8rhz3c9g66vvz4qvih4vd29rhfk2phmcwpnvmh")))) (build-system r-build-system) - (inputs `(("python" ,python))) + (inputs (list python)) (propagated-inputs - `(("r-here" ,r-here) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-png" ,r-png) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-withr" ,r-withr))) + (list r-here + r-jsonlite + r-matrix + r-png + r-rappdirs + r-rcpp + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description @@ -8231,7 +8014,7 @@ (define-public r-bibtex (base32 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv")))) (build-system r-build-system) - (propagated-inputs `(("r-stringr" ,r-stringr))) + (propagated-inputs (list r-stringr)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex @@ -8250,7 +8033,7 @@ (define-public r-ggseqlogo (base32 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) + (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/omarwagih/ggseqlogo") (synopsis "ggplot2 extension for drawing genetic sequence logos") (description @@ -8275,8 +8058,7 @@ (define-public r-ggsci "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description @@ -8298,9 +8080,9 @@ (define-public r-ggsignif "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") (synopsis "Significance brackets for ggplot2") (description @@ -8326,17 +8108,17 @@ (define-public r-rstatix (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-car" ,r-car) - ("r-corrplot" ,r-corrplot) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + (list r-broom + r-car + r-corrplot + r-dplyr + r-generics + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description @@ -8362,22 +8144,22 @@ (define-public r-ggpubr "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb")))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggsci" ,r-ggsci) - ("r-ggsignif" ,r-ggsignif) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-polynom" ,r-polynom) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-rstatix" ,r-rstatix) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-cowplot + r-dplyr + r-ggplot2 + r-ggrepel + r-ggsci + r-ggsignif + r-glue + r-gridextra + r-magrittr + r-polynom + r-purrr + r-rlang + r-scales + r-rstatix + r-tibble + r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description @@ -8424,7 +8206,7 @@ (define-public r-flashclust "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) (properties `((upstream-name . "flashClust"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/flashClust/") (synopsis "Implementation of optimal hierarchical clustering") (description @@ -8446,19 +8228,19 @@ (define-public r-factominer (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-cluster" ,r-cluster) - ("r-dt" ,r-dt) - ("r-ellipse" ,r-ellipse) - ("r-flashclust" ,r-flashclust) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-leaps" ,r-leaps) - ("r-mass" ,r-mass) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-car + r-cluster + r-dt + r-ellipse + r-flashclust + r-ggplot2 + r-ggrepel + r-lattice + r-leaps + r-mass + r-scatterplot3d)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://factominer.free.fr") (synopsis "Multivariate exploratory data analysis and data mining") (description @@ -8484,15 +8266,15 @@ (define-public r-factoextra "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-cluster" ,r-cluster) - ("r-dendextend" ,r-dendextend) - ("r-factominer" ,r-factominer) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) + (list r-abind + r-cluster + r-dendextend + r-factominer + r-ggplot2 + r-ggpubr + r-ggrepel + r-reshape2 + r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/factoextra") (synopsis "Extract and visualize the results of multivariate data analyses") (description @@ -8519,7 +8301,7 @@ (define-public r-fansi "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description @@ -8561,13 +8343,11 @@ (define-public r-hdf5r "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7")))) (build-system r-build-system) (inputs - `(("hdf5" ,hdf5) - ("zlib" ,zlib))) + (list hdf5 zlib)) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-r6" ,r-r6))) + (list r-bit64 r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://hhoeflin.github.io/hdf5r") (synopsis "Interface to the HDF5 binary data format") (description @@ -8591,7 +8371,7 @@ (define-public r-itertools "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) (build-system r-build-system) (propagated-inputs - `(("r-iterators" ,r-iterators))) + (list r-iterators)) (home-page "https://cran.r-project.org/web/packages/itertools/") (synopsis "Iterator tools") (description @@ -8653,11 +8433,11 @@ (define-public r-rjags "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr")))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda))) + (list r-coda)) (inputs - `(("jags" ,jags))) + (list jags)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://mcmc-jags.sourceforge.net") (synopsis "Bayesian graphical models using MCMC") (description @@ -8702,7 +8482,7 @@ (define-public r-rdpack (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs - `(("r-rbibutils" ,r-rbibutils))) + (list r-rbibutils)) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description @@ -8727,12 +8507,9 @@ (define-public r-officer "1gfx299zr4q2264q37994pirv5bd5isn1cszccz603ij3q40wajr")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-uuid" ,r-uuid) - ("r-xml2" ,r-xml2) - ("r-zip" ,r-zip))) + (list r-r6 r-uuid r-xml2 r-zip)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description @@ -8783,7 +8560,7 @@ (define-public r-brglm (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs - `(("r-profilemodel" ,r-profilemodel))) + (list r-profilemodel)) (home-page "https://github.com/ikosmidis/brglm") (synopsis "Bias reduction in binomial-response generalized linear models") (description @@ -8859,11 +8636,7 @@ (define-public r-acdm (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rsolnp" ,r-rsolnp) - ("r-zoo" ,r-zoo))) + (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo)) (home-page "https://cran.r-project.org/web/packages/ACDm/") (synopsis "Tools for Autoregressive Conditional Duration Models") (description @@ -8907,8 +8680,7 @@ (define-public r-snakecase "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r")))) (build-system r-build-system) (propagated-inputs - `(("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr))) + (list r-stringi r-stringr)) (home-page "https://github.com/Tazinho/snakecase") (synopsis "Convert strings into any case") (description @@ -8929,7 +8701,7 @@ (define-public r-prediction "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://github.com/leeper/prediction") (synopsis "Tidy, type-safe prediction methods") (description @@ -8953,7 +8725,7 @@ (define-public r-insight "10kc72g2hfsiipba4kalda1wxsb01nq2ax2yim386bkk0vjszwfx")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") (description @@ -8981,9 +8753,9 @@ (define-public r-sjlabelled "17gskxr43rgbg7syla3b78g2qgksq2kj07iad4139xycqxblxya0")))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight))) + (list r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description @@ -9007,15 +8779,15 @@ (define-public r-sjmisc "17hcjb2j690qi2zrkwc14sr1wsid6dy6v7bfsf0bc94ql812k8g2")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-insight" ,r-insight) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-sjlabelled" ,r-sjlabelled) - ("r-tidyselect" ,r-tidyselect))) + (list r-dplyr + r-insight + r-magrittr + r-purrr + r-rlang + r-sjlabelled + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description @@ -9059,14 +8831,14 @@ (define-public r-moonbook (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-nortest" ,r-nortest) - ("r-sjmisc" ,r-sjmisc) - ("r-stringr" ,r-stringr) - ("r-survival" ,r-survival) - ("r-ztable" ,r-ztable))) + (list r-magrittr + r-nortest + r-sjmisc + r-stringr + r-survival + r-ztable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/cardiomoon/moonBook") (synopsis "Functions and datasets for the book by Keon-Woong Moon") (description @@ -9089,18 +8861,18 @@ (define-public r-flextable "01nm0357b0z4dgrplbq9ms63j51n0rgvvxyy068zdsc5p7j3lql2")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-data-table" ,r-data-table) - ("r-gdtools" ,r-gdtools) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-officer" ,r-officer) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-uuid" ,r-uuid) - ("r-xml2" ,r-xml2))) + (list r-base64enc + r-data-table + r-gdtools + r-htmltools + r-knitr + r-officer + r-rlang + r-rmarkdown + r-uuid + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description @@ -9123,7 +8895,7 @@ (define-public r-writexl (base32 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry")))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description @@ -9168,10 +8940,7 @@ (define-public r-goplot (properties `((upstream-name . "GOplot"))) (build-system r-build-system) (propagated-inputs - `(("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer)) (home-page "https://github.com/wencke/wencke.github.io") (synopsis "Visualization of functional analysis data") (description @@ -9240,13 +9009,11 @@ (define-public r-argparse (base32 "1cz5qlxw3v8smd5vb00wlzy02mx5i0infm5hnq55hnakffd3b5wr")))) (build-system r-build-system) - (inputs `(("python" ,python))) + (inputs (list python)) (propagated-inputs - `(("r-findpython" ,r-findpython) - ("r-jsonlite" ,r-jsonlite) - ("r-r6" ,r-r6))) + (list r-findpython r-jsonlite r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description @@ -9288,7 +9055,7 @@ (define-public r-orddom (base32 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) (build-system r-build-system) - (propagated-inputs `(("r-psych" ,r-psych))) + (propagated-inputs (list r-psych)) (home-page "https://cran.r-project.org/web/packages/orddom/") (synopsis "Ordinal dominance statistics") (description @@ -9338,19 +9105,19 @@ (define-public r-doby (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-curry" ,r-curry) - ("r-deriv" ,r-deriv) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-microbenchmark" ,r-microbenchmark) - ("r-pbkrtest" ,r-pbkrtest) - ("r-tibble" ,r-tibble))) + (list r-broom + r-curry + r-deriv + r-dplyr + r-ggplot2 + r-magrittr + r-mass + r-matrix + r-microbenchmark + r-pbkrtest + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description @@ -9378,9 +9145,7 @@ (define-public r-refgenome (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi) - ("r-doby" ,r-doby) - ("r-rsqlite" ,r-rsqlite))) + (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") (synopsis "Gene and splice site annotation using annotation data from Ensembl and UCSC") @@ -9425,7 +9190,7 @@ (define-public r-blockfest "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) - (propagated-inputs `(("r-basix" ,r-basix))) + (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description @@ -9450,8 +9215,7 @@ (define-public r-proc (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp))) + (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description @@ -9474,7 +9238,7 @@ (define-public r-rootsolve "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description @@ -9507,7 +9271,7 @@ (define-public r-abcanalysis (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . "ABCanalysis"))) (build-system r-build-system) - (propagated-inputs `(("r-plotrix" ,r-plotrix))) + (propagated-inputs (list r-plotrix)) (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") (synopsis "Computed ABC Analysis") (description @@ -9551,17 +9315,17 @@ (define-public r-manipulatewidget `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-codetools" ,r-codetools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-knitr" ,r-knitr) - ("r-miniui" ,r-miniui) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-webshot" ,r-webshot))) + (list r-base64enc + r-codetools + r-htmltools + r-htmlwidgets + r-knitr + r-miniui + r-shiny + r-shinyjs + r-webshot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description @@ -9584,8 +9348,7 @@ (define-public r-a3 (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs - `(("r-pbapply" ,r-pbapply) - ("r-xtable" ,r-xtable))) + (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description @@ -9679,13 +9442,13 @@ (define-public r-precrec (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rcpp" ,r-rcpp) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-data-table + r-ggplot2 + r-gridextra + r-rcpp + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description @@ -9707,15 +9470,15 @@ (define-public r-netrep (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bh" ,r-bh) - ("r-foreach" ,r-foreach) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-statmod" ,r-statmod))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-bh + r-foreach + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-statmod)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description @@ -9738,10 +9501,9 @@ (define-public r-intergraph (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-network" ,r-network))) + (list r-igraph r-network)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description @@ -9763,7 +9525,7 @@ (define-public r-abcoptim (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description @@ -9788,7 +9550,7 @@ (define-public r-abcp2 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description @@ -9809,15 +9571,15 @@ (define-public r-abcrf (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27")))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-ranger" ,r-ranger) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-readr" ,r-readr) - ("r-stringr" ,r-stringr))) + (list r-doparallel + r-foreach + r-mass + r-matrixstats + r-ranger + r-rcpp + r-rcpparmadillo + r-readr + r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description @@ -9839,10 +9601,7 @@ (define-public r-abctools (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) (build-system r-build-system) (propagated-inputs - `(("r-abc" ,r-abc) - ("r-abind" ,r-abind) - ("r-hmisc" ,r-hmisc) - ("r-plyr" ,r-plyr))) + (list r-abc r-abind r-hmisc r-plyr)) (home-page "https://github.com/dennisprangle/abctools/") (synopsis "Tools for ABC analyses") (description @@ -9864,10 +9623,7 @@ (define-public r-ggstance (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-withr" ,r-withr))) + (list r-ggplot2 r-plyr r-rlang r-withr)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description @@ -9892,12 +9648,8 @@ (define-public r-ggnetwork (properties `((upstream-name . "ggnetwork"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-network" ,r-network) - ("r-sna" ,r-sna))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-ggrepel r-igraph r-network r-sna)) + (native-inputs (list r-knitr)) (home-page "https://github.com/briatte/ggnetwork") (synopsis "Geometries to plot networks with ggplot2") (description @@ -9919,8 +9671,7 @@ (define-public r-cvauc (properties `((upstream-name . "cvAUC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-rocr" ,r-rocr))) + (list r-data-table r-rocr)) (home-page "https://github.com/ledell/cvAUC") (synopsis "Cross-validated area under the ROC curve confidence intervals") (description @@ -9946,9 +9697,9 @@ (define-public r-gam (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach))) + (list r-foreach)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/package=gam") (synopsis "Generalized additive models") (description @@ -9972,11 +9723,9 @@ (define-public r-superlearner (properties `((upstream-name . "SuperLearner"))) (build-system r-build-system) (propagated-inputs - `(("r-cvauc" ,r-cvauc) - ("r-gam" ,r-gam) - ("r-nnls" ,r-nnls))) + (list r-cvauc r-gam r-nnls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ecpolley/SuperLearner") (synopsis "Super learner prediction") (description @@ -9998,11 +9747,9 @@ (define-public r-drtmle (properties `((upstream-name . "drtmle"))) (build-system r-build-system) (propagated-inputs - `(("r-future-apply" ,r-future-apply) - ("r-np" ,r-np) - ("r-superlearner" ,r-superlearner))) + (list r-future-apply r-np r-superlearner)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/benkeser/drtmle") (synopsis "Doubly-robust nonparametric estimation and inference") (description @@ -10030,12 +9777,9 @@ (define-public r-dofuture (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-future" ,r-future) - ("r-globals" ,r-globals) - ("r-iterators" ,r-iterators))) + (list r-foreach r-future r-globals r-iterators)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/doFuture") (synopsis "Foreach parallel adapter using the future API") (description @@ -10057,13 +9801,13 @@ (define-public r-superheat (properties `((upstream-name . "superheat"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + (list r-dplyr + r-ggdendro + r-ggplot2 + r-gtable + r-magrittr + r-plyr + r-scales)) (home-page "https://cran.r-project.org/package=superheat") (synopsis "Graphical tool for exploring complex datasets using heatmaps") (description @@ -10086,7 +9830,7 @@ (define-public r-qualv (properties `((upstream-name . "qualV"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "http://qualV.R-Forge.R-Project.org/") (synopsis "Qualitative Validation Methods") (description @@ -10118,10 +9862,7 @@ (define-public r-mosaiccore (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-mass" ,r-mass) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-mass r-rlang r-tidyr)) (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") (synopsis "Common utilities for mosaic family packages") (description @@ -10142,15 +9883,15 @@ (define-public r-labelled (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-haven" ,r-haven) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs))) + (list r-dplyr + r-haven + r-lifecycle + r-rlang + r-stringr + r-tidyr + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://larmarange.github.io/labelled/") (synopsis "Manipulating labelled data") (description @@ -10171,19 +9912,19 @@ (define-public r-ggformula (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges) - ("r-ggstance" ,r-ggstance) - ("r-labelled" ,r-labelled) - ("r-magrittr" ,r-magrittr) - ("r-mosaiccore" ,r-mosaiccore) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-ggforce + r-ggplot2 + r-ggridges + r-ggstance + r-labelled + r-magrittr + r-mosaiccore + r-rlang + r-scales + r-stringr + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description @@ -10225,9 +9966,7 @@ (define-public r-raster "0wixw1ixnmcmkwczpj8m90c76727zira2rl4ighashggydkm2mlr")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp) - ("r-terra" ,r-terra))) + (list r-rcpp r-sp r-terra)) (home-page "https://www.rspatial.org/") (synopsis "Geographic data analysis and modeling") (description @@ -10248,25 +9987,25 @@ (define-public r-mosaic (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggdendro" ,r-ggdendro) - ("r-ggformula" ,r-ggformula) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-lazyeval" ,r-lazyeval) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mosaiccore" ,r-mosaiccore) - ("r-mosaicdata" ,r-mosaicdata) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-dplyr + r-ggdendro + r-ggformula + r-ggplot2 + r-ggrepel + r-glue + r-gridextra + r-lattice + r-latticeextra + r-lazyeval + r-mass + r-matrix + r-mosaiccore + r-mosaicdata + r-readr + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/mosaic/") (synopsis "Mathematics, statistics, and computation teaching utilities") (description @@ -10290,9 +10029,7 @@ (define-public r-abd (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mosaic" ,r-mosaic) - ("r-nlme" ,r-nlme))) + (list r-lattice r-mosaic r-nlme)) (home-page "https://cran.r-project.org/web/packages/abd/") (synopsis "Analysis of biological data") (description @@ -10313,7 +10050,7 @@ (define-public r-svgui (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description @@ -10336,13 +10073,11 @@ (define-public r-svdialogs (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs - `(("yad" ,yad) - ("zenity" ,zenity))) + (list yad zenity)) (propagated-inputs - `(("r-rstudioapi" ,r-rstudioapi) - ("r-svgui" ,r-svgui))) + (list r-rstudioapi r-svgui)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description @@ -10406,8 +10141,7 @@ (define-public r-abhgenotyper (properties `((upstream-name . "ABHgenotypeR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") (synopsis "Visualize and manipulate ABH genotypes") (description @@ -10432,13 +10166,13 @@ (define-public r-furrr "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-future" ,r-future) - ("r-globals" ,r-globals) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis + r-future + r-globals + r-lifecycle + r-purrr + r-rlang + r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description @@ -10460,14 +10194,14 @@ (define-public r-abjutils (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-magrittr + r-purrr + r-rlang + r-rstudioapi + r-stringi + r-stringr + r-tidyr)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description @@ -10489,8 +10223,7 @@ (define-public r-abnormality (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description @@ -10515,7 +10248,7 @@ (define-public r-abodoutlier (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster))) + (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description @@ -10543,7 +10276,7 @@ (define-public r-abps (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) - (propagated-inputs `(("r-kernlab" ,r-kernlab))) + (propagated-inputs (list r-kernlab)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description @@ -10587,7 +10320,7 @@ (define-public r-pscl (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description @@ -10613,8 +10346,7 @@ (define-public r-accelmissing (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs - `(("r-mice" ,r-mice) - ("r-pscl" ,r-pscl))) + (list r-mice r-pscl)) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description @@ -10637,7 +10369,7 @@ (define-public r-mhsmm (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (build-system r-build-system) - (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description @@ -10660,7 +10392,7 @@ (define-public r-nleqslv (sha256 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description @@ -10716,19 +10448,19 @@ (define-public r-acc (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-dbi" ,r-dbi) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-mhsmm" ,r-mhsmm) - ("r-nleqslv" ,r-nleqslv) - ("r-physicalactivity" ,r-physicalactivity) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsqlite" ,r-rsqlite) - ("r-zoo" ,r-zoo))) + (list r-circlize + r-dbi + r-ggplot2 + r-iterators + r-mhsmm + r-nleqslv + r-physicalactivity + r-plyr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rsqlite + r-zoo)) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description @@ -10773,7 +10505,7 @@ (define-public r-mitools (base32 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) (build-system r-build-system) - (propagated-inputs `(("r-dbi" ,r-dbi))) + (propagated-inputs (list r-dbi)) (home-page "https://cran.r-project.org/web/packages/mitools/") (synopsis "Tools for multiple imputation of missing data") (description @@ -10794,11 +10526,9 @@ (define-public r-mixsqp (properties `((upstream-name . "mixsqp"))) (build-system r-build-system) (propagated-inputs - `(("r-irlba" ,r-irlba) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") @@ -10825,15 +10555,11 @@ (define-public r-magick "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) (build-system r-build-system) (inputs - `(("imagemagick" ,imagemagick) - ("zlib" ,zlib))) + (list imagemagick zlib)) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp))) + (list r-curl r-magrittr r-rcpp)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description @@ -10859,12 +10585,12 @@ (define-public r-survey "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-minqa" ,r-minqa) - ("r-mitools" ,r-mitools) - ("r-numderiv" ,r-numderiv) - ("r-survival" ,r-survival))) + (list r-lattice + r-matrix + r-minqa + r-mitools + r-numderiv + r-survival)) (home-page "http://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description @@ -10894,7 +10620,7 @@ (define-public r-gee (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description @@ -10915,13 +10641,9 @@ (define-public r-tab (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-kableextra" ,r-kableextra) - ("r-knitr" ,r-knitr) - ("r-mass" ,r-mass) - ("r-survey" ,r-survey))) + (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description @@ -10944,17 +10666,17 @@ (define-public r-dvmisc (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs - `(("r-cubature" ,r-cubature) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-mass" ,r-mass) - ("r-mvtnorm" ,r-mvtnorm) - ("r-pracma" ,r-pracma) - ("r-rbenchmark" ,r-rbenchmark) - ("r-rcpp" ,r-rcpp) - ("r-survey" ,r-survey) - ("r-tab" ,r-tab))) + (list r-cubature + r-data-table + r-dplyr + r-ggplot2 + r-mass + r-mvtnorm + r-pracma + r-rbenchmark + r-rcpp + r-survey + r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description @@ -10978,8 +10700,7 @@ (define-public r-accelerometry (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs - `(("r-dvmisc" ,r-dvmisc) - ("r-rcpp" ,r-rcpp))) + (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description @@ -11003,8 +10724,7 @@ (define-public r-absim (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-powerlaw" ,r-powerlaw))) + (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description @@ -11053,7 +10773,7 @@ (define-public r-abundant (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) (build-system r-build-system) (propagated-inputs - `(("r-quic" ,r-quic))) + (list r-quic)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description @@ -11077,7 +10797,7 @@ (define-public r-ac3net (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core @@ -11194,7 +10914,7 @@ (define-public r-sandwich "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description @@ -11217,10 +10937,9 @@ (define-public r-th-data (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-survival" ,r-survival))) + (list r-mass r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description @@ -11241,11 +10960,7 @@ (define-public r-multcomp "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sandwich" ,r-sandwich) - ("r-survival" ,r-survival) - ("r-th-data" ,r-th-data))) + (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description @@ -11269,12 +10984,9 @@ (define-public r-emmeans "1ig94mjifhhygznv2xv1gl8hdvk618w5fcmkaj1xmpwpc64m9dnl")))) (build-system r-build-system) (propagated-inputs - `(("r-estimability" ,r-estimability) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv) - ("r-xtable" ,r-xtable))) + (list r-estimability r-mvtnorm r-numderiv r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description @@ -11298,7 +11010,7 @@ (define-public r-pwr "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description @@ -11317,7 +11029,7 @@ (define-public r-libcoin (sha256 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d")))) (build-system r-build-system) - (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description @@ -11338,12 +11050,12 @@ (define-public r-coin "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm")))) (build-system r-build-system) (propagated-inputs - `(("r-libcoin" ,r-libcoin) - ("r-matrixstats" ,r-matrixstats) - ("r-modeltools" ,r-modeltools) - ("r-multcomp" ,r-multcomp) - ("r-mvtnorm" ,r-mvtnorm) - ("r-survival" ,r-survival))) + (list r-libcoin + r-matrixstats + r-modeltools + r-multcomp + r-mvtnorm + r-survival)) (home-page "http://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description @@ -11365,18 +11077,18 @@ (define-public r-bayesplot "0aman4273i8hy3z0qay1nrsr7v27m4icm1j6f4w59ylix80l5myq")))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges) - ("r-glue" ,r-glue) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + (list pandoc)) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-ggridges + r-glue + r-reshape2 + r-rlang + r-tibble + r-tidyselect)) (home-page "https://mc-stan.org/bayesplot") (synopsis "Plotting for Bayesian models") (description @@ -11401,8 +11113,7 @@ (define-public r-tmb (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcppeigen)) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description @@ -11427,23 +11138,23 @@ (define-public r-sjstats (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-effectsize" ,r-effectsize) - ("r-emmeans" ,r-emmeans) - ("r-insight" ,r-insight) - ("r-lme4" ,r-lme4) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-modelr" ,r-modelr) - ("r-parameters" ,r-parameters) - ("r-performance" ,r-performance) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-sjlabelled" ,r-sjlabelled) - ("r-sjmisc" ,r-sjmisc) - ("r-tidyr" ,r-tidyr))) + (list r-bayestestr + r-broom + r-dplyr + r-effectsize + r-emmeans + r-insight + r-lme4 + r-magrittr + r-mass + r-modelr + r-parameters + r-performance + r-purrr + r-rlang + r-sjlabelled + r-sjmisc + r-tidyr)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description @@ -11472,14 +11183,14 @@ (define-public r-glmmtmb (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-numderiv" ,r-numderiv) - ("r-rcppeigen" ,r-rcppeigen) - ("r-tmb" ,r-tmb))) + (list r-lme4 + r-matrix + r-nlme + r-numderiv + r-rcppeigen + r-tmb)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description @@ -11505,10 +11216,9 @@ (define-public r-bayestestr (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs - `(("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight))) + (list r-datawizard r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description @@ -11532,9 +11242,7 @@ (define-public r-performance "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2")))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight))) + (list r-bayestestr r-datawizard r-insight)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description @@ -11560,11 +11268,9 @@ (define-public r-ggeffects "0xrb105kblkj3l9zlj9yy52rjlmx5x2aai1wwb5zvjr1f6nlc84l")))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight) - ("r-mass" ,r-mass) - ("r-sjlabelled" ,r-sjlabelled))) + (list r-insight r-mass r-sjlabelled)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description @@ -11591,13 +11297,10 @@ (define-public r-effectsize (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight) - ("r-parameters" ,r-parameters) - ("r-performance" ,r-performance))) + (list r-bayestestr r-datawizard r-insight r-parameters + r-performance)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/easystats/effectsize") (synopsis "Indices of effect size and standardized parameters") (description @@ -11619,26 +11322,26 @@ (define-public r-sjplot (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-dplyr" ,r-dplyr) - ("r-effectsize" ,r-effectsize) - ("r-ggeffects" ,r-ggeffects) - ("r-ggplot2" ,r-ggplot2) - ("r-insight" ,r-insight) - ("r-knitr" ,r-knitr) - ("r-mass" ,r-mass) - ("r-parameters" ,r-parameters) - ("r-performance" ,r-performance) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-sjlabelled" ,r-sjlabelled) - ("r-sjmisc" ,r-sjmisc) - ("r-sjstats" ,r-sjstats) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bayestestr + r-datawizard + r-dplyr + r-effectsize + r-ggeffects + r-ggplot2 + r-insight + r-knitr + r-mass + r-parameters + r-performance + r-purrr + r-rlang + r-scales + r-sjlabelled + r-sjmisc + r-sjstats + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description @@ -11687,7 +11390,7 @@ (define-public r-gitcreds (properties `((upstream-name . "gitcreds"))) (build-system r-build-system) (inputs `(("git" ,git-minimal))) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") (description @@ -11710,13 +11413,9 @@ (define-public r-gh "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-gitcreds" ,r-gitcreds) - ("r-httr" ,r-httr) - ("r-ini" ,r-ini) - ("r-jsonlite" ,r-jsonlite))) + (list r-cli r-gitcreds r-httr r-ini r-jsonlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description @@ -11736,7 +11435,7 @@ (define-public r-fs "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://fs.r-lib.org") (synopsis "Cross-platform file system operations based on libuv") (description @@ -11788,13 +11487,9 @@ (define-public r-credentials (inputs `(("git" ,git-minimal))) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite) - ("r-openssl" ,r-openssl) - ("r-sys" ,r-sys))) + (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/credentials/") (synopsis "Tools for managing SSH and Git credentials") (description @@ -11822,18 +11517,16 @@ (define-public r-gert (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs - `(("libgit2" ,libgit2) - ("zlib" ,zlib))) + (list libgit2 zlib)) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-credentials" ,r-credentials) - ("r-openssl" ,r-openssl) - ("r-rstudioapi" ,r-rstudioapi) - ("r-sys" ,r-sys) - ("r-zip" ,r-zip))) + (list r-askpass + r-credentials + r-openssl + r-rstudioapi + r-sys + r-zip)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://docs.ropensci.org/gert/") (synopsis "Simple Git client for R") (description @@ -11857,25 +11550,25 @@ (define-public r-usethis "1gwvirp53pa0zychd7d47d56a2vfdzz7l3p61l8m9n270ac7bc1d")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-clipr" ,r-clipr) - ("r-crayon" ,r-crayon) - ("r-curl" ,r-curl) - ("r-desc" ,r-desc) - ("r-fs" ,r-fs) - ("r-gert" ,r-gert) - ("r-gh" ,r-gh) - ("r-glue" ,r-glue) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-rstudioapi" ,r-rstudioapi) - ("r-whisker" ,r-whisker) - ("r-withr" ,r-withr) - ("r-yaml" ,r-yaml))) + (list r-cli + r-clipr + r-crayon + r-curl + r-desc + r-fs + r-gert + r-gh + r-glue + r-jsonlite + r-lifecycle + r-purrr + r-rappdirs + r-rlang + r-rprojroot + r-rstudioapi + r-whisker + r-withr + r-yaml)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description @@ -11898,7 +11591,7 @@ (define-public r-sessioninfo "0w3vhp652524348a4cfyvvs8z9xpxkcznw8x406nvkwfh0gdyka2")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli))) + (list r-cli)) (home-page "https://github.com/r-lib/sessioninfo#readme") (synopsis "R session information") (description @@ -11920,7 +11613,7 @@ (define-public r-remotes "0xij8x4ga0r7rp2lxx9hw1zlzv48mfg56v8nf03gsw0dw6r7gmym")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description @@ -11943,7 +11636,7 @@ (define-public r-xopen "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) (build-system r-build-system) (propagated-inputs - `(("r-processx" ,r-processx))) + (list r-processx)) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description @@ -11964,18 +11657,18 @@ (define-public r-rcmdcheck "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-curl" ,r-curl) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-pkgbuild" ,r-pkgbuild) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6) - ("r-rprojroot" ,r-rprojroot) - ("r-sessioninfo" ,r-sessioninfo) - ("r-withr" ,r-withr) - ("r-xopen" ,r-xopen))) + (list r-callr + r-cli + r-curl + r-desc + r-digest + r-pkgbuild + r-prettyunits + r-r6 + r-rprojroot + r-sessioninfo + r-withr + r-xopen)) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description @@ -11996,9 +11689,7 @@ (define-public r-rapportools "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) (build-system r-build-system) (propagated-inputs - `(("r-pander" ,r-pander) - ("r-plyr" ,r-plyr) - ("r-reshape" ,r-reshape))) + (list r-pander r-plyr r-reshape)) (home-page "https://cran.r-project.org/web/packages/rapportools/") (synopsis "Miscellaneous helper functions with sane defaults for reporting") (description @@ -12020,10 +11711,9 @@ (define-public r-pander "1knjcr50xxns3w3kh15myjpsizn4d7fdqx071a4yj90imif07qjh")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp))) + (list r-digest r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description @@ -12048,20 +11738,20 @@ (define-public r-summarytools "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-lubridate" ,r-lubridate) - ("r-magick" ,r-magick) - ("r-matrixstats" ,r-matrixstats) - ("r-pander" ,r-pander) - ("r-pryr" ,r-pryr) - ("r-rapportools" ,r-rapportools) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-checkmate + r-dplyr + r-htmltools + r-lubridate + r-magick + r-matrixstats + r-pander + r-pryr + r-rapportools + r-tibble + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description @@ -12085,7 +11775,7 @@ (define-public r-lsei "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Solve regression problems under equality/inequality constraints") (description @@ -12108,7 +11798,7 @@ (define-public r-npsurv "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw")))) (build-system r-build-system) (propagated-inputs - `(("r-lsei" ,r-lsei))) + (list r-lsei)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Nonparametric survival analysis") (description @@ -12129,8 +11819,7 @@ (define-public r-clusteval "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp))) + (list r-mvtnorm r-rcpp)) (home-page "https://cran.r-project.org/web/packages/clusteval/") (synopsis "Evaluation of clustering algorithms") (description @@ -12150,7 +11839,7 @@ (define-public r-tweedie (base32 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tweedie/") (synopsis "Evaluation of Tweedie exponential family models") (description @@ -12173,8 +11862,7 @@ (define-public r-rcppgsl (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("gsl" ,gsl))) + (list r-rcpp gsl)) (home-page "https://cran.r-project.org/web/packages/RcppGSL/") (synopsis "Rcpp integration for GSL vectors and matrices") (description @@ -12200,11 +11888,7 @@ (define-public r-mvabund "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppgsl" ,r-rcppgsl) - ("r-statmod" ,r-statmod) - ("r-tweedie" ,r-tweedie))) + (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie)) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description @@ -12225,13 +11909,9 @@ (define-public r-afex "1k04n6gwk2n8kg0l3yk5j3wrqgkv5f6w04yjpif9y451hx5w7svg")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-pbkrtest" ,r-pbkrtest) - ("r-reshape2" ,r-reshape2))) + (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description @@ -12253,10 +11933,7 @@ (define-public r-lmertest (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-numderiv" ,r-numderiv))) + (list r-ggplot2 r-lme4 r-mass r-numderiv)) (home-page "https://github.com/runehaubo/lmerTestR") (synopsis "Tests in linear mixed effects models") (description @@ -12281,16 +11958,16 @@ (define-public r-r2glmm "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) (build-system r-build-system) (propagated-inputs - `(("r-afex" ,r-afex) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-pbkrtest" ,r-pbkrtest))) + (list r-afex + r-data-table + r-dplyr + r-ggplot2 + r-gridextra + r-lmertest + r-mass + r-matrix + r-mgcv + r-pbkrtest)) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description @@ -12315,14 +11992,14 @@ (define-public r-cmdfun (properties `((upstream-name . "cmdfun"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-r-utils" ,r-r-utils) - ("r-rlang" ,r-rlang) - ("r-testthat" ,r-testthat) - ("r-usethis" ,r-usethis))) + (list r-magrittr + r-purrr + r-r-utils + r-rlang + r-testthat + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://snystrom.github.io/cmdfun/") (synopsis "Framework for building interfaces to shell commands") (description @@ -12348,8 +12025,8 @@ (define-public r-rslurm "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf")))) (properties `((upstream-name . "rslurm"))) (build-system r-build-system) - (propagated-inputs `(("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-whisker)) + (native-inputs (list r-knitr)) (home-page "http://cyberhelp.sesync.org/rslurm/") (synopsis "Submit R calculations to a Slurm cluster") (description @@ -12372,9 +12049,8 @@ (define-public r-chk (properties `((upstream-name . "chk"))) (build-system r-build-system) (propagated-inputs - `(("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-lifecycle r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://github.com/poissonconsulting/chk") (synopsis "Check user-supplied function arguments") (description @@ -12396,10 +12072,7 @@ (define-public r-weights "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg")))) (build-system r-build-system) (propagated-inputs - `(("r-gdata" ,r-gdata) - ("r-hmisc" ,r-hmisc) - ("r-lme4" ,r-lme4) - ("r-mice" ,r-mice))) + (list r-gdata r-hmisc r-lme4 r-mice)) (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing @@ -12425,7 +12098,7 @@ (define-public r-rcppannoy (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") (description @@ -12449,7 +12122,7 @@ (define-public r-rcpphnsw "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description @@ -12494,8 +12167,7 @@ (define-public r-ncdf4 "1fyjhp2zkvp7ls1sxn623far7473lpkfsqqvj3a1fczpmqs6iw4m")))) (build-system r-build-system) (inputs - `(("netcdf" ,netcdf) - ("zlib" ,zlib))) + (list netcdf zlib)) (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") (synopsis "R interface to Unidata netCDF format data files") (description @@ -12521,7 +12193,7 @@ (define-public r-biocmanager (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description @@ -12542,22 +12214,21 @@ (define-public r-rgl "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("glu" ,glu) - ("libx11" ,libx11) - ("pandoc" ,pandoc) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6))) + (list freetype + libpng + glu + libx11 + pandoc + zlib)) + (propagated-inputs + (list r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-magrittr + r-r6)) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description @@ -12582,7 +12253,7 @@ (define-public r-multicool (base32 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description @@ -12623,16 +12294,16 @@ (define-public r-ks (base32 "02gnpyjqdlj6dl2x9i7mmks4f5nrh85j3h0kfa0v1v6wi8blx7kw")))) (build-system r-build-system) (propagated-inputs - `(("r-fnn" ,r-fnn) - ("r-kernlab" ,r-kernlab) - ("r-kernsmooth" ,r-kernsmooth) - ("r-matrix" ,r-matrix) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-multicool" ,r-multicool) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plot3d" ,r-plot3d) - ("r-pracma" ,r-pracma))) + (list r-fnn + r-kernlab + r-kernsmooth + r-matrix + r-mclust + r-mgcv + r-multicool + r-mvtnorm + r-plot3d + r-pracma)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description @@ -12656,10 +12327,9 @@ (define-public r-feature "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs - `(("r-ks" ,r-ks) - ("r-plot3d" ,r-plot3d))) + (list r-ks r-plot3d)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description @@ -12683,12 +12353,12 @@ (define-public r-arm "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-coda" ,r-coda) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme))) + (list r-abind + r-coda + r-lme4 + r-mass + r-matrix + r-nlme)) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description @@ -12710,10 +12380,9 @@ (define-public r-circular "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-boot r-mvtnorm)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description @@ -12735,9 +12404,7 @@ (define-public r-activity "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5")))) (build-system r-build-system) (propagated-inputs - `(("r-circular" ,r-circular) - ("r-insol" ,r-insol) - ("r-pbapply" ,r-pbapply))) + (list r-circular r-insol r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description @@ -12760,7 +12427,7 @@ (define-public r-ouch (base32 "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf")))) (build-system r-build-system) - (propagated-inputs `(("r-subplex" ,r-subplex))) + (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description @@ -12822,7 +12489,7 @@ (define-public r-gsl "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description @@ -12866,10 +12533,9 @@ (define-public r-sodium (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs - `(("libsodium" ,libsodium))) + (list libsodium)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description @@ -12893,10 +12559,9 @@ (define-public r-softimpute (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description @@ -12919,9 +12584,9 @@ (define-public r-fftwtools (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) - (inputs `(("fftw" ,fftw))) + (inputs (list fftw)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description @@ -12951,7 +12616,7 @@ (define-public r-tiff ("libjpeg" ,libjpeg-turbo) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description @@ -12995,11 +12660,7 @@ (define-public r-tm (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-nlp" ,r-nlp) - ("r-rcpp" ,r-rcpp) - ("r-slam" ,r-slam) - ("r-xml2" ,r-xml2))) + (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "http://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description @@ -13019,7 +12680,7 @@ (define-public r-waveslim "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description @@ -13044,11 +12705,10 @@ (define-public r-wordcloud "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ;; The "tm" package is only "suggested" according to CRAN, but the - ;; wordcloud package cannot be loaded without it. - ("r-tm" ,r-tm))) + (list r-rcolorbrewer r-rcpp + ;; The "tm" package is only "suggested" according to CRAN, but the + ;; wordcloud package cannot be loaded without it. + r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description @@ -13089,17 +12749,17 @@ (define-public r-tidytree (base32 "1gnpm4zz0kvqng5s179301q0h5993ajynm8y0zbdz38qcmzfpsdk")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-ape + r-dplyr + r-lazyeval + r-magrittr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-yulab-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description @@ -13121,8 +12781,7 @@ (define-public r-rvcheck (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description @@ -13161,7 +12820,7 @@ (define-public r-sparsesvd (base32 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) (build-system r-build-system) - (propagated-inputs `(("r-matrix" ,r-matrix))) + (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description @@ -13185,8 +12844,7 @@ (define-public r-speedglm "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description @@ -13209,13 +12867,13 @@ (define-public r-densityclust (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs - `(("r-fnn" ,r-fnn) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rtsne" ,r-rtsne))) + (list r-fnn + r-ggplot2 + r-ggrepel + r-gridextra + r-rcolorbrewer + r-rcpp + r-rtsne)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description @@ -13256,10 +12914,7 @@ (define-public r-qlcmatrix (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-docopt" ,r-docopt) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-sparsesvd" ,r-sparsesvd))) + (list r-docopt r-matrix r-slam r-sparsesvd)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description @@ -13283,10 +12938,7 @@ (define-public r-ddrtree (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-irlba" ,r-irlba) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description @@ -13336,9 +12988,7 @@ (define-public r-rspectra (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcpp r-rcppeigen)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description @@ -13384,10 +13034,7 @@ (define-public r-flare "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description @@ -13408,7 +13055,7 @@ (define-public r-lassopv (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) - (propagated-inputs `(("r-lars" ,r-lars))) + (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description @@ -13431,7 +13078,7 @@ (define-public r-splitstackshape "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description @@ -13458,7 +13105,7 @@ (define-public r-tfmpvalue "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description @@ -13483,8 +13130,7 @@ (define-public r-rncl "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb")))) (build-system r-build-system) (propagated-inputs - `(("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp))) + (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class @@ -13507,13 +13153,9 @@ (define-public r-phylobase "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-rcpp" ,r-rcpp) - ("r-rncl" ,r-rncl) - ("r-rnexml" ,r-rnexml))) + (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative @@ -13532,20 +13174,20 @@ (define-public r-rnexml "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-lazyeval" ,r-lazyeval) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("r-uuid" ,r-uuid) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-httr + r-lazyeval + r-plyr + r-reshape2 + r-stringi + r-stringr + r-tidyr + r-uuid + r-xml + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in @@ -13567,7 +13209,7 @@ (define-public r-rnifti "0bz10ar6hrgkvlzh9j2im24kwi3s2nnax668z40a2wj6s5xghqlr")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description @@ -13628,7 +13270,7 @@ (define-public r-reportr (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) - (propagated-inputs `(("r-ore" ,r-ore))) + (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description @@ -13653,10 +13295,7 @@ (define-public r-tractor-base (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs - `(("r-ore" ,r-ore) - ("r-reportr" ,r-reportr) - ("r-rnifti" ,r-rnifti) - ("r-shades" ,r-shades))) + (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description @@ -13681,9 +13320,9 @@ (define-public r-grimport (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs - `(("ghostscript" ,ghostscript))) + (list ghostscript)) (propagated-inputs - `(("r-xml" ,r-xml))) + (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description @@ -13705,10 +13344,7 @@ (define-public r-grimport2 (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-jpeg" ,r-jpeg) - ("r-png" ,r-png) - ("r-xml" ,r-xml))) + (list r-base64enc r-jpeg r-png r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description @@ -13735,7 +13371,7 @@ (define-public r-kohonen "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description @@ -13757,7 +13393,7 @@ (define-public r-nnls (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description @@ -13779,7 +13415,7 @@ (define-public r-iso "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description @@ -13803,10 +13439,7 @@ (define-public r-chemometricswithr `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-kohonen" ,r-kohonen) - ("r-mass" ,r-mass) - ("r-pls" ,r-pls))) + (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description @@ -13829,8 +13462,7 @@ (define-public r-als (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs - `(("r-iso" ,r-iso) - ("r-nnls" ,r-nnls))) + (list r-iso r-nnls)) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description @@ -13859,8 +13491,7 @@ (define-public r-strucchange "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) (build-system r-build-system) (propagated-inputs - `(("r-sandwich" ,r-sandwich) - ("r-zoo" ,r-zoo))) + (list r-sandwich r-zoo)) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description @@ -13928,7 +13559,7 @@ (define-public r-ontologyindex (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") (synopsis "Functions for processing ontologies in R") (description @@ -13949,17 +13580,17 @@ (define-public r-gargle "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-cli + r-fs + r-glue + r-httr + r-jsonlite + r-rappdirs + r-rlang + r-rstudioapi + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://gargle.r-lib.org") (synopsis "Utilities for working with Google APIs") (description @@ -13981,21 +13612,21 @@ (define-public r-bigrquery "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-bit64" ,r-bit64) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-prettyunits" ,r-prettyunits) - ("r-progress" ,r-progress) - ("r-rapidjsonr" ,r-rapidjsonr) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-assertthat + r-bit64 + r-curl + r-dbi + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-prettyunits + r-progress + r-rapidjsonr + r-rcpp + r-rlang + r-tibble)) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") (description @@ -14019,7 +13650,7 @@ (define-public r-gmp (modify-phases %standard-phases (add-after 'unpack 'set-CC (lambda _ (setenv "CC" "gcc") #t))))) - (inputs `(("gmp" ,gmp))) + (inputs (list gmp)) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") (description @@ -14043,12 +13674,11 @@ (define-public r-rmpfr (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs - `(("mpfr" ,mpfr) - ("gmp" ,gmp))) + (list mpfr gmp)) (propagated-inputs - `(("r-gmp" ,r-gmp))) + (list r-gmp)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description @@ -14095,7 +13725,7 @@ (define-public r-assertive-properties `((upstream-name . "assertive.properties"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.properties") (synopsis "Assertions to check properties of variables") (description @@ -14120,7 +13750,7 @@ (define-public r-assertive-numbers `((upstream-name . "assertive.numbers"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.numbers") (synopsis "Assertions to check properties of numbers") (description @@ -14144,7 +13774,7 @@ (define-public r-assertive-sets `((upstream-name . "assertive.sets"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.sets") (synopsis "Assertions to check properties of sets") (description @@ -14168,7 +13798,7 @@ (define-public r-assertive-matrices `((upstream-name . "assertive.matrices"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.matrices") (synopsis "Assertions to check properties of matrices") (description @@ -14193,7 +13823,7 @@ (define-public r-assertive-models `((upstream-name . "assertive.models"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.models") (synopsis "Assertions to check properties of models") (description @@ -14217,7 +13847,7 @@ (define-public r-assertive-reflection `((upstream-name . "assertive.reflection"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.reflection") (synopsis "Assertions for checking the state of R") (description @@ -14242,9 +13872,7 @@ (define-public r-assertive-types `((upstream-name . "assertive.types"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-properties" ,r-assertive-properties) - ("r-codetools" ,r-codetools))) + (list r-assertive-base r-assertive-properties r-codetools)) (home-page "https://bitbucket.org/richierocks/assertive.types") (synopsis "Assertions to check types of variables") (description @@ -14268,8 +13896,7 @@ (define-public r-assertive-files `((upstream-name . "assertive.files"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-numbers" ,r-assertive-numbers))) + (list r-assertive-base r-assertive-numbers)) (home-page "https://bitbucket.org/richierocks/assertive.files") (synopsis "Assertions to check properties of files") (description @@ -14294,9 +13921,7 @@ (define-public r-assertive-code `((upstream-name . "assertive.code"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-properties" ,r-assertive-properties) - ("r-assertive-types" ,r-assertive-types))) + (list r-assertive-base r-assertive-properties r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.code") (synopsis "Assertions to check properties of code") (description @@ -14320,8 +13945,7 @@ (define-public r-assertive-datetimes `((upstream-name . "assertive.datetimes"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-types" ,r-assertive-types))) + (list r-assertive-base r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.datetimes") (synopsis "Assertions to check properties of dates and times") (description @@ -14346,9 +13970,7 @@ (define-public r-assertive-strings `((upstream-name . "assertive.strings"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-types" ,r-assertive-types) - ("r-stringi" ,r-stringi))) + (list r-assertive-base r-assertive-types r-stringi)) (home-page "https://bitbucket.org/richierocks/assertive.strings") (synopsis "Assertions to check properties of strings") (description @@ -14372,8 +13994,7 @@ (define-public r-assertive-data-us `((upstream-name . "assertive.data.us"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.us") (synopsis "Assertions to check properties of strings") (description @@ -14398,8 +14019,7 @@ (define-public r-assertive-data-uk `((upstream-name . "assertive.data.uk"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.uk") (synopsis "Assertions to check properties of strings") (description @@ -14424,8 +14044,7 @@ (define-public r-assertive-data `((upstream-name . "assertive.data"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data") (synopsis "Assertions to check properties of data") (description @@ -14448,24 +14067,24 @@ (define-public r-assertive "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-code" ,r-assertive-code) - ("r-assertive-data" ,r-assertive-data) - ("r-assertive-data-uk" ,r-assertive-data-uk) - ("r-assertive-data-us" ,r-assertive-data-us) - ("r-assertive-datetimes" ,r-assertive-datetimes) - ("r-assertive-files" ,r-assertive-files) - ("r-assertive-matrices" ,r-assertive-matrices) - ("r-assertive-models" ,r-assertive-models) - ("r-assertive-numbers" ,r-assertive-numbers) - ("r-assertive-properties" ,r-assertive-properties) - ("r-assertive-reflection" ,r-assertive-reflection) - ("r-assertive-sets" ,r-assertive-sets) - ("r-assertive-strings" ,r-assertive-strings) - ("r-assertive-types" ,r-assertive-types) - ("r-knitr" ,r-knitr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertive-base + r-assertive-code + r-assertive-data + r-assertive-data-uk + r-assertive-data-us + r-assertive-datetimes + r-assertive-files + r-assertive-matrices + r-assertive-models + r-assertive-numbers + r-assertive-properties + r-assertive-reflection + r-assertive-sets + r-assertive-strings + r-assertive-types + r-knitr)) + (native-inputs + (list r-knitr)) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description @@ -14487,7 +14106,7 @@ (define-public r-dotcall64 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description @@ -14510,10 +14129,9 @@ (define-public r-spam (base32 "03c50wfyrzcmrcv9mkgj8dmdg2cwkh4p4ys8gaclr8w7ym45qav3")))) (build-system r-build-system) (propagated-inputs - `(("r-dotcall64" ,r-dotcall64))) + (list r-dotcall64)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description @@ -14541,11 +14159,9 @@ (define-public r-fields (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6")))) (build-system r-build-system) (propagated-inputs - `(("r-maps" ,r-maps) - ("r-spam" ,r-spam) - ("r-viridis" ,r-viridis))) + (list r-maps r-spam r-viridis)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://www.image.ucar.edu/fields") (synopsis "Tools for spatial data") (description @@ -14570,8 +14186,7 @@ (define-public r-spatialextremes `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs - `(("r-fields" ,r-fields) - ("r-maps" ,r-maps))) + (list r-fields r-maps)) (home-page "http://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description @@ -14596,12 +14211,12 @@ (define-public r-drc "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-gtools" ,r-gtools) - ("r-mass" ,r-mass) - ("r-multcomp" ,r-multcomp) - ("r-plotrix" ,r-plotrix) - ("r-scales" ,r-scales))) + (list r-car + r-gtools + r-mass + r-multcomp + r-plotrix + r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description @@ -14642,7 +14257,7 @@ (define-public r-bootstrap (base32 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/bootstrap") (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") (description @@ -14703,7 +14318,7 @@ (define-public r-longitudinal (base32 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) - (propagated-inputs `(("r-corpcor" ,r-corpcor))) + (propagated-inputs (list r-corpcor)) (home-page "http://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description @@ -14727,9 +14342,7 @@ (define-public r-genenet (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs - `(("r-corpcor" ,r-corpcor) - ("r-fdrtool" ,r-fdrtool) - ("r-longitudinal" ,r-longitudinal))) + (list r-corpcor r-fdrtool r-longitudinal)) (home-page "http://strimmerlab.org/software/genenet/") (synopsis "Modeling and inferring gene networks") (description @@ -14752,9 +14365,9 @@ (define-public r-rbamtools (base32 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-refgenome" ,r-refgenome))) + (list r-refgenome)) (home-page "https://cran.r-project.org/web/packages/rbamtools") (synopsis "Read and write BAM (binary alignment) files") (description @@ -14775,7 +14388,7 @@ (define-public r-protviz "0l1pmfr9kmc90rl5s9b0141451rxrjmiiasp3lsvl2x3ps0smqaj")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") (description @@ -14798,9 +14411,9 @@ (define-public r-cmprsk (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cmprsk") (synopsis "Subdistribution analysis of competing risks") (description @@ -14825,11 +14438,7 @@ (define-public r-etm "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description @@ -14852,18 +14461,18 @@ (define-public r-epi (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs - `(("r-cmprsk" ,r-cmprsk) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-etm" ,r-etm) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-numderiv" ,r-numderiv) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-survival" ,r-survival) - ("r-zoo" ,r-zoo))) + (list r-cmprsk + r-data-table + r-dplyr + r-etm + r-mass + r-matrix + r-mgcv + r-numderiv + r-plyr + r-purrr + r-survival + r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description @@ -14889,7 +14498,7 @@ (define-public r-ppls (base32 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppls") (synopsis "Penalized partial least squares") (description @@ -14911,11 +14520,7 @@ (define-public r-huge (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/huge") (synopsis "High-dimensional undirected graph estimation") (description @@ -14937,11 +14542,7 @@ (define-public r-parcor "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) (build-system r-build-system) (propagated-inputs - `(("r-epi" ,r-epi) - ("r-genenet" ,r-genenet) - ("r-glmnet" ,r-glmnet) - ("r-mass" ,r-mass) - ("r-ppls" ,r-ppls))) + (list r-epi r-genenet r-glmnet r-mass r-ppls)) (home-page "https://cran.r-project.org/web/packages/parcor") (synopsis "Regularized estimation of partial correlation matrices") (description @@ -14993,7 +14594,7 @@ (define-public r-listenv (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") (synopsis "Environments behaving (almost) as lists") (description @@ -15016,7 +14617,7 @@ (define-public r-globals "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools))) + (list r-codetools)) (home-page "https://github.com/HenrikBengtsson/globals") (synopsis "Identify global objects in R expressions") (description @@ -15073,12 +14674,9 @@ (define-public r-future (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-globals" ,r-globals) - ("r-listenv" ,r-listenv) - ("r-parallelly" ,r-parallelly))) + (list r-digest r-globals r-listenv r-parallelly)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") (synopsis "Unified parallel and distributed processing in R") (description @@ -15112,10 +14710,9 @@ (define-public r-future-apply (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-future" ,r-future) - ("r-globals" ,r-globals))) + (list r-future r-globals)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future.apply") (synopsis "Apply function to elements in parallel using futures") (description @@ -15139,7 +14736,7 @@ (define-public r-rsvd "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description @@ -15171,11 +14768,7 @@ (define-public r-sloop "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-crayon" ,r-crayon) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-codetools r-crayon r-purrr r-rlang r-tibble)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description @@ -15196,7 +14789,7 @@ (define-public r-capushe (base32 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/capushe/index.html") (synopsis "Calibrating penalties using slope heuristics") (description @@ -15219,9 +14812,7 @@ (define-public r-dorng (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-rngtools" ,r-rngtools))) + (list r-foreach r-iterators r-rngtools)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description @@ -15246,8 +14837,8 @@ (define-public r-blockmodeling "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-matrix)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/blockmodeling") (synopsis "Generalized and classical blockmodeling of valued networks") (description @@ -15271,10 +14862,7 @@ (define-public r-upsetr (properties `((upstream-name . "UpSetR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-gridextra r-plyr r-scales)) (home-page "https://github.com/hms-dbmi/UpSetR") (synopsis "Visualize intersecting sets") (description @@ -15303,8 +14891,7 @@ (define-public r-shinybs ;; non-interactively. (arguments '(#:tests? #f)) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-shiny)) (home-page "https://ebailey78.github.io/shinyBS/") (synopsis "Twitter Bootstrap components for Shiny") (description @@ -15340,13 +14927,9 @@ (define-public r-shinyjqui (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-htmlwidgets r-jsonlite r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr) - ("esbuild" ,esbuild))) + (list r-knitr esbuild)) (home-page "https://github.com/yang-tang/shinyjqui") (synopsis "jQuery UI interactions and effects for Shiny") (description @@ -15385,8 +14968,7 @@ (define-public r-bayesm (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "http://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description @@ -15443,7 +15025,7 @@ (define-public r-rarpack "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) (properties `((upstream-name . "rARPACK"))) (build-system r-build-system) - (propagated-inputs `(("r-rspectra" ,r-rspectra))) + (propagated-inputs (list r-rspectra)) (home-page "https://github.com/yixuan/rARPACK") (synopsis "Solvers for large scale eigenvalue and SVD problems") (description @@ -15467,12 +15049,9 @@ (define-public r-compositions "05pji62pzgfk9dyiybmr16q0h6mdzsmvyzxdni3hn0dvl4a7mr5m")))) (build-system r-build-system) (propagated-inputs - `(("r-bayesm" ,r-bayesm) - ("r-mass" ,r-mass) - ("r-robustbase" ,r-robustbase) - ("r-tensora" ,r-tensora))) + (list r-bayesm r-mass r-robustbase r-tensora)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description @@ -15494,8 +15073,7 @@ (define-public r-cobs "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1")))) (build-system r-build-system) (propagated-inputs - `(("r-quantreg" ,r-quantreg) - ("r-sparsem" ,r-sparsem))) + (list r-quantreg r-sparsem)) (home-page "https://cran.r-project.org/web/packages/cobs") (synopsis "Constrained B-Splines (sparse matrix based)") (description @@ -15517,8 +15095,7 @@ (define-public r-drimpute (properties `((upstream-name . "DrImpute"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ikwak2/DrImpute") (synopsis "Imputing dropout events in single-cell RNA-Seq data") (description @@ -15540,7 +15117,7 @@ (define-public r-gamlss-dist (base32 "0m41n7zf7m0mh1w9ql70wqnzsf2f013ql699im7zmp6fdggb8qxm")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "http://www.gamlss.org/") (synopsis "Distributions for Generalized Additive Models for location scale and shape") (description @@ -15569,12 +15146,9 @@ (define-public r-shinyjs "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-digest r-htmltools r-jsonlite r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description @@ -15622,13 +15196,13 @@ (define-public r-colourpicker (map car mapping) (map cdr mapping))))))))) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-miniui" ,r-miniui) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs))) + (list r-ggplot2 + r-htmltools + r-htmlwidgets + r-jsonlite + r-miniui + r-shiny + r-shinyjs)) (native-inputs `(("esbuild" ,esbuild) ("js-jquery" @@ -15670,16 +15244,16 @@ (define-public r-ggextra (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-colourpicker" ,r-colourpicker) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-miniui" ,r-miniui) - ("r-r6" ,r-r6) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs))) + (list r-colourpicker + r-ggplot2 + r-gtable + r-miniui + r-r6 + r-scales + r-shiny + r-shinyjs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description @@ -15701,7 +15275,7 @@ (define-public r-minpack-lm "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/minpack.lm") (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") (description @@ -15745,9 +15319,9 @@ (define-public r-msir "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs - `(("r-mclust" ,r-mclust))) + (list r-mclust)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description @@ -15767,7 +15341,7 @@ (define-public r-pbivnorm (base32 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://github.com/brentonk/pbivnorm") (synopsis "Vectorized bivariate normal CDF") (description @@ -15788,10 +15362,7 @@ (define-public r-lavaan "12hhbwxaiprs9bmclwhhdpv42h4mrl4gj92zq3wk8rb883mw816l")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-mnormt" ,r-mnormt) - ("r-numderiv" ,r-numderiv) - ("r-pbivnorm" ,r-pbivnorm))) + (list r-mass r-mnormt r-numderiv r-pbivnorm)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description @@ -15813,12 +15384,9 @@ (define-public r-nonnest2 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (build-system r-build-system) (propagated-inputs - `(("r-compquadform" ,r-compquadform) - ("r-lavaan" ,r-lavaan) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sandwich" ,r-sandwich))) + (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description @@ -15842,9 +15410,7 @@ (define-public r-penalized "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/penalized/") (synopsis "Penalized estimation in GLMs and in the Cox model") (description @@ -15870,7 +15436,7 @@ (define-public r-zim "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) (properties `((upstream-name . "ZIM"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://github.com/biostatstudio/ZIM") (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") (description @@ -15940,10 +15506,9 @@ (define-public r-pbdzmq (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs - `(("zeromq" ,zeromq) - ("zlib" ,zlib))) + (list zeromq zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "R interface to ZeroMQ") (description @@ -15967,10 +15532,7 @@ (define-public r-repr "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-pillar" ,r-pillar))) + (list r-base64enc r-htmltools r-jsonlite r-pillar)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description @@ -15992,7 +15554,7 @@ (define-public r-irdisplay (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs - `(("r-repr" ,r-repr))) + (list r-repr)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description @@ -16033,18 +15595,18 @@ (define-public r-irkernel (string-append "[\"" (which "R") "\","))) #t)))))) (inputs - `(("jupyter" ,jupyter))) - (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) - ("r-irdisplay" ,r-irdisplay) - ("r-jsonlite" ,r-jsonlite) - ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) - ("r-minimal" ,r-minimal) - ("r-pbdzmq" ,r-pbdzmq) - ("r-repr" ,r-repr) - ("r-uuid" ,r-uuid))) + (list jupyter)) + (propagated-inputs + (list r-crayon + r-digest + r-evaluate + r-irdisplay + r-jsonlite + ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) + r-minimal + r-pbdzmq + r-repr + r-uuid)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description @@ -16066,8 +15628,7 @@ (define-public r-gmodels "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) (build-system r-build-system) (propagated-inputs - `(("r-gdata" ,r-gdata) - ("r-mass" ,r-mass))) + (list r-gdata r-mass)) (home-page "https://cran.r-project.org/web/packages/gmodels/") (synopsis "Various R programming tools for model fitting") (description @@ -16087,8 +15648,7 @@ (define-public r-apcluster "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-matrix r-rcpp)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description @@ -16112,16 +15672,16 @@ (define-public r-valr "1lzdlw0mw06rymyjzwf4i8rx1z6zxpwxxqfsc9ggqlnhq6bfhy93")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-broom + r-dplyr + r-ggplot2 + r-rcpp + r-readr + r-rlang + r-stringr + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description @@ -16143,7 +15703,7 @@ (define-public r-rematch2 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y")))) (build-system r-build-system) (propagated-inputs - `(("r-tibble" ,r-tibble))) + (list r-tibble)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description @@ -16164,9 +15724,7 @@ (define-public r-picante "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-nlme" ,r-nlme) - ("r-vegan" ,r-vegan))) + (list r-ape r-nlme r-vegan)) (home-page "https://cran.r-project.org/web/packages/picante/") (synopsis "Integrating phylogenies and ecology") (description @@ -16193,10 +15751,7 @@ (define-public r-reinforcelearn "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-nnet" ,r-nnet) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6))) + (list r-checkmate r-nnet r-purrr r-r6)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description @@ -16219,16 +15774,16 @@ (define-public r-lemon "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 + r-gridextra + r-gtable + r-knitr + r-lattice + r-plyr + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description @@ -16249,8 +15804,7 @@ (define-public r-wgaim (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-qtl" ,r-qtl))) + (list r-ggplot2 r-qtl)) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") (description @@ -16271,16 +15825,16 @@ (define-public r-bedr "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-r-utils" ,r-r-utils) - ("r-testthat" ,r-testthat) - ("r-venndiagram" ,r-venndiagram) - ("r-yaml" ,r-yaml) - ("bedops" ,bedops) - ("bedtools" ,bedtools) - ("htslib" ,htslib))) ; for tabix + (list r-data-table + r-r-utils + r-testthat + r-venndiagram + r-yaml + bedops + bedtools + htslib)) ; for tabix (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description @@ -16325,9 +15879,7 @@ (define-public r-partitions "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns")))) (build-system r-build-system) (propagated-inputs - `(("r-gmp" ,r-gmp) - ("r-polynom" ,r-polynom) - ("r-sets" ,r-sets))) + (list r-gmp r-polynom r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description @@ -16373,9 +15925,7 @@ (define-public r-untb "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) (build-system r-build-system) (propagated-inputs - `(("r-brobdingnag" ,r-brobdingnag) - ("r-partitions" ,r-partitions) - ("r-polynom" ,r-polynom))) + (list r-brobdingnag r-partitions r-polynom)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description @@ -16416,8 +15966,7 @@ (define-public r-snpmaxsel (properties `((upstream-name . "SNPmaxsel"))) (build-system r-build-system) (propagated-inputs - `(("r-combinat" ,r-combinat) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-combinat r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") (synopsis "Maximally selected statistics for SNP data") (description @@ -16439,8 +15988,7 @@ (define-public r-acsnminer (properties `((upstream-name . "ACSNMineR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra))) + (list r-ggplot2 r-gridextra)) (home-page "https://cran.r-project.org/web/packages/ACSNMineR") (synopsis "Gene enrichment analysis") (description @@ -16465,10 +16013,9 @@ (define-public r-seqinr "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-segmented" ,r-segmented))) + (list r-ade4 r-segmented)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://seqinr.r-forge.r-project.org/") (synopsis "Biological sequences retrieval and analysis") (description @@ -16490,11 +16037,11 @@ (define-public r-units "1ss0f15h4yqzk488ilsa5d2ibrj3wzwplx4160mn600i8ciy02xr")))) (build-system r-build-system) (inputs - `(("udunits" ,udunits))) + (list udunits)) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description @@ -16519,7 +16066,7 @@ (define-public r-udunits2 (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs - `(("udunits" ,udunits))) + (list udunits)) (home-page "https://cran.r-project.org/package=udunits2") (synopsis "Udunits-2 bindings for R") (description @@ -16540,12 +16087,9 @@ (define-public r-classint (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-e1071" ,r-e1071) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-class r-e1071 r-kernsmooth)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://github.com/r-spatial/classInt/") (synopsis "Choose univariate class intervals") (description @@ -16567,8 +16111,7 @@ (define-public r-spdata (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-sp" ,r-sp))) + (list r-raster r-sp)) (home-page "https://github.com/Nowosad/spData") (synopsis "Datasets for spatial analysis") (description @@ -16618,7 +16161,7 @@ (define-public r-deldir (base32 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/deldir") (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") (description @@ -16644,7 +16187,7 @@ (define-public r-wk (properties `((upstream-name . "wk"))) (build-system r-build-system) (propagated-inputs - `(("r-cpp11" ,r-cpp11))) + (list r-cpp11)) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description @@ -16670,12 +16213,11 @@ (define-public r-s2 (properties `((upstream-name . "s2"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-wk" ,r-wk))) + (list r-rcpp r-wk)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description @@ -16700,21 +16242,16 @@ (define-public r-sf "0dxln3ikqmwczz0ri63xwj05v09hkpljw2qvma6n03nzczyg2713")))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list gdal geos proj sqlite zlib)) (propagated-inputs - `(("r-classint" ,r-classint) - ("r-dbi" ,r-dbi) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-s2" ,r-s2) - ("r-units" ,r-units))) + (list r-classint + r-dbi + r-magrittr + r-rcpp + r-s2 + r-units)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description @@ -16750,23 +16287,23 @@ (define-public r-spdep "inst/doc/nb_sf.Rmd"))))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-coda" ,r-coda) - ("r-deldir" ,r-deldir) - ("r-e1071" ,r-e1071) - ("r-expm" ,r-expm) - ("r-gmodels" ,r-gmodels) - ("r-learnbayes" ,r-learnbayes) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-s2" ,r-s2) - ("r-sf" ,r-sf) - ("r-sp" ,r-sp) - ("r-spdata" ,r-spdata) - ("r-units" ,r-units))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-boot + r-coda + r-deldir + r-e1071 + r-expm + r-gmodels + r-learnbayes + r-mass + r-matrix + r-nlme + r-s2 + r-sf + r-sp + r-spdata + r-units)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description @@ -16790,17 +16327,17 @@ (define-public r-adegenet "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-boot" ,r-boot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-reshape2" ,r-reshape2) - ("r-seqinr" ,r-seqinr) - ("r-shiny" ,r-shiny) - ("r-vegan" ,r-vegan))) + (list r-ade4 + r-ape + r-boot + r-dplyr + r-ggplot2 + r-igraph + r-mass + r-reshape2 + r-seqinr + r-shiny + r-vegan)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description @@ -16827,8 +16364,7 @@ (define-public r-pegas (base32 "0ykx84p7c8cad5d1mj8cm1d5cz2paacdjx4ll4qzmq827lcyycz1")))) (build-system r-build-system) (propagated-inputs - `(("r-adegenet" ,r-adegenet) - ("r-ape" ,r-ape))) + (list r-adegenet r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description @@ -16853,10 +16389,7 @@ (define-public r-rmetasim "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-adegenet" ,r-adegenet) - ("r-gtools" ,r-gtools) - ("r-pegas" ,r-pegas))) + (list r-ade4 r-adegenet r-gtools r-pegas)) (home-page "https://cran.r-project.org/web/packages/rmetasim") (synopsis "Individual-based population genetic simulation environment") (description @@ -16880,11 +16413,7 @@ (define-public r-genetics "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs - `(("r-combinat" ,r-combinat) - ("r-gdata" ,r-gdata) - ("r-gtools" ,r-gtools) - ("r-mass" ,r-mass) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-combinat r-gdata r-gtools r-mass r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/genetics/") (synopsis "Population genetics") (description @@ -16910,7 +16439,7 @@ (define-public r-snp-plotter "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) (properties `((upstream-name . "snp.plotter"))) (build-system r-build-system) - (propagated-inputs `(("r-genetics" ,r-genetics))) + (propagated-inputs (list r-genetics)) (home-page "https://cran.r-project.org/web/packages/snp.plotter/") (synopsis "Plot p-values using single SNP and/or haplotype data") (description @@ -16933,7 +16462,7 @@ (define-public r-polspline (sha256 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") (synopsis "Polynomial spline routines") (description @@ -16954,22 +16483,22 @@ (define-public r-rms (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-htmltable" ,r-htmltable) - ("r-htmltools" ,r-htmltools) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-multcomp" ,r-multcomp) - ("r-nlme" ,r-nlme) - ("r-polspline" ,r-polspline) - ("r-quantreg" ,r-quantreg) - ("r-rpart" ,r-rpart) - ("r-sparsem" ,r-sparsem) - ("r-survival" ,r-survival))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster + r-digest + r-ggplot2 + r-hmisc + r-htmltable + r-htmltools + r-lattice + r-mass + r-multcomp + r-nlme + r-polspline + r-quantreg + r-rpart + r-sparsem + r-survival)) + (native-inputs (list gfortran)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description @@ -17001,8 +16530,8 @@ (define-public r-arsenal "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) - (propagated-inputs `(("r-knitr" ,r-knitr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-knitr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description @@ -17041,10 +16570,9 @@ (define-public r-haplo-stats (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs - `(("r-arsenal" ,r-arsenal) - ("r-rms" ,r-rms))) + (list r-arsenal r-rms)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; for vignettes + (list r-r-rsp)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description @@ -17068,7 +16596,7 @@ (define-public r-bqtl (base32 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") (synopsis "Bayesian QTL mapping toolkit") (description @@ -17111,11 +16639,7 @@ (define-public r-dlmap "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) (build-system r-build-system) (propagated-inputs - `(("r-ibdreg" ,r-ibdreg) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-qtl" ,r-qtl) - ("r-wgaim" ,r-wgaim))) + (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim)) (home-page "https://cran.r-project.org/web/packages/dlmap/") (synopsis "Detection localization mapping for QTL") (description @@ -17184,8 +16708,7 @@ (define-public r-sparql (properties `((upstream-name . "SPARQL"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-rcurl r-xml)) (home-page "https://cran.r-project.org/web/packages/SPARQL") (synopsis "SPARQL client for R") (description "This package provides an interface to use SPARQL to pose @@ -17206,14 +16729,14 @@ (define-public r-bookdown "1qqvvfbpbd6sin8vpvr3zzlhlyx1i6b98yp77xj5zl220nid5slb")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jquerylib" ,r-jquerylib) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tinytex" ,r-tinytex) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml) - ("pandoc" ,pandoc))) + (list r-htmltools + r-jquerylib + r-knitr + r-rmarkdown + r-tinytex + r-xfun + r-yaml + pandoc)) ;; We cannot add knitr because this package depends on xfun, which is an ;; input to knitr. #; @@ -17238,9 +16761,9 @@ (define-public r-optparse "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij")))) (build-system r-build-system) (propagated-inputs - `(("r-getopt" ,r-getopt))) + (list r-getopt)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description @@ -17283,12 +16806,9 @@ (define-public r-hierfstat "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-adegenet" ,r-adegenet) - ("r-gaston" ,r-gaston) - ("r-gtools" ,r-gtools))) + (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description @@ -17334,8 +16854,7 @@ (define-public r-sampling "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-mass" ,r-mass))) + (list r-lpsolve r-mass)) (home-page "https://cran.r-project.org/web/packages/sampling/") (synopsis "Survey sampling") (description @@ -17428,7 +16947,7 @@ (define-public r-svmisc (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description @@ -17451,7 +16970,7 @@ (define-public r-xyz "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/xyz/") (synopsis "Algorithm for fast interaction search in high-dimensional data") (description @@ -17518,8 +17037,7 @@ (define-public r-extrafont "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) (build-system r-build-system) (propagated-inputs - `(("r-extrafontdb" ,r-extrafontdb) - ("r-rttf2pt1" ,r-rttf2pt1))) + (list r-extrafontdb r-rttf2pt1)) (home-page "https://github.com/wch/extrafont") (synopsis "Tools for using fonts in R") (description @@ -17551,9 +17069,7 @@ (define-public r-xkcd "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) (build-system r-build-system) (propagated-inputs - `(("r-extrafont" ,r-extrafont) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc))) + (list r-extrafont r-ggplot2 r-hmisc)) (home-page "https://cran.r-project.org/web/packages/xkcd/") (synopsis "Plot ggplot2 graphics in the XKCD style") (description @@ -17575,10 +17091,9 @@ (define-public r-babelgene (properties `((upstream-name . "babelgene"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-rlang" ,r-rlang))) + (list r-dplyr r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://igordot.github.io/babelgene/") (synopsis "Gene orthologs for model organisms in a Tidy data format") @@ -17605,14 +17120,14 @@ (define-public r-msigdbr "103m52av68pkjfh8f81qh6j3cs1mj1lg831ciwybr34cax767jr1")))) (build-system r-build-system) (propagated-inputs - `(("r-babelgene" ,r-babelgene) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + (list r-babelgene + r-dplyr + r-magrittr + r-rlang + r-tibble + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description @@ -17707,11 +17222,9 @@ (define-public r-ggplotify "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridgraphics" ,r-gridgraphics) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-ggplot2 r-gridgraphics r-yulab-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description @@ -17735,7 +17248,7 @@ (define-public r-triebeard (base32 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description @@ -17758,10 +17271,7 @@ (define-public r-tweenr "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) (propagated-inputs - `(("r-farver" ,r-farver) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-farver r-magrittr r-rcpp r-rlang)) (home-page "https://github.com/thomasp85/tweenr") (synopsis "Interpolate data for smooth animations") (description @@ -17784,7 +17294,7 @@ (define-public r-polyclip (base32 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) (build-system r-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") (synopsis "Polygon clipping") (description @@ -17810,8 +17320,7 @@ (define-public r-urltools "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-triebeard" ,r-triebeard))) + (list r-rcpp r-triebeard)) (home-page "https://github.com/Ironholds/urltools/") (synopsis "Vectorized tools for URL handling and parsing") (description @@ -17836,17 +17345,17 @@ (define-public r-ggforce "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-mass" ,r-mass) - ("r-polyclip" ,r-polyclip) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyselect" ,r-tidyselect) - ("r-tweenr" ,r-tweenr) - ("r-withr" ,r-withr))) + (list r-ggplot2 + r-gtable + r-mass + r-polyclip + r-rcpp + r-rcppeigen + r-rlang + r-scales + r-tidyselect + r-tweenr + r-withr)) (home-page "https://ggforce.data-imaginist.com") (synopsis "Accelerating ggplot2") (description @@ -17869,19 +17378,19 @@ (define-public r-europepmc "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-urltools" ,r-urltools) - ("r-xml2" ,r-xml2))) + (list r-dplyr + r-httr + r-jsonlite + r-plyr + r-progress + r-purrr + r-rlang + r-tibble + r-tidyr + r-urltools + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/europepmc/") (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") (description @@ -17909,23 +17418,23 @@ (define-public r-ggraph "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-graphlayouts" ,r-graphlayouts) - ("r-gtable" ,r-gtable) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-digest + r-dplyr + r-ggforce + r-ggplot2 + r-ggrepel + r-graphlayouts + r-gtable + r-igraph + r-mass + r-rcpp + r-rlang + r-scales + r-tidygraph + r-viridis + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ggraph/") (synopsis "Implementation of grammar of graphics for graphs and networks") (description @@ -17950,10 +17459,7 @@ (define-public r-gkmsvm (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs - `(("r-kernlab" ,r-kernlab) - ("r-rcpp" ,r-rcpp) - ("r-rocr" ,r-rocr) - ("r-seqinr" ,r-seqinr))) + (list r-kernlab r-rcpp r-rocr r-seqinr)) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description @@ -17976,7 +17482,7 @@ (define-public r-varselrf (properties `((upstream-name . "varSelRF"))) (build-system r-build-system) (propagated-inputs - `(("r-randomforest" ,r-randomforest))) + (list r-randomforest)) (home-page "https://www.ligarto.org/rdiaz/software/software") (synopsis "Variable selection using random forests") (description @@ -18002,9 +17508,8 @@ (define-public r-pamr "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-survival" ,r-survival))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster r-survival)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pamr/") (synopsis "Prediction Analysis for Microarrays") (description @@ -18044,13 +17549,13 @@ (define-public r-ggvis "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-shiny" ,r-shiny))) + (list r-assertthat + r-dplyr + r-htmltools + r-jsonlite + r-magrittr + r-rlang + r-shiny)) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") (description @@ -18073,10 +17578,9 @@ (define-public r-gbm "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-survival" ,r-survival))) + (list r-lattice r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description @@ -18129,10 +17633,7 @@ (define-public r-threejs sources targets)))) #t))))) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-crosstalk" ,r-crosstalk) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph))) + (list r-base64enc r-crosstalk r-htmlwidgets r-igraph)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" @@ -18189,8 +17690,7 @@ (define-public r-mpm "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-mass" ,r-mass))) + (list r-kernsmooth r-mass)) (home-page "http://mpm.r-forge.r-project.org") (synopsis "Multivariate projection methods") (description @@ -18212,8 +17712,7 @@ (define-public r-png "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) (build-system r-build-system) (inputs - `(("libpng" ,libpng) - ("zlib" ,zlib))) + (list libpng zlib)) (home-page "https://www.rforge.net/png/") (synopsis "Read and write PNG images") (description @@ -18236,8 +17735,7 @@ (define-public r-ggcorrplot "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (home-page "http://www.sthda.com/english/wiki/ggcorrplot") (synopsis "Visualization of a correlation matrix using ggplot2") (description @@ -18261,9 +17759,8 @@ (define-public r-ggfun (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggfun") (synopsis "Miscellaneous functions for ggplot2") (description @@ -18286,14 +17783,14 @@ (define-public r-gridtext (properties `((upstream-name . "gridtext"))) (build-system r-build-system) (propagated-inputs - `(("r-jpeg" ,r-jpeg) - ("r-markdown" ,r-markdown) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-xml2" ,r-xml2))) + (list r-jpeg + r-markdown + r-png + r-rcpp + r-rcurl + r-rlang + r-stringr + r-xml2)) (home-page "https://wilkelab.org/gridtext/") (synopsis "Improved text rendering support for Grid graphics") (description @@ -18317,11 +17814,8 @@ (define-public r-ggtext (properties `((upstream-name . "ggtext"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridtext" ,r-gridtext) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gridtext r-rlang r-scales)) + (native-inputs (list r-knitr)) (home-page "https://wilkelab.org/ggtext/") (synopsis "Improved text rendering support for ggplot2") (description @@ -18401,12 +17895,12 @@ (define-public r-flexdashboard sources targets)))) #t))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny))) + (list r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-rmarkdown + r-shiny)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-raphael" @@ -18466,7 +17960,7 @@ (define-public r-preseqr (properties `((upstream-name . "preseqR"))) (build-system r-build-system) (propagated-inputs - `(("r-polynom" ,r-polynom))) + (list r-polynom)) (home-page "https://cran.r-project.org/web/packages/preseqR/") (synopsis "Predicting species accumulation curves") (description @@ -18534,7 +18028,7 @@ (define-public r-downloader "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest))) + (list r-digest)) (home-page "https://github.com/wch/downloader") (synopsis "Download files over HTTP and HTTPS") (description @@ -18558,12 +18052,12 @@ (define-public r-aplot (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs - `(("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-ggplotify" ,r-ggplotify) - ("r-magrittr" ,r-magrittr) - ("r-patchwork" ,r-patchwork) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-ggfun + r-ggplot2 + r-ggplotify + r-magrittr + r-patchwork + r-yulab-utils)) (home-page "https://github.com/YuLab-SMU/aplot") (synopsis "Decorate a ggplot with associated information") (description @@ -18588,7 +18082,7 @@ (define-public r-ggnewscale (properties `((upstream-name . "ggnewscale"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://cran.r-project.org/package=ggnewscale") (synopsis "Multiple fill and color scales in ggplot2") (description @@ -18610,7 +18104,7 @@ (define-public r-ggpointdensity `((upstream-name . "ggpointdensity"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://github.com/LKremer/ggpointdensity") (synopsis "Cross between a 2D density plot and a scatter plot") (description @@ -18634,19 +18128,17 @@ (define-public r-arrow (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs - `(("apache-arrow" ,apache-arrow "lib") - ("zlib" ,zlib))) + (list `(,apache-arrow "lib") zlib)) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-bit64" ,r-bit64) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-assertthat + r-bit64 + r-purrr + r-r6 + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description @@ -18670,9 +18162,9 @@ (define-public r-rex "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval))) + (list r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description @@ -18696,10 +18188,9 @@ (define-public r-mlapi (properties `((upstream-name . "mlapi"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-r6" ,r-r6))) + (list r-matrix r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=mlapi") (synopsis "Abstract classes for building scikit-learn like API") (description @@ -18723,7 +18214,7 @@ (define-public r-float (properties `((upstream-name . "float"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://github.com/wrathematics/float") (synopsis "32-bit floats") (description @@ -18750,13 +18241,13 @@ (define-public r-rsparse (properties `((upstream-name . "rsparse"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-float" ,r-float) - ("r-lgr" ,r-lgr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhpcblasctl" ,r-rhpcblasctl))) + (list r-data-table + r-float + r-lgr + r-matrix + r-rcpp + r-rcpparmadillo + r-rhpcblasctl)) (home-page "https://github.com/rexyai/rsparse") (synopsis "Statistical learning on sparse matrices") (description @@ -18782,17 +18273,17 @@ (define-public r-text2vec (properties `((upstream-name . "text2vec"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-lgr" ,r-lgr) - ("r-matrix" ,r-matrix) - ("r-mlapi" ,r-mlapi) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rsparse" ,r-rsparse) - ("r-stringi" ,r-stringi))) + (list r-data-table + r-digest + r-lgr + r-matrix + r-mlapi + r-r6 + r-rcpp + r-rsparse + r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://text2vec.org") (synopsis "Text mining framework for R") (description @@ -18818,11 +18309,7 @@ (define-public r-mcmcpack (properties `((upstream-name . "MCMCpack"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-mcmc" ,r-mcmc) - ("r-quantreg" ,r-quantreg))) + (list r-coda r-lattice r-mass r-mcmc r-quantreg)) (home-page "https://cran.r-project.org/package=MCMCpack") (synopsis "Markov Chain Monte Carlo (MCMC) package") (description @@ -18871,11 +18358,7 @@ (define-public r-cyclocomp (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-remotes" ,r-remotes) - ("r-withr" ,r-withr))) + (list r-callr r-crayon r-desc r-remotes r-withr)) (home-page "https://github.com/MangoTheCat/cyclocomp") (synopsis "Cyclomatic complexity of R code") (description @@ -18899,18 +18382,18 @@ (define-public r-lintr (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-crayon" ,r-crayon) - ("r-cyclocomp" ,r-cyclocomp) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-rex" ,r-rex) - ("r-rstudioapi" ,r-rstudioapi) - ("r-testthat" ,r-testthat) - ("r-xml2" ,r-xml2) - ("r-xmlparsedata" ,r-xmlparsedata))) + (list r-codetools + r-crayon + r-cyclocomp + r-digest + r-httr + r-jsonlite + r-knitr + r-rex + r-rstudioapi + r-testthat + r-xml2 + r-xmlparsedata)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax @@ -18931,16 +18414,16 @@ (define-public r-sctransform "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx")))) (build-system r-build-system) (propagated-inputs - `(("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-reshape2" ,r-reshape2))) + (list r-future + r-future-apply + r-ggplot2 + r-gridextra + r-mass + r-matrix + r-matrixstats + r-rcpp + r-rcpparmadillo + r-reshape2)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description @@ -18969,20 +18452,20 @@ (define-public r-styler (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-cli" ,r-cli) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-tibble" ,r-tibble) - ("r-withr" ,r-withr) - ("r-xfun" ,r-xfun))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-backports + r-cli + r-glue + r-magrittr + r-purrr + r-r-cache + r-rematch2 + r-rlang + r-rprojroot + r-tibble + r-withr + r-xfun)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description @@ -19042,7 +18525,7 @@ (define-public r-blme (base32 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) - (propagated-inputs `(("r-lme4" ,r-lme4))) + (propagated-inputs (list r-lme4)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description @@ -19064,20 +18547,20 @@ (define-public r-batchtools "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-base64url" ,r-base64url) - ("r-brew" ,r-brew) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-fs" ,r-fs) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-stringi" ,r-stringi) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-backports + r-base64url + r-brew + r-checkmate + r-data-table + r-digest + r-fs + r-progress + r-r6 + r-rappdirs + r-stringi + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description @@ -19102,7 +18585,7 @@ (define-public r-clue (base32 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd")))) (build-system r-build-system) - (propagated-inputs `(("r-cluster" ,r-cluster))) + (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") (synopsis "Tools for analyzing cluster ensembles") (description "Cluster ensembles are collections of individual solutions to @@ -19126,9 +18609,9 @@ (define-public r-sitmo (base32 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description @@ -19150,11 +18633,9 @@ (define-public r-dqrng "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-sitmo" ,r-sitmo))) + (list r-bh r-rcpp r-sitmo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description @@ -19185,10 +18666,8 @@ (define-public r-ingredients (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-scales" ,r-scales))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gridextra r-scales)) + (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description @@ -19224,8 +18703,8 @@ (define-public r-ibreakdown "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-ggplot2)) + (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description @@ -19250,10 +18729,9 @@ (define-public r-dae "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr))) + (list r-ggplot2 r-plyr)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description @@ -19290,9 +18768,7 @@ (define-public r-dalex (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ibreakdown" ,r-ibreakdown) - ("r-ingredients" ,r-ingredients))) + (list r-ggplot2 r-ibreakdown r-ingredients)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description @@ -19319,11 +18795,9 @@ (define-public r-enrichr (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-httr" ,r-httr) - ("r-rjson" ,r-rjson))) + (list r-ggplot2 r-httr r-rjson)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description @@ -19345,7 +18819,7 @@ (define-public r-plot3d "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) - (propagated-inputs `(("r-misc3d" ,r-misc3d))) + (propagated-inputs (list r-misc3d)) (home-page "https://cran.r-project.org/web/packages/plot3D") (synopsis "Plot multi-dimensional data") (description @@ -19367,15 +18841,15 @@ (define-public r-ggfortify "0qls8pyndrlwx75wzlc0xmk04qq263d7065r3d6kvay7haa4nm40")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-ggplot2 + r-gridextra + r-scales + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description @@ -19399,14 +18873,14 @@ (define-public r-refmanager (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lubridate" ,r-lubridate) - ("r-plyr" ,r-plyr) - ("r-stringr" ,r-stringr) - ("r-xml2" ,r-xml2))) + (list r-httr + r-jsonlite + r-lubridate + r-plyr + r-stringr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description @@ -19434,15 +18908,15 @@ (define-public r-citr "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-curl" ,r-curl) - ("r-httr" ,r-httr) - ("r-miniui" ,r-miniui) - ("r-refmanager" ,r-refmanager) - ("r-rstudioapi" ,r-rstudioapi) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-yaml" ,r-yaml))) + (list r-assertthat + r-curl + r-httr + r-miniui + r-refmanager + r-rstudioapi + r-shiny + r-shinyjs + r-yaml)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description @@ -19464,11 +18938,9 @@ (define-public r-xgboost "04xbgrrb3aq067hrivslq5f2rd1v95yfv7lkj596ijyqi6ibjl27")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix))) + (list r-data-table r-jsonlite r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description @@ -19495,12 +18967,9 @@ (define-public r-umap "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab")))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-rcpp" ,r-rcpp) - ("r-reticulate" ,r-reticulate) - ("r-rspectra" ,r-rspectra))) + (list r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description @@ -19522,14 +18991,14 @@ (define-public r-uwot "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf")))) (build-system r-build-system) (propagated-inputs - `(("r-dqrng" ,r-dqrng) - ("r-fnn" ,r-fnn) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppprogress" ,r-rcppprogress) - ("r-rspectra" ,r-rspectra))) + (list r-dqrng + r-fnn + r-irlba + r-matrix + r-rcpp + r-rcppannoy + r-rcppprogress + r-rspectra)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description @@ -19554,22 +19023,22 @@ (define-public r-kableextra (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rvest" ,r-rvest) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-svglite" ,r-svglite) - ("r-viridislite" ,r-viridislite) - ("r-webshot" ,r-webshot) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-digest + r-glue + r-htmltools + r-knitr + r-magrittr + r-rmarkdown + r-rstudioapi + r-rvest + r-scales + r-stringr + r-svglite + r-viridislite + r-webshot + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description @@ -19592,7 +19061,7 @@ (define-public r-glasso (sha256 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/glasso/") (synopsis "Graphical Lasso: estimation of Gaussian graphical models") (description @@ -19683,11 +19152,9 @@ (define-public r-leiden (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-reticulate" ,r-reticulate))) + (list r-igraph r-matrix r-reticulate)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description @@ -19710,10 +19177,9 @@ (define-public r-patchwork "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable))) + (list r-ggplot2 r-gtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description @@ -19756,26 +19222,26 @@ (define-public r-liger (find-files "." "\\.class$")) #t))))) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-hmisc" ,r-hmisc) - ("r-ica" ,r-ica) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-mclust" ,r-mclust) - ("r-patchwork" ,r-patchwork) - ("r-plyr" ,r-plyr) - ("r-rann-l1" ,r-rann-l1) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-riverplot" ,r-riverplot) - ("r-rtsne" ,r-rtsne) - ("r-snow" ,r-snow))) + (list r-cowplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-ggrepel + r-hmisc + r-ica + r-irlba + r-matrix + r-mclust + r-patchwork + r-plyr + r-rann-l1 + r-rcpp + r-rcpparmadillo + r-riverplot + r-rtsne + r-snow)) (native-inputs `(("jdk" ,icedtea "jdk") ;; See https://github.com/MacoskoLab/liger/issues/96 @@ -19819,19 +19285,19 @@ (define-public r-harmony #t)))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppprogress" ,r-rcppprogress) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-cowplot + r-dplyr + r-ggplot2 + r-irlba + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-rlang + r-tibble + r-tidyr)) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (home-page "https://github.com/immunogenomics/harmony") (synopsis "Integration of single cell sequencing data") (description @@ -19854,15 +19320,15 @@ (define-public r-covr (properties `((upstream-name . "covr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rex" ,r-rex) - ("r-withr" ,r-withr) - ("r-yaml" ,r-yaml))) + (list r-crayon + r-digest + r-httr + r-jsonlite + r-rex + r-withr + r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description @@ -19888,13 +19354,12 @@ (define-public r-systemfonts (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs - `(("r-cpp11" ,r-cpp11))) + (list r-cpp11)) (inputs `(("fontconfig" ,fontconfig) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description @@ -19919,9 +19384,7 @@ (define-public r-graphlayouts (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-igraph r-rcpp r-rcpparmadillo)) (home-page "https://github.com/schochastics/graphlayouts") (synopsis "Additional layout algorithms for network visualizations") (description @@ -19946,15 +19409,15 @@ (define-public r-terra (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) ; needed for proj - ("zlib" ,zlib))) + (list gdal + geos + proj + sqlite ; needed for proj + zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://rspatial.org/terra") (synopsis "Spatial data analysis") (description @@ -19980,15 +19443,15 @@ (define-public r-tidygraph (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-igraph + r-magrittr + r-pillar + r-r6 + r-rcpp + r-rlang + r-tibble + r-tidyr)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description @@ -20018,9 +19481,7 @@ (define-public r-soupx (properties `((upstream-name . "SoupX"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-seurat" ,r-seurat))) + (list r-ggplot2 r-matrix r-seurat)) (home-page "https://github.com/constantAmateur/SoupX") (synopsis "Single cell mRNA Soup eXterminator") (description @@ -20042,11 +19503,9 @@ (define-public r-assertr "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-mass" ,r-mass) - ("r-rlang" ,r-rlang))) + (list r-dplyr r-mass r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) ; needed for vignette + (list r-knitr)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description @@ -20070,11 +19529,9 @@ (define-public r-parameters (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight))) + (list r-bayestestr r-datawizard r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description @@ -20099,14 +19556,11 @@ (define-public r-rgdal (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("proj" ,proj) - ("zlib" ,zlib))) + (list gdal proj zlib)) (propagated-inputs - `(("r-sp" ,r-sp))) + (list r-sp)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "http://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description @@ -20129,9 +19583,9 @@ (define-public r-insol (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster))) + (list r-raster)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://meteoexploration.com/R/insol/index.html") (synopsis "Tools for calculating solar radiation") (description @@ -20156,10 +19610,9 @@ (define-public r-lifecycle (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) - ("r-rlang" ,r-rlang))) + (list r-glue r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description @@ -20185,9 +19638,9 @@ (define-public r-assertable "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on @@ -20213,7 +19666,7 @@ (define-public r-quadprog (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/quadprog") (synopsis "Functions to solve quadratic programming problems") (description @@ -20234,7 +19687,7 @@ (define-public r-desolve (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") (description "This package provides functions that solve initial value @@ -20281,7 +19734,7 @@ (define-public r-subplex "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/subplex") (synopsis "Unconstrained optimization using the subplex algorithm") (description @@ -20324,10 +19777,10 @@ (define-public r-bio3d "1jvcmpzi9knhxq5jsbhg8slm8hnlx2y8smmwwrbnbyd0rmk5fhci")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (inputs (list zlib)) + (propagated-inputs (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description @@ -20358,10 +19811,7 @@ (define-public r-bios2cor (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory) - ("r-bio3d" ,r-bio3d) - ("r-circular" ,r-circular) - ("r-igraph" ,r-igraph))) + (list r-bigmemory r-bio3d r-circular r-igraph)) (home-page "https://cran.r-project.org/web/packages/Bios2cor/") (synopsis "From biological sequences and simulations to correlation analysis") (description @@ -20433,9 +19883,7 @@ (define-public r-networkd3 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (propagated-inputs - `(("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr))) + (list r-htmlwidgets r-igraph r-magrittr)) (home-page "https://cran.r-project.org/package=networkD3") (synopsis "D3 JavaScript network graphs from R") (description @@ -20457,15 +19905,15 @@ (define-public r-aasea (properties `((upstream-name . "aaSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-bios2cor" ,r-bios2cor) - ("r-dt" ,r-dt) - ("r-hmisc" ,r-hmisc) - ("r-magrittr" ,r-magrittr) - ("r-networkd3" ,r-networkd3) - ("r-plotly" ,r-plotly) - ("r-seqinr" ,r-seqinr) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard))) + (list r-bios2cor + r-dt + r-hmisc + r-magrittr + r-networkd3 + r-plotly + r-seqinr + r-shiny + r-shinydashboard)) (home-page "https://cran.r-project.org/web/packages/aaSEA/") (synopsis "Amino acid substitution effect analyzer") (description @@ -20489,8 +19937,7 @@ (define-public r-abacus (properties `((upstream-name . "ABACUS"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-shiny" ,r-shiny))) + (list r-ggplot2 r-shiny)) (home-page "https://shiny.abdn.ac.uk/Stats/apps/") (synopsis "Apps-based activities for communicating and understanding statistics") (description @@ -20535,8 +19982,7 @@ (define-public r-abcadm (properties `((upstream-name . "abcADM"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-rcpp)) (home-page "https://cran.r-project.org/web/packages/abcADM/") (synopsis "Fit accumulated damage models and estimate reliability using ABC") (description @@ -20560,9 +20006,9 @@ (define-public r-rglpk (properties `((upstream-name . "Rglpk"))) (build-system r-build-system) (propagated-inputs - `(("r-slam" ,r-slam))) + (list r-slam)) (inputs - `(("glpk" ,glpk))) + (list glpk)) (home-page "https://r-forge.r-project.org/projects/rglp/") (synopsis "R interface to the GNU Linear Programming Kit") (description @@ -20586,10 +20032,7 @@ (define-public r-abcdefba (properties `((upstream-name . "abcdeFBA"))) (build-system r-build-system) (propagated-inputs - `(("r-corrplot" ,r-corrplot) - ("r-lattice" ,r-lattice) - ("r-rgl" ,r-rgl) - ("r-rglpk" ,r-rglpk))) + (list r-corrplot r-lattice r-rgl r-rglpk)) (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") (description @@ -20635,7 +20078,7 @@ (define-public r-abemus (properties `((upstream-name . "abemus"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/abemus/") (synopsis "Adaptive base error model in ultra-deep sequencing data") (description @@ -20685,8 +20128,7 @@ (define-public r-rintrojs (base32 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-jsonlite r-shiny)) (home-page "https://github.com/carlganz/rintrojs") (synopsis "Wrapper for the Intro.js library") (description @@ -20712,11 +20154,9 @@ (define-public r-sysfonts (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list freetype libpng zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/yixuan/sysfonts") (synopsis "Loading fonts into R") (description @@ -20738,7 +20178,7 @@ (define-public r-showtextdb (properties `((upstream-name . "showtextdb"))) (build-system r-build-system) (propagated-inputs - `(("r-sysfonts" ,r-sysfonts))) + (list r-sysfonts)) (home-page "https://cran.r-project.org/web/packages/showtextdb/") (synopsis "Font files for the 'showtext' package") (description @@ -20760,15 +20200,11 @@ (define-public r-showtext (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list freetype libpng zlib)) (propagated-inputs - `(("r-showtextdb" ,r-showtextdb) - ("r-sysfonts" ,r-sysfonts))) + (list r-showtextdb r-sysfonts)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/yixuan/showtext") (synopsis "Using fonts more easily in R graphs") (description @@ -20794,12 +20230,9 @@ (define-public r-emojifont (properties `((upstream-name . "emojifont"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-proto" ,r-proto) - ("r-showtext" ,r-showtext) - ("r-sysfonts" ,r-sysfonts))) + (list r-ggplot2 r-proto r-showtext r-sysfonts)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/emojifont") (synopsis "Emoji and Font Awesome in R graphics") (description @@ -20821,13 +20254,13 @@ (define-public r-abstractr (properties `((upstream-name . "abstractr"))) (build-system r-build-system) (propagated-inputs - `(("r-colourpicker" ,r-colourpicker) - ("r-emojifont" ,r-emojifont) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rintrojs" ,r-rintrojs) - ("r-shiny" ,r-shiny) - ("r-shinythemes" ,r-shinythemes))) + (list r-colourpicker + r-emojifont + r-ggplot2 + r-gridextra + r-rintrojs + r-shiny + r-shinythemes)) (home-page "https://matt-kumar.shinyapps.io/portfolio") (synopsis "R-Shiny application for creating visual abstracts") (description @@ -20850,11 +20283,8 @@ (define-public r-qgam (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-mgcv" ,r-mgcv) - ("r-plyr" ,r-plyr) - ("r-shiny" ,r-shiny))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-doparallel r-mgcv r-plyr r-shiny)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qgam/") (synopsis "Smooth additive quantile regression models") (description @@ -20883,14 +20313,14 @@ (define-public r-abtest (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix) - ("r-qgam" ,r-qgam) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-sn" ,r-sn) - ("r-truncnorm" ,r-truncnorm))) + (list r-matrix + r-mvtnorm + r-plotrix + r-qgam + r-rcolorbrewer + r-rcpp + r-sn + r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description @@ -20913,8 +20343,7 @@ (define-public r-reldist (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs - `(("r-hmisc" ,r-hmisc) - ("r-mgcv" ,r-mgcv))) + (list r-hmisc r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description @@ -20941,8 +20370,7 @@ (define-public r-accept (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reldist" ,r-reldist))) + (list r-dplyr r-reldist)) (home-page "https://cran.r-project.org/web/packages/accept/") (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") (description @@ -20966,10 +20394,7 @@ (define-public r-smpracticals (properties `((upstream-name . "SMPracticals"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipse" ,r-ellipse) - ("r-mass" ,r-mass) - ("r-nlme" ,r-nlme) - ("r-survival" ,r-survival))) + (list r-ellipse r-mass r-nlme r-survival)) (home-page "http://statwww.epfl.ch/davison/SM/") (synopsis "Practicals for use with Davison (2003) Statistical Models") (description @@ -21020,8 +20445,7 @@ (define-public r-tcltk2 (properties `((upstream-name . "tcltk2"))) (build-system r-build-system) (inputs - `(("tcl" ,tcl) - ("tk" ,tk))) + (list tcl tk)) (home-page "https://www.sciviews.org/SciViews-R") (synopsis "Tcl/Tk additions") (description @@ -21043,9 +20467,7 @@ (define-public r-accrual (properties `((upstream-name . "accrual"))) (build-system r-build-system) (propagated-inputs - `(("r-fgui" ,r-fgui) - ("r-smpracticals" ,r-smpracticals) - ("r-tcltk2" ,r-tcltk2))) + (list r-fgui r-smpracticals r-tcltk2)) (home-page "https://cran.r-project.org/web/packages/accrual/") (synopsis "Bayesian accrual prediction") (description @@ -21092,8 +20514,8 @@ (define-public r-mda "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) - (propagated-inputs `(("r-class" ,r-class))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-class)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/mda/") (synopsis "Mixture and flexible discriminant analysis") (description @@ -21115,7 +20537,7 @@ (define-public r-elasticnet (properties `((upstream-name . "elasticnet"))) (build-system r-build-system) (propagated-inputs - `(("r-lars" ,r-lars))) + (list r-lars)) (home-page "http://users.stat.umn.edu/~zouxx019/") (synopsis "Elastic-Net for sparse estimation and sparse PCA") (description @@ -21138,9 +20560,7 @@ (define-public r-sparselda (properties `((upstream-name . "sparseLDA"))) (build-system r-build-system) (propagated-inputs - `(("r-elasticnet" ,r-elasticnet) - ("r-mass" ,r-mass) - ("r-mda" ,r-mda))) + (list r-elasticnet r-mass r-mda)) (home-page "https://www.imm.dtu.dk/~lkhc/") (synopsis "Sparse discriminant analysis") (description @@ -21162,12 +20582,12 @@ (define-public r-accsda (properties `((upstream-name . "accSDA"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-gridextra" ,r-gridextra) - ("r-mass" ,r-mass) - ("r-rarpack" ,r-rarpack) - ("r-sparselda" ,r-sparselda))) + (list r-ggplot2 + r-ggthemes + r-gridextra + r-mass + r-rarpack + r-sparselda)) (home-page "https://github.com/gumeo/accSDA/wiki") (synopsis "Accelerated sparse discriminant analysis") (description @@ -21195,7 +20615,7 @@ (define-public r-ace2fastq (properties `((upstream-name . "ace2fastq"))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr))) + (list r-stringr)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description @@ -21240,8 +20660,7 @@ (define-public r-rnmf "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-nnls" ,r-nnls))) + (list r-knitr r-nnls)) (home-page "https://cran.r-project.org/web/packages/rNMF/") (synopsis "Robust nonnegative matrix factorization") (description @@ -21267,9 +20686,9 @@ (define-public r-randtoolbox (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs - `(("r-rngwell" ,r-rngwell))) + (list r-rngwell)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/randtoolbox/") (synopsis "Toolbox for pseudo and quasi random number generation") (description @@ -21303,9 +20722,9 @@ (define-public r-lhs "1l861h76q5w0nbnbybhgg7hiw7fks677jakyd49n1whwvd48sfz4")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description @@ -21327,11 +20746,7 @@ (define-public r-acebayes (properties `((upstream-name . "acebayes"))) (build-system r-build-system) (propagated-inputs - `(("r-compare" ,r-compare) - ("r-lhs" ,r-lhs) - ("r-randtoolbox" ,r-randtoolbox) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/acebayes/") (synopsis "Optimal Bayesian experimental design using the ACE algorithm") (description @@ -21358,10 +20773,7 @@ (define-public r-acet (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-bh r-mass r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description @@ -21384,7 +20796,7 @@ (define-public r-acfmperiod (properties `((upstream-name . "acfMPeriod"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") (synopsis "Estimation of the ACF from the M-periodogram") (description @@ -21434,11 +20846,7 @@ (define-public r-gamlss (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs - `(("r-gamlss-data" ,r-gamlss-data) - ("r-gamlss-dist" ,r-gamlss-dist) - ("r-mass" ,r-mass) - ("r-nlme" ,r-nlme) - ("r-survival" ,r-survival))) + (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival)) (home-page "http://www.gamlss.org/") (synopsis "Generalized additive models for location scale and shape") (description @@ -21465,9 +20873,7 @@ (define-public r-acid (properties `((upstream-name . "acid"))) (build-system r-build-system) (propagated-inputs - `(("r-gamlss" ,r-gamlss) - ("r-gamlss-dist" ,r-gamlss-dist) - ("r-hmisc" ,r-hmisc))) + (list r-gamlss r-gamlss-dist r-hmisc)) (home-page "https://cran.r-project.org/web/packages/acid/") (synopsis "Analysing conditional income distributions") (description @@ -21493,7 +20899,7 @@ (define-public r-acm4r "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) (properties `((upstream-name . "acm4r"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acm4r/") (synopsis "Align-and-count method comparisons of RFLP data") (description @@ -21539,8 +20945,7 @@ (define-public r-filematrix (build-system r-build-system) ;; These inputs are needed for vignettes (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-knitr r-rmarkdown)) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description @@ -21567,7 +20972,7 @@ (define-public r-acmeeqtl (properties `((upstream-name . "ACMEeqtl"))) (build-system r-build-system) (propagated-inputs - `(("r-filematrix" ,r-filematrix))) + (list r-filematrix)) (home-page "https://github.com/andreyshabalin/ACMEeqtl") (synopsis "Estimation of interpretable eQTL effect sizes") (description @@ -21591,7 +20996,7 @@ (define-public r-acmer "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) (properties `((upstream-name . "acmeR"))) (build-system r-build-system) - (propagated-inputs `(("r-foreign" ,r-foreign))) + (propagated-inputs (list r-foreign)) (home-page "https://cran.r-project.org/web/packages/acmeR/") (synopsis "ACME estimator of bird and bat mortality by wind turbines") (description @@ -21619,9 +21024,7 @@ (define-public r-r-huge (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs - `(("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.huge") (synopsis "Methods for accessing huge amounts of data") (description @@ -21650,11 +21053,7 @@ (define-public r-r-filesets (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-r-cache" ,r-r-cache) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.filesets") (synopsis "Easy handling of and access to files") (description @@ -21682,10 +21081,7 @@ (define-public r-r-devices (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.devices") (synopsis "Unified handling of graphics devices") (description @@ -21758,7 +21154,7 @@ (define-public r-tuner "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) - (propagated-inputs `(("r-signal" ,r-signal))) + (propagated-inputs (list r-signal)) (home-page "https://cran.r-project.org/web/packages/tuneR/") (synopsis "Analysis of music and speech") (description @@ -21783,9 +21179,9 @@ (define-public r-seewave (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (propagated-inputs - `(("r-tuner" ,r-tuner))) + (list r-tuner)) (home-page "http://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description @@ -21812,9 +21208,7 @@ (define-public r-acousticndlcoder `((upstream-name . "AcousticNDLCodeR"))) (build-system r-build-system) (propagated-inputs - `(("r-seewave" ,r-seewave) - ("r-tuner" ,r-tuner) - ("r-zoo" ,r-zoo))) + (list r-seewave r-tuner r-zoo)) (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") (synopsis "Coding sound files for use with NDL") (description @@ -21840,8 +21234,7 @@ (define-public r-acp (properties `((upstream-name . "acp"))) (build-system r-build-system) (propagated-inputs - `(("r-quantmod" ,r-quantmod) - ("r-tseries" ,r-tseries))) + (list r-quantmod r-tseries)) (home-page "https://cran.r-project.org/web/packages/acp/") (synopsis "Autoregressive conditional Poisson") (description @@ -21863,7 +21256,7 @@ (define-public r-ada "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) (properties `((upstream-name . "ada"))) (build-system r-build-system) - (propagated-inputs `(("r-rpart" ,r-rpart))) + (propagated-inputs (list r-rpart)) (home-page "https://cran.r-project.org/web/packages/ada/") (synopsis "Stochastic boosting") (description @@ -21908,10 +21301,7 @@ (define-public r-kernelfactory (properties `((upstream-name . "kernelFactory"))) (build-system r-build-system) (propagated-inputs - `(("r-auc" ,r-auc) - ("r-genalg" ,r-genalg) - ("r-kernlab" ,r-kernlab) - ("r-randomforest" ,r-randomforest))) + (list r-auc r-genalg r-kernlab r-randomforest)) (home-page "https://cran.r-project.org/web/packages/kernelFactory/") (synopsis "Ensemble of kernel machines") (description @@ -21953,10 +21343,7 @@ (define-public r-acrm (properties `((upstream-name . "aCRM"))) (build-system r-build-system) (propagated-inputs - `(("r-ada" ,r-ada) - ("r-dummies" ,r-dummies) - ("r-kernelfactory" ,r-kernelfactory) - ("r-randomforest" ,r-randomforest))) + (list r-ada r-dummies r-kernelfactory r-randomforest)) (home-page "https://cran.r-project.org/web/packages/aCRM/") (synopsis "Convenience functions for analytical customer relationship management") (description @@ -21996,8 +21383,7 @@ (define-public r-treeclust (properties `((upstream-name . "treeClust"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-rpart" ,r-rpart))) + (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/web/packages/treeClust/") (synopsis "Cluster distances through trees") (description @@ -22020,8 +21406,7 @@ (define-public r-acrosstic (properties `((upstream-name . "AcrossTic"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-treeclust" ,r-treeclust))) + (list r-lpsolve r-treeclust)) (home-page "https://cran.r-project.org/web/packages/AcrossTic/") (synopsis "Cost-minimal regular spanning subgraph with TreeClust") (description @@ -22044,9 +21429,7 @@ (define-public r-acrt (properties `((upstream-name . "acrt"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-sandwich" ,r-sandwich))) + (list r-rcpp r-rcppeigen r-sandwich)) (home-page "https://cran.r-project.org/web/packages/acrt/") (synopsis "Autocorrelation robust testing") (description @@ -22069,11 +21452,7 @@ (define-public r-acs (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml))) + (list r-httr r-plyr r-rcpp r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description @@ -22129,8 +21508,7 @@ (define-public r-acss (properties `((upstream-name . "acss"))) (build-system r-build-system) (propagated-inputs - `(("r-acss-data" ,r-acss-data) - ("r-zoo" ,r-zoo))) + (list r-acss-data r-zoo)) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Algorithmic complexity for short strings") (description @@ -22158,7 +21536,7 @@ (define-public r-acswr (properties `((upstream-name . "ACSWR"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ACSWR/") (synopsis "Companion package for the book \"A Course in Statistics with R\"") (description @@ -22179,7 +21557,7 @@ (define-public r-alabama "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) - (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (propagated-inputs (list r-numderiv)) (home-page "https://cran.r-project.org/web/packages/alabama/") (synopsis "Constrained nonlinear optimization") (description @@ -22203,18 +21581,18 @@ (define-public r-gdina (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs - `(("r-alabama" ,r-alabama) - ("r-ggplot2" ,r-ggplot2) - ("r-mass" ,r-mass) - ("r-nloptr" ,r-nloptr) - ("r-numderiv" ,r-numderiv) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsolnp" ,r-rsolnp) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard))) + (list r-alabama + r-ggplot2 + r-mass + r-nloptr + r-numderiv + r-rcpp + r-rcpparmadillo + r-rsolnp + r-shiny + r-shinydashboard)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description @@ -22245,10 +21623,9 @@ (define-public r-actcd (properties `((upstream-name . "ACTCD"))) (build-system r-build-system) (propagated-inputs - `(("r-gdina" ,r-gdina) - ("r-r-methodss3" ,r-r-methodss3))) + (list r-gdina r-r-methodss3)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ACTCD/") (synopsis "Asymptotic classification theory for cognitive diagnosis") (description @@ -22296,11 +21673,7 @@ (define-public r-actfrag (properties `((upstream-name . "ActFrag"))) (build-system r-build-system) (propagated-inputs - `(("r-accelerometry" ,r-accelerometry) - ("r-dplyr" ,r-dplyr) - ("r-ineq" ,r-ineq) - ("r-survival" ,r-survival) - ("r-tidyr" ,r-tidyr))) + (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description @@ -22322,7 +21695,7 @@ (define-public r-ash "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) (properties `((upstream-name . "ash"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ash/") (synopsis "David Scott's ASH routines") (description @@ -22344,13 +21717,13 @@ (define-public r-hdrcde (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs - `(("r-ash" ,r-ash) - ("r-ggplot2" ,r-ggplot2) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-ash + r-ggplot2 + r-kernsmooth + r-ks + r-locfit + r-rcolorbrewer)) + (native-inputs (list gfortran)) (home-page "http://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description @@ -22373,12 +21746,12 @@ (define-public r-rainbow (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-colorspace" ,r-colorspace) - ("r-hdrcde" ,r-hdrcde) - ("r-ks" ,r-ks) - ("r-mass" ,r-mass) - ("r-pcapp" ,r-pcapp))) + (list r-cluster + r-colorspace + r-hdrcde + r-ks + r-mass + r-pcapp)) (home-page "https://cran.r-project.org/web/packages/rainbow/") (synopsis "Bagplots, boxplots and rainbow plots for functional data") (description @@ -22400,8 +21773,7 @@ (define-public r-fds (properties `((upstream-name . "fds"))) (build-system r-build-system) (propagated-inputs - `(("r-rainbow" ,r-rainbow) - ("r-rcurl" ,r-rcurl))) + (list r-rainbow r-rcurl)) (home-page "https://cran.r-project.org/web/packages/fds/") (synopsis "Functional data sets") (description "This package contains a list of functional time series, @@ -22425,9 +21797,7 @@ (define-public r-fda (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - `(("r-desolve" ,r-desolve) - ("r-fds" ,r-fds) - ("r-matrix" ,r-matrix))) + (list r-desolve r-fds r-matrix)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description @@ -22451,7 +21821,7 @@ (define-public r-actigraphy (properties `((upstream-name . "Actigraphy"))) (build-system r-build-system) (propagated-inputs - `(("r-fda" ,r-fda))) + (list r-fda)) (home-page "https://cran.r-project.org/web/packages/Actigraphy/") (synopsis "Actigraphy data analysis") (description @@ -22473,7 +21843,7 @@ (define-public r-activedriver (properties `((upstream-name . "ActiveDriver"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") (synopsis "Tools for finding cancer driver proteins") (description @@ -22502,11 +21872,7 @@ (define-public r-activitycounts `((upstream-name . "activityCounts"))) (build-system r-build-system) (propagated-inputs - `(("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-seewave" ,r-seewave) - ("r-signal" ,r-signal) - ("r-tibble" ,r-tibble))) + (list r-lubridate r-magrittr r-seewave r-signal r-tibble)) (home-page "https://github.com/walkabillylab/activityCounts") (synopsis "Generate ActiLife counts") (description @@ -22533,11 +21899,9 @@ (define-public r-activityindex (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils))) + (list r-data-table r-matrixstats r-r-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description @@ -22560,12 +21924,12 @@ (define-public r-activpal (properties `((upstream-name . "activPAL"))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-tidyr" ,r-tidyr))) + (list r-devtools + r-dplyr + r-ggplot2 + r-lubridate + r-magrittr + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description @@ -22592,7 +21956,7 @@ (define-public r-activpalprocessing `((upstream-name . "activpalProcessing"))) (build-system r-build-system) (propagated-inputs - `(("r-chron" ,r-chron))) + (list r-chron)) (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") (synopsis "Process activPAL events files") (description @@ -22615,11 +21979,7 @@ (define-public r-actogrammr (properties `((upstream-name . "actogrammr"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description @@ -22666,7 +22026,7 @@ (define-public r-actuar "015brjjgmkwmjajdjdw8gs02jrd96if425pk9a97d499hzsq3xds")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) - (propagated-inputs `(("r-expint" ,r-expint))) + (propagated-inputs (list r-expint)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description @@ -22718,10 +22078,7 @@ (define-public r-readbitmap `(("libjpeg" ,libjpeg-turbo) ("libpng" ,libpng))) (propagated-inputs - `(("r-bmp" ,r-bmp) - ("r-jpeg" ,r-jpeg) - ("r-png" ,r-png) - ("r-tiff" ,r-tiff))) + (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description @@ -22744,23 +22101,19 @@ (define-public r-imager (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs - `(("fftw" ,fftw) - ("libtiff" ,libtiff) - ("libx11" ,libx11) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-downloader" ,r-downloader) - ("r-igraph" ,r-igraph) - ("r-jpeg" ,r-jpeg) - ("r-magrittr" ,r-magrittr) - ("r-png" ,r-png) - ("r-purrr" ,r-purrr) - ("r-rcpp" ,r-rcpp) - ("r-readbitmap" ,r-readbitmap) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list fftw libtiff libx11 zlib)) + (propagated-inputs + (list r-downloader + r-igraph + r-jpeg + r-magrittr + r-png + r-purrr + r-rcpp + r-readbitmap + r-stringr)) + (native-inputs + (list pkg-config r-knitr)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description @@ -22786,9 +22139,7 @@ (define-public r-acuityview (properties `((upstream-name . "AcuityView"))) (build-system r-build-system) (propagated-inputs - `(("r-fftwtools" ,r-fftwtools) - ("r-imager" ,r-imager) - ("r-plotrix" ,r-plotrix))) + (list r-fftwtools r-imager r-plotrix)) (home-page "https://cran.r-project.org/web/packages/AcuityView/") (synopsis "Display scenes as seen by an animal with less acute vision") (description @@ -22809,19 +22160,19 @@ (define-public r-caret "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8")))) (build-system r-build-system) (propagated-inputs - `(("r-e1071" ,r-e1071) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-modelmetrics" ,r-modelmetrics) - ("r-nlme" ,r-nlme) - ("r-plyr" ,r-plyr) - ("r-proc" ,r-proc) - ("r-recipes" ,r-recipes) - ("r-reshape2" ,r-reshape2) - ("r-withr" ,r-withr))) + (list r-e1071 + r-foreach + r-ggplot2 + r-lattice + r-modelmetrics + r-nlme + r-plyr + r-proc + r-recipes + r-reshape2 + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description @@ -22843,10 +22194,7 @@ (define-public r-adabag (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs - `(("r-caret" ,r-caret) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-rpart" ,r-rpart))) + (list r-caret r-doparallel r-foreach r-rpart)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description @@ -22871,7 +22219,7 @@ (define-public r-adagio (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve))) + (list r-lpsolve)) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description @@ -22895,8 +22243,7 @@ (define-public r-univoutl (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs - `(("r-hmisc" ,r-hmisc) - ("r-robustbase" ,r-robustbase))) + (list r-hmisc r-robustbase)) (home-page "https://github.com/marcellodo/univOutl") (synopsis "Detection of univariate outliers") (description @@ -22921,8 +22268,7 @@ (define-public r-tolerance (properties `((upstream-name . "tolerance"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-rgl" ,r-rgl))) + (list r-mass r-rgl)) (home-page "https://cran.r-project.org/web/packages/tolerance/") (synopsis "Statistical tolerance intervals and regions") (description @@ -22973,9 +22319,7 @@ (define-public r-flexclust (properties `((upstream-name . "flexclust"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-lattice" ,r-lattice) - ("r-modeltools" ,r-modeltools))) + (list r-class r-lattice r-modeltools)) (home-page "https://cran.r-project.org/web/packages/flexclust/") (synopsis "Flexible cluster algorithms") (description @@ -23002,13 +22346,13 @@ (define-public r-biclust (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs - `(("r-additivitytests" ,r-additivitytests) - ("r-colorspace" ,r-colorspace) - ("r-flexclust" ,r-flexclust) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-tidyr" ,r-tidyr))) + (list r-additivitytests + r-colorspace + r-flexclust + r-ggplot2 + r-lattice + r-mass + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/biclust/") (synopsis "BiCluster algorithms") (description @@ -23033,9 +22377,7 @@ (define-public r-icge (properties `((upstream-name . "ICGE"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-fastcluster" ,r-fastcluster) - ("r-mass" ,r-mass))) + (list r-cluster r-fastcluster r-mass)) (home-page "https://cran.r-project.org/web/packages/ICGE/") (synopsis "Cluster estimation and identification of atypical units") (description @@ -23058,11 +22400,9 @@ (define-public r-depth (properties `((upstream-name . "depth"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-circular" ,r-circular) - ("r-rgl" ,r-rgl))) + (list r-abind r-circular r-rgl)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/depth/") (synopsis "Nonparametric depth functions for multivariate analysis") (description @@ -23087,8 +22427,7 @@ (define-public r-archetypes (properties `((upstream-name . "archetypes"))) (build-system r-build-system) (propagated-inputs - `(("r-modeltools" ,r-modeltools) - ("r-nnls" ,r-nnls))) + (list r-modeltools r-nnls)) (home-page "https://cran.r-project.org/web/packages/archetypes") (synopsis "Archetypal analysis") (description @@ -23111,10 +22450,7 @@ (define-public r-shapes (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-minpack-lm" ,r-minpack-lm) - ("r-rgl" ,r-rgl) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-mass r-minpack-lm r-rgl r-scatterplot3d)) (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") (synopsis "Statistical shape analysis") (description @@ -23140,17 +22476,17 @@ (define-public r-anthropometry (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs - `(("r-archetypes" ,r-archetypes) - ("r-biclust" ,r-biclust) - ("r-cluster" ,r-cluster) - ("r-depth" ,r-depth) - ("r-fnn" ,r-fnn) - ("r-icge" ,r-icge) - ("r-nnls" ,r-nnls) - ("r-rgl" ,r-rgl) - ("r-shapes" ,r-shapes))) + (list r-archetypes + r-biclust + r-cluster + r-depth + r-fnn + r-icge + r-nnls + r-rgl + r-shapes)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Anthropometry/") (synopsis "Statistical methods for anthropometric data") (description @@ -23175,13 +22511,13 @@ (define-public r-adamethods (properties `((upstream-name . "adamethods"))) (build-system r-build-system) (propagated-inputs - `(("r-anthropometry" ,r-anthropometry) - ("r-archetypes" ,r-archetypes) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-nnls" ,r-nnls) - ("r-tolerance" ,r-tolerance) - ("r-univoutl" ,r-univoutl))) + (list r-anthropometry + r-archetypes + r-fnn + r-foreach + r-nnls + r-tolerance + r-univoutl)) (home-page "https://cran.r-project.org/web/packages/adamethods/") (synopsis "Archetypoid algorithms and anomaly detection") (description @@ -23205,7 +22541,7 @@ (define-public r-idpmisc (properties `((upstream-name . "IDPmisc"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/IDPmisc/") (synopsis "Functions for data analyses and visualization") (description @@ -23234,9 +22570,9 @@ (define-public r-qqman (properties `((upstream-name . "qqman"))) (build-system r-build-system) (propagated-inputs - `(("r-calibrate" ,r-calibrate))) + (list r-calibrate)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qqman/") (synopsis "Q-Q and Manhattan plots for GWAS data") (description @@ -23259,10 +22595,7 @@ (define-public r-ggplot-multistats `((upstream-name . "ggplot.multistats"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-hexbin r-rlang r-scales)) (home-page "https://github.com/flying-sheep/ggplot.multistats") (synopsis "Multiple summary statistics for binned stats/geometries") (description @@ -23286,9 +22619,7 @@ (define-public r-knn-covertree (properties `((upstream-name . "knn.covertree"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcpp r-rcppeigen)) (home-page "https://github.com/flying-sheep/knn.covertree") (synopsis "Accurate kNN Implementation with multiple distance measures") (description @@ -23335,7 +22666,7 @@ (define-public r-diagram (properties `((upstream-name . "diagram"))) (build-system r-build-system) (propagated-inputs - `(("r-shape" ,r-shape))) + (list r-shape)) (home-page "https://cran.r-project.org/web/packages/diagram/") (synopsis "Visualize simple graphs (networks) and plot flow diagrams") (description @@ -23362,8 +22693,7 @@ (define-public r-lim (properties `((upstream-name . "LIM"))) (build-system r-build-system) (propagated-inputs - `(("r-diagram" ,r-diagram) - ("r-limsolve" ,r-limsolve))) + (list r-diagram r-limsolve)) (home-page "https://cran.r-project.org/web/packages/LIM/") (synopsis "Linear inverse model examples and solution methods") (description @@ -23386,9 +22716,7 @@ (define-public r-shinycssloaders `((upstream-name . "shinycssloaders"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-glue" ,r-glue) - ("r-shiny" ,r-shiny))) + (list r-digest r-glue r-shiny)) (home-page "https://github.com/andrewsali/shinycssloaders") (synopsis "Add CSS loading animations to Shiny outputs") (description @@ -23412,11 +22740,9 @@ (define-public r-rsvg (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs - `(("librsvg" ,librsvg) - ("zlib" ,zlib))) + (list librsvg zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/rsvg#readme") (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") (description @@ -23441,8 +22767,7 @@ (define-public r-influencer (properties `((upstream-name . "influenceR"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix))) + (list r-igraph r-matrix)) (home-page "https://github.com/rcc-uchicago/influenceR") (synopsis "Tools to quantify structural importance of nodes in a network") (description @@ -23469,7 +22794,7 @@ (define-public r-emplik (properties `((upstream-name . "emplik"))) (build-system r-build-system) (propagated-inputs - `(("r-quantreg" ,r-quantreg))) + (list r-quantreg)) (home-page "https://www.ms.uky.edu/~mai/EmpLik.html") (synopsis "Empirical likelihood ratio for censored/truncated data") (description @@ -23492,11 +22817,7 @@ (define-public r-imputeyn (properties `((upstream-name . "imputeYn"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-emplik" ,r-emplik) - ("r-mvtnorm" ,r-mvtnorm) - ("r-quadprog" ,r-quadprog) - ("r-survival" ,r-survival))) + (list r-boot r-emplik r-mvtnorm r-quadprog r-survival)) (home-page "https://cran.r-project.org/web/packages/imputeYn/") (synopsis "Impute last largest censored observation under weighted least squares") (description @@ -23519,10 +22840,7 @@ (define-public r-adapenetclass (properties `((upstream-name . "AdapEnetClass"))) (build-system r-build-system) (propagated-inputs - `(("r-glmnet" ,r-glmnet) - ("r-imputeyn" ,r-imputeyn) - ("r-lars" ,r-lars) - ("r-quadprog" ,r-quadprog))) + (list r-glmnet r-imputeyn r-lars r-quadprog)) (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") (synopsis "Class of adaptive elastic net methods for censored data") (description @@ -23542,7 +22860,7 @@ (define-public r-flock "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) (properties `((upstream-name . "flock"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/flock/") (synopsis "Process synchronization using file locks") (description @@ -23565,16 +22883,16 @@ (define-public r-archivist (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-flock" ,r-flock) - ("r-httr" ,r-httr) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite))) + (list r-dbi + r-digest + r-flock + r-httr + r-lubridate + r-magrittr + r-rcurl + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://pbiecek.github.io/archivist/") (synopsis "Tools for storing, restoring and searching for R objects") (description @@ -23624,21 +22942,21 @@ (define-public r-adapr (properties `((upstream-name . "adapr"))) (build-system r-build-system) (propagated-inputs - `(("r-archivist" ,r-archivist) - ("r-devtools" ,r-devtools) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-gdata" ,r-gdata) - ("r-ggplot2" ,r-ggplot2) - ("r-git2r" ,r-git2r) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard) - ("r-versions" ,r-versions))) + (list r-archivist + r-devtools + r-digest + r-doparallel + r-gdata + r-ggplot2 + r-git2r + r-igraph + r-knitr + r-plotly + r-plyr + r-rmarkdown + r-shiny + r-shinydashboard + r-versions)) (home-page "https://cran.r-project.org/web/packages/adapr/") (synopsis "Implementation of an accountable data analysis process") (description @@ -23661,7 +22979,7 @@ (define-public r-adapsamp "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) (properties `((upstream-name . "AdapSamp"))) (build-system r-build-system) - (propagated-inputs `(("r-pracma" ,r-pracma))) + (propagated-inputs (list r-pracma)) (home-page "https://cran.r-project.org/web/packages/AdapSamp/") (synopsis "Adaptive sampling algorithms") (description @@ -23689,9 +23007,7 @@ (define-public r-adaptalint (properties `((upstream-name . "adaptalint"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-lintr" ,r-lintr) - ("r-purrr" ,r-purrr))) + (list r-dplyr r-lintr r-purrr)) (home-page "https://cran.r-project.org/web/packages/adaptalint/") (synopsis "Check R code style") (description @@ -23737,20 +23053,20 @@ (define-public r-forecast (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-fracdiff" ,r-fracdiff) - ("r-ggplot2" ,r-ggplot2) - ("r-lmtest" ,r-lmtest) - ("r-magrittr" ,r-magrittr) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-timedate" ,r-timedate) - ("r-tseries" ,r-tseries) - ("r-urca" ,r-urca) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; needed for vignettes + (list r-colorspace + r-fracdiff + r-ggplot2 + r-lmtest + r-magrittr + r-nnet + r-rcpp + r-rcpparmadillo + r-timedate + r-tseries + r-urca + r-zoo)) + (native-inputs + (list r-knitr)) ; needed for vignettes (home-page "https://pkg.robjhyndman.com/forecast/") (synopsis "Forecasting functions for time series and linear models") (description @@ -23772,12 +23088,9 @@ (define-public r-formattable (properties `((upstream-name . "formattable"))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-lifecycle" ,r-lifecycle) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/renkun-ken/formattable") (synopsis "Print vectors and data frames with text fromatting") (description @@ -23824,10 +23137,7 @@ (define-public r-proxyc (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel)) (home-page "https://cran.r-project.org/package=proxyC") (synopsis "Compute proximity in large sparse matrices") (description @@ -23874,7 +23184,7 @@ (define-public r-stopwords (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs - `(("r-isocodes" ,r-isocodes))) + (list r-isocodes)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description @@ -23896,8 +23206,7 @@ (define-public r-spacyr (properties `((upstream-name . "spacyr"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-reticulate" ,r-reticulate))) + (list r-data-table r-reticulate)) (home-page "https://spacyr.quanteda.io") (synopsis "R wrapper for the spaCy NLP library") (description @@ -23942,19 +23251,19 @@ (define-public r-quanteda (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs - `(("r-fastmatch" ,r-fastmatch) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-snowballc" ,r-snowballc) - ("r-stopwords" ,r-stopwords) - ("r-stringi" ,r-stringi) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) + (list r-fastmatch + r-magrittr + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-snowballc + r-stopwords + r-stringi + r-xml2 + r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://quanteda.io") (synopsis "Quantitative analysis of textual data") (description @@ -23981,11 +23290,9 @@ (define-public r-topicmodels (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-modeltools" ,r-modeltools) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) + (list r-modeltools r-slam r-tm)) (home-page "https://cran.r-project.org/package=topicmodels") (synopsis "Topic models") (description @@ -24009,17 +23316,17 @@ (define-public r-stm (properties `((upstream-name . "stm"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-glmnet" ,r-glmnet) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-quadprog" ,r-quadprog) - ("r-quanteda" ,r-quanteda) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr))) + (list r-data-table + r-glmnet + r-lda + r-matrix + r-matrixstats + r-quadprog + r-quanteda + r-rcpp + r-rcpparmadillo + r-slam + r-stringr)) (home-page "http://www.structuraltopicmodel.com/") (synopsis "Estimation of the Structural Topic Model") (description @@ -24043,8 +23350,7 @@ (define-public r-polycor (properties `((upstream-name . "polycor"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-matrix r-mvtnorm)) (home-page "https://r-forge.r-project.org/projects/polycor/") (synopsis "Polychoric and polyserial correlations") (description @@ -24067,9 +23373,7 @@ (define-public r-msm (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs - `(("r-expm" ,r-expm) - ("r-mvtnorm" ,r-mvtnorm) - ("r-survival" ,r-survival))) + (list r-expm r-mvtnorm r-survival)) (home-page "https://github.com/chjackson/msm") (synopsis "Multi-state Markov and hidden Markov models in continuous time") (description @@ -24095,9 +23399,7 @@ (define-public r-ltm (properties `((upstream-name . "ltm"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-msm" ,r-msm) - ("r-polycor" ,r-polycor))) + (list r-mass r-msm r-polycor)) (home-page "https://github.com/drizopoulos/ltm") (synopsis "Latent trait models under IRT") (description @@ -24122,8 +23424,7 @@ (define-public r-mi (properties `((upstream-name . "mi"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-matrix" ,r-matrix))) + (list r-arm r-matrix)) (home-page "http://www.stat.columbia.edu/~gelman/") (synopsis "Missing data imputation and model checking") (description @@ -24170,9 +23471,7 @@ (define-public r-sem (properties `((upstream-name . "sem"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mass" ,r-mass) - ("r-mi" ,r-mi))) + (list r-boot r-mass r-mi)) (home-page "https://cran.r-project.org/package=sem") (synopsis "Structural equation models") (description @@ -24196,8 +23495,7 @@ (define-public r-semtools (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs - `(("r-lavaan" ,r-lavaan) - ("r-pbivnorm" ,r-pbivnorm))) + (list r-lavaan r-pbivnorm)) (home-page "https://github.com/simsem/semTools/wiki") (synopsis "Useful tools for structural equation modeling") (description @@ -24218,12 +23516,9 @@ (define-public r-regsem (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs - `(("r-lavaan" ,r-lavaan) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsolnp" ,r-rsolnp))) + (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=regsem") (synopsis "Regularized structural equation modeling") (description @@ -24247,13 +23542,11 @@ (define-public r-stanheaders "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) + (inputs (list pandoc)) (propagated-inputs - `(("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-rcppeigen r-rcppparallel)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) ; for vignettes + (list gfortran r-knitr)) ; for vignettes (home-page "https://mc-stan.org/") (synopsis "C++ header files for Stan") (description @@ -24289,12 +23582,9 @@ (define-public r-rpf (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs - `(("r-lifecycle" ,r-lifecycle) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jpritikin/rpf") (synopsis "Response probability functions") (description @@ -24319,17 +23609,17 @@ (define-public r-openmx (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-digest" ,r-digest) - ("r-lifecycle" ,r-lifecycle) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rpf" ,r-rpf) - ("r-stanheaders" ,r-stanheaders))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-bh + r-digest + r-lifecycle + r-mass + r-matrix + r-rcpp + r-rcppeigen + r-rcppparallel + r-rpf + r-stanheaders)) + (native-inputs (list gfortran)) (home-page "http://openmx.ssri.psu.edu") (synopsis "Extended structural equation modelling") (description @@ -24353,11 +23643,7 @@ (define-public r-kutils (properties `((upstream-name . "kutils"))) (build-system r-build-system) (propagated-inputs - `(("r-foreign" ,r-foreign) - ("r-openxlsx" ,r-openxlsx) - ("r-plyr" ,r-plyr) - ("r-runit" ,r-runit) - ("r-xtable" ,r-xtable))) + (list r-foreign r-openxlsx r-plyr r-runit r-xtable)) (home-page "https://cran.r-project.org/package=kutils") (synopsis "Project management tools") (description @@ -24383,10 +23669,7 @@ (define-public r-rockchalk (properties `((upstream-name . "rockchalk"))) (build-system r-build-system) (propagated-inputs - `(("r-cardata" ,r-cardata) - ("r-kutils" ,r-kutils) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass))) + (list r-cardata r-kutils r-lme4 r-mass)) (home-page "https://cran.r-project.org/package=rockchalk") (synopsis "Regression estimation and presentation") (description @@ -24433,7 +23716,7 @@ (define-public r-bdgraph (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://www.uva.nl/profile/a.mohammadi") (synopsis "Bayesian structure learning in graphical models") (description @@ -24457,9 +23740,7 @@ (define-public r-d3network (properties `((upstream-name . "d3Network"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rjson" ,r-rjson) - ("r-whisker" ,r-whisker))) + (list r-plyr r-rjson r-whisker)) (home-page "http://christophergandrud.github.io/d3Network/") (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs") (description @@ -24481,24 +23762,24 @@ (define-public r-qgraph (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-colorspace" ,r-colorspace) - ("r-corpcor" ,r-corpcor) - ("r-fdrtool" ,r-fdrtool) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gtools" ,r-gtools) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-jpeg" ,r-jpeg) - ("r-lavaan" ,r-lavaan) - ("r-matrix" ,r-matrix) - ("r-pbapply" ,r-pbapply) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-psych" ,r-psych) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) + (list r-abind + r-colorspace + r-corpcor + r-fdrtool + r-ggplot2 + r-glasso + r-gtools + r-hmisc + r-igraph + r-jpeg + r-lavaan + r-matrix + r-pbapply + r-plyr + r-png + r-psych + r-rcpp + r-reshape2)) (home-page "http://sachaepskamp.com/qgraph/") (synopsis "Weighted network visualization and analysis") (description @@ -24523,18 +23804,18 @@ (define-public r-semplot (properties `((upstream-name . "semPlot"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-corpcor" ,r-corpcor) - ("r-igraph" ,r-igraph) - ("r-lavaan" ,r-lavaan) - ("r-lisreltor" ,r-lisreltor) - ("r-openmx" ,r-openmx) - ("r-plyr" ,r-plyr) - ("r-qgraph" ,r-qgraph) - ("r-regsem" ,r-regsem) - ("r-rockchalk" ,r-rockchalk) - ("r-sem" ,r-sem) - ("r-xml" ,r-xml))) + (list r-colorspace + r-corpcor + r-igraph + r-lavaan + r-lisreltor + r-openmx + r-plyr + r-qgraph + r-regsem + r-rockchalk + r-sem + r-xml)) (home-page "https://github.com/SachaEpskamp/semPlot") (synopsis "Unified visualizations of structural equation models") (description @@ -24562,10 +23843,7 @@ (define-public r-cdm (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm) - ("r-polycor" ,r-polycor) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo)) (home-page "https://github.com/alexanderrobitzsch/CDM") (synopsis "Cognitive diagnosis modeling") @@ -24596,9 +23874,7 @@ (define-public r-tam (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs - `(("r-cdm" ,r-cdm) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-cdm r-rcpp r-rcpparmadillo)) (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/") (synopsis "Test analysis modules") (description @@ -24625,12 +23901,8 @@ (define-public r-erm (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-psych" ,r-psych))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-colorspace r-lattice r-mass r-matrix r-psych)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=eRm") (synopsis "Extended Rasch modeling") (description @@ -24659,8 +23931,7 @@ (define-public r-irtoys (properties `((upstream-name . "irtoys"))) (build-system r-build-system) (propagated-inputs - `(("r-ltm" ,r-ltm) - ("r-sm" ,r-sm))) + (list r-ltm r-sm)) (home-page "https://cran.r-project.org/package=irtoys") (synopsis "Collection of functions related to Item Response Theory (IRT)") (description @@ -24689,16 +23960,16 @@ (define-public r-iheatmapr (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) (propagated-inputs - `(("r-fastcluster" ,r-fastcluster) - ("r-ggdendro" ,r-ggdendro) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-scales" ,r-scales))) + (list r-fastcluster + r-ggdendro + r-htmlwidgets + r-jsonlite + r-knitr + r-magrittr + r-rcolorbrewer + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description @@ -24748,13 +24019,13 @@ (define-public r-rsconnect (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-jsonlite" ,r-jsonlite) - ("r-openssl" ,r-openssl) - ("r-packrat" ,r-packrat) - ("r-rstudioapi" ,r-rstudioapi) - ("r-yaml" ,r-yaml))) + (list r-curl + r-digest + r-jsonlite + r-openssl + r-packrat + r-rstudioapi + r-yaml)) (home-page "https://github.com/rstudio/rsconnect") (synopsis "Deployment interface for R Markdown documents and Shiny applications") (description @@ -24827,11 +24098,7 @@ (define-public r-dygraphs (base32 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo)) (home-page "https://github.com/rstudio/dygraphs") (synopsis "Interface to Dygraphs interactive time series charting library") (description @@ -24856,23 +24123,23 @@ (define-public r-shinystan (properties `((upstream-name . "shinystan"))) (build-system r-build-system) (propagated-inputs - `(("r-bayesplot" ,r-bayesplot) - ("r-colourpicker" ,r-colourpicker) - ("r-dt" ,r-dt) - ("r-dygraphs" ,r-dygraphs) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-markdown" ,r-markdown) - ("r-reshape2" ,r-reshape2) - ("r-rsconnect" ,r-rsconnect) - ("r-rstan" ,r-rstan) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-threejs" ,r-threejs) - ("r-xtable" ,r-xtable) - ("r-xts" ,r-xts))) + (list r-bayesplot + r-colourpicker + r-dt + r-dygraphs + r-ggplot2 + r-gridextra + r-gtools + r-markdown + r-reshape2 + r-rsconnect + r-rstan + r-shiny + r-shinyjs + r-shinythemes + r-threejs + r-xtable + r-xts)) (home-page "https://mc-stan.org/") (synopsis "Interactive visual and numerical analysis for Bayesian models") (description @@ -24897,13 +24164,11 @@ (define-public r-rstantools "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) + (inputs (list pandoc)) (propagated-inputs - `(("r-desc" ,r-desc) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-desc r-rcpp r-rcppparallel)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/rstantools/") (synopsis "Tools for developing R packages interfacing with Stan") (description @@ -24927,12 +24192,11 @@ (define-public r-loo (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) + (list pandoc)) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-matrixstats" ,r-matrixstats))) + (list r-checkmate r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description @@ -24971,22 +24235,20 @@ (define-public r-rstan (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - `(("tzdata" ,tzdata-for-tests) - ("pandoc" ,pandoc) - ("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-bh" ,r-bh) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-inline" ,r-inline) - ("r-loo" ,r-loo) - ("r-pkgbuild" ,r-pkgbuild) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-stanheaders" ,r-stanheaders) - ("r-v8" ,r-v8) - ("r-withr" ,r-withr))) + (list tzdata-for-tests pandoc r-knitr)) + (propagated-inputs + (list r-bh + r-ggplot2 + r-gridextra + r-inline + r-loo + r-pkgbuild + r-rcpp + r-rcppeigen + r-rcppparallel + r-stanheaders + r-v8 + r-withr)) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description @@ -25015,25 +24277,25 @@ (define-public r-rstanarm (properties `((upstream-name . "rstanarm"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-bayesplot" ,r-bayesplot) - ("r-bh" ,r-bh) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-loo" ,r-loo) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rstan" ,r-rstan) - ("r-rstantools" ,r-rstantools) - ("r-shinystan" ,r-shinystan) - ("r-stanheaders" ,r-stanheaders) - ("r-survival" ,r-survival))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-bayesplot + r-bh + r-ggplot2 + r-lme4 + r-loo + r-matrix + r-nlme + r-rcpp + r-rcppeigen + r-rcppparallel + r-rstan + r-rstantools + r-shinystan + r-stanheaders + r-survival)) + (native-inputs + (list r-knitr)) (home-page "https://mc-stan.org/rstanarm/") (synopsis "Bayesian applied regression modeling via Stan") (description @@ -25057,9 +24319,9 @@ (define-public r-kendall (properties `((upstream-name . "Kendall"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot))) + (list r-boot)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/Kendall/") (synopsis "Kendall rank correlation and Mann-Kendall trend test") (description @@ -25081,15 +24343,15 @@ (define-public r-keyring (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-assertthat" ,r-assertthat) - ("r-filelock" ,r-filelock) - ("r-openssl" ,r-openssl) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-sodium" ,r-sodium) - ("r-yaml" ,r-yaml))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-askpass + r-assertthat + r-filelock + r-openssl + r-r6 + r-rappdirs + r-sodium + r-yaml)) + (native-inputs (list pkg-config)) (home-page "https://github.com/r-lib/keyring") (synopsis "Access the system credential store from R") (description @@ -25114,7 +24376,7 @@ (define-public r-zyp (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs - `(("r-kendall" ,r-kendall))) + (list r-kendall)) (home-page "https://cran.r-project.org/web/packages/zyp/") (synopsis "Zhang + Yue-Pilon Trends Package") (description @@ -25138,10 +24400,7 @@ (define-public r-rlinsolve (properties `((upstream-name . "Rlinsolve"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rdpack" ,r-rdpack))) + (list r-matrix r-rcpp r-rcpparmadillo r-rdpack)) (home-page "https://cran.r-project.org/web/packages/Rlinsolve/") (synopsis "Iterative solvers for (sparse) linear system of equations") (description @@ -25170,15 +24429,15 @@ (define-public r-zvcv (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bh" ,r-bh) - ("r-dplyr" ,r-dplyr) - ("r-glmnet" ,r-glmnet) - ("r-magrittr" ,r-magrittr) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rlinsolve" ,r-rlinsolve))) + (list r-abind + r-bh + r-dplyr + r-glmnet + r-magrittr + r-mvtnorm + r-rcpp + r-rcpparmadillo + r-rlinsolve)) (home-page "https://cran.r-project.org/web/packages/ZVCV/") (synopsis "Zero-Variance Control Variates") (description @@ -25207,13 +24466,13 @@ (define-public r-ztype (properties `((upstream-name . "ztype"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr))) + (list r-assertthat + r-dplyr + r-ggplot2 + r-lubridate + r-magrittr + r-rvest + r-stringr)) (home-page "https://cran.r-project.org/web/packages/ztype/") (synopsis "Run a Ztype game loaded with R functions") (description @@ -25236,7 +24495,7 @@ (define-public r-zseq (properties `((upstream-name . "Zseq"))) (build-system r-build-system) (propagated-inputs - `(("r-gmp" ,r-gmp))) + (list r-gmp)) (home-page "https://cran.r-project.org/web/packages/Zseq/") (synopsis "Integer sequence generator") (description @@ -25260,7 +24519,7 @@ (define-public r-isoband (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/wilkelab/isoband") (synopsis "Generate isolines and isobands from regularly spaced elevation grids") (description @@ -25283,7 +24542,7 @@ (define-public r-ppcor (properties `((upstream-name . "ppcor"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppcor/") (synopsis "Partial and semi-partial correlation") (description @@ -25305,16 +24564,16 @@ (define-public r-hrbrthemes (properties `((upstream-name . "hrbrthemes"))) (build-system r-build-system) (propagated-inputs - `(("r-extrafont" ,r-extrafont) - ("r-gdtools" ,r-gdtools) - ("r-ggplot2" ,r-ggplot2) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-scales" ,r-scales))) + (list r-extrafont + r-gdtools + r-ggplot2 + r-htmltools + r-knitr + r-magrittr + r-rmarkdown + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hrbrmstr/hrbrthemes/") (synopsis "Additional themes, theme components and utilities for @code{ggplot2}") (description @@ -25336,7 +24595,7 @@ (define-public r-crochet "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/agrueneberg/crochet") (synopsis "Implementation Helper for Matrix-Like Types") (description @@ -25398,10 +24657,9 @@ (define-public r-latex2exp "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-magrittr" ,r-magrittr))) + (list r-stringr r-magrittr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -25421,13 +24679,9 @@ (define-public r-oai "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb")))) (build-system r-build-system) (propagated-inputs - `(("r-xml2" ,r-xml2) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-xml2 r-httr r-plyr r-stringr r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/oai/") (synopsis "General purpose OAI-PMH services client") (description "@code{oai} provides a general purpose client to work with @@ -25471,7 +24725,7 @@ (define-public r-getpass (properties `((upstream-name . "getPass"))) (build-system r-build-system) (propagated-inputs - `(("r-rstudioapi" ,r-rstudioapi))) + (list r-rstudioapi)) (home-page "https://github.com/wrathematics/getPass") (synopsis "Masked user input") (description @@ -25495,10 +24749,7 @@ (define-public r-remoter (properties `((upstream-name . "remoter"))) (build-system r-build-system) (propagated-inputs - `(("r-argon2" ,r-argon2) - ("r-getpass" ,r-getpass) - ("r-pbdzmq" ,r-pbdzmq) - ("r-png" ,r-png))) + (list r-argon2 r-getpass r-pbdzmq r-png)) (home-page "https://github.com/RBigData/remoter") (synopsis "Control a remote R session from a local one") (description @@ -25521,7 +24772,7 @@ (define-public r-asd (properties `((upstream-name . "asd"))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm))) + (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/asd") (synopsis "Simulations for Adaptive Seamless Designs") (description @@ -25570,14 +24821,14 @@ (define-public r-bridgesampling `((upstream-name . "bridgesampling"))) (build-system r-build-system) (propagated-inputs - `(("r-brobdingnag" ,r-brobdingnag) - ("r-coda" ,r-coda) - ("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + (list r-brobdingnag + r-coda + r-matrix + r-mvtnorm + r-scales + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/quentingronau/bridgesampling") (synopsis "Bridge sampling for marginal likelihoods and Bayes factors") (description @@ -25601,7 +24852,7 @@ (define-public r-tea `((upstream-name . "tea"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/tea/") (synopsis "Threshold estimation approaches") (description @@ -25652,10 +24903,9 @@ (define-public r-aws `((upstream-name . "aws"))) (build-system r-build-system) (propagated-inputs - `(("r-awsmethods" ,r-awsmethods) - ("r-gsl" ,r-gsl))) + (list r-awsmethods r-gsl)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/aws/") (synopsis "Adaptive weights smoothing") (description @@ -25681,15 +24931,15 @@ (define-public r-sgloptim `((upstream-name . "sglOptim"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppprogress" ,r-rcppprogress))) + (list r-bh + r-doparallel + r-foreach + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/nielsrhansen/sglOptim") (synopsis "Generic sparse group Lasso solver") (description @@ -25717,7 +24967,7 @@ (define-public r-grouped `((upstream-name . "grouped"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/grouped/") (synopsis "Regression analysis of grouped and coarse data") (description @@ -25740,8 +24990,7 @@ (define-public r-stam `((upstream-name . "stam"))) (build-system r-build-system) (propagated-inputs - `(("r-np" ,r-np) - ("r-sp" ,r-sp))) + (list r-np r-sp)) (home-page "https://cran.r-project.org/web/packages/stam") (synopsis "Spatio-temporal analysis and modelling") (description @@ -25765,7 +25014,7 @@ (define-public r-dcv `((upstream-name . "dcv"))) (build-system r-build-system) (propagated-inputs - `(("r-lmtest" ,r-lmtest))) + (list r-lmtest)) (home-page "https://cran.r-project.org/web/packages/dcv/") (synopsis "Conventional cross-validation statistics for climate-growth model") (description @@ -25790,7 +25039,7 @@ (define-public r-rcdd `((upstream-name . "rcdd"))) (build-system r-build-system) (inputs - `(("gmp" ,gmp))) + (list gmp)) (home-page "https://www.stat.umn.edu/geyer/rcdd/") (synopsis "Computational geometry") (description @@ -25816,11 +25065,9 @@ (define-public r-rxnat `((upstream-name . "Rxnat"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-rcurl" ,r-rcurl) - ("r-tibble" ,r-tibble))) + (list r-httr r-rcurl r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Rxnat/") (synopsis "Queries and extracts images from neuroimaging datasets") (description @@ -25854,16 +25101,15 @@ (define-public r-rserve (("\\$\\(R_HOME\\)") out)) (mkdir-p bin))))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-mime" ,r-mime) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-uuid" ,r-uuid))) + (list r-checkmate + r-mime + r-jsonlite + r-knitr + r-r6 + r-rcpp + r-uuid)) (inputs - `(("openssl" ,openssl) - ("zlib" ,zlib))) + (list openssl zlib)) (home-page "https://github.com/s-u/Rserve") (synopsis "Server providing access to R from many languages and systems") @@ -25891,9 +25137,7 @@ (define-public r-gamm4 (properties `((upstream-name . "gamm4"))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv))) + (list r-lme4 r-matrix r-mgcv)) (home-page "https://cran.r-project.org/web/packages/gamm4/") (synopsis "Generalized additive mixed models using mgcv and lme4") (description @@ -25915,8 +25159,8 @@ (define-public r-optimx "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) - (propagated-inputs `(("r-numderiv" ,r-numderiv))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-numderiv)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/optimx/") (synopsis "Expanded replacement and extension of the optim function") (description @@ -25944,21 +25188,21 @@ (define-public r-projpred (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-gamm4" ,r-gamm4) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-loo" ,r-loo) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-optimx" ,r-optimx) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rngtools" ,r-rngtools) - ("r-rstantools" ,r-rstantools) - ("r-tidyverse" ,r-tidyverse))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-gamm4 + r-ggplot2 + r-lme4 + r-loo + r-magrittr + r-mass + r-mgcv + r-optimx + r-rcpp + r-rcpparmadillo + r-rngtools + r-rstantools + r-tidyverse)) + (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description @@ -25984,16 +25228,16 @@ (define-public r-distributional `((upstream-name . "distributional"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) - ("r-farver" ,r-farver) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-lifecycle" ,r-lifecycle) - ("r-numderiv" ,r-numderiv) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-vctrs" ,r-vctrs))) + (list r-digest + r-ellipsis + r-farver + r-generics + r-ggplot2 + r-lifecycle + r-numderiv + r-rlang + r-scales + r-vctrs)) (home-page "https://pkg.mitchelloharawild.com/distributional/") (synopsis "Vectorized probability distributions") (description @@ -26020,17 +25264,17 @@ (define-public r-posterior (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-checkmate" ,r-checkmate) - ("r-distributional" ,r-distributional) - ("r-matrixstats" ,r-matrixstats) - ("r-pillar" ,r-pillar) - ("r-rlang" ,r-rlang) - ("r-tensora" ,r-tensora) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-abind + r-checkmate + r-distributional + r-matrixstats + r-pillar + r-rlang + r-tensora + r-tibble + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/posterior/") (synopsis "Tools for working with posterior distributions") (description @@ -26067,27 +25311,27 @@ (define-public r-brms (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-backports" ,r-backports) - ("r-bayesplot" ,r-bayesplot) - ("r-bridgesampling" ,r-bridgesampling) - ("r-coda" ,r-coda) - ("r-future" ,r-future) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-loo" ,r-loo) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-nlme" ,r-nlme) - ("r-posterior" ,r-posterior) - ("r-projpred" ,r-projpred) - ("r-rcpp" ,r-rcpp) - ("r-rstan" ,r-rstan) - ("r-rstantools" ,r-rstantools) - ("r-shinystan" ,r-shinystan))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-backports + r-bayesplot + r-bridgesampling + r-coda + r-future + r-ggplot2 + r-glue + r-loo + r-matrix + r-matrixstats + r-mgcv + r-nleqslv + r-nlme + r-posterior + r-projpred + r-rcpp + r-rstan + r-rstantools + r-shinystan)) + (native-inputs (list r-knitr)) (home-page "https://github.com/paul-buerkner/brms") (synopsis @@ -26121,14 +25365,14 @@ (define-public r-mstate (properties `((upstream-name . "mstate"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-survival" ,r-survival) - ("r-viridislite" ,r-viridislite))) + (list r-data-table + r-lattice + r-rcolorbrewer + r-rlang + r-survival + r-viridislite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/") (synopsis @@ -26153,13 +25397,9 @@ (define-public r-scatterpie (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs - `(("r-ggforce" ,r-ggforce) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/scatterpie/") (synopsis "Scatter pie plot") (description @@ -26181,7 +25421,7 @@ (define-public r-scrypt (properties `((upstream-name . "scrypt"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/rstudio/rscrypt") (synopsis "Key derivation functions for R based on Scrypt") (description @@ -26205,7 +25445,7 @@ (define-public r-boruta "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg")))) (properties `((upstream-name . "Boruta"))) (build-system r-build-system) - (propagated-inputs `(("r-ranger" ,r-ranger))) + (propagated-inputs (list r-ranger)) (home-page "https://gitlab.com/mbq/Boruta/") (synopsis "Wrapper algorithm for all relevant feature selection") (description @@ -26228,9 +25468,9 @@ (define-public r-directlabels "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w")))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog))) + (list r-quadprog)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description @@ -26273,7 +25513,7 @@ (define-public r-phylogram (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v")))) (properties `((upstream-name . "phylogram"))) (build-system r-build-system) - (propagated-inputs `(("r-ape" ,r-ape))) + (propagated-inputs (list r-ape)) (home-page "https://github.com/ropensci/phylogram/") (synopsis "Dendrograms for evolutionary analysis") (description @@ -26299,9 +25539,7 @@ (define-public r-kmer (properties `((upstream-name . "kmer"))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-phylogram" ,r-phylogram) - ("r-rcpp" ,r-rcpp))) + (list r-openssl r-phylogram r-rcpp)) (home-page "https://github.com/shaunpwilkinson/kmer/") (synopsis "Fast K-Mer counting and clustering for biological sequence analysis") (description @@ -26324,12 +25562,9 @@ (define-public r-hardhat (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-glue r-rlang r-tibble r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/hardhat") (synopsis "Construct modeling packages") (description @@ -26357,10 +25592,7 @@ (define-public r-lightgbm (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-r6" ,r-r6))) + (list r-data-table r-jsonlite r-matrix r-r6)) (home-page "https://github.com/Microsoft/LightGBM") (synopsis "Light gradient boosting machine") (description @@ -26394,16 +25626,16 @@ (define-public r-shapforxgboost `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) (propagated-inputs - `(("r-bbmisc" ,r-bbmisc) - ("r-data-table" ,r-data-table) - ("r-ggextra" ,r-ggextra) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-xgboost" ,r-xgboost))) + (list r-bbmisc + r-data-table + r-ggextra + r-ggforce + r-ggplot2 + r-ggpubr + r-rcolorbrewer + r-xgboost)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/liuyanguu/SHAPforxgboost") (synopsis "SHAP Plots for XGBoost") (description @@ -26428,8 +25660,7 @@ (define-public r-rismed (properties `((upstream-name . "RISmed"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-xml2" ,r-xml2))) + (list r-httr r-xml2)) (home-page "https://cran.r-project.org/web/packages/RISmed") (synopsis "Download content from NCBI databases") (description @@ -26454,9 +25685,8 @@ (define-public r-semver (properties `((upstream-name . "semver"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/johndharrison/semver") (synopsis "Parser for Semantic Versioning 2.0.0") (description @@ -26480,14 +25710,14 @@ (define-public r-binman (properties `((upstream-name . "binman"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rappdirs" ,r-rappdirs) - ("r-semver" ,r-semver) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-httr + r-jsonlite + r-rappdirs + r-semver + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/binman") (synopsis "Binary download manager") (description @@ -26511,12 +25741,8 @@ (define-public r-wdman (properties `((upstream-name . "wdman"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-binman" ,r-binman) - ("r-processx" ,r-processx) - ("r-semver" ,r-semver) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat r-binman r-processx r-semver r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/wdman/") (synopsis "Webdriver/Selenium binary manager") (description @@ -26544,13 +25770,13 @@ (define-public r-rselenium (properties `((upstream-name . "RSelenium"))) (build-system r-build-system) (propagated-inputs - `(("r-binman" ,r-binman) - ("r-catools" ,r-catools) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-wdman" ,r-wdman) - ("r-xml" ,r-xml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-binman + r-catools + r-httr + r-openssl + r-wdman + r-xml)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RSelenium/") (synopsis "R bindings for Selenium WebDriver") (description @@ -26579,11 +25805,7 @@ (define-public r-conquer (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs - `(("r-caret" ,r-caret) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-caret r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://github.com/XiaoouPan/conquer") (synopsis "Convolution-type smoothed quantile regression") (description @@ -26607,14 +25829,14 @@ (define-public r-fastshap (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrixstats" ,r-matrixstats) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-tibble" ,r-tibble))) + (list r-abind + r-ggplot2 + r-gridextra + r-matrixstats + r-plyr + r-rcpp + r-rcpparmadillo + r-tibble)) (home-page "https://github.com/bgreenwell/fastshap") (synopsis "Fast approximate Shapley values") (description @@ -26682,17 +25904,17 @@ (define-public r-iml (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-formula" ,r-formula) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-keras" ,r-keras) - ("r-metrics" ,r-metrics) - ("r-prediction" ,r-prediction) - ("r-r6" ,r-r6))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-data-table + r-formula + r-future + r-future-apply + r-ggplot2 + r-keras + r-metrics + r-prediction + r-r6)) + (native-inputs (list r-knitr)) (home-page "https://github.com/christophM/iml") (synopsis "Interpretable machine learning") (description @@ -26792,10 +26014,7 @@ (define-public r-spatstat-sparse `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-matrix" ,r-matrix) - ("r-spatstat-utils" ,r-spatstat-utils) - ("r-tensor" ,r-tensor))) + (list r-abind r-matrix r-spatstat-utils r-tensor)) (home-page "http://spatstat.org/") (synopsis "Sparse three-dimensional arrays and linear algebra utilities") (description @@ -26818,8 +26037,7 @@ (define-public r-spatstat-data (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-matrix r-spatstat-utils)) (home-page "http://www.spatstat.org") (synopsis "Datasets for spatstat") (description @@ -26841,10 +26059,7 @@ (define-public r-spatstat-geom (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs - `(("r-deldir" ,r-deldir) - ("r-polyclip" ,r-polyclip) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils)) (home-page "http://spatstat.org/") (synopsis "Geometrical functionality of the spatstat package") (description @@ -26867,17 +26082,17 @@ (define-public r-spatstat-core (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-goftest" ,r-goftest) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-rpart" ,r-rpart) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-sparse" ,r-spatstat-sparse) - ("r-spatstat-utils" ,r-spatstat-utils) - ("r-tensor" ,r-tensor))) + (list r-abind + r-goftest + r-matrix + r-mgcv + r-nlme + r-rpart + r-spatstat-data + r-spatstat-geom + r-spatstat-sparse + r-spatstat-utils + r-tensor)) (home-page "http://spatstat.org/") (synopsis "Core functionality of the spatstat package") (description @@ -26900,12 +26115,12 @@ (define-public r-spatstat-linnet `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-sparse" ,r-spatstat-sparse) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-matrix + r-spatstat-core + r-spatstat-data + r-spatstat-geom + r-spatstat-sparse + r-spatstat-utils)) (home-page "http://spatstat.org/") (synopsis "Linear networks functionality of the spatstat package") (description @@ -26927,11 +26142,8 @@ (define-public r-spatstat (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs - `(("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-linnet" ,r-spatstat-linnet) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-spatstat-core r-spatstat-data r-spatstat-geom + r-spatstat-linnet r-spatstat-utils)) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -26959,12 +26171,10 @@ (define-public r-gaston "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-rcpp r-rcppeigen r-rcppparallel)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gaston/") (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models") (description @@ -26987,7 +26197,7 @@ (define-public r-cpp11 "1nk47xkab7i17h7917l4cfyfvnxf782dfq67wwxa6n0r4jqqxzz9")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/cpp11") (synopsis "C++11 Interface for R's C Interface") (description @@ -27011,9 +26221,8 @@ (define-public r-rcppziggurat (properties `((upstream-name . "RcppZiggurat"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppgsl" ,r-rcppgsl))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-rcpp r-rcppgsl)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/") (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations") (description @@ -27040,9 +26249,7 @@ (define-public r-rfast (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppziggurat" ,r-rcppziggurat))) + (list r-rcpp r-rcpparmadillo r-rcppziggurat)) (home-page "https://github.com/RfastOfficial/Rfast") (synopsis "Collection of efficient and fast R functions") (description @@ -27066,7 +26273,7 @@ (define-public r-rffc "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) (build-system r-build-system) (propagated-inputs - `(("r-randomforest",r-randomforest))) + (list r-randomforest)) (home-page "https://r-forge.r-project.org/projects/rffc/") (synopsis "Random Forest Feature Contributions") (description "This package provides functions for extracting feature @@ -27090,12 +26297,8 @@ (define-public r-clusterr (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gmp" ,r-gmp) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") (description @@ -27136,11 +26339,8 @@ (define-public r-spectrum (properties `((upstream-name . "Spectrum"))) (build-system r-build-system) (propagated-inputs - `(("r-clusterr" ,r-clusterr) - ("r-diptest" ,r-diptest) - ("r-ggplot2" ,r-ggplot2) - ("r-rfast" ,r-rfast))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-clusterr r-diptest r-ggplot2 r-rfast)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Spectrum/") (synopsis "Fast adaptive spectral clustering for single and multi-view data") (description @@ -27169,9 +26369,7 @@ (define-public r-nabor (properties `((upstream-name . "nabor"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-bh r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/nabor/") (synopsis "Wrapper for K nearest neighbour library for low dimensions") (description @@ -27214,16 +26412,16 @@ (define-public r-visdat "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-ggplot2 + r-glue + r-magrittr + r-purrr + r-readr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://visdat.njtierney.com/") (synopsis "Preliminary Visualisation of Data") (description "This package provides procedures to create preliminary exploratory @@ -27245,9 +26443,9 @@ (define-public r-muhaz (properties `((upstream-name . "muhaz"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/muhaz/") (synopsis "Hazard function estimation in survival analysis") (description @@ -27270,27 +26468,27 @@ (define-public r-flexsurv (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-desolve" ,r-desolve) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-mstate" ,r-mstate) - ("r-muhaz" ,r-muhaz) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv) - ("r-purrr" ,r-purrr) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-rstpm2" ,r-rstpm2) - ("r-survival" ,r-survival) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-desolve + r-dplyr + r-generics + r-magrittr + r-matrix + r-mstate + r-muhaz + r-mvtnorm + r-numderiv + r-purrr + r-quadprog + r-rcpp + r-rlang + r-rstpm2 + r-survival + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/chjackson/flexsurv-dev") (synopsis "Flexible parametric survival and multi-state models") (description @@ -27316,10 +26514,9 @@ (define-public r-transphylo (properties `((upstream-name . "TransPhylo"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-rcpp" ,r-rcpp))) + (list r-ape r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TransPhylo/") (synopsis "Inference of transmission tree from a dated phylogeny") (description @@ -27343,7 +26540,7 @@ (define-public r-km-ci (properties `((upstream-name . "km.ci"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://cran.r-project.org/web/packages/km.ci/") (synopsis "Confidence intervals for the Kaplan-Meier estimator") (description @@ -27388,17 +26585,17 @@ (define-public r-survmisc (properties `((upstream-name . "survMisc"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-km-ci" ,r-km-ci) - ("r-kmsurv" ,r-kmsurv) - ("r-knitr" ,r-knitr) - ("r-survival" ,r-survival) - ("r-xtable" ,r-xtable) - ("r-zoo" ,r-zoo))) + (list r-data-table + r-ggplot2 + r-gridextra + r-km-ci + r-kmsurv + r-knitr + r-survival + r-xtable + r-zoo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/survMisc/") (synopsis "Miscellaneous functions for survival data") (description @@ -27442,8 +26639,7 @@ (define-public r-maxstat (properties `((upstream-name . "maxstat"))) (build-system r-build-system) (propagated-inputs - `(("r-exactranktests" ,r-exactranktests) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-exactranktests r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/maxstat/") (synopsis "Maximally selected rank statistics") (description @@ -27465,23 +26661,23 @@ (define-public r-survminer (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggtext" ,r-ggtext) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-maxstat" ,r-maxstat) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-survival" ,r-survival) - ("r-survmisc" ,r-survmisc) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-broom + r-dplyr + r-ggplot2 + r-ggpubr + r-ggtext + r-gridextra + r-magrittr + r-maxstat + r-purrr + r-rlang + r-scales + r-survival + r-survmisc + r-tibble + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://rpkgs.datanovia.com/survminer/index.html") (synopsis "Drawing survival curves using ggplot2") (description @@ -27506,8 +26702,7 @@ (define-public r-forge (properties `((upstream-name . "forge"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang))) + (list r-magrittr r-rlang)) (home-page "https://cran.r-project.org/web/packages/forge/") (synopsis "Cast values into shape") (description @@ -27529,9 +26724,9 @@ (define-public r-config (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs - `(("r-yaml" ,r-yaml))) + (list r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstudio/config") (synopsis "Manage environment specific configuration values") (description @@ -27564,12 +26759,9 @@ (define-public r-adaptivesparsity (string-append prefix "-larmadillo"))) #t))))) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-mass r-matrix r-rcpp r-rcpparmadillo)) (inputs - `(("armadillo" ,armadillo))) + (list armadillo)) (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity") (synopsis "Adaptive sparsity models") (description @@ -27592,9 +26784,7 @@ (define-public r-diffusionmap (properties `((upstream-name . "diffusionMap"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-igraph r-matrix r-scatterplot3d)) (home-page "https://www.r-project.org") (synopsis "Diffusion map") (description "This package implements the diffusion map method of data @@ -27616,16 +26806,11 @@ (define-public r-igraph "01hvphaf5mx9xvwiazcw39kp6gc1lafqrbjwczy6f7hr145dn1pl")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (inputs - `(("gmp" ,gmp) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list gmp glpk libxml2 zlib)) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-pkgconfig" ,r-pkgconfig))) + (list r-magrittr r-matrix r-pkgconfig)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -27649,18 +26834,18 @@ (define-public r-workflows (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-parsnip" ,r-parsnip) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-cli + r-ellipsis + r-generics + r-glue + r-hardhat + r-lifecycle + r-parsnip + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/workflows") (synopsis "Modeling workflows") (description @@ -27695,9 +26880,7 @@ (define-public r-lobstr (properties `((upstream-name . "lobstr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-crayon r-rcpp r-rlang)) (home-page "https://github.com/r-lib/lobstr") (synopsis "Visualize R data structures with trees") (description @@ -27722,8 +26905,7 @@ (define-public r-gpfit (properties `((upstream-name . "GPfit"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-lhs" ,r-lhs))) + (list r-lattice r-lhs)) (home-page "https://cran.r-project.org/web/packages/GPfit/") (synopsis "Gaussian Processes modeling") (description @@ -27745,14 +26927,14 @@ (define-public r-yardstick (properties `((upstream-name . "yardstick"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-proc" ,r-proc) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-dplyr + r-generics + r-proc + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/yardstick") (synopsis "Tidy characterizations of model performance") (description @@ -27774,7 +26956,7 @@ (define-public r-warp "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f")))) (properties `((upstream-name . "warp"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/warp") (synopsis "Group dates") (description @@ -27800,12 +26982,8 @@ (define-public r-slider (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs) - ("r-warp" ,r-warp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ellipsis r-glue r-rlang r-vctrs r-warp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/slider") (synopsis "Sliding window functions") (description @@ -27829,20 +27007,20 @@ (define-public r-rsample (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-furrr" ,r-furrr) - ("r-generics" ,r-generics) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-slider" ,r-slider) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-ellipsis + r-furrr + r-generics + r-lifecycle + r-purrr + r-rlang + r-slider + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://rsample.tidymodels.org") (synopsis "General resampling infrastructure") (description @@ -27884,16 +27062,16 @@ (define-public r-dials (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs - `(("r-dicedesign" ,r-dicedesign) - ("r-dplyr" ,r-dplyr) - ("r-glue" ,r-glue) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dicedesign + r-dplyr + r-glue + r-purrr + r-rlang + r-scales + r-tibble + r-vctrs + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://dials.tidymodels.org/") (synopsis "Tools for creating tuning parameter values") (description @@ -27916,27 +27094,27 @@ (define-public r-tune (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-dials" ,r-dials) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gpfit" ,r-gpfit) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-parsnip" ,r-parsnip) - ("r-purrr" ,r-purrr) - ("r-recipes" ,r-recipes) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr) - ("r-workflows" ,r-workflows) - ("r-yardstick" ,r-yardstick))) + (list r-cli + r-dials + r-dplyr + r-foreach + r-generics + r-ggplot2 + r-glue + r-gpfit + r-hardhat + r-lifecycle + r-parsnip + r-purrr + r-recipes + r-rlang + r-rsample + r-tibble + r-tidyr + r-vctrs + r-withr + r-workflows + r-yardstick)) (home-page "https://github.com/tidymodels/tune") (synopsis "Tidy tuning tools") (description @@ -27960,24 +27138,24 @@ (define-public r-workflowsets (properties `((upstream-name . "workflowsets"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-dplyr" ,r-dplyr) - ("r-hardhat" ,r-hardhat) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-lifecycle" ,r-lifecycle) - ("r-prettyunits" ,r-prettyunits) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr) - ("r-workflows" ,r-workflows))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cli + r-dplyr + r-hardhat + r-generics + r-ggplot2 + r-lifecycle + r-prettyunits + r-purrr + r-rlang + r-rsample + r-tibble + r-tidyr + r-tune + r-vctrs + r-withr + r-workflows)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tidymodels/workflowsets") (synopsis "Create a collection of tidymodels workflows") (description @@ -28002,20 +27180,20 @@ (define-public r-tidyposterior (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-rstanarm" ,r-rstanarm) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-vctrs" ,r-vctrs) - ("r-workflowsets" ,r-workflowsets))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-ggplot2 + r-purrr + r-rlang + r-rsample + r-rstanarm + r-tibble + r-tidyr + r-tune + r-vctrs + r-workflowsets)) + (native-inputs + (list r-knitr)) (home-page "https://tidyposterior.tidymodels.org") (synopsis "Bayesian analysis to compare models using resampling statistics") (description @@ -28040,16 +27218,16 @@ (define-public r-tidypredict (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-knitr" ,r-knitr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-generics + r-knitr + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://tidypredict.tidymodels.org") (synopsis "Run predictions inside the database") (description @@ -28097,11 +27275,9 @@ (define-public r-tokenizers (properties `((upstream-name . "tokenizers"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-snowballc" ,r-snowballc) - ("r-stringi" ,r-stringi))) + (list r-rcpp r-snowballc r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://lincolnmullen.com/software/tokenizers/") (synopsis "Fast, consistent tokenization of natural language text") (description @@ -28129,10 +27305,9 @@ (define-public r-hunspell (properties `((upstream-name . "hunspell"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp))) + (list r-digest r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/hunspell#readme") (synopsis "High-performance stemmer, tokenizer, and spell checker") (description @@ -28164,20 +27339,20 @@ (define-public r-tidytext (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-hunspell" ,r-hunspell) - ("r-janeaustenr" ,r-janeaustenr) - ("r-lifecycle" ,r-lifecycle) - ("r-matrix" ,r-matrix) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tokenizers" ,r-tokenizers) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-hunspell + r-janeaustenr + r-lifecycle + r-matrix + r-purrr + r-rlang + r-stringr + r-tibble + r-tokenizers + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliasilge/tidytext") (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools") (description @@ -28199,21 +27374,21 @@ (define-public r-parsnip (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-globals" ,r-globals) - ("r-glue" ,r-glue) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-prettyunits" ,r-prettyunits) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-globals + r-glue + r-hardhat + r-lifecycle + r-magrittr + r-prettyunits + r-purrr + r-rlang + r-tibble + r-tidyr + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://parsnip.tidymodels.org") (synopsis "Common API to modeling and analysis functions") (description @@ -28236,19 +27411,19 @@ (define-public r-infer (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-patchwork" ,r-patchwork) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-dplyr + r-generics + r-ggplot2 + r-glue + r-magrittr + r-patchwork + r-purrr + r-rlang + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/infer") (synopsis "Tidy statistical inference") (description @@ -28290,8 +27465,7 @@ (define-public r-conflicted (properties `((upstream-name . "conflicted"))) (build-system r-build-system) (propagated-inputs - `(("r-memoise" ,r-memoise) - ("r-rlang" ,r-rlang))) + (list r-memoise r-rlang)) (home-page "https://github.com/r-lib/conflicted") (synopsis "Alternative conflict resolution strategy") (description @@ -28317,31 +27491,29 @@ (define-public r-tidymodels (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cli" ,r-cli) - ("r-conflicted" ,r-conflicted) - ("r-dials" ,r-dials) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-hardhat" ,r-hardhat) - ("r-infer" ,r-infer) - ("r-modeldata" ,r-modeldata) - ("r-parsnip" ,r-parsnip) - ("r-purrr" ,r-purrr) - ("r-recipes" ,r-recipes) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-workflows" ,r-workflows) - ("r-workflowsets" ,r-workflowsets) - ("r-yardstick" ,r-yardstick))) - (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("pandoc" ,pandoc))) + (list r-broom + r-cli + r-conflicted + r-dials + r-dplyr + r-ggplot2 + r-hardhat + r-infer + r-modeldata + r-parsnip + r-purrr + r-recipes + r-rlang + r-rsample + r-rstudioapi + r-tibble + r-tidyr + r-tune + r-workflows + r-workflowsets + r-yardstick)) + (native-inputs + (list r-knitr r-rmarkdown pandoc)) (home-page "https://github.com/tidymodels/tidymodels") (synopsis "Tidy collection for modeling and statistical analysis") (description @@ -28364,7 +27536,7 @@ (define-public r-lsa (properties `((upstream-name . "lsa"))) (build-system r-build-system) (propagated-inputs - `(("r-snowballc" ,r-snowballc))) + (list r-snowballc)) (home-page "https://cran.r-project.org/package=lsa") (synopsis "Latent semantic analysis") (description @@ -28417,8 +27589,7 @@ (define-public r-metafor (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme))) + (list r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description @@ -28454,11 +27625,7 @@ (define-public r-altmeta (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-metafor" ,r-metafor) - ("r-rjags" ,r-rjags))) + (list r-coda r-lme4 r-matrix r-metafor r-rjags)) (home-page "https://cran.r-project.org/web/packages/altmeta/") (synopsis "Alternative meta-analysis methods") (description @@ -28536,12 +27703,12 @@ (define-public r-qtl2 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rsqlite" ,r-rsqlite) - ("r-yaml" ,r-yaml))) + (list r-data-table + r-jsonlite + r-rcpp + r-rcppeigen + r-rsqlite + r-yaml)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description @@ -28564,7 +27731,7 @@ (define-public r-seqminer "097313x72jr2q6dp8ma33w8kyp3gfw71snf1qx2maxbwwnysk085")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://seqminer.genomic.codes") (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") (description @@ -28587,7 +27754,7 @@ (define-public r-maldiquant (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description @@ -28615,8 +27782,7 @@ (define-public r-scattermore (properties `((upstream-name . "scattermore"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (home-page "https://github.com/exaexa/scattermore") (synopsis "Scatterplots with more points") (description @@ -28638,10 +27804,7 @@ (define-public r-seuratobject (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rlang" ,r-rlang))) + (list r-matrix r-rcpp r-rcppeigen r-rlang)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description @@ -28665,49 +27828,49 @@ (define-public r-seurat (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-jsonlite" ,r-jsonlite) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-miniui" ,r-miniui) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-scattermore" ,r-scattermore) - ("r-sctransform" ,r-sctransform) - ("r-seuratobject" ,r-seuratobject) - ("r-shiny" ,r-shiny) - ("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-tibble" ,r-tibble) - ("r-uwot" ,r-uwot))) + (list r-cluster + r-cowplot + r-fitdistrplus + r-future + r-future-apply + r-ggplot2 + r-ggrepel + r-ggridges + r-httr + r-ica + r-igraph + r-irlba + r-jsonlite + r-kernsmooth + r-leiden + r-lmtest + r-mass + r-matrix + r-matrixstats + r-miniui + r-patchwork + r-pbapply + r-plotly + r-png + r-rann + r-rcolorbrewer + r-rcpp + r-rcppannoy + r-rcppeigen + r-rcppprogress + r-reticulate + r-rlang + r-rocr + r-rtsne + r-scales + r-scattermore + r-sctransform + r-seuratobject + r-shiny + r-spatstat-core + r-spatstat-geom + r-tibble + r-uwot)) (home-page "http://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description @@ -28737,18 +27900,18 @@ (define-public r-seuratdisk (properties `((upstream-name . "SeuratDisk"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-hdf5r" ,r-hdf5r) - ("r-matrix" ,r-matrix) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-seurat" ,r-seurat) - ("r-seuratobject" ,r-seuratobject) - ("r-stringi" ,r-stringi) - ("r-withr" ,r-withr))) + (list r-cli + r-crayon + r-hdf5r + r-matrix + r-r6 + r-rlang + r-seurat + r-seuratobject + r-stringi + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/mojaveazure/seurat-disk") (synopsis "Interfaces for HDF5-based single cell file formats") (description @@ -28787,9 +27950,7 @@ (define-public r-seuratdata (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-rappdirs" ,r-rappdirs))) + (list r-cli r-crayon r-rappdirs)) (home-page "https://github.com/satijalab/seurat-data") (synopsis "Install and manage Seurat datasets") (description @@ -28813,14 +27974,14 @@ (define-public r-phangorn "1pg5lfc5m4ccphswbfbihj91ppmqhf4084kbjlmfsrqxylsyy8ch")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-fastmatch" ,r-fastmatch) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp))) + (list r-ape + r-fastmatch + r-igraph + r-matrix + r-quadprog + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description @@ -28842,13 +28003,10 @@ (define-public r-diversitree "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) - (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (list gfortran)) + (inputs (list fftw gsl)) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-desolve" ,r-desolve) - ("r-rcpp" ,r-rcpp) - ("r-subplex" ,r-subplex))) + (list r-ape r-desolve r-rcpp r-subplex)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" @@ -28874,9 +28032,9 @@ (define-public r-calculus (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description @@ -28904,7 +28062,7 @@ (define-public r-decon (properties `((upstream-name . "decon"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/decon/") (synopsis "Deconvolution Estimation in Measurement Error Models") @@ -28963,11 +28121,7 @@ (define-public r-lpme (properties `((upstream-name . "lpme"))) (build-system r-build-system) (propagated-inputs - `(("r-decon" ,r-decon) - ("r-flexmix" ,r-flexmix) - ("r-locpol" ,r-locpol) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/lpme/") (synopsis "Nonparametric Estimation of Measurement Error Models") @@ -28992,8 +28146,7 @@ (define-public r-aws-signature (properties `((upstream-name . "aws.signature"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest))) + (list r-base64enc r-digest)) (home-page "https://github.com/cloudyr/aws.signature") (synopsis "Amazon Web Services Request Signatures") (description @@ -29017,12 +28170,12 @@ (define-public r-aws-s3 (properties `((upstream-name . "aws.s3"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-signature" ,r-aws-signature) - ("r-base64enc" ,r-base64enc) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-xml2" ,r-xml2))) + (list r-aws-signature + r-base64enc + r-curl + r-digest + r-httr + r-xml2)) (home-page "https://github.com/cloudyr/aws.s3") (synopsis "AWS S3 Client Package") (description @@ -29042,9 +28195,9 @@ (define-public r-lgr "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6))) + (list r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet @@ -29086,8 +28239,7 @@ (define-public r-mlr3measures "1qlqfan5akz42zwkcz3ncln6rd9c302dy4cyp7nx0jcafr5i459f")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-prroc" ,r-prroc))) + (list r-checkmate r-prroc)) (home-page "https://mlr3measures.mlr-org.com/") (synopsis "Performance measures for mlr3") (description "This package implements multiple performance measures for @@ -29109,11 +28261,7 @@ (define-public r-mlr3misc "1ax1mvnm8xjcskq12x63jkal766v1zwilpgrkdv6yawd7yrww4q9")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-r6" ,r-r6))) + (list r-backports r-checkmate r-data-table r-digest r-r6)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions @@ -29135,11 +28283,7 @@ (define-public r-paradox "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-mlr3misc" ,r-mlr3misc) - ("r-r6" ,r-r6))) + (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, @@ -29160,20 +28304,20 @@ (define-public r-mlr3 "1729wbdp62cjjk775qxrahyskp191s9qqnmqbxncfjrpdxphxk34")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-lgr" ,r-lgr) - ("r-mlbench" ,r-mlbench) - ("r-mlr3measures" ,r-mlr3measures) - ("r-mlr3misc" ,r-mlr3misc) - ("r-palmerpenguins" ,r-palmerpenguins) - ("r-paradox" ,r-paradox) - ("r-parallelly" ,r-parallelly) - ("r-uuid" ,r-uuid))) + (list r-r6 + r-backports + r-checkmate + r-data-table + r-future + r-future-apply + r-lgr + r-mlbench + r-mlr3measures + r-mlr3misc + r-palmerpenguins + r-paradox + r-parallelly + r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming @@ -29196,12 +28340,12 @@ (define-public r-mlr3learners "1yc3mrk1b9h1k342wnw7sm4zmcw7w31l5ybh558g88f5hmibdl98")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-mlr3" ,r-mlr3) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + (list r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} @@ -29225,14 +28369,14 @@ (define-public r-bbotk (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-lgr" ,r-lgr) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + (list r-checkmate + r-data-table + r-lgr + r-mlr3misc + r-paradox + r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of @@ -29253,15 +28397,15 @@ (define-public r-mlr3tuning "0i428kdbak81j1wlwmdf9y40hqi63azhyny802ms2z04wl8lwnvs")))) (build-system r-build-system) (propagated-inputs - `(("r-bbotk" ,r-bbotk) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-lgr" ,r-lgr) - ("r-mlr3" ,r-mlr3) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + (list r-bbotk + r-checkmate + r-data-table + r-digest + r-lgr + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter @@ -29333,8 +28477,7 @@ (define-public r-fontquiver (properties `((upstream-name . "fontquiver"))) (build-system r-build-system) (propagated-inputs - `(("r-fontbitstreamvera" ,r-fontbitstreamvera) - ("r-fontliberation" ,r-fontliberation))) + (list r-fontbitstreamvera r-fontliberation)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description @@ -29375,7 +28518,7 @@ (define-public r-freetypeharfbuzz (copy-recursively (string-append harfbuzz "/include") "src/target/include"))))))) (propagated-inputs - `(("r-fontquiver" ,r-fontquiver))) + (list r-fontquiver)) ;; This may defeat the purpose of this package as our versions of freetype ;; and harfbuzz obviously differ from the tarballs offered by this ;; project. On the other hand, Guix arguably does a better job at @@ -29407,7 +28550,7 @@ (define-public r-freetypeharfbuzz "--without-fontconfig" "--without-glib"))))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://cran.r-project.org/package=freetypeharfbuzz") (synopsis "Deterministic computation of text box metrics") (description @@ -29432,17 +28575,16 @@ (define-public r-vdiffr (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs - `(("libpng" ,libpng) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-diffobj" ,r-diffobj) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-testthat" ,r-testthat) - ("r-xml2" ,r-xml2))) + (list libpng zlib)) + (propagated-inputs + (list r-cpp11 + r-diffobj + r-glue + r-htmltools + r-lifecycle + r-rlang + r-testthat + r-xml2)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description @@ -29487,17 +28629,17 @@ (define-public r-clustree (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-rlang" ,r-rlang) - ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis))) + (list r-checkmate + r-dplyr + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-rlang + r-tidygraph + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description @@ -29522,16 +28664,11 @@ (define-public r-textshaping (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("fribidi" ,fribidi) - ("harfbuzz" ,harfbuzz) - ("zlib" ,zlib))) + (list freetype fribidi harfbuzz zlib)) (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-systemfonts" ,r-systemfonts))) + (list r-cpp11 r-systemfonts)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/textshaping") (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") (description @@ -29561,10 +28698,9 @@ (define-public r-ragg ("libtiff" ,libtiff) ("zlib" ,zlib))) (propagated-inputs - `(("r-systemfonts" ,r-systemfonts) - ("r-textshaping" ,r-textshaping))) + (list r-systemfonts r-textshaping)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description @@ -29588,15 +28724,15 @@ (define-public r-downlit (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs - `(("r-brio" ,r-brio) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) - ("r-fansi" ,r-fansi) - ("r-memoise" ,r-memoise) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs) - ("r-yaml" ,r-yaml))) + (list r-brio + r-desc + r-digest + r-evaluate + r-fansi + r-memoise + r-rlang + r-vctrs + r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description @@ -29620,30 +28756,30 @@ (define-public r-pkgdown "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-callr" ,r-callr) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-downlit" ,r-downlit) - ("r-fs" ,r-fs) - ("r-httr" ,r-httr) - ("r-magrittr" ,r-magrittr) - ("r-memoise" ,r-memoise) - ("r-openssl" ,r-openssl) - ("r-purrr" ,r-purrr) - ("r-ragg" ,r-ragg) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tibble" ,r-tibble) - ("r-whisker" ,r-whisker) - ("r-withr" ,r-withr) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list pandoc)) + (propagated-inputs + (list r-callr + r-crayon + r-desc + r-digest + r-downlit + r-fs + r-httr + r-magrittr + r-memoise + r-openssl + r-purrr + r-ragg + r-rematch2 + r-rlang + r-rmarkdown + r-tibble + r-whisker + r-withr + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description @@ -29667,7 +28803,7 @@ (define-public r-prereg (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs - `(("r-rmarkdown" ,r-rmarkdown))) + (list r-rmarkdown)) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") @@ -29690,16 +28826,16 @@ (define-public r-ez (properties `((upstream-name . "ez"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + (list r-car + r-ggplot2 + r-lme4 + r-mass + r-matrix + r-mgcv + r-plyr + r-reshape2 + r-scales + r-stringr)) (home-page "https://github.com/mike-lawrence/ez") (synopsis "Easy Analysis and Visualization of Factorial Experiments") (description @@ -29729,7 +28865,7 @@ (define-public r-qdapregex "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) - (propagated-inputs `(("r-stringi" ,r-stringi))) + (propagated-inputs (list r-stringi)) (home-page "https://trinker.github.com/qdapRegex/") (synopsis @@ -29755,7 +28891,7 @@ (define-public r-mgsub "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis @@ -29780,9 +28916,7 @@ (define-public r-textshape (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-slam" ,r-slam) - ("r-stringi" ,r-stringi))) + (list r-data-table r-slam r-stringi)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description @@ -29803,14 +28937,14 @@ (define-public r-syuzhet (properties `((upstream-name . "syuzhet"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dtt" ,r-dtt) - ("r-nlp" ,r-nlp) - ("r-rlang" ,r-rlang) - ("r-textshape" ,r-textshape) - ("r-tidyr" ,r-tidyr) - ("r-zoo" ,r-zoo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-dtt + r-nlp + r-rlang + r-textshape + r-tidyr + r-zoo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") @@ -29841,8 +28975,7 @@ (define-public r-lexicon (properties `((upstream-name . "lexicon"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-syuzhet" ,r-syuzhet))) + (list r-data-table r-syuzhet)) (home-page "https://github.com/trinker/lexicon") (synopsis "Lexicons for Text Analysis") (description @@ -29863,7 +28996,7 @@ (define-public r-english "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=english") (synopsis "Translate Integers into English") @@ -29887,14 +29020,14 @@ (define-public r-textclean (properties `((upstream-name . "textclean"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-english" ,r-english) - ("r-glue" ,r-glue) - ("r-lexicon" ,r-lexicon) - ("r-mgsub" ,r-mgsub) - ("r-qdapregex" ,r-qdapregex) - ("r-stringi" ,r-stringi) - ("r-textshape" ,r-textshape))) + (list r-data-table + r-english + r-glue + r-lexicon + r-mgsub + r-qdapregex + r-stringi + r-textshape)) (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") @@ -29922,9 +29055,7 @@ (define-public r-striprtf (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr))) + (list r-magrittr r-rcpp r-stringr)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description @@ -29959,11 +29090,9 @@ (define-public r-ndjson (("PKG_LIBS = " all) (string-append all "-lgzstream "))) #t))))) - (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream))) + (inputs (list zlib gzstream)) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-data-table r-rcpp r-tibble)) (home-page "https://gitlab.com/hrbrmstr/ndjson") (synopsis "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") @@ -29992,9 +29121,7 @@ (define-public r-streamr (properties `((upstream-name . "streamR"))) (build-system r-build-system) (propagated-inputs - `(("r-ndjson" ,r-ndjson) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) + (list r-ndjson r-rcurl r-rjson)) (home-page "https://cran.r-project.org/package=streamR") (synopsis @@ -30018,11 +29145,8 @@ (define-public r-readods (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-readr" ,r-readr) - ("r-stringi" ,r-stringi) - ("r-xml2" ,r-xml2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cellranger r-readr r-stringi r-xml2)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") @@ -30059,13 +29183,10 @@ (define-public r-qpdf (setenv "EXTERNAL_QPDF" "1") #t))))) (inputs - `(("zlib" ,zlib) - ("qpdf" ,qpdf))) + (list zlib qpdf)) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-curl" ,r-curl) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-askpass r-curl r-rcpp)) + (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") @@ -30091,11 +29212,10 @@ (define-public r-pdftools (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib) - ("poppler" ,poppler))) + (list zlib poppler)) (propagated-inputs - `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-qpdf r-rcpp)) + (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis @@ -30135,8 +29255,8 @@ (define-public r-antiword (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) #t))))) - (inputs `(("antiword" ,antiword))) - (propagated-inputs `(("r-sys" ,r-sys))) + (inputs (list antiword)) + (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis @@ -30162,20 +29282,20 @@ (define-public r-readtext (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs - `(("r-antiword" ,r-antiword) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-pdftools" ,r-pdftools) - ("r-readods" ,r-readods) - ("r-readxl" ,r-readxl) - ("r-streamr" ,r-streamr) - ("r-stringi" ,r-stringi) - ("r-striprtf" ,r-striprtf) - ("r-tibble" ,r-tibble) - ("r-xml2" ,r-xml2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-antiword + r-data-table + r-digest + r-httr + r-jsonlite + r-pdftools + r-readods + r-readxl + r-streamr + r-stringi + r-striprtf + r-tibble + r-xml2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/quanteda/readtext") (synopsis @@ -30200,8 +29320,8 @@ (define-public r-packcircles "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mbedward/packcircles") (synopsis "Circle Packing") @@ -30225,15 +29345,10 @@ (define-public r-lwgeom (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs - `(("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list geos proj sqlite zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-sf" ,r-sf) - ("r-units" ,r-units))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-rcpp r-sf r-units)) + (native-inputs (list pkg-config)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description @@ -30256,13 +29371,13 @@ (define-public r-stars (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-classint" ,r-classint) - ("r-lwgeom" ,r-lwgeom) - ("r-rlang" ,r-rlang) - ("r-sf" ,r-sf) - ("r-units" ,r-units))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-classint + r-lwgeom + r-rlang + r-sf + r-units)) + (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") @@ -30286,15 +29401,15 @@ (define-public r-tmaptools (properties `((upstream-name . "tmaptools"))) (build-system r-build-system) (propagated-inputs - `(("r-dichromat" ,r-dichromat) - ("r-lwgeom" ,r-lwgeom) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sf" ,r-sf) - ("r-stars" ,r-stars) - ("r-units" ,r-units) - ("r-viridislite" ,r-viridislite) - ("r-xml" ,r-xml))) + (list r-dichromat + r-lwgeom + r-magrittr + r-rcolorbrewer + r-sf + r-stars + r-units + r-viridislite + r-xml)) (home-page "https://github.com/mtennekes/tmaptools") (synopsis "Thematic Map Tools") @@ -30318,9 +29433,7 @@ (define-public r-rworldmap (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs - `(("r-fields" ,r-fields) - ("r-maptools" ,r-maptools) - ("r-sp" ,r-sp))) + (list r-fields r-maptools r-sp)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") @@ -30342,14 +29455,14 @@ (define-public r-rtweet (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv + r-httr + r-jsonlite + r-magrittr + r-progress + r-rcpp + r-tibble)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collecting Twitter Data") @@ -30393,12 +29506,8 @@ (define-public r-eyelinker (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs - `(("r-intervals" ,r-intervals) - ("r-readr" ,r-readr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-intervals r-readr r-stringi r-stringr r-tibble)) + (native-inputs (list r-knitr)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis @@ -30421,7 +29530,7 @@ (define-public r-btm "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/BTM") (synopsis "Biterm Topic Models for Short Text") (description @@ -30452,7 +29561,7 @@ (define-public r-delaporte "0ijhmwclpg5czs2sl2vykcw8qj2pxy26xf6knh62rqq6p6sm43f4")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://github.com/aadler/Delaporte") (synopsis "Statistical functions for the Delaporte distribution") (description @@ -30504,8 +29613,7 @@ (define-public r-revgeo (properties `((upstream-name . "revgeo"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjsonio" ,r-rjsonio))) + (list r-rcurl r-rjsonio)) (home-page "https://cran.r-project.org/package=revgeo") (synopsis "Reverse geocoding") (description @@ -30528,11 +29636,7 @@ (define-public r-qpcr (properties `((upstream-name . "qpcR"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-minpack-lm" ,r-minpack-lm) - ("r-rgl" ,r-rgl) - ("r-robustbase" ,r-robustbase))) + (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase)) (home-page "https://cran.r-project.org/package=qpcR") (synopsis "Modelling and analysis of real-time PCR data") (description @@ -30555,10 +29659,8 @@ (define-public r-textplot (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-lattice r-matrix)) + (native-inputs (list r-knitr)) (home-page "https://github.com/bnosac/textplot") (synopsis "Text Plots") (description @@ -30648,8 +29750,8 @@ (define-public r-elliptic "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) (properties `((upstream-name . "elliptic"))) (build-system r-build-system) - (inputs `(("pari-gp" ,pari-gp))) - (propagated-inputs `(("r-mass" ,r-mass))) + (inputs (list pari-gp)) + (propagated-inputs (list r-mass)) (home-page "https://github.com/RobinHankin/elliptic") (synopsis @@ -30674,9 +29776,7 @@ (define-public r-hypergeo (properties `((upstream-name . "hypergeo"))) (build-system r-build-system) (propagated-inputs - `(("r-contfrac" ,r-contfrac) - ("r-desolve" ,r-desolve) - ("r-elliptic" ,r-elliptic))) + (list r-contfrac r-desolve r-elliptic)) (home-page "https://cran.r-project.org/web/packages/hypergeo/") (synopsis "The Gauss Hypergeometric Function") @@ -30707,22 +29807,22 @@ (define-public r-gganimate (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) (inputs ;; For video output. - `(("ffmpeg" ,ffmpeg))) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringi" ,r-stringi) - ("r-tweenr" ,r-tweenr) - ;; For GIF/SVG output. gifski is faster, but depends on Rust. - ("r-magick" ,r-magick) - ;; For HTML output. - ("r-base64enc" ,r-base64enc) - ("r-htmltools" ,r-htmltools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list ffmpeg)) + (propagated-inputs + (list r-ggplot2 + r-glue + r-plyr + r-progress + r-rlang + r-scales + r-stringi + r-tweenr + ;; For GIF/SVG output. gifski is faster, but depends on Rust. + r-magick + ;; For HTML output. + r-base64enc + r-htmltools)) + (native-inputs (list r-knitr)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description @@ -30748,7 +29848,7 @@ (define-public r-tzdb "1afmav7s29fb5cd920h6vrzg9cvc4jsidfalxpvhlh1b8mfr0df3")))) (properties `((upstream-name . "tzdb"))) (build-system r-build-system) - (propagated-inputs `(("r-cpp11" ,r-cpp11))) + (propagated-inputs (list r-cpp11)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description @@ -30777,21 +29877,21 @@ (define-public r-vroom (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-cli" ,r-cli) - ("r-cpp11" ,r-cpp11) - ("r-crayon" ,r-crayon) - ("r-glue" ,r-glue) - ("r-hms" ,r-hms) - ("r-lifecycle" ,r-lifecycle) - ("r-progress" ,r-progress) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-tzdb" ,r-tzdb) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bit64 + r-cli + r-cpp11 + r-crayon + r-glue + r-hms + r-lifecycle + r-progress + r-rlang + r-tibble + r-tidyselect + r-tzdb + r-vctrs + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") @@ -30815,9 +29915,7 @@ (define-public r-rmisc "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8")))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-lattice" ,r-lattice))) + (list r-plyr r-rcpp r-lattice)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and @@ -30837,8 +29935,7 @@ (define-public r-webutils (properties `((upstream-name . "webutils"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite))) + (list r-curl r-jsonlite)) (home-page "https://github.com/jeroen/webutils") (synopsis "Utility functions for developing web applications") (description @@ -30861,13 +29958,11 @@ (define-public r-protolite (properties `((upstream-name . "protolite"))) (build-system r-build-system) (inputs - `(("protobuf" ,protobuf))) + (list protobuf)) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp))) + (list r-jsonlite r-rcpp)) (native-inputs - `(("protobuf" ,protobuf) - ("pkg-config" ,pkg-config))) + (list protobuf pkg-config)) (home-page "https://github.com/jeroen/protolite") (synopsis "Highly optimized protocol buffer serializers") (description @@ -30894,24 +29989,24 @@ (define-public r-opencpu (properties `((upstream-name . "opencpu"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-brew" ,r-brew) - ("r-curl" ,r-curl) - ("r-evaluate" ,r-evaluate) - ("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-mime" ,r-mime) - ("r-openssl" ,r-openssl) - ("r-protolite" ,r-protolite) - ("r-rappdirs" ,r-rappdirs) - ("r-remotes" ,r-remotes) - ("r-sys" ,r-sys) - ("r-webutils" ,r-webutils) - ("r-zip" ,r-zip))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-brew + r-curl + r-evaluate + r-httpuv + r-jsonlite + r-knitr + r-mime + r-openssl + r-protolite + r-rappdirs + r-remotes + r-sys + r-webutils + r-zip)) + (native-inputs + (list r-knitr)) (home-page "https://www.opencpu.org") (synopsis "API for embedded scientific computing") (description @@ -30937,13 +30032,11 @@ (define-public r-exactextractr "1gc1p9pgazhblk8jgykxxjpblylbaq5r9hdlw3ilz5g45yjjwcnc")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) - (inputs `(("geos" ,geos))) + (inputs (list geos)) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp) - ("r-sf" ,r-sf))) + (list r-raster r-rcpp r-sf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://isciences.gitlab.io/exactextractr/") (synopsis "Fast extraction from raster datasets using polygons") (description @@ -30966,11 +30059,9 @@ (define-public r-stringfish (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-rcpp r-rcppparallel)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/traversc/stringfish") (synopsis "Alternative string implementation") (description @@ -31015,14 +30106,11 @@ (define-public r-qs "077i181vh0izvsdy2d4366yir0ajg531g6d1s7ab044ssbphg38x")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-rapiserialize" ,r-rapiserialize) - ("r-rcpp" ,r-rcpp) - ("r-stringfish" ,r-stringfish))) + (list r-rapiserialize r-rcpp r-stringfish)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/traversc/qs") (synopsis "Quick serialization of R objects") (description @@ -31044,9 +30132,9 @@ (define-public r-rgeos (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs - `(("geos" ,geos))) + (list geos)) (propagated-inputs - `(("r-sp" ,r-sp))) + (list r-sp)) (home-page "https://cran.r-project.org/package=rgeos") (synopsis "Interface to Geometry Engine (GEOS)") (description @@ -31068,17 +30156,17 @@ (define-public r-tfruns (properties `((upstream-name . "tfruns"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-config" ,r-config) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tidyselect" ,r-tidyselect) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-config + r-jsonlite + r-magrittr + r-reticulate + r-rlang + r-rstudioapi + r-tidyselect + r-whisker + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/tfruns") (synopsis "Training run tools for TensorFlow") (description @@ -31101,10 +30189,9 @@ (define-public r-tfautograph "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2")))) (properties `((upstream-name . "tfautograph"))) (build-system r-build-system) - (inputs `(("tensorflow" ,tensorflow))) + (inputs (list tensorflow)) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-reticulate" ,r-reticulate))) + (list r-backports r-reticulate)) (home-page "https://t-kalinowski.github.io/tfautograph/") (synopsis "Autograph R for Tensorflow") (description @@ -31125,15 +30212,15 @@ (define-public r-tensorflow "0xgm8jb1hl8564vviqys3aqwzvfbh0d43m154cj07j9spdz306ng")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) - (inputs `(("tensorflow" ,tensorflow))) + (inputs (list tensorflow)) (propagated-inputs - `(("r-config" ,r-config) - ("r-processx" ,r-processx) - ("r-reticulate" ,r-reticulate) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tfautograph" ,r-tfautograph) - ("r-tfruns" ,r-tfruns) - ("r-yaml" ,r-yaml))) + (list r-config + r-processx + r-reticulate + r-rstudioapi + r-tfautograph + r-tfruns + r-yaml)) (home-page "https://github.com/rstudio/tensorflow") (synopsis "R interface to TensorFlow") (description @@ -31157,17 +30244,17 @@ (define-public r-keras (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-tensorflow" ,r-tensorflow) - ("r-tfruns" ,r-tfruns) - ("r-zeallot" ,r-zeallot))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ellipsis + r-generics + r-glue + r-magrittr + r-r6 + r-reticulate + r-rlang + r-tensorflow + r-tfruns + r-zeallot)) + (native-inputs (list r-knitr)) (home-page "https://keras.rstudio.com") (synopsis "R Interface to 'Keras'") (description @@ -31192,10 +30279,9 @@ (define-public r-zzlite (properties `((upstream-name . "zzlite"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite))) + (list r-httr r-jsonlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=zzlite") (synopsis "Wrapper for the Zamzar file conversion API") (description @@ -31219,7 +30305,7 @@ (define-public r-ztree (properties `((upstream-name . "zTree"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr))) + (list r-plyr)) (home-page "https://cran.r-project.org/package=zTree") (synopsis "Functions to import data from z-Tree into R") (description @@ -31243,7 +30329,7 @@ (define-public r-distributionutils `((upstream-name . "DistributionUtils"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/package=DistributionUtils") (synopsis "Distribution utilities") (description @@ -31269,13 +30355,10 @@ (define-public r-ztpln (properties `((upstream-name . "ztpln"))) (build-system r-build-system) (propagated-inputs - `(("r-distributionutils" ,r-distributionutils) - ("r-mixtools" ,r-mixtools) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical))) + (list r-distributionutils r-mixtools r-rcpp r-rcppeigen + r-rcppnumerical)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/mattocci27/ztpln") (synopsis "Zero-truncated Poisson lognormal distribution") (description @@ -31298,9 +30381,9 @@ (define-public r-zscorer (properties `((upstream-name . "zscorer"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny))) + (list r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/nutriverse/zscorer") (synopsis "Child Anthropometry z-Score Calculator") (description @@ -31325,8 +30408,7 @@ (define-public r-zra (properties `((upstream-name . "ZRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dygraphs" ,r-dygraphs) - ("r-forecast" ,r-forecast))) + (list r-dygraphs r-forecast)) (home-page "https://cran.r-project.org/package=ZRA") (synopsis "Dynamic plots for time series forecasting") (description @@ -31348,13 +30430,13 @@ (define-public r-rfigshare (properties `((upstream-name . "rfigshare"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-rjsonio" ,r-rjsonio) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-ggplot2 + r-httpuv + r-httr + r-plyr + r-rjsonio + r-xml + r-yaml)) (home-page "https://github.com/ropensci/rfigshare") (synopsis "R Interface to figshare") (description @@ -31376,10 +30458,7 @@ (define-public r-dismo (properties `((upstream-name . "dismo"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp) - ("r-terra" ,r-terra))) + (list r-raster r-rcpp r-sp r-terra)) (home-page "https://rspatial.org/raster/sdm/") (synopsis "Species distribution modeling") (description @@ -31402,19 +30481,19 @@ (define-public r-zoon (properties `((upstream-name . "zoon"))) (build-system r-build-system) (propagated-inputs - `(("r-dismo" ,r-dismo) - ("r-plyr" ,r-plyr) - ("r-randomforest" ,r-randomforest) - ("r-raster" ,r-raster) - ("r-rcurl" ,r-rcurl) - ("r-rfigshare" ,r-rfigshare) - ("r-rgdal" ,r-rgdal) - ("r-roxygen2" ,r-roxygen2) - ("r-rworldmap" ,r-rworldmap) - ("r-sp" ,r-sp) - ("r-testthat" ,r-testthat))) + (list r-dismo + r-plyr + r-randomforest + r-raster + r-rcurl + r-rfigshare + r-rgdal + r-roxygen2 + r-rworldmap + r-sp + r-testthat)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/zoonproject/zoon") (synopsis "Reproducible, accessible and shareable species distribution modelling") (description @@ -31437,11 +30516,7 @@ (define-public r-paws-common (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-xml2" ,r-xml2))) + (list r-base64enc r-digest r-httr r-jsonlite r-xml2)) (home-page "https://cran.r-project.org/package=paws.common") (synopsis "Paws low-level Amazon Web Services API") (description @@ -31467,7 +30542,7 @@ (define-public r-paws-customer-engagement `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services customer engagement services") (description @@ -31491,7 +30566,7 @@ (define-public r-paws-cost-management `((upstream-name . "paws.cost.management"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services cost management services") (description @@ -31513,7 +30588,7 @@ (define-public r-paws-developer-tools (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services developer tools services") (description @@ -31535,7 +30610,7 @@ (define-public r-paws-end-user-computing (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services end user computing services") (description @@ -31559,7 +30634,7 @@ (define-public r-paws-application-integration `((upstream-name . "paws.application.integration"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services application integration services") (description @@ -31583,7 +30658,7 @@ (define-public r-paws-security-identity `((upstream-name . "paws.security.identity"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services security, identity, and compliance services") (description @@ -31608,7 +30683,7 @@ (define-public r-paws-analytics `((upstream-name . "paws.analytics"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services analytics services") (description @@ -31632,7 +30707,7 @@ (define-public r-paws-machine-learning `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services machine learning services") (description @@ -31656,7 +30731,7 @@ (define-public r-paws-management `((upstream-name . "paws.management"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services management and governance services") (description @@ -31680,7 +30755,7 @@ (define-public r-paws-networking `((upstream-name . "paws.networking"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services networking and content delivery services") (description @@ -31703,7 +30778,7 @@ (define-public r-paws-database (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services Database Services") @@ -31727,7 +30802,7 @@ (define-public r-paws-storage (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services storage services") (description @@ -31749,7 +30824,7 @@ (define-public r-paws-compute (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description @@ -31772,19 +30847,19 @@ (define-public r-paws (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-analytics" ,r-paws-analytics) - ("r-paws-application-integration" ,r-paws-application-integration) - ("r-paws-compute" ,r-paws-compute) - ("r-paws-cost-management" ,r-paws-cost-management) - ("r-paws-customer-engagement" ,r-paws-customer-engagement) - ("r-paws-database" ,r-paws-database) - ("r-paws-developer-tools" ,r-paws-developer-tools) - ("r-paws-end-user-computing" ,r-paws-end-user-computing) - ("r-paws-machine-learning" ,r-paws-machine-learning) - ("r-paws-management" ,r-paws-management) - ("r-paws-networking" ,r-paws-networking) - ("r-paws-security-identity" ,r-paws-security-identity) - ("r-paws-storage" ,r-paws-storage))) + (list r-paws-analytics + r-paws-application-integration + r-paws-compute + r-paws-cost-management + r-paws-customer-engagement + r-paws-database + r-paws-developer-tools + r-paws-end-user-computing + r-paws-machine-learning + r-paws-management + r-paws-networking + r-paws-security-identity + r-paws-storage)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services software development kit") (description @@ -31808,16 +30883,16 @@ (define-public r-zoomgroupstats `((upstream-name . "zoomGroupStats"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-lubridate" ,r-lubridate) - ("r-magick" ,r-magick) - ("r-openxlsx" ,r-openxlsx) - ("r-paws" ,r-paws) - ("r-pbapply" ,r-pbapply) - ("r-stringr" ,r-stringr) - ("r-syuzhet" ,r-syuzhet))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table + r-dplyr + r-lubridate + r-magick + r-openxlsx + r-paws + r-pbapply + r-stringr + r-syuzhet)) + (native-inputs (list r-knitr)) (home-page "http://zoomgroupstats.org") (synopsis "Analyze text, audio, and video from Zoom meetings") (description @@ -31862,10 +30937,9 @@ (define-public r-zoolog (properties `((upstream-name . "zoolog"))) (build-system r-build-system) (propagated-inputs - `(("r-rdpack" ,r-rdpack) - ("r-stringi" ,r-stringi))) + (list r-rdpack r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://josempozo.github.io/zoolog/") (synopsis "Zooarchaeological analysis with log-ratios") (description @@ -31917,12 +30991,12 @@ (define-public r-mlearning (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-e1071" ,r-e1071) - ("r-ipred" ,r-ipred) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-randomforest" ,r-randomforest))) + (list r-class + r-e1071 + r-ipred + r-mass + r-nnet + r-randomforest)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description @@ -31944,18 +31018,18 @@ (define-public r-zooimage (properties `((upstream-name . "zooimage"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-filehash" ,r-filehash) - ("r-jpeg" ,r-jpeg) - ("r-mass" ,r-mass) - ("r-mda" ,r-mda) - ("r-mlearning" ,r-mlearning) - ("r-png" ,r-png) - ("r-shiny" ,r-shiny) - ("r-svdialogs" ,r-svdialogs) - ("r-svmisc" ,r-svmisc) - ("r-tiff" ,r-tiff))) + (list r-digest + r-dt + r-filehash + r-jpeg + r-mass + r-mda + r-mlearning + r-png + r-shiny + r-svdialogs + r-svmisc + r-tiff)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description @@ -31979,8 +31053,8 @@ (define-public r-zooarch "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) (properties `((upstream-name . "zooaRch"))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-ggplot2)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zooaRch") (synopsis @@ -32007,10 +31081,9 @@ (define-public r-zonebuilder (properties `((upstream-name . "zonebuilder"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sf" ,r-sf))) + (list r-rcolorbrewer r-sf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/zonebuilders/zonebuilder") (synopsis "Create and explore geographic zoning systems") (description @@ -32035,12 +31108,8 @@ (define-public r-zonator (properties `((upstream-name . "zonator"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rgdal" ,r-rgdal))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal)) + (native-inputs (list r-knitr)) (home-page "https://cbig.github.io/zonator/") (synopsis "Utilities for Zonation spatial conservation prioritization") (description @@ -32085,13 +31154,13 @@ (define-public r-crul (properties `((upstream-name . "crul"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-httpcode" ,r-httpcode) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-r6" ,r-r6) - ("r-urltools" ,r-urltools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-curl + r-httpcode + r-jsonlite + r-mime + r-r6 + r-urltools)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/crul") (synopsis "HTTP client") (description @@ -32114,15 +31183,15 @@ (define-public r-gistr (properties `((upstream-name . "gistr"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crul" ,r-crul) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rmarkdown" ,r-rmarkdown))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-crul + r-dplyr + r-httr + r-jsonlite + r-knitr + r-magrittr + r-rmarkdown)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/gistr") (synopsis "Work with Gists in browser") (description @@ -32168,16 +31237,16 @@ (define-public r-rbokeh (map car mapping) (map cdr mapping))))))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-gistr" ,r-gistr) - ("r-hexbin" ,r-hexbin) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) - ("r-magrittr" ,r-magrittr) - ("r-maps" ,r-maps) - ("r-pryr" ,r-pryr) - ("r-scales" ,r-scales))) + (list r-digest + r-gistr + r-hexbin + r-htmlwidgets + r-jsonlite + r-lazyeval + r-magrittr + r-maps + r-pryr + r-scales)) ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml. (native-inputs `(("esbuild" ,esbuild) @@ -32218,11 +31287,9 @@ (define-public r-fauxpas (properties `((upstream-name . "fauxpas"))) (build-system r-build-system) (propagated-inputs - `(("r-httpcode" ,r-httpcode) - ("r-r6" ,r-r6) - ("r-whisker" ,r-whisker))) + (list r-httpcode r-r6 r-whisker)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/fauxpas") (synopsis "HTTP error helpers") (description @@ -32248,14 +31315,14 @@ (define-public r-webmockr (properties `((upstream-name . "webmockr"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-crul" ,r-crul) - ("r-curl" ,r-curl) - ("r-fauxpas" ,r-fauxpas) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-urltools" ,r-urltools))) + (list r-base64enc + r-crul + r-curl + r-fauxpas + r-jsonlite + r-magrittr + r-r6 + r-urltools)) (home-page "https://github.com/ropensci/webmockr") (synopsis "Stubbing and setting expectations on HTTP Requests") (description @@ -32280,9 +31347,9 @@ (define-public r-mockery (properties `((upstream-name . "mockery"))) (build-system r-build-system) (propagated-inputs - `(("r-testthat" ,r-testthat))) + (list r-testthat)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jfiksel/mockery") (synopsis "Mocking library for R") (description @@ -32308,17 +31375,17 @@ (define-public r-zoltr (properties `((upstream-name . "zoltr"))) (build-system r-build-system) (propagated-inputs - `(("r-base64url" ,r-base64url) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-mmwrweek" ,r-mmwrweek) - ("r-mockery" ,r-mockery) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-webmockr" ,r-webmockr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-base64url + r-dplyr + r-httr + r-jsonlite + r-magrittr + r-mmwrweek + r-mockery + r-readr + r-rlang + r-webmockr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/reichlab/zoltr") (synopsis "Interface to the Zoltar forecast repository API") (description @@ -32345,10 +31412,7 @@ (define-public r-zoib (properties `((upstream-name . "zoib"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-coda" ,r-coda) - ("r-formula" ,r-formula) - ("r-rjags" ,r-rjags))) + (list r-abind r-coda r-formula r-rjags)) (home-page "https://www.r-project.org") (synopsis "Bayesian inference for beta regression") (description @@ -32369,7 +31433,7 @@ (define-public r-logger (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg")))) (properties `((upstream-name . "logger"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://daroczig.github.io/logger/") (synopsis "Lightweight and flexible logging utility") (description @@ -32391,11 +31455,8 @@ (define-public r-fasterize (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-sp" ,r-sp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-raster r-rcpp r-rcpparmadillo r-sp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ecohealthalliance/fasterize") (synopsis "Fast Polygon to Raster Conversion") (description @@ -32419,20 +31480,19 @@ (define-public r-bien (properties `((upstream-name . "BIEN"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-testthat" ,r-testthat))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dbi" ,r-dbi) - ("r-doparallel" ,r-doparallel) - ("r-fasterize" ,r-fasterize) - ("r-foreach" ,r-foreach) - ("r-raster" ,r-raster) - ("r-rgdal" ,r-rgdal) - ("r-rgeos" ,r-rgeos) - ("r-rpostgresql" ,r-rpostgresql) - ("r-sf" ,r-sf) - ("r-sp" ,r-sp))) + (list r-knitr r-testthat)) + (propagated-inputs + (list r-ape + r-dbi + r-doparallel + r-fasterize + r-foreach + r-raster + r-rgdal + r-rgeos + r-rpostgresql + r-sf + r-sp)) (home-page "https://cran.r-project.org/package=BIEN") (synopsis "Tools for accessing the BIEN database") (description @@ -32457,13 +31517,9 @@ (define-public r-ggh4x (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-vctrs" ,r-vctrs))) + (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/teunbrand/ggh4x") (synopsis "Extension for ggplot2") (description "This package is a @code{ggplot2} extension. It provides some diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm index 75479ef592..065ff6c8e8 100644 --- a/gnu/packages/crates-graphics.scm +++ b/gnu/packages/crates-graphics.scm @@ -97,7 +97,7 @@ (define-public rust-andrew-0.2 #:cargo-development-inputs (("rust-smithay-client-toolkit" ,rust-smithay-client-toolkit-0.4)))) (inputs - `(("wayland" ,wayland))))) + (list wayland)))) (define-public rust-ansi-colours-1 (package @@ -211,11 +211,9 @@ (define-public rust-aom-sys-0.2 (("rust-bindgen" ,rust-bindgen-0.54) ("rust-metadeps" ,rust-metadeps-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libaom" ,libaom) - ("clang" ,clang) - ("llvm" ,llvm))) + (list libaom clang llvm)) (home-page "https://github.com/rust-av/aom-rs") (synopsis "FFI bindings to aom") (description "This package provides FFI bindings to aom.") @@ -241,11 +239,9 @@ (define-public rust-aom-sys-0.1 (("rust-bindgen" ,rust-bindgen-0.53) ("rust-metadeps" ,rust-metadeps-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libaom" ,libaom) - ("clang" ,clang) - ("llvm" ,llvm))))) + (list libaom clang llvm)))) (define-public rust-ascii-canvas-2 (package @@ -593,11 +589,9 @@ (define-public rust-dav1d-sys-0.3 (("rust-bindgen" ,rust-bindgen-0.54) ("rust-metadeps" ,rust-metadeps-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dav1d" ,dav1d) - ("clang" ,clang) - ("llvm" ,llvm))) + (list dav1d clang llvm)) (home-page "https://github.com/rust-av/dav1d-rs") (synopsis "FFI bindings to dav1d") (description "This package provides FFI bindings to dav1d.") @@ -984,8 +978,7 @@ (define-public rust-glutin-0.26 ("rust-winapi" ,rust-winapi-0.3) ("rust-winit" ,rust-winit-0.24)))) (inputs - `(("rust-wayland-client" ,rust-wayland-client-0.28) - ("rust-wayland-egl" ,rust-wayland-egl-0.28))) + (list rust-wayland-client-0.28 rust-wayland-egl-0.28)) (home-page "https://github.com/tomaka/glutin") (synopsis "Cross-platform OpenGL context provider") (description "This package provides an OpenGL context provider.") @@ -1996,7 +1989,7 @@ (define-public rust-ravif-0.6 #:cargo-development-inputs (("rust-avif-parse" ,rust-avif-parse-0.13)))) (native-inputs - `(("nasm" ,nasm))) ;for building rav1e + (list nasm)) ;for building rav1e (home-page "https://lib.rs/ravif") (synopsis "Library for encoding images in AVIF format") (description "This package is a rav1e-based pure Rust library for encoding @@ -2213,7 +2206,7 @@ (define-public rust-smithay-clipboard-0.3 #:cargo-development-inputs (("rust-andrew" ,rust-andrew-0.2)))) (inputs - `(("wayland" ,wayland))))) + (list wayland)))) (define-public rust-tiff-0.6 (package @@ -2327,14 +2320,14 @@ (define-public rust-wayland-client-0.28 #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("rust-bitflags" ,rust-bitflags-1) - ("rust-downcast-rs" ,rust-downcast-rs-1) - ("rust-libc" ,rust-libc-0.2) - ("rust-nix" ,rust-nix-0.18) - ("rust-scoped-tls" ,rust-scoped-tls-1) - ("rust-wayland-commons" ,rust-wayland-commons-0.28) - ("rust-wayland-scanner" ,rust-wayland-scanner-0.28) - ("rust-wayland-sys" ,rust-wayland-sys-0.28))) + (list rust-bitflags-1 + rust-downcast-rs-1 + rust-libc-0.2 + rust-nix-0.18 + rust-scoped-tls-1 + rust-wayland-commons-0.28 + rust-wayland-scanner-0.28 + rust-wayland-sys-0.28)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Rust bindings to the standard C implementation of the wayland protocol") @@ -2421,10 +2414,8 @@ (define-public rust-wayland-commons-0.28 ("rust-once-cell" ,rust-once-cell-1) ("rust-smallvec" ,rust-smallvec-1)))) (inputs - `(("rust-nix" ,rust-nix-0.18) - ("rust-once-cell" ,rust-once-cell-1) - ("rust-smallvec" ,rust-smallvec-1) - ("rust-wayland-sys" ,rust-wayland-sys-0.28))) + (list rust-nix-0.18 rust-once-cell-1 rust-smallvec-1 + rust-wayland-sys-0.28)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Types and structures used by wayland-client and wayland-server") (description @@ -2489,9 +2480,7 @@ (define-public rust-wayland-cursor-0.28 (("rust-nix" ,rust-nix-0.18) ("rust-xcursor" ,rust-xcursor-0.3)))) (inputs - `(("rust-nix" ,rust-nix-0.18) - ("rust-wayland-client" ,rust-wayland-client-0.28) - ("rust-xcursor" ,rust-xcursor-0.3))) + (list rust-nix-0.18 rust-wayland-client-0.28 rust-xcursor-0.3)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Bindings to libwayland-cursor") (description @@ -2513,11 +2502,10 @@ (define-public rust-wayland-egl-0.28 (base32 "1xd7iap0x4sidmy9dv02cdnxjhnbk9li7r7f39x9cg0i8xs50ly6")))) (build-system cargo-build-system) (inputs - `(("rust-wayland-client" ,rust-wayland-client-0.28) - ("rust-wayland-sys" ,rust-wayland-sys-0.28))) + (list rust-wayland-client-0.28 rust-wayland-sys-0.28)) ;; For the PKG_CONFIG_PATH environment variable. (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Bindings to libwayland-egl") (description @@ -2543,11 +2531,9 @@ (define-public rust-wayland-protocols-0.28 `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)))) (inputs - `(("rust-bitflags" ,rust-bitflags-1) - ("rust-wayland-client" ,rust-wayland-client-0.28) - ("rust-wayland-commons" ,rust-wayland-commons-0.28) - ("rust-wayland-scanner" ,rust-wayland-scanner-0.28) - ("rust-wayland-server" ,rust-wayland-server-0.28))) + (list rust-bitflags-1 rust-wayland-client-0.28 + rust-wayland-commons-0.28 rust-wayland-scanner-0.28 + rust-wayland-server-0.28)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Generated API for the officials Wayland protocol extensions") (description @@ -2615,9 +2601,7 @@ (define-public rust-wayland-scanner-0.28 (base32 "0g8ky63qk27in7zajycj3fyydsxlj19hanfcvr8d7z5kcxbvl43h")))) (build-system cargo-build-system) (inputs - `(("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quote" ,rust-quote-1) - ("rust-xml-rs" ,rust-xml-rs-0.8))) + (list rust-proc-macro2-1 rust-quote-1 rust-xml-rs-0.8)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Generate Rust APIs from XML Wayland protocol files") (description @@ -2685,16 +2669,16 @@ (define-public rust-wayland-server-0.28 ("rust-parking-lot" ,rust-parking-lot-0.11) ("rust-scoped-tls" ,rust-scoped-tls-1)))) (inputs - `(("rust-bitflags" ,rust-bitflags-1) - ("rust-downcast-rs" ,rust-downcast-rs-1) - ("rust-lazy-static" ,rust-lazy-static-1) - ("rust-libc" ,rust-libc-0.2) - ("rust-nix" ,rust-nix-0.18) - ("rust-parking-lot" ,rust-parking-lot-0.11) - ("rust-scoped-tls" ,rust-scoped-tls-1) - ("rust-wayland-commons" ,rust-wayland-commons-0.28) - ("rust-wayland-scanner" ,rust-wayland-scanner-0.28) - ("rust-wayland-sys" ,rust-wayland-sys-0.28))) + (list rust-bitflags-1 + rust-downcast-rs-1 + rust-lazy-static-1 + rust-libc-0.2 + rust-nix-0.18 + rust-parking-lot-0.11 + rust-scoped-tls-1 + rust-wayland-commons-0.28 + rust-wayland-scanner-0.28 + rust-wayland-sys-0.28)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "Bindings to the standard C implementation of the wayland protocol") @@ -2785,12 +2769,10 @@ (define-public rust-wayland-sys-0.28 (string-append libwayland "/lib/" shared-lib))) #t)))))) (inputs - `(("rust-dlib" ,rust-dlib-0.4) - ("rust-lazy-static" ,rust-lazy-static-1) - ("rust-libc" ,rust-libc-0.2) - ("rust-pkg-config" ,rust-pkg-config-0.3))) + (list rust-dlib-0.4 rust-lazy-static-1 rust-libc-0.2 + rust-pkg-config-0.3)) (propagated-inputs - `(("wayland" ,wayland))) + (list wayland)) (home-page "https://github.com/smithay/wayland-rs") (synopsis "FFI bindings to the various @file{libwayland-*.so} libraries") (description @@ -2880,7 +2862,7 @@ (define-public rust-winit-0.24 ("rust-winapi" ,rust-winapi-0.3) ("rust-x11-dl" ,rust-x11-dl-2)))) (inputs - `(("rust-wayland-client" ,rust-wayland-client-0.28))) + (list rust-wayland-client-0.28)) (home-page "https://github.com/rust-windowing/winit") (synopsis "Window creation library") (description @@ -3072,7 +3054,7 @@ (define-public rust-x11-clipboard-0.4 `(#:tests? #f ; Tests require display server. #:cargo-inputs (("rust-xcb" ,rust-xcb-0.9)))) (native-inputs - `(("python" ,python))))) + (list python)))) (define-public rust-x11-dl-2 (package diff --git a/gnu/packages/crates-gtk.scm b/gnu/packages/crates-gtk.scm index 0d72fbf321..b22905629f 100644 --- a/gnu/packages/crates-gtk.scm +++ b/gnu/packages/crates-gtk.scm @@ -55,8 +55,7 @@ (define-public rust-atk-sys-0.9 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("atk" ,atk) - ("glib" ,glib))) + (list atk glib)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libatk-1") (description "FFI bindings to libatk-1") @@ -86,8 +85,7 @@ (define-public rust-atk-0.8 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("atk" ,atk) - ("glib" ,glib))) + (list atk glib)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the ATK library") (description "Rust bindings for the ATK library") @@ -119,7 +117,7 @@ (define-public rust-cairo-rs-0.9 #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("cairo" ,cairo))) + (list cairo)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the Cairo library") (description "Rust bindings for the Cairo library") @@ -198,7 +196,7 @@ (define-public rust-cairo-sys-rs-0.10 ("rust-winapi" ,rust-winapi-0.3) ("rust-x11" ,rust-x11-2)))) (inputs - `(("cairo" ,cairo))) + (list cairo)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libcairo") (description "This package provides FFI bindings to libcairo.") @@ -255,11 +253,7 @@ (define-public rust-gdk-0.13 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("cairo" ,cairo) - ("gdk-pixbuf" ,gdk-pixbuf) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("pango" ,pango))) + (list cairo gdk-pixbuf glib gtk+ pango)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the GDK 3 library") (description "This package provides Rust bindings for the GDK 3 library.") @@ -321,7 +315,7 @@ (define-public rust-gdk-pixbuf-0.9 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("gdk-pixbuf" ,gdk-pixbuf))) + (list gdk-pixbuf)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the GdkPixbuf library") (description "Rust bindings for the GdkPixbuf library") @@ -405,7 +399,7 @@ (define-public rust-gdk-pixbuf-sys-0.10 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("gdk-pixbuf" ,gdk-pixbuf))) + (list gdk-pixbuf)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgdk_pixbuf-2.0") (description "This package provides FFI bindings to @code{libgdk_pixbuf-2.0}.") @@ -463,11 +457,7 @@ (define-public rust-gdk-sys-0.10 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("cairo" ,cairo) - ("gdk-pixbuf" ,gdk-pixbuf) - ("gtk+" ,gtk+) - ("glib" ,glib) - ("pango" ,pango))) + (list cairo gdk-pixbuf gtk+ glib pango)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgdk-3") (description "FFI bindings to libgdk-3") @@ -533,7 +523,7 @@ (define-public rust-gio-0.9 (("rust-gir-format-check" ,rust-gir-format-check-0.1) ("rust-serial-test" ,rust-serial-test-0.4)))) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the Gio library") (description "Rust bindings for the Gio library") @@ -621,7 +611,7 @@ (define-public rust-gio-sys-0.10 ("rust-system-deps" ,rust-system-deps-1) ("rust-winapi" ,rust-winapi-0.3)))) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgio-2.0") (description "This package provides FFI bindings to libgio-2.0.") @@ -697,7 +687,7 @@ (define-public rust-glib-0.10 ("rust-libc" ,rust-libc-0.2) ("rust-once-cell" ,rust-once-cell-1)))) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the GLib library") (description "Rust bindings for the GLib library") @@ -807,7 +797,7 @@ (define-public rust-glib-sys-0.10 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libglib-2.0") (description "This package provides FFI bindings to libglib-2.0.") @@ -858,7 +848,7 @@ (define-public rust-gobject-sys-0.10 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgobject-2.0") (description "This package provides FFI bindings to libgobject-2.0.") @@ -925,11 +915,7 @@ (define-public rust-gtk-0.8 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("atk" ,atk) - ("cairo" ,cairo) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("pango" ,pango))) + (list atk cairo glib gtk+ pango)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the GTK+ 3 library") (description "This package provides Rust bindings for the GTK+ 3 library.") @@ -985,7 +971,7 @@ (define-public rust-gtk-sys-0.9 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("gtk+" ,gtk+))) + (list gtk+)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgtk-3") (description "This package provides FFI bindings to libgtk-3.") @@ -1017,7 +1003,7 @@ (define-public rust-pango-0.9 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("pango" ,pango))) + (list pango)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the Pango library") (description "Rust bindings for the Pango library") @@ -1097,7 +1083,7 @@ (define-public rust-pango-sys-0.10 ("rust-libc" ,rust-libc-0.2) ("rust-system-deps" ,rust-system-deps-1)))) (inputs - `(("pango" ,pango))) + (list pango)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libpango-1.0") (description "This package provides FFI bindings to @code{libpango-1.0}.") @@ -1156,7 +1142,7 @@ (define-public rust-pangocairo-0.9 #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)))) (inputs - `(("gtk+" ,gtk+))) + (list gtk+)) (home-page "https://gtk-rs.org/") (synopsis "Rust bindings for the PangoCairo library") (description @@ -1218,7 +1204,7 @@ (define-public rust-pangocairo-sys-0.10 (("rust-shell-words" ,rust-shell-words-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("gtk+" ,gtk+))) + (list gtk+)) (home-page "https://gtk-rs.org/") (synopsis "FFI bindings to libgtk-3") (description "This package provides FFI bindings to libgtk-3.") diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index dd96d2be38..28bc88c887 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1033,8 +1033,7 @@ (define-public rust-adblock-0.4 ("rust-serde-json" ,rust-serde-json-1) ("rust-sha2" ,rust-sha2-0.9) ("rust-tokio" ,rust-tokio-1.8)))) - (native-inputs `(("pkg-config" ,pkg-config) - ("openssl" ,openssl))) + (native-inputs (list pkg-config openssl)) (home-page "https://github.com/brave/adblock-rust/") (synopsis "Adblock Plus syntax filter parsing and matching") (description "This package provides native Rust module for Adblock Plus @@ -2772,10 +2771,9 @@ (define-public rust-article-scraper-1 ("rust-tokio" ,rust-tokio-1) ("rust-url" ,rust-url-2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libxml2" ,libxml2) - ("openssl" ,openssl))) + (list libxml2 openssl)) (home-page "https://gitlab.com/news-flash/article_scraper") (synopsis "Scrap article contents from the web") (description "This package provides a crate to scrap article contents from @@ -5084,7 +5082,7 @@ (define-public rust-bindgen-0.55 (base32 "0hxlvy9q9984rr3rqaxwmgxjrd9wh11mcc161hv3shz6b7jkrcbm")))) (inputs - `(("clang" ,clang))) + (list clang)) (arguments `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-1) @@ -5153,7 +5151,7 @@ (define-public rust-bindgen-0.54 ("rust-diff" ,rust-diff-0.1) ("rust-shlex" ,rust-shlex-0.1)))) (inputs - `(("clang" ,clang))))) + (list clang)))) (define-public rust-bindgen-0.53 (package @@ -8104,7 +8102,7 @@ (define-public rust-capnp-rpc-0.13 (base32 "17p0y0yk68pzsnpmaklhiqrrlrrv0ld8nhbg4qflmgibshi8b69p")))) (build-system cargo-build-system) (native-inputs - `(("capnproto" ,capnproto))) + (list capnproto)) (arguments `(#:cargo-inputs (("rust-capnp" ,rust-capnp-0.13) @@ -8300,12 +8298,9 @@ (define-public rust-cargo-0.53 ("rust-walkdir" ,rust-walkdir-2) ("rust-winapi" ,rust-winapi-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("libssh2" ,libssh2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl libssh2 openssl zlib)) (home-page "https://crates.io") (synopsis "Package manager for Rust") (description "Cargo, a package manager for Rust. This package provides @@ -8583,7 +8578,7 @@ (define-public rust-cexpr-0.4 #:cargo-development-inputs (("rust-clang-sys" ,rust-clang-sys-0.28)))) (inputs - `(("clang" ,clang))) + (list clang)) (home-page "https://github.com/jethrogb/rust-cexpr") (synopsis "C expression parser and evaluator") (description @@ -9051,7 +9046,7 @@ (define-public rust-clang-sys-1 "0695kfrqx7n091fzm6msbqg2q2kyhka64q08lm63f3l9d964i8cx")))) (build-system cargo-build-system) (inputs - `(("clang" ,clang))) + (list clang)) (arguments `(#:cargo-inputs (("rust-glob" ,rust-glob-0.3) @@ -11287,7 +11282,7 @@ (define-public rust-cpuprofiler-0.0 ("rust-lazy-static" ,rust-lazy-static-1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (inputs - `(("gperftools" ,gperftools))) + (list gperftools)) (home-page "https://github.com/AtheMathmo/cpuprofiler") (synopsis "Bindings to Google's cpu profiler") (description "This package provides bindings to Google's cpu profiler.") @@ -11349,10 +11344,7 @@ (define-public rust-crates-io-0.33 ("rust-serde-json" ,rust-serde-json-1) ("rust-url" ,rust-url-2)))) (native-inputs - `(("curl" ,curl) - ("openssl" ,openssl) - ("pkg-config" ,pkg-config) - ("zlib" ,zlib))) + (list curl openssl pkg-config zlib)) (home-page "https://github.com/rust-lang/cargo") (synopsis "Helpers for interacting with @url{crates.io}") (description "This package provides helpers for interacting with @@ -12501,7 +12493,7 @@ (define-public rust-crypto-hash-0.3 ("rust-openssl" ,rust-openssl-0.10) ("rust-winapi" ,rust-winapi-0.3)))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://github.com/malept/crypto-hash") (synopsis "Wrapper for OS-level cryptographic hash functions") (description "This package provides a wrapper for OS-level cryptographic @@ -12970,12 +12962,9 @@ (define-public rust-curl-0.4 ("rust-mio" ,rust-mio-0.6) ("rust-mio-extras" ,rust-mio-extras-2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("nghttp2" ,nghttp2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl nghttp2 openssl zlib)) (home-page "https://github.com/alexcrichton/curl-rust") (synopsis "Rust bindings to libcurl for making HTTP requests") (description @@ -13013,12 +13002,9 @@ (define-public rust-curl-sys-0.4 #:cargo-development-inputs (("rust-cfg-if" ,rust-cfg-if-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("nghttp2" ,nghttp2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl nghttp2 openssl zlib)) (home-page "https://github.com/alexcrichton/curl-rust") (synopsis "Native bindings to the libcurl library") (description @@ -13784,9 +13770,9 @@ (define-public rust-dbus-0.9 #:cargo-development-inputs (("rust-tempfile" ,rust-tempfile-3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dbus" ,dbus))) + (list dbus)) (home-page "https://github.com/diwic/dbus-rs") (synopsis "Rust bindings to D-Bus") (description "This package provides Rust bindings to D-Bus.") @@ -13829,9 +13815,9 @@ (define-public rust-dbus-tree-0.9 (arguments `(#:cargo-inputs (("rust-dbus" ,rust-dbus-0.9)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dbus" ,dbus))) + (list dbus)) (home-page "https://github.com/diwic/dbus-rs") (synopsis "Framework for writing D-Bus method handlers (legacy)") (description @@ -14711,7 +14697,7 @@ (define-public rust-diesel-1 "0hpmwrc0zx3zvpgwp9zrm6wj8d8i8q8990grlrnfzlivbi6zqyq4")))) (build-system cargo-build-system) (native-inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:cargo-inputs (("rust-bigdecimal" ,rust-bigdecimal-0.1) @@ -15206,8 +15192,7 @@ (define-public rust-dirs-2 (("rust-cfg-if" ,rust-cfg-if-0.1) ("rust-dirs-sys" ,rust-dirs-sys-0.3)))) (inputs - `(("rust-cfg-if" ,rust-cfg-if-0.1) - ("rust-dirs-sys" ,rust-dirs-sys-0.3))))) + (list rust-cfg-if-0.1 rust-dirs-sys-0.3)))) (define-public rust-dirs-1 (package @@ -15297,10 +15282,8 @@ (define-public rust-dirs-sys-0.3 ("rust-redox-users" ,rust-redox-users-0.3) ("rust-winapi" ,rust-winapi-0.3)))) (inputs - `(("rust-cfg-if" ,rust-cfg-if-0.1) - ("rust-libc" ,rust-libc-0.2) - ("rust-redox-users" ,rust-redox-users-0.3) - ("rust-winapi" ,rust-winapi-0.3))) + (list rust-cfg-if-0.1 rust-libc-0.2 rust-redox-users-0.3 + rust-winapi-0.3)) (home-page "https://github.com/soc/dirs-sys-rs") (synopsis "System-level helper functions for the dirs and directories crates") @@ -15425,7 +15408,7 @@ (define-public rust-dlib-0.4 `(#:cargo-inputs (("rust-libloading" ,rust-libloading-0.6)))) (inputs - `(("rust-libloading" ,rust-libloading-0.6))) + (list rust-libloading-0.6)) (home-page "https://github.com/vberger/dlib") (synopsis "Helper macros for manually loading optional system libraries") (description @@ -16291,7 +16274,7 @@ (define-public rust-emacs-0.11 ("rust-failure-derive" ,rust-failure-derive-0.1) ("rust-lazy-static" ,rust-lazy-static-1)))) (inputs - `(("clang" ,clang))) + (list clang)) (home-page "https://github.com/ubolonton/emacs-module-rs") (synopsis "Library for creating Emacs's dynamic modules") (description @@ -16341,7 +16324,7 @@ (define-public rust-emacs-module-0.10 `(#:cargo-inputs (("rust-bindgen" ,rust-bindgen-0.48)))) (inputs - `(("clang" ,clang))) + (list clang)) (home-page "https://github.com/ubolonton/emacs-module-rs") (synopsis "Raw FFI for emacs-module") (description "This module provides a high-level binding to emacs-module: @@ -17525,9 +17508,9 @@ (define-public rust-expat-sys-2 (("rust-cmake" ,rust-cmake-0.1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("expat" ,expat))) + (list expat)) (home-page "http://www.libexpat.org/") (synopsis "XML parser library written in C") (description "XML parser library written in C") @@ -17879,9 +17862,9 @@ (define-public rust-fastq-0.6 (("rust-bio" ,rust-bio-0.33) ("rust-parasailors" ,rust-parasailors-0.3)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("libtool" ,libtool))) + (list libtool)) (home-page "https://github.com/aseyboldt/fastq-rs") (synopsis "Parser for fastq files") (description "This package provides a parser for fastq files.") @@ -18060,9 +18043,9 @@ (define-public rust-feedbin-api-0.1 ("rust-rand" ,rust-rand-0.8) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://gitlab.com/news-flash/feedbin_api") (synopsis "Rust implementation of the Feedbin REST API") (description @@ -18099,9 +18082,9 @@ (define-public rust-feedly-api-0.4 (("rust-dotenv" ,rust-dotenv-0.15) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://gitlab.com/news-flash/feedly_api") (synopsis "Rust implementation of the feedly REST API") (description @@ -18253,9 +18236,9 @@ (define-public rust-fever-api-0.2 (("rust-dotenv" ,rust-dotenv-0.15) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://gitlab.com/news-flash/fever_api") (synopsis "Rust implementation of the Fever API") (description @@ -19099,8 +19082,7 @@ (define-public rust-freetype-rs-0.23 #:cargo-development-inputs (("rust-unicode-normalization" ,rust-unicode-normalization-0.1)))) (inputs - `(("freetype" ,freetype) - ("zlib" ,zlib))))) + (list freetype zlib)))) (define-public rust-freetype-sys-0.13 (package @@ -19146,8 +19128,7 @@ (define-public rust-freetype-sys-0.9 ("rust-libz-sys" ,rust-libz-sys-1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (inputs - `(("freetype" ,freetype) - ("zlib" ,zlib))))) + (list freetype zlib)))) (define-public rust-fs2-0.4 (package @@ -21251,10 +21232,7 @@ (define-public rust-git2-0.13 `(("pkg-config" ,pkg-config) ("git" ,git-minimal))) ;for a single test (inputs - `(("libgit2" ,libgit2) - ("libssh2" ,libssh2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list libgit2 libssh2 openssl zlib)) (home-page "https://github.com/rust-lang/git2-rs") (synopsis "Rust bindings to libgit2") (description @@ -21888,8 +21866,7 @@ (define-public rust-grep-pcre2-0.1 (("rust-grep-matcher" ,rust-grep-matcher-0.1) ("rust-pcre2" ,rust-pcre2-0.2)))) (native-inputs - `(("pcre2" ,pcre2) - ("pkg-config" ,pkg-config))) + (list pcre2 pkg-config)) (home-page "https://github.com/BurntSushi/ripgrep") (synopsis "Use PCRE2 with the grep crate") @@ -24038,9 +24015,9 @@ (define-public rust-hyper-tls-0.4 (base32 "1vcfyz7dxavf4brns15afmj5fxz88lbn05rrpbfqsnybdp2sqyfr")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (arguments `(#:cargo-inputs (("rust-bytes" ,rust-bytes-0.5) @@ -25050,11 +25027,9 @@ (define-public rust-isahc-0.9 ("rust-test-case" ,rust-test-case-1) ("rust-tracing-subscriber" ,rust-tracing-subscriber-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("curl" ,curl) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl openssl zlib)) (home-page "https://github.com/sagebind/isahc") (synopsis "Practical HTTP client") (description @@ -25484,7 +25459,7 @@ (define-public rust-jemalloc-sys-0.3 (string-append jemalloc "/lib/libjemalloc_pic.a"))) #t))))) (native-inputs - `(("jemalloc" ,jemalloc))) + (list jemalloc)) (home-page "https://github.com/gnzlbg/jemallocator") (synopsis "Rust FFI bindings to jemalloc") (description "This package provides Rust FFI bindings to jemalloc.") @@ -25564,7 +25539,7 @@ (define-public rust-jemallocator-0.1 (string-append jemalloc "/lib/libjemalloc_pic.a"))) #t))))) (native-inputs - `(("jemalloc" ,jemalloc))))) + (list jemalloc)))) (define-public rust-jetscii-0.5 (package @@ -26282,7 +26257,7 @@ (define-public rust-lazy-static-1 #:cargo-development-inputs (("rust-doc-comment" ,rust-doc-comment-0.3)))) (inputs - `(("rust-spin" ,rust-spin-0.5))) + (list rust-spin-0.5)) (home-page "https://github.com/rust-lang-nursery/lazy-static.rs") (synopsis "Macro for declaring lazily evaluated statics in Rust") (description @@ -26694,9 +26669,9 @@ (define-public rust-libdbus-sys-0.2 `(#:cargo-inputs (("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dbus" ,dbus))) + (list dbus)) (home-page "https://github.com/diwic/dbus-rs") (synopsis "FFI bindings to libdbus") (description "This package provides FFI bindings to libdbus.") @@ -26820,11 +26795,9 @@ (define-public rust-libgit2-sys-0.12 ("rust-openssl-sys" ,rust-openssl-sys-0.9) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libgit2" ,libgit2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list libgit2 openssl zlib)) (home-page "https://github.com/rust-lang/git2-rs") (synopsis "Native bindings to the libgit2 library") (description @@ -26925,8 +26898,7 @@ (define-public rust-libloading-0.6 (("rust-libc" ,rust-libc-0.2) ("rust-static-assertions" ,rust-static-assertions-1)))) (inputs - `(("rust-cfg-if" ,rust-cfg-if-1) - ("rust-winapi" ,rust-winapi-0.3))))) + (list rust-cfg-if-1 rust-winapi-0.3)))) (define-public rust-libloading-0.5 (package @@ -27075,8 +27047,7 @@ (define-public rust-libnghttp2-sys-0.1 ("rust-cc" ,rust-cc-1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (inputs - `(("nghttp2" ,nghttp2 "lib") - ("pkg-config" ,pkg-config))) + (list `(,nghttp2 "lib") pkg-config)) (home-page "https://github.com/alexcrichton/nghttp2-rs") (synopsis "FFI bindings for libnghttp2 (nghttp2)") (description @@ -27123,11 +27094,9 @@ (define-public rust-libpijul-0.12 ("rust-tempdir" ,rust-tempdir-0.3) ("rust-toml" ,rust-toml-0.4)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("clang" ,clang) - ("nettle" ,nettle) - ("openssl" ,openssl))) + (list clang nettle openssl)) (home-page "https://pijul.org/") (synopsis "Library component of the pijul version control system") (description @@ -27176,9 +27145,9 @@ (define-public rust-libpulse-binding-2 (add-before 'check 'set-HOME (lambda _ (setenv "HOME" "/tmp") #t))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("pulseaudio" ,pulseaudio))) + (list pulseaudio)) (home-page "https://github.com/jnqnfe/pulse-binding-rust") (synopsis "Binding for the PulseAudio libpulse library") (description @@ -27208,9 +27177,9 @@ (define-public rust-libpulse-sys-1 ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-winapi" ,rust-winapi-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("pulseaudio" ,pulseaudio))) + (list pulseaudio)) (home-page "https://github.com/jnqnfe/pulse-binding-rust") (synopsis "FFI bindings for the PulseAudio") (description @@ -27231,7 +27200,7 @@ (define-public rust-libsqlite3-sys-0.22 (base32 "17gqc2mwih81j3ds479gl5zmsxqzzrcrj3yyv62vh34bgy8n82r9")))) (build-system cargo-build-system) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:skip-build? #t #:cargo-inputs @@ -27258,7 +27227,7 @@ (define-public rust-libsqlite3-sys-0.20 (sha256 (base32 "1g9gbjjpm9phhs991abkzmacszibp94m5nrh331ycd99y9ci1lv4")))) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:skip-build? #t #:cargo-inputs @@ -27318,7 +27287,7 @@ (define-public rust-libsqlite3-sys-0.15 (base32 "104n0s4f46zprppjq6y82y0wjh1r2cgwzw26w914yj30rizy1cbj")))) (build-system cargo-build-system) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:cargo-inputs ;; build dependencies @@ -27349,9 +27318,9 @@ (define-public rust-libxml-0.3 (("rust-criterion" ,rust-criterion-0.3) ("rust-rayon" ,rust-rayon-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libxml2" ,libxml2))) + (list libxml2)) (home-page "https://github.com/KWARC/rust-libxml") (synopsis "Rust wrapper for libxml2") (description "This package provides a Rust wrapper for libxml2, the XML @@ -27399,8 +27368,7 @@ (define-public rust-libz-sys-1 ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config) - ("zlib" ,zlib))) + (list pkg-config zlib)) (home-page "https://github.com/rust-lang/libz-sys") (synopsis "Bindings to the system libz library") (description @@ -27628,11 +27596,9 @@ (define-public rust-libssh2-sys-0.2 ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libssh2" ,libssh2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list libssh2 openssl zlib)) (home-page "https://github.com/alexcrichton/ssh2-rs") (synopsis "Native bindings to the libssh2 library") (description @@ -27664,9 +27630,9 @@ (define-public rust-lmdb-rkv-0.14 (("rust-rand" ,rust-rand-0.4) ("rust-tempdir" ,rust-tempdir-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("lmdb" ,lmdb))) + (list lmdb)) (home-page "https://github.com/mozilla/lmdb-rs") (synopsis "Safe Rust bindings for LMDB") (description "This package provides idiomatic and safe APIs for interacting @@ -27700,9 +27666,9 @@ (define-public rust-lmdb-rkv-sys-0.11 ("rust-cc" ,rust-cc-1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("lmdb" ,lmdb))) + (list lmdb)) (home-page "https://github.com/mozilla/lmdb-rs") (synopsis "Rust bindings for liblmdb") (description "This package provides rust bindings for liblmdb.") @@ -28382,8 +28348,7 @@ (define-public rust-lzma-sys-0.1 ("rust-cc" ,rust-cc-1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config) - ("xz" ,xz))) + (list pkg-config xz)) (home-page "https://github.com/alexcrichton/xz2-rs") (synopsis "Bindings to liblzma for lzma and xz stream encoding/decoding") (description @@ -29814,9 +29779,9 @@ (define-public rust-migrations-macros-1 #:cargo-development-inputs (("rust-tempdir" ,rust-tempdir-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (home-page "https://diesel.rs") (synopsis "Code generation macros for Diesel's embedded migrations") (description "This package provides code generation macros for Diesel's @@ -29959,9 +29924,9 @@ (define-public rust-miniflux-api-0.3 (("rust-dotenv" ,rust-dotenv-0.15) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://gitlab.com/news-flash/miniflux_api") (synopsis "Rust implementation of the Miniflux REST API") (description @@ -30599,10 +30564,9 @@ (define-public rust-mpris-player-0.6 (("rust-dbus" ,rust-dbus-0.6) ("rust-glib" ,rust-glib-0.10)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dbus" ,dbus) - ("glib" ,glib))) + (list dbus glib)) (home-page "https://gitlab.gnome.org/World/Rust/mpris-player") (synopsis "Library for creating MPRIS2 media players over D-Bus") (description "This package provides a library for creating MPRIS2 media @@ -30822,7 +30786,7 @@ (define-public rust-mysqlclient-sys-0.2 (("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))) (native-inputs - `(("mariadb" ,mariadb "lib"))) + (list `(,mariadb "lib"))) (home-page "https://github.com/sgrif/mysqlclient-sys") (synopsis "Auto-generated rust bindings for libmysqlclient") (description "This package provides auto-generated rust bindings for @@ -31249,9 +31213,9 @@ (define-public rust-napi-sys-0.4 "0cjirf6n4i2lw65iaww8d4hahv3cbfm5ka9hlansvnbfgzwadzq9")))) (build-system cargo-build-system) (inputs - `(("openssl" ,openssl))) + (list openssl)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (arguments `(#:cargo-inputs (("rust-bindgen" ,rust-bindgen-0.55) @@ -31296,9 +31260,9 @@ (define-public rust-native-tls-0.2 (("rust-hex" ,rust-hex-0.4) ("rust-test-cert-gen" ,rust-test-cert-gen-0.1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://github.com/sfackler/rust-native-tls") (synopsis "Wrapper over a platform's native TLS implementation") (description @@ -31691,11 +31655,9 @@ (define-public rust-nettle-7 (patches (search-patches "rust-nettle-disable-vendor.patch")))) (build-system cargo-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("clang" ,clang) - ("gmp" ,gmp) - ("nettle" ,nettle))) + (list clang gmp nettle)) (arguments `(#:skip-build? #t ;; provides nothing, has no tests #:cargo-inputs @@ -31740,10 +31702,9 @@ (define-public rust-nettle-sys-2 (patches (search-patches "rust-nettle-sys-disable-vendor.patch")))) (build-system cargo-build-system) (native-inputs - `(("clang" ,clang) - ("pkg-config" ,pkg-config))) + (list clang pkg-config)) (inputs - `(("nettle" ,nettle))) + (list nettle)) (arguments `(#:cargo-inputs (("rust-bindgen" ,rust-bindgen-0.51) @@ -31838,11 +31799,9 @@ (define-public rust-news-flash-1 (("rust-tempfile" ,rust-tempfile-3) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libxml2" ,libxml2) - ("openssl" ,openssl) - ("sqlite" ,sqlite))) + (list libxml2 openssl sqlite)) (home-page "https://gitlab.com/news-flash/news_flash") (synopsis "Base library for NewsFlash") (description "This package provides the base library for the NewsFlash @@ -31875,9 +31834,9 @@ (define-public rust-newsblur-api-0.1 (("rust-dotenv" ,rust-dotenv-0.15) ("rust-tokio" ,rust-tokio-1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://gitlab.com/news-flash/newsblur_api/") (synopsis "Rust implementation of the NewsBlur API") (description @@ -32211,10 +32170,7 @@ (define-public rust-nix-0.18 ("rust-sysctl" ,rust-sysctl-0.1) ("rust-tempfile" ,rust-tempfile-3)))) (inputs - `(("rust-bitflags" ,rust-bitflags-1) - ("rust-cc" ,rust-cc-1) - ("rust-cfg-if" ,rust-cfg-if-0.1) - ("rust-libc" ,rust-libc-0.2))))) + (list rust-bitflags-1 rust-cc-1 rust-cfg-if-0.1 rust-libc-0.2)))) (define-public rust-nix-0.17 (package @@ -32457,7 +32413,7 @@ (define-public rust-nom-7 (string-append jemalloc "/lib/libjemalloc_pic.a"))) #t))))) (native-inputs - `(("jemalloc" ,jemalloc))) + (list jemalloc)) (home-page "https://github.com/Geal/nom") (synopsis "Byte-oriented, zero-copy, parser combinators library") @@ -32857,10 +32813,9 @@ (define-public rust-notmuch-0.6 (substitute* "Cargo.toml" (("version = \"0.3.2\"") "version = \"0.5.0\""))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl) - ("notmuch" ,notmuch))) + (list openssl notmuch)) (home-page "https://github.com/vhdirk/notmuch-rs") (synopsis "Rust interface and bindings for Notmuch") (description @@ -34427,9 +34382,9 @@ (define-public rust-openssl-sys-0.9 ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://github.com/sfackler/rust-openssl") (synopsis "FFI bindings to OpenSSL") (description @@ -35038,9 +34993,9 @@ (define-public rust-parasail-sys-0.2 #:cargo-inputs (("rust-libc" ,rust-libc-0.2)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("libtool" ,libtool))) + (list libtool)) (home-page "https://github.com/anp/parasailors") (synopsis "Bindings to the parasail pairwise genetic sequence alignment library") (description @@ -35072,9 +35027,9 @@ (define-public rust-parasailors-0.3 (("rust-libc" ,rust-libc-0.2) ("rust-parasail-sys" ,rust-parasail-sys-0.2)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("libtool" ,libtool))) + (list libtool)) (home-page "https://github.com/anp/parasailors") (synopsis "SIMD accelerated pairwise genetic sequence alignment") (description "This package provides SIMD accelerated pairwise genetic @@ -35921,7 +35876,7 @@ (define-public rust-pcap-sys-0.1 (("rust-libc" ,rust-libc-0.2) ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-winapi" ,rust-winapi-0.3)))) - (inputs `(("libpcap" ,libpcap))) + (inputs (list libpcap)) (home-page "https://github.com/jmmk/rustcap") (synopsis "Low-level bindings to libpcap") (description "This package provides low-level Rust bindings to the libpcap @@ -35949,8 +35904,7 @@ (define-public rust-pcre2-0.2 ("rust-pcre2-sys" ,rust-pcre2-sys-0.2) ("rust-thread-local" ,rust-thread-local-1)))) (native-inputs - `(("pcre2" ,pcre2) - ("pkg-config" ,pkg-config))) + (list pcre2 pkg-config)) (home-page "https://github.com/BurntSushi/rust-pcre2") (synopsis "High level wrapper library for PCRE2") (description @@ -35980,8 +35934,7 @@ (define-public rust-pcre2-sys-0.2 ("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-cc" ,rust-cc-1)))) (native-inputs - `(("pcre2" ,pcre2) - ("pkg-config" ,pkg-config))) + (list pcre2 pkg-config)) (home-page "https://github.com/BurntSushi/rust-pcre2") (synopsis "Low level bindings to PCRE2") @@ -36964,7 +36917,7 @@ (define-public rust-pkg-config-0.3 "/bin/pkg-config\""))) #t))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/rust-lang/pkg-config-rs") (synopsis "Library to run the pkg-config system tool") (description @@ -38137,7 +38090,7 @@ (define-public rust-pq-sys-0.4 (("rust-pkg-config" ,rust-pkg-config-0.3) ("rust-vcpkg" ,rust-vcpkg-0.2)))) (native-inputs - `(("postgresql" ,postgresql))) + (list postgresql)) (home-page "https://crates.io/crates/pq-sys") (synopsis "Auto-generated rust bindings for libpq") (description "This package provides auto-generated rust bindings for @@ -38791,7 +38744,7 @@ (define-public rust-proc-macro2-1 #:cargo-development-inputs (("rust-quote" ,rust-quote-1)))) (inputs - `(("rust-unicode-xid" ,rust-unicode-xid-0.2))) + (list rust-unicode-xid-0.2)) (home-page "https://github.com/alexcrichton/proc-macro2") (synopsis "Stable implementation of the upcoming new `proc_macro` API") (description "This package provides a stable implementation of the upcoming new @@ -42230,9 +42183,9 @@ (define-public rust-reqwest-0.10 ("rust-tokio" ,rust-tokio-0.2) ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))))) + (list openssl)))) (define-public rust-reqwest-0.9 (package @@ -42528,9 +42481,9 @@ (define-public rust-rkv-0.10 (("rust-byteorder" ,rust-byteorder-1) ("rust-tempfile" ,rust-tempfile-3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("lmdb" ,lmdb))) + (list lmdb)) (home-page "https://github.com/mozilla/rkv") (synopsis "Typed key-value storage") (description "This package provides a typed key-value storage solution.") @@ -43315,7 +43268,7 @@ (define-public rust-rusqlite-0.23 (setenv "RUSTC_BOOTSTRAP" "1") #t))))) (native-inputs - `(("pkg-config" ,pkg-config))))) + (list pkg-config)))) (define-public rust-rusqlite-0.19 (package @@ -43353,7 +43306,7 @@ (define-public rust-rusqlite-0.19 ("rust-unicase" ,rust-unicase-2) ("rust-uuid" ,rust-uuid-0.7)))) (inputs - `(("sqlite" ,sqlite))))) + (list sqlite)))) (define-public rust-rust-argon2-0.7 (package @@ -46097,7 +46050,7 @@ (define-public rust-seccomp-sys-0.1 (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-libc" ,rust-libc-0.2)))) - (inputs `(("libseccomp" ,libseccomp))) + (inputs (list libseccomp)) (home-page "https://github.com/polachok/seccomp-sys") (synopsis "Low-level bindings to libseccomp") (description "This package provides low-level bindings to libseccomp.") @@ -46643,7 +46596,7 @@ (define-public rust-seq-io-0.3 ("rust-rand" ,rust-rand-0.7) ("rust-rand-isaac" ,rust-rand-isaac-0.2)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/markschl/seq_io") (synopsis "Fast FASTA, FASTQ and FASTX parsing") (description "This library provides readers for the the following sequence @@ -46718,10 +46671,9 @@ (define-public rust-sequoia-openpgp-0.9 #:cargo-development-inputs (("rust-rpassword" ,rust-rpassword-3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("clang" ,clang) - ("nettle" ,nettle))) + (list clang nettle)) (home-page "https://sequoia-pgp.org/") (synopsis "OpenPGP data types and associated machinery") (description @@ -47904,7 +47856,7 @@ (define-public rust-servo-fontconfig-0.4 (("rust-libc" ,rust-libc-0.2) ("rust-servo-fontconfig-sys" ,rust-servo-fontconfig-sys-4)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("fontconfig" ,fontconfig))))) @@ -47958,7 +47910,7 @@ (define-public rust-servo-fontconfig-sys-4 ("rust-servo-freetype-sys" ,rust-servo-freetype-sys-4) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("fontconfig" ,fontconfig))))) @@ -47984,9 +47936,9 @@ (define-public rust-servo-freetype-sys-4 (("rust-cmake" ,rust-cmake-0.1) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("freetype" ,freetype))) + (list freetype)) (home-page "https://www.freetype.org/") (synopsis "Rust wrapper around freetype") (description @@ -52597,7 +52549,7 @@ (define-public rust-syscallz-0.15 ("rust-seccomp-sys" ,rust-seccomp-sys-0.1) ("rust-strum" ,rust-strum-0.19) ("rust-strum-macros" ,rust-strum-macros-0.19)))) - (inputs `(("libseccomp" ,libseccomp))) + (inputs (list libseccomp)) (home-page "https://github.com/kpcyrd/syscallz-rs") (synopsis "Simple seccomp library for rust") (description "Simple seccomp library for rust") @@ -53501,9 +53453,9 @@ (define-public rust-tectonic-pdf-io-0.1 ("rust-tectonic-cfg-support" ,rust-tectonic-cfg-support-0.1) ("rust-tectonic-dep-support" ,rust-tectonic-dep-support-0.1)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libpng" ,libpng))) + (list libpng)) (home-page "https://tectonic-typesetting.github.io/") (synopsis "Xdvipdfmx's PDF, XDV, and image I/O APIs in C, as a Rust crate") (description @@ -54589,9 +54541,9 @@ (define-public rust-thrussh-libsodium-0.1 (("rust-libc" ,rust-libc-0.2) ("rust-pkg-config" ,rust-pkg-config-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libsodium" ,libsodium))) + (list libsodium)) (home-page "https://nest.pijul.com/pijul_org/thrussh") (synopsis "Straightforward bindings to libsodium") (description @@ -55844,9 +55796,9 @@ (define-public rust-tokio-openssl-0.4 (("rust-futures" ,rust-futures-0.3) ("rust-tokio" ,rust-tokio-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))))) + (list openssl)))) (define-public rust-tokio-openssl-0.3 (package @@ -56608,9 +56560,9 @@ (define-public rust-tokio-tls-0.3 ("rust-tokio-util" ,rust-tokio-util-0.3) ("rust-winapi" ,rust-winapi-0.3)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://tokio.rs") (synopsis "TLS/SSL streams for Tokio") (description "An implementation of TLS/SSL streams for Tokio giving an @@ -57750,9 +57702,9 @@ (define-public rust-trust-dns-native-tls-0.19 ("rust-tokio-tls" ,rust-tokio-tls-0.3) ("rust-trust-dns-proto" ,rust-trust-dns-proto-0.19)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))))) + (list openssl)))) (define-public rust-trust-dns-native-tls-0.18 (package @@ -57850,9 +57802,9 @@ (define-public rust-trust-dns-openssl-0.19 (("rust-openssl" ,rust-openssl-0.10) ("rust-tokio" ,rust-tokio-0.2)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))))) + (list openssl)))) (define-public rust-trust-dns-openssl-0.18 (package @@ -58280,9 +58232,9 @@ (define-public rust-trust-dns-rustls-0.19 #:cargo-development-inputs (("rust-openssl" ,rust-openssl-0.10)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))))) + (list openssl)))) (define-public rust-trust-dns-rustls-0.18 (package @@ -58325,9 +58277,9 @@ (define-public rust-trust-dns-rustls-0.6 (base32 "0vbh2y7w2s5gcw33fn4hb5f927kgjm6603vw63slg9riikmsiq43")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (arguments `(#:cargo-test-flags '("--release" "--" "--skip=tests::test_tls_client_stream_ipv4") @@ -61794,8 +61746,8 @@ (define-public rust-winapi-0.3 (("winapi-i686-pc-windows-gnu" ,rust-winapi-i686-pc-windows-gnu-0.4) ("winapi-x86-64-pc-windows-gnu" ,rust-winapi-x86-64-pc-windows-gnu-0.4)))) (inputs - `(("rust-winapi-i686-pc-windows-gnu" ,rust-winapi-i686-pc-windows-gnu-0.4) - ("rust-winapi-x86-64-pc-windows-gnu" ,rust-winapi-x86-64-pc-windows-gnu-0.4))) + (list rust-winapi-i686-pc-windows-gnu-0.4 + rust-winapi-x86-64-pc-windows-gnu-0.4)) (home-page "https://github.com/retep998/winapi-rs") (synopsis "Raw FFI bindings for all of Windows API") (description @@ -62352,12 +62304,9 @@ (define-public rust-xcb-0.9 ("rust-log" ,rust-log-0.4) ("rust-x11" ,rust-x11-2)))) (inputs - `(("libx11" ,libx11) - ("libxcb" ,libxcb) - ("xcb-proto" ,xcb-proto))) + (list libx11 libxcb xcb-proto)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python))) + (list pkg-config python)) (home-page "https://github.com/rtbo/rust-xcb") (synopsis "Rust bindings and wrappers for XCB") (description @@ -62632,8 +62581,7 @@ (define-public rust-xz2-0.1 ("rust-rand" ,rust-rand-0.5) ("rust-tokio-core" ,rust-tokio-core-0.1)))) (native-inputs - `(("pkg-config" ,pkg-config) - ("xz" ,xz))) + (list pkg-config xz)) (home-page "https://github.com/alexcrichton/xz2-rs") (synopsis "Rust bindings to liblzma") (description "This package provides Rust bindings to liblzma providing diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 1a26d7ab37..ba10a6c732 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -231,9 +231,9 @@ (define-public signify (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libbsd" ,libbsd))) + (list libbsd)) (synopsis "Create and verify cryptographic signatures") (description "The signify utility creates and verifies cryptographic signatures using the elliptic curve Ed25519. This is a Linux port of the @@ -292,7 +292,7 @@ (define-public go-minisign (arguments '(#:import-path "github.com/jedisct1/go-minisign")) (propagated-inputs - `(("go-golang-org-x-crypto" ,go-golang-org-x-crypto))) + (list go-golang-org-x-crypto)) (home-page "https://github.com/jedisct1/go-minisign") (synopsis "Minisign verification library for Golang") (description "A Golang library to verify Minisign signatures.") @@ -327,10 +327,7 @@ (define-public encfs ("googletest-source" ,(package-source googletest)) ("perl" ,perl))) (inputs - `(("attr" ,attr) - ("fuse" ,fuse) - ("openssl" ,openssl) - ("tinyxml2" ,tinyxml2))) + (list attr fuse openssl tinyxml2)) (arguments `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF") #:phases @@ -397,7 +394,7 @@ (define-public keyutils "SHAREDIR=/share/keyutils") #:test-target "test")) (inputs - `(("mit-krb5" ,mit-krb5))) + (list mit-krb5)) (home-page "https://people.redhat.com/dhowells/keyutils/") (synopsis "Linux key management utilities") (description @@ -440,9 +437,9 @@ (define-public ssss (install-file "ssss.1.html" docdir) #t)))))) (inputs - `(("gmp" ,gmp))) + (list gmp)) (native-inputs - `(("xmltoman" ,xmltoman))) + (list xmltoman)) (home-page "http://point-at-infinity.org/ssss/") (synopsis "Shamir's secret sharing scheme implementation") (description "@command{ssss-split} and @command{ssss-combine} are utilities that split @@ -463,7 +460,7 @@ (define-public tomb (base32 "136nfnpaz29hngwwnzrmc858gpnvnb977gf4ldbpapw1h1k3r8mk")))) (build-system gnu-build-system) - (native-inputs `(("sudo" ,sudo))) ;presence needed for 'check' phase + (native-inputs (list sudo)) ;presence needed for 'check' phase (inputs `(("zsh" ,zsh) ("gnupg" ,gnupg) @@ -556,7 +553,7 @@ (define-public scrypt (install-file "FORMAT" doc) #t)))))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://www.tarsnap.com/scrypt.html") (synopsis "Memory-hard encryption tool based on scrypt") (description "This package provides a simple password-based encryption @@ -614,8 +611,7 @@ (define-public perl-math-random-isaac-xs "0yxqqcqvj51fn7b7j5xqhz65v74arzgainn66c6k7inijbmr1xws")))) (build-system perl-build-system) (native-inputs - `(("perl-module-build" ,perl-module-build) - ("perl-test-nowarnings" ,perl-test-nowarnings))) + (list perl-module-build perl-test-nowarnings)) (home-page "https://metacpan.org/release/Math-Random-ISAAC-XS") (synopsis "C implementation of the ISAAC PRNG algorithm") (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a @@ -641,9 +637,9 @@ (define-public perl-math-random-isaac "0z1b3xbb3xz71h25fg6jgsccra7migq7s0vawx2rfzi0pwpz0wr7")))) (build-system perl-build-system) (native-inputs - `(("perl-test-nowarnings" ,perl-test-nowarnings))) + (list perl-test-nowarnings)) (propagated-inputs - `(("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs))) + (list perl-math-random-isaac-xs)) (home-page "https://metacpan.org/release/Math-Random-ISAAC") (synopsis "Perl interface to the ISAAC PRNG algorithm") (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a @@ -669,16 +665,15 @@ (define-public perl-crypt-random-source (base32 "1rpdds3sy5l1fhngnkrsgwsmwd54wpicx3i9ds69blcskwkcwkpc")))) (build-system perl-build-system) (native-inputs - `(("perl-module-build-tiny" ,perl-module-build-tiny) - ("perl-test-fatal" ,perl-test-fatal))) + (list perl-module-build-tiny perl-test-fatal)) (propagated-inputs - `(("perl-capture-tiny" ,perl-capture-tiny) - ("perl-module-find" ,perl-module-find) - ("perl-module-runtime" ,perl-module-runtime) - ("perl-moo" ,perl-moo) - ("perl-namespace-clean" ,perl-namespace-clean) - ("perl-sub-exporter" ,perl-sub-exporter) - ("perl-type-tiny" ,perl-type-tiny))) + (list perl-capture-tiny + perl-module-find + perl-module-runtime + perl-moo + perl-namespace-clean + perl-sub-exporter + perl-type-tiny)) (home-page "https://metacpan.org/release/Crypt-Random-Source") (synopsis "Get weak or strong random data from pluggable sources") (description "This module provides implementations for a number of @@ -699,15 +694,11 @@ (define-public perl-math-random-secure "0dgbf4ncll4kmgkyb9fsaxn0vf2smc9dmwqzgh3259zc2zla995z")))) (build-system perl-build-system) (native-inputs - `(("perl-list-moreutils" ,perl-list-moreutils) - ("perl-test-leaktrace" ,perl-test-leaktrace) - ("perl-test-sharedfork" ,perl-test-sharedfork) - ("perl-test-warn" ,perl-test-warn))) + (list perl-list-moreutils perl-test-leaktrace perl-test-sharedfork + perl-test-warn)) (inputs - `(("perl-crypt-random-source" ,perl-crypt-random-source) - ("perl-math-random-isaac" ,perl-math-random-isaac) - ("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs) - ("perl-moo" ,perl-moo))) + (list perl-crypt-random-source perl-math-random-isaac + perl-math-random-isaac-xs perl-moo)) (home-page "https://metacpan.org/release/Math-Random-Secure") (synopsis "Cryptographically secure replacement for rand()") (description "This module is intended to provide a @@ -796,7 +787,7 @@ (define-public crypto++ "Cflags: -I${includedir}\n")) #t)))))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://cryptopp.com/") (synopsis "C++ class library of cryptographic schemes") (description "Crypto++ is a C++ class library of cryptographic schemes.") @@ -974,9 +965,7 @@ (define-public botan `(("python" ,python-wrapper) ("python-docutils" ,python-docutils))) (inputs - `(("sqlite" ,sqlite) - ("bzip2" ,bzip2) - ("zlib" ,zlib))) + (list sqlite bzip2 zlib)) (synopsis "Cryptographic library in C++11") (description "Botan is a cryptography library, written in C++11, offering the tools necessary to implement a range of practical systems, such as TLS/DTLS, @@ -1032,11 +1021,9 @@ (define-public asignify (string-append "--with-openssl=" (assoc-ref %build-inputs "openssl"))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (home-page "https://github.com/vstakhov/asignify") (synopsis "Cryptographic authentication and encryption tool and library") (description "Asignify offers public cryptographic signatures and @@ -1104,9 +1091,7 @@ (define-public libsecp256k1 "--enable-module-ecdh" "--enable-shared"))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) ;; WARNING: This package might need additional configure flags to run properly. ;; See https://github.com/archlinux/svntogit-community/blob/packages/libsecp256k1/trunk/PKGBUILD. (synopsis "C library for EC operations on curve secp256k1") @@ -1144,9 +1129,7 @@ (define-public libsecp256k1-bitcoin-cash (base32 "1rnif3iny6pz1r3g69bagzr342mm3x0v66b60csnmm1rg44bd5v1")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (arguments '(#:configure-flags '("--enable-module-recovery" "--enable-experimental" @@ -1194,10 +1177,9 @@ (define-public stoken "0npgr6y85gzwksy8jkwa4yzvqwjprwnplx3yiw3ayk4f0ldlhaxa")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("nettle" ,nettle) - ("libxml2" ,libxml2))) + (list nettle libxml2)) (home-page "http://stoken.sf.net") (synopsis "Software Token for cryptographic authentication") (description @@ -1244,8 +1226,7 @@ (define-public hpenc (mkdir-p man1) #t)))))) (inputs - `(("libsodium" ,libsodium) - ("openssl" ,openssl))) + (list libsodium openssl)) (synopsis "High-performance command-line tool for stream encryption") (description "Hpenc is a command-line tool for performing authenticated encryption (AES-GCM and ChaCha20-Poly1305) of streaming data. It does not @@ -1272,9 +1253,9 @@ (define-public minisign ; No test suite `(#:tests? #f)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libsodium" ,libsodium))) + (list libsodium)) (home-page "https://jedisct1.github.io/minisign") (synopsis "Tool to sign files and verify signatures") (description @@ -1340,14 +1321,11 @@ (define-public python-olm (when tests? (add-installed-pythonpath inputs outputs) (invoke "pytest"))))))) - (inputs `(("libolm" ,libolm))) + (inputs (list libolm)) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-future" ,python-future))) + (list python-cffi python-future)) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-benchmark" ,python-pytest-benchmark) - ("python-aspectlib" ,python-aspectlib))) + (list python-pytest python-pytest-benchmark python-aspectlib)) (synopsis "Python bindings for libolm") (description "The libolm library implements the Double Ratchet cryptographic ratchet. It is written in C and C++11, and exposed as a C @@ -1387,7 +1365,7 @@ (define-public hash-extender (install-file "README.md" docdir) #t)))))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (synopsis "Tool for hash length extension attacks") (description "@command{hash_extender} is a utility for performing hash length extension attacks supporting MD4, MD5, RIPEMD-160, SHA-0, SHA-1, @@ -1420,9 +1398,9 @@ (define-public mkp224o (install-file "mkp224o" bindir) #t)))))) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (inputs - `(("libsodium" ,libsodium))) + (list libsodium)) (synopsis "Tor hidden service v3 name generator") (description "@code{mkp224o} generates valid ed25519 (hidden service version 3) onion addresses. It allows one to produce customized vanity .onion @@ -1444,8 +1422,7 @@ (define-public transcrypt (base32 "0bpz1hazbhfb6pqi68x55kq6a31bgh6vwij836slmi4jqiwvnh5a")) (file-name (git-file-name name version)))) (inputs - `(("git" ,git) - ("openssl" ,openssl))) + (list git openssl)) (build-system copy-build-system) (arguments `(#:install-plan @@ -1524,11 +1501,7 @@ (define-public cryfs `(("python" ,python-wrapper) ("pkg-config" ,pkg-config))) (inputs - `(("boost" ,boost) - ("curl" ,curl) - ("fuse" ,fuse) - ("range-v3" ,range-v3) - ("spdlog" ,spdlog))) + (list boost curl fuse range-v3 spdlog)) (home-page "https://www.cryfs.org/") (synopsis "Encrypted FUSE filesystem for the cloud") (description "CryFS encrypts your files, so you can safely store them anywhere. diff --git a/gnu/packages/cryptsetup.scm b/gnu/packages/cryptsetup.scm index 49b82090f0..c8853dca30 100644 --- a/gnu/packages/cryptsetup.scm +++ b/gnu/packages/cryptsetup.scm @@ -55,14 +55,14 @@ (define-public cryptsetup ;; GRUB 2.06 supports LUKS2, but does it reliably support all set-ups…? "--with-default-luks-format=LUKS1"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("argon2" ,argon2) - ("json-c" ,json-c) - ("libgcrypt" ,libgcrypt) - ("lvm2" ,lvm2) ; device-mapper - ("popt" ,popt) - ("util-linux" ,util-linux "lib"))) ;libuuid + (list argon2 + json-c + libgcrypt + lvm2 ; device-mapper + popt + `(,util-linux "lib"))) ;libuuid (synopsis "Set up transparent encryption of block devices using dm-crypt") (description "Cryptsetup is a utility used to conveniently set up disk encryption based diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index 193c808b1e..6342f85404 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -84,9 +84,7 @@ (define-public brlaser (assoc-ref %outputs "out") "/lib/cups")))) (inputs - `(("ghostscript" ,ghostscript) - ("cups" ,cups) - ("zlib" ,zlib))) + (list ghostscript cups zlib)) (home-page "https://github.com/pdewacht/brlaser") (synopsis "Brother laser printer driver") (description "Brlaser is a CUPS driver for Brother laser printers. This @@ -213,8 +211,8 @@ (define-public cups-filters out "/lib/cups/filter"))) #t)))))) (native-inputs - `(("glib" ,glib "bin") ; for gdbus-codegen - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") ; for gdbus-codegen + pkg-config)) (inputs `(("avahi" ,avahi) ("fontconfig" ,fontconfig) @@ -327,10 +325,9 @@ (define-public cups-minimal "#elif defined(HAVE_AVAHI)")) #t))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("zlib" ,zlib) - ("gnutls" ,gnutls))) + (list zlib gnutls)) (home-page "https://openprinting.github.io/") (synopsis "The Common Unix Printing System") (description @@ -486,11 +483,7 @@ (define-public cups-pk-helper "0a52jw6rm7lr5nbyksiia0rn7sasyb5cjqcb95z1wxm2yprgi6lm")))) (build-system gnu-build-system) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("glib" ,glib) - ("polkit" ,polkit) - ("cups" ,cups))) + (list intltool pkg-config glib polkit cups)) (home-page "https://www.freedesktop.org/wiki/Software/cups-pk-helper/") (synopsis "PolicyKit helper to configure CUPS with fine-grained privileges") (description @@ -692,8 +685,7 @@ (define-public hplip ("sane-backends" ,sane-backends-minimal) ("zlib" ,zlib))) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config))))) + (list perl pkg-config)))) (define-public hplip-minimal (package/inherit hplip @@ -735,11 +727,9 @@ (define-public foomatic-filters (home-page "https://wiki.linuxfoundation.org/openprinting/database/foomatic") (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list perl pkg-config)) (inputs - `(("dbus" ,dbus) - ("a2ps" ,a2ps))) + (list dbus a2ps)) (arguments '( ;; Specify the installation directories. #:configure-flags (list (string-append "ac_cv_path_CUPS_BACKENDS=" @@ -853,13 +843,9 @@ (define-public foo2zjs #:tests? #f ;no tests #:make-flags '("CC=gcc"))) (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("ghostscript" ,ghostscript) - ("foomatic-filters" ,foomatic-filters))) ;for 'foomatic-rip' + (list coreutils sed ghostscript foomatic-filters)) ;for 'foomatic-rip' (native-inputs - `(("bc" ,bc) - ("groff" ,groff))) + (list bc groff)) ;; The domain has expired and no one has meaningfully taken up the torch. (home-page (string-append "https://web.archive.org/web/20210129024712/" "http://foo2zjs.rkkda.com/")) @@ -923,8 +909,7 @@ (define-public epson-inkjet-printer-escpr (for-each (cut invoke "gzip" "-9" <>) (find-files "share/cups" "\\.ppd$"))))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (inputs `(("cups" ,cups-minimal))) (synopsis "ESC/P-R printer driver") @@ -1024,7 +1009,7 @@ (define-public python-pycups '(;; Tests require CUPS to be running #:tests? #f)) (inputs - `(("cups" ,cups))) + (list cups)) (home-page "https://github.com/zdohnal/pycups") (synopsis "Python bindings for libcups") (description diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 6d2f36397f..9a9d788ceb 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -69,11 +69,8 @@ (define-public curl (build-system gnu-build-system) (outputs '("out" "doc")) ;1.2 MiB of man3 pages - (inputs `(("gnutls" ,gnutls) - ("libidn" ,libidn) - ("mit-krb5" ,mit-krb5) - ("nghttp2" ,nghttp2 "lib") - ("zlib" ,zlib))) + (inputs (list gnutls libidn mit-krb5 + `(,nghttp2 "lib") zlib)) (native-inputs `(("nghttp2" ,nghttp2) ("perl" ,perl) @@ -190,9 +187,8 @@ (define-public kurly (string-append man "/kurly.1"))) #t)))))) (inputs - `(("go-github-com-alsm-ioprogress" ,go-github-com-alsm-ioprogress) - ("go-github-com-aki237-nscjar" ,go-github-com-aki237-nscjar) - ("go-github-com-urfave-cli" ,go-github-com-urfave-cli))) + (list go-github-com-alsm-ioprogress go-github-com-aki237-nscjar + go-github-com-urfave-cli)) (synopsis "Command-line HTTP client") (description "kurly is an alternative to the @code{curl} program written in Go. kurly is designed to operate in a similar manner to curl, with select @@ -263,10 +259,9 @@ (define-public guile-curl ;; The build system does not actually compile the Scheme module. ;; So we can compile it and put it in the right place in one go. (invoke "guild" "compile" curl.scm "-o" curl.go))))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (inputs - `(("curl" ,curl) - ("guile" ,guile-3.0))) + (list curl guile-3.0)) (home-page "http://www.lonelycactus.com/guile-curl.html") (synopsis "Curl bindings for Guile") (description "@code{guile-curl} is a project that has procedures that allow @@ -279,8 +274,7 @@ (define-public guile2.2-curl (inherit guile-curl) (name "guile2.2-curl") (inputs - `(("curl" ,curl) - ("guile" ,guile-2.2))))) + (list curl guile-2.2)))) (define-public curlpp (package @@ -301,7 +295,7 @@ (define-public curlpp '(#:tests? #f)) ;; The installed version needs the header files from the C library. (propagated-inputs - `(("curl" ,curl))) + (list curl)) (synopsis "C++ wrapper around libcURL") (description "This package provides a free and easy-to-use client-side C++ URL @@ -332,7 +326,7 @@ (define-public h2c '(#:install-plan '(("./h2c" "bin/")))) (inputs - `(("perl" ,perl))) + (list perl)) (home-page "https://curl.se/h2c/") (synopsis "Convert HTTP headers to a curl command line") (description diff --git a/gnu/packages/cvassistant.scm b/gnu/packages/cvassistant.scm index e7ad411b6f..9af5c7976f 100644 --- a/gnu/packages/cvassistant.scm +++ b/gnu/packages/cvassistant.scm @@ -69,9 +69,7 @@ (define-public cvassistant (replace 'configure (lambda _ (invoke "qmake")))))) (inputs - `(("qtbase" ,qtbase-5) - ("quazip" ,quazip-0) - ("zlib" ,zlib))) + (list qtbase-5 quazip-0 zlib)) (home-page "https://cvassistant.sourceforge.io/") (synopsis "Job application organizer") (description "Whether you're looking for a job or trying to help diff --git a/gnu/packages/cybersecurity.scm b/gnu/packages/cybersecurity.scm index e4614e908e..c61342c0ba 100644 --- a/gnu/packages/cybersecurity.scm +++ b/gnu/packages/cybersecurity.scm @@ -44,7 +44,7 @@ (define-public ropgadget (base32 "08ms7x4af07970ij9899l75sghnxsa7xyx73gkn6gv0l05p1hqfw")))) (build-system python-build-system) (propagated-inputs - `(("python-capstone" ,python-capstone))) + (list python-capstone)) (home-page "http://shell-storm.org/project/ROPgadget/") (synopsis "Semiautomatic return oriented programming") (description @@ -68,23 +68,22 @@ (define-public pwntools (arguments '(#:tests? #f)) ;XXX: needs a specific version of unicorn (propagated-inputs - `(("capstone" ,capstone) - ("python-dateutil" ,python-dateutil) - ("python-intervaltree" ,python-intervaltree) - ("python-mako" ,python-mako) - ("python-packaging" ,python-packaging) - ("python-paramiko" ,python-paramiko) - ("python-psutil" ,python-psutil) - ("python-pyelftools" ,python-pyelftools) - ("python-pygments" ,python-pygments) - ("python-pyserial" ,python-pyserial) - ("python-pysocks" ,python-pysocks) - ("python-requests" ,python-requests) - ("ropgadget" ,ropgadget) - ("python-six" ,python-six) - ("python-sortedcontainers" - ,python-sortedcontainers) - ("unicorn" ,unicorn))) + (list capstone + python-dateutil + python-intervaltree + python-mako + python-packaging + python-paramiko + python-psutil + python-pyelftools + python-pygments + python-pyserial + python-pysocks + python-requests + ropgadget + python-six + python-sortedcontainers + unicorn)) (home-page "https://github.com/Gallopsled/pwntools") (synopsis "Capture-the-flag (CTF) framework and exploit development library") diff --git a/gnu/packages/cyrus-sasl.scm b/gnu/packages/cyrus-sasl.scm index 43c2099968..2cd18f3e5e 100644 --- a/gnu/packages/cyrus-sasl.scm +++ b/gnu/packages/cyrus-sasl.scm @@ -48,14 +48,11 @@ (define-public cyrus-sasl "cyrus-sasl-CVE-2019-19906.patch")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - (inputs `(("gdbm" ,gdbm) - ("openssl" ,openssl))) + (list autoconf automake libtool)) + (inputs (list gdbm openssl)) (propagated-inputs - `(;; cyrus-sasl.pc refers to -lkrb5, so propagate it. - ("mit-krb5" ,mit-krb5))) + (list ;; cyrus-sasl.pc refers to -lkrb5, so propagate it. + mit-krb5)) (arguments '(#:configure-flags (list (string-append "--with-plugindir=" (assoc-ref %outputs "out") diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 6b552f688f..0f766e1738 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -194,15 +194,15 @@ (define-public 4store ("pcre" ,pcre "bin") ;for 'pcre-config' ("pkg-config" ,pkg-config))) (inputs - `(("glib" ,glib) - ("rasqal" ,rasqal) - ("libxml2" ,libxml2) - ("raptor2" ,raptor2) - ("readline" ,readline) - ("avahi" ,avahi) - ("cyrus-sasl" ,cyrus-sasl) - ("openssl" ,openssl) - ("util-linux" ,util-linux "lib"))) + (list glib + rasqal + libxml2 + raptor2 + readline + avahi + cyrus-sasl + openssl + `(,util-linux "lib"))) ;; http://www.4store.org has been down for a while now. (home-page "https://github.com/4store/4store") (synopsis "Clustered RDF storage and query engine") @@ -243,12 +243,10 @@ (define-public ephemeralpg #t))) #:test-target "test")) (inputs - `(("postgresql" ,postgresql) - ("util-linux" ,util-linux))) + (list postgresql util-linux)) (native-inputs ;; For tests. - `(("ruby" ,ruby) - ("which" ,which))) + (list ruby which)) (home-page "https://eradman.com/ephemeralpg/") (synopsis "Run temporary PostgreSQL databases") (description @@ -274,11 +272,8 @@ (define-public es-dump-restore (arguments '(#:tests? #f)) ;; No testsuite. (propagated-inputs - `(("ruby-httpclient" ,ruby-httpclient) - ("ruby-multi-json" ,ruby-multi-json) - ("ruby-progress_bar" ,ruby-progress_bar) - ("ruby-rubyzip" ,ruby-rubyzip) - ("ruby-thor" ,ruby-thor))) + (list ruby-httpclient ruby-multi-json ruby-progress_bar ruby-rubyzip + ruby-thor)) (synopsis "Utility for dumping and restoring ElasticSearch indexes") (description "This package provides a utility for dumping the contents of an @@ -424,12 +419,12 @@ (define-public firebird "lib/firebird/plugins/udr")) #t))))))) (inputs - `(("boost" ,boost) - ("editline" ,editline) - ("icu4c" ,icu4c-67) - ("libtommath" ,libtommath) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) + (list boost + editline + icu4c-67 + libtommath + ncurses + zlib)) (home-page "https://www.firebirdsql.org") (synopsis "Relational database with many ANSI SQL standard features") (description @@ -481,7 +476,7 @@ (define-public leveldb (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" "-DLEVELDB_BUILD_TESTS=ON"))) (inputs - `(("snappy" ,snappy))) + (list snappy)) (home-page "https://github.com/google/leveldb") (synopsis "Fast key-value storage library") (description @@ -502,8 +497,7 @@ (define-public memcached (base32 "0ii3z2mhjrimc6mv5z5x6bwp1s2bbzppja4m3pnmd5zgh9gs74gj")))) (build-system gnu-build-system) (inputs - `(("libevent" ,libevent) - ("cyrus-sasl" ,cyrus-sasl))) + (list libevent cyrus-sasl)) (home-page "https://memcached.org/") (synopsis "In-memory caching service") (description "Memcached is an in-memory key-value store. It has a small @@ -530,17 +524,16 @@ (define-public libmemcached (search-patches "libmemcached-build-with-gcc7.patch")))) (build-system gnu-build-system) (native-inputs - `(("memcached" ,memcached) - ("libtool" ,libtool) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("bison" ,bison) - ("flex" ,flex) - ("perl" ,perl) - ("python-sphinx" ,python-sphinx))) ;to build the HTML doc. + (list memcached + libtool + autoconf + automake + bison + flex + perl + python-sphinx)) ;to build the HTML doc. (inputs - `(("libevent" ,libevent) - ("cyrus-sasl" ,cyrus-sasl))) + (list libevent cyrus-sasl)) (outputs '("out" "doc")) (arguments '(#:tests? #f ;many tests fail and use too much time @@ -600,12 +593,9 @@ (define-public python-pylibmc (lambda _ (invoke "memcached" "-d")))))) (native-inputs - `(("memcached" ,memcached) - ("python-nose" ,python-nose))) + (list memcached python-nose)) (inputs - `(("libmemcached" ,libmemcached) - ("zlib" ,zlib) - ("cyrus-sasl" ,cyrus-sasl))) + (list libmemcached zlib cyrus-sasl)) (home-page "http://sendapatch.se/projects/pylibmc/") (synopsis "Python client for memcached") (description @@ -626,15 +616,14 @@ (define-public litecli (base32 "1yb706mgzizzijm1k0fbny98jf58qh5q6f2870rbplxlfla4w9sd")))) (build-system python-build-system) (propagated-inputs - `(("python-cli-helpers" ,python-cli-helpers) - ("python-click" ,python-click) - ("python-configobj" ,python-configobj) - ("python-prompt-toolkit" ,python-prompt-toolkit) - ("python-pygments" ,python-pygments) - ("python-sqlparse" ,python-sqlparse))) + (list python-cli-helpers + python-click + python-configobj + python-prompt-toolkit + python-pygments + python-sqlparse)) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + (list python-mock python-pytest)) (home-page "https://litecli.com") (synopsis "CLI for SQLite databases") (description @@ -656,16 +645,16 @@ (define-public mycli (arguments `(#:tests? #f)) ; tests expect a running MySQL (propagated-inputs - `(("python-cli-helpers" ,python-cli-helpers) - ("python-click" ,python-click) - ("python-configobj" ,python-configobj) - ("python-cryptography" ,python-cryptography) - ("python-prompt-toolkit" ,python-prompt-toolkit) - ("python-pyaes" ,python-pyaes) - ("python-pygments" ,python-pygments) - ("python-pymysql" ,python-pymysql) - ("python-pyperclip" ,python-pyperclip) - ("python-sqlparse" ,python-sqlparse))) + (list python-cli-helpers + python-click + python-configobj + python-cryptography + python-prompt-toolkit + python-pyaes + python-pygments + python-pymysql + python-pyperclip + python-sqlparse)) (home-page "https://www.mycli.net") (synopsis "Terminal Client for MySQL with AutoCompletion and Syntax Highlighting") @@ -750,22 +739,20 @@ (define-public mysql ,(string-append sed "/bin")))) #t)))))) (native-inputs - `(("bison" ,bison) - ("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list bison perl pkg-config)) (inputs - `(("boost" ,boost-for-mysql) - ("coreutils" ,coreutils) - ("gawk" ,gawk) - ("grep" ,grep) - ("libaio" ,libaio) - ("libtirpc" ,libtirpc) - ("ncurses" ,ncurses) - ("openssl" ,openssl) - ("procps" ,procps) - ("rpcsvc-proto" ,rpcsvc-proto) ; rpcgen - ("sed" ,sed) - ("zlib" ,zlib))) + (list boost-for-mysql + coreutils + gawk + grep + libaio + libtirpc + ncurses + openssl + procps + rpcsvc-proto ; rpcgen + sed + zlib)) (home-page "https://www.mysql.com/") (synopsis "Fast, easy to use, and popular database") (description @@ -1015,8 +1002,7 @@ (define-public mariadb (("-lssl -lcrypto" all) (string-append "-L" openssl "/lib " all))))))))) (native-inputs - `(("bison" ,bison) - ("perl" ,perl))) + (list bison perl)) (inputs `(("jemalloc" ,jemalloc) ("libaio" ,libaio) @@ -1052,7 +1038,7 @@ (define-public mariadb-connector-c (sha256 (base32 "0xb8fiissblxb319y5ifqqp86zblwis789ipb753pcb4zpnsaw82")))) (inputs - `(("openssl" ,openssl))) + (list openssl)) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests @@ -1077,9 +1063,7 @@ (define-public galera (base32 "0h7s670pcasq8wzprhyxqfca2cghi62b8xz2kikb2a86wd453qil")))) (build-system cmake-build-system) (inputs - `(("check" ,check) - ("boost" ,boost) - ("openssl" ,openssl))) + (list check boost openssl)) (home-page "https://github.com/codership/galera/") (synopsis "Extension to the MariaDB database server") (description @@ -1226,8 +1210,7 @@ (define-public pgloader (install-file "build/bin/pgloader" bin)) #t))))) (native-inputs - `(("buildapp" ,buildapp) - ("sbcl" ,sbcl))) + (list buildapp sbcl)) (inputs `(("alexandria" ,sbcl-alexandria) ("cl-abnf" ,sbcl-cl-abnf) @@ -1279,9 +1262,9 @@ (define-public python-pymysql (base32 "1ry8lxgdc1p3k7gbw20r405jqi5lvhi5wk83kxdbiv8xv3f5kh6q")))) (build-system python-build-system) (native-inputs - `(("python-unittest2" ,python-unittest2))) + (list python-unittest2)) (inputs - `(("python-cryptography" ,python-cryptography))) + (list python-cryptography)) (arguments `(#:tests? #f)) ; tests expect a running MySQL (home-page "https://github.com/PyMySQL/PyMySQL/") @@ -1464,18 +1447,14 @@ (define-public rocksdb '()) ,@make-flags))))))) (native-inputs - `(("parallel" ,parallel) - ("perl" ,perl) - ("procps" ,procps) - ("python" ,python) - ("which" ,which))) + (list parallel perl procps python which)) (inputs - `(("bzip2" ,bzip2) - ("gflags" ,gflags) - ("jemalloc" ,jemalloc) - ("lz4" ,lz4) - ("snappy" ,snappy) - ("zlib" ,zlib))) + (list bzip2 + gflags + jemalloc + lz4 + snappy + zlib)) (home-page "https://rocksdb.org/") (synopsis "Persistent key-value store for fast storage") (description @@ -1504,13 +1483,9 @@ (define-public sparql-query (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("curl" ,curl) - ("glib" ,glib) - ("libxml2" ,libxml2) - ("ncurses" ,ncurses) - ("readline" ,readline))) + (list curl glib libxml2 ncurses readline)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (arguments `(#:make-flags '("CC=gcc") #:phases @@ -1584,20 +1559,20 @@ (define-public sqitch path))))) #t))))) (native-inputs - `(("perl-capture-tiny" ,perl-capture-tiny) - ("perl-io-pager" ,perl-io-pager) - ("perl-module-build" ,perl-module-build) - ("perl-module-runtime" ,perl-module-runtime) - ("perl-path-class" ,perl-path-class) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-dir" ,perl-test-dir) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-file" ,perl-test-file) - ("perl-test-file-contents" ,perl-test-file-contents) - ("perl-test-mockmodule" ,perl-test-mockmodule) - ("perl-test-mockobject" ,perl-test-mockobject) - ("perl-test-nowarnings" ,perl-test-nowarnings) - ("perl-test-warn" ,perl-test-warn))) + (list perl-capture-tiny + perl-io-pager + perl-module-build + perl-module-runtime + perl-path-class + perl-test-deep + perl-test-dir + perl-test-exception + perl-test-file + perl-test-file-contents + perl-test-mockmodule + perl-test-mockobject + perl-test-nowarnings + perl-test-warn)) (inputs `(("perl-class-xsaccessor" ,perl-class-xsaccessor) ("perl-clone" ,perl-clone) @@ -1656,10 +1631,8 @@ (define-public sqlcrush "0x3wy40r93p0jv3nbwj9a77wa4ff697d13r0wffmm7q9h3mzsww8")))) (build-system python-build-system) (inputs - `(("python-cryptography" ,python-cryptography) - ("python-psycopg2" ,python-psycopg2) - ("python-pymysql" ,python-pymysql) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-cryptography python-psycopg2 python-pymysql + python-sqlalchemy)) (home-page "https://github.com/coffeeandscripts/sqlcrush") (synopsis "Text console-based database viewer and editor") (description @@ -1692,12 +1665,12 @@ (define-public tdb (invoke "./configure" (string-append "--prefix=" out)))))))) (native-inputs - `(;; TODO: Build the documentation. - ;; ("docbook-xsl" ,docbook-xsl) - ;; ("libxml2" ,libxml2) - ;; ("libxslt" ,libxslt) - ("python" ,python) ;for the Waf build system - ("which" ,which))) + (list ;; TODO: Build the documentation. + ;; ("docbook-xsl" ,docbook-xsl) + ;; ("libxml2" ,libxml2) + ;; ("libxslt" ,libxslt) + python ;for the Waf build system + which)) (home-page "https://tdb.samba.org/") (synopsis "Trivial database") (description @@ -1738,35 +1711,35 @@ (define-public perl-dbix-class (base32 "1rh7idjjbibc1zmiaaarask434lh0lx7f2xyfwmy37k9fa0xcpmh")))) (build-system perl-build-system) (native-inputs - `(("perl-dbd-sqlite" ,perl-dbd-sqlite) - ("perl-file-temp" ,perl-file-temp) - ("perl-module-install" ,perl-module-install) - ("perl-package-stash" ,perl-package-stash) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-warn" ,perl-test-warn))) + (list perl-dbd-sqlite + perl-file-temp + perl-module-install + perl-package-stash + perl-test-deep + perl-test-exception + perl-test-warn)) (propagated-inputs - `(("perl-class-accessor-grouped" ,perl-class-accessor-grouped) - ("perl-class-c3-componentised" ,perl-class-c3-componentised) - ("perl-class-inspector" ,perl-class-inspector) - ("perl-config-any" ,perl-config-any) - ("perl-context-preserve" ,perl-context-preserve) - ("perl-data-dumper-concise" ,perl-data-dumper-concise) - ("perl-data-page" ,perl-data-page) - ("perl-dbi" ,perl-dbi) - ("perl-devel-globaldestruction" ,perl-devel-globaldestruction) - ("perl-hash-merge" ,perl-hash-merge) - ("perl-module-find" ,perl-module-find) - ("perl-moo" ,perl-moo) - ("perl-mro-compat" ,perl-mro-compat) - ("perl-namespace-clean" ,perl-namespace-clean) - ("perl-path-class" ,perl-path-class) - ("perl-scalar-list-utils" ,perl-scalar-list-utils) - ("perl-scope-guard" ,perl-scope-guard) - ("perl-sql-abstract-classic" ,perl-sql-abstract-classic) - ("perl-sub-name" ,perl-sub-name) - ("perl-text-balanced" ,perl-text-balanced) - ("perl-try-tiny" ,perl-try-tiny))) + (list perl-class-accessor-grouped + perl-class-c3-componentised + perl-class-inspector + perl-config-any + perl-context-preserve + perl-data-dumper-concise + perl-data-page + perl-dbi + perl-devel-globaldestruction + perl-hash-merge + perl-module-find + perl-moo + perl-mro-compat + perl-namespace-clean + perl-path-class + perl-scalar-list-utils + perl-scope-guard + perl-sql-abstract-classic + perl-sub-name + perl-text-balanced + perl-try-tiny)) (home-page "https://metacpan.org/release/DBIx-Class") (synopsis "Extensible and flexible object <-> relational mapper") (description "An SQL to OO mapper with an object API inspired by @@ -1793,12 +1766,9 @@ (define-public perl-dbix-class-cursor-cached "09b2jahn2x12qm4f7qm1jzsxbz7qn1czp6a3fnl5l2i3l4r5421p")))) (build-system perl-build-system) (native-inputs - `(("perl-cache-cache" ,perl-cache-cache) - ("perl-dbd-sqlite" ,perl-dbd-sqlite) - ("perl-module-install" ,perl-module-install))) + (list perl-cache-cache perl-dbd-sqlite perl-module-install)) (propagated-inputs - `(("perl-carp-clan" ,perl-carp-clan) - ("perl-dbix-class" ,perl-dbix-class))) + (list perl-carp-clan perl-dbix-class)) (home-page "https://metacpan.org/release/DBIx-Class-Cursor-Cached") (synopsis "Cursor with built-in caching support") (description "DBIx::Class::Cursor::Cached provides a cursor class with @@ -1819,9 +1789,9 @@ (define-public perl-dbix-class-introspectablem2m "1w47rh2241iy5x3a9bqsyd5kdp9sk43dksr99frzv4qn4jsazfn6")))) (build-system perl-build-system) (native-inputs - `(("perl-module-install" ,perl-module-install))) + (list perl-module-install)) (propagated-inputs - `(("perl-dbix-class" ,perl-dbix-class))) + (list perl-dbix-class)) (home-page "https://metacpan.org/release/DBIx-Class-IntrospectableM2M") (synopsis "Introspect many-to-many relationships") (description "Because the many-to-many relationships are not real @@ -1846,40 +1816,40 @@ (define-public perl-dbix-class-schema-loader "0r57fv71ypxafb85cpxph1hdqii7ipjwvc19yb6fpkvq2ggcssg8")))) (build-system perl-build-system) (native-inputs - `(("perl-config-any" ,perl-config-any) - ("perl-config-general" ,perl-config-general) - ("perl-dbd-sqlite" ,perl-dbd-sqlite) - ("perl-dbix-class-introspectablem2m" ,perl-dbix-class-introspectablem2m) - ("perl-module-install" ,perl-module-install) - ("perl-moose" ,perl-moose) - ("perl-moosex-markasmethods" ,perl-moosex-markasmethods) - ("perl-moosex-nonmoose" ,perl-moosex-nonmoose) - ("perl-namespace-autoclean" ,perl-namespace-autoclean) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-differences" ,perl-test-differences) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-pod" ,perl-test-pod) - ("perl-test-warn" ,perl-test-warn))) + (list perl-config-any + perl-config-general + perl-dbd-sqlite + perl-dbix-class-introspectablem2m + perl-module-install + perl-moose + perl-moosex-markasmethods + perl-moosex-nonmoose + perl-namespace-autoclean + perl-test-deep + perl-test-differences + perl-test-exception + perl-test-pod + perl-test-warn)) (propagated-inputs - `(("perl-class-unload" ,perl-class-unload) - ("perl-class-inspector" ,perl-class-inspector) - ("perl-class-accessor-grouped" ,perl-class-accessor-grouped) - ("perl-class-c3-componentised" ,perl-class-c3-componentised) - ("perl-carp-clan" ,perl-carp-clan) - ("perl-data-dump" ,perl-data-dump) - ("perl-dbix-class" ,perl-dbix-class) - ("perl-hash-merge" ,perl-hash-merge) - ("perl-list-moreutils" ,perl-list-moreutils) - ("perl-lingua-en-inflect-phrase" ,perl-lingua-en-inflect-phrase) - ("perl-lingua-en-inflect-number" ,perl-lingua-en-inflect-number) - ("perl-lingua-en-tagger" ,perl-lingua-en-tagger) - ("perl-namespace-clean" ,perl-namespace-clean) - ("perl-mro-compat" ,perl-mro-compat) - ("perl-scope-guard" ,perl-scope-guard) - ("perl-string-camelcase" ,perl-string-camelcase) - ("perl-string-toidentifier-en" ,perl-string-toidentifier-en) - ("perl-sub-name" ,perl-sub-name) - ("perl-try-tiny" ,perl-try-tiny))) + (list perl-class-unload + perl-class-inspector + perl-class-accessor-grouped + perl-class-c3-componentised + perl-carp-clan + perl-data-dump + perl-dbix-class + perl-hash-merge + perl-list-moreutils + perl-lingua-en-inflect-phrase + perl-lingua-en-inflect-number + perl-lingua-en-tagger + perl-namespace-clean + perl-mro-compat + perl-scope-guard + perl-string-camelcase + perl-string-toidentifier-en + perl-sub-name + perl-try-tiny)) (arguments `(#:tests? #f)) ;TODO: t/20invocations.t fails (home-page "https://metacpan.org/release/DBIx-Class-Schema-Loader") (synopsis "Create a DBIx::Class::Schema based on a database") @@ -1902,10 +1872,9 @@ (define-public perl-dbd-pg "0kcfqq7g3832wiix0sbyvlc885qghjrp2ah3akn7h2lnb22fjwy9")))) (build-system perl-build-system) (native-inputs - `(("perl-dbi" ,perl-dbi))) + (list perl-dbi)) (propagated-inputs - `(("perl-dbi" ,perl-dbi) - ("postgresql" ,postgresql))) + (list perl-dbi postgresql)) (home-page "https://metacpan.org/release/DBD-Pg") (synopsis "DBI PostgreSQL interface") (description "This package provides a PostgreSQL driver for the Perl5 @@ -1963,8 +1932,8 @@ (define-public perl-dbd-sqlite (base32 "1zljln5nh61gj3k22a1fv2vhx5l83waizmarwkh77hk6kzzmvrw9")))) (build-system perl-build-system) - (inputs `(("sqlite" ,sqlite))) - (propagated-inputs `(("perl-dbi" ,perl-dbi))) + (inputs (list sqlite)) + (propagated-inputs (list perl-dbi)) (synopsis "SQlite interface for Perl") (description "DBD::SQLite is a Perl DBI driver for SQLite, that includes the entire thing in the distribution. So in order to get a fast transaction @@ -2009,15 +1978,10 @@ (define-public perl-sql-abstract (base32 "0jhw91b23wc9bkfwcgvka4x5ddxk58m9bcp5ay7a3vx77nla09p9")))) (build-system perl-build-system) (native-inputs - `(("perl-module-install" ,perl-module-install) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-warn" ,perl-test-warn))) + (list perl-module-install perl-test-deep perl-test-exception + perl-test-warn)) (propagated-inputs - `(("perl-hash-merge" ,perl-hash-merge) - ("perl-moo" ,perl-moo) - ("perl-mro-compat" ,perl-mro-compat) - ("perl-text-balanced" ,perl-text-balanced))) + (list perl-hash-merge perl-moo perl-mro-compat perl-text-balanced)) (home-page "https://metacpan.org/release/SQL-Abstract") (synopsis "Generate SQL from Perl data structures") (description "This module was inspired by the excellent DBIx::Abstract. @@ -2041,12 +2005,9 @@ (define-public perl-sql-abstract-classic (base32 "0a7g13hs3kdxrjn43sfli09mgsi9d6w0dfw6hlk268av17yisgaf")))) (build-system perl-build-system) (native-inputs - `(("perl-test-deep" ,perl-test-deep) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-warn" ,perl-test-warn))) + (list perl-test-deep perl-test-exception perl-test-warn)) (propagated-inputs - `(("perl-mro-compat" ,perl-mro-compat) - ("perl-sql-abstract" ,perl-sql-abstract))) + (list perl-mro-compat perl-sql-abstract)) (home-page "https://metacpan.org/release/SQL-Abstract-Classic") (synopsis "Generate SQL from Perl data structures") (description @@ -2077,14 +2038,10 @@ (define-public perl-sql-splitstatement (base32 "0ppkx46nydzlnsxf9a8pkyb74wggfrdiiwafab143lrarlh88x0s")))) (build-system perl-build-system) (native-inputs - `(("perl-test-differences" ,perl-test-differences) - ("perl-test-exception" ,perl-test-exception) - ("perl-test-script" ,perl-test-script))) + (list perl-test-differences perl-test-exception perl-test-script)) (propagated-inputs - `(("perl-class-accessor" ,perl-class-accessor) - ("perl-list-moreutils" ,perl-list-moreutils) - ("perl-regexp-common" ,perl-regexp-common) - ("perl-sql-tokenizer" ,perl-sql-tokenizer))) + (list perl-class-accessor perl-list-moreutils perl-regexp-common + perl-sql-tokenizer)) (home-page "https://metacpan.org/release/SQL-SplitStatement") (synopsis "Split SQL code into atomic statements") (description "This module tries to split any SQL code, even including @@ -2154,7 +2111,7 @@ (define-public nanodbc "-DBUILD_SHARED_LIBS=ON") #:tests? #false)) (inputs - `(("unixodbc" ,unixodbc))) + (list unixodbc)) (home-page "https://nanodbc.io/") (synopsis "C++ wrapper for the native C ODBC API") (description "The goal for nanodbc is to make developers happy by providing @@ -2242,8 +2199,8 @@ (define-public redis '(begin (delete-file-recursively "deps/jemalloc"))))) (build-system gnu-build-system) (native-inputs - `(("procps" ,procps) ; for tests - ("tcl" ,tcl))) ; for tests + (list procps ; for tests + tcl)) ; for tests (arguments '(#:phases (modify-phases %standard-phases @@ -2314,7 +2271,7 @@ (define-public kyotocabinet "--disable-opt" ;"-march=native". XXX this also turns off -O0. (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib")))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://fallabs.com/kyotocabinet/") (synopsis "Kyoto Cabinet is a modern implementation of the DBM database") @@ -2343,7 +2300,7 @@ (define-public tokyocabinet (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib")))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://fallabs.com/tokyocabinet/") (synopsis "Tokyo Cabinet is a modern implementation of the DBM database") (description @@ -2379,9 +2336,7 @@ (define-public wiredtiger (("test/fops") "")) #t))))) (inputs - `(("lz4" ,lz4) - ("zlib" ,zlib) - ("snappy" ,snappy))) + (list lz4 zlib snappy)) (home-page "http://source.wiredtiger.com/") (synopsis "NoSQL data engine") (description @@ -2428,14 +2383,11 @@ (define-public guile-wiredtiger (assoc-ref %build-inputs "wiredtiger"))) #:make-flags '("GUILE_AUTO_COMPILE=0"))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config))) + (list autoconf automake pkg-config)) (inputs - `(("wiredtiger" ,wiredtiger-3) - ("guile" ,guile-2.2))) + (list wiredtiger-3 guile-2.2)) (propagated-inputs - `(("guile-bytestructures" ,guile-bytestructures))) + (list guile-bytestructures)) (synopsis "WiredTiger bindings for GNU Guile") (description "This package provides Guile bindings to the WiredTiger ``NoSQL'' @@ -2455,8 +2407,8 @@ (define-public perl-db-file (sha256 (base32 "1ab6rm2b8lz0g3gc8k9y79gkgajyby0zpybkdg9mk4g35y9bmyfd")))) (build-system perl-build-system) - (inputs `(("bdb" ,bdb))) - (native-inputs `(("perl-test-pod" ,perl-test-pod))) + (inputs (list bdb)) + (native-inputs (list perl-test-pod)) (arguments `(#:phases (modify-phases %standard-phases (add-before @@ -2547,7 +2499,7 @@ (define-public lmdbxx (modify-phases %standard-phases (delete 'configure)))) (build-system gnu-build-system) - (inputs `(("lmdb" ,lmdb))) + (inputs (list lmdb)) (home-page "https://github.com/hoytech/lmdbxx") (synopsis "C++11 wrapper for the LMDB embedded B+ tree database library") (description "@code{lmdbxx} is a comprehensive @code{C++} wrapper for the @@ -2571,7 +2523,7 @@ (define-public libpqxx (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) - (inputs `(("postgresql" ,postgresql))) + (inputs (list postgresql)) (arguments `(#:tests? #f ; # FAIL: 1 #:phases @@ -2604,9 +2556,9 @@ (define-public python-peewee (arguments `(#:tests? #f)) ; fails to import test data (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/coleifer/peewee/") (synopsis "Small object-relational mapping utility") (description @@ -2778,7 +2730,7 @@ (define-public sqlcipher `(("libcrypto" ,openssl) ("libtcl8.6" ,tcl))) ; required for running the tests (native-inputs - `(("tcl" ,tcl))) + (list tcl)) (arguments '(#:configure-flags '("--enable-tempstore=yes" @@ -2825,7 +2777,7 @@ (define-public python-pyodbc-c (file-name (string-append name "-" version ".tar.gz")))) (build-system python-build-system) (inputs - `(("unixodbc" ,unixodbc))) + (list unixodbc)) (arguments `(;; No unit tests exist. #:tests? #f)) @@ -2851,7 +2803,7 @@ (define-public python-pyodbc (file-name (string-append name "-" version ".tar.gz")))) (build-system python-build-system) (inputs - `(("unixodbc" ,unixodbc))) + (list unixodbc)) (arguments `(#:tests? #f)) ; no unit tests exist (home-page "https://github.com/mkleehammer/pyodbc") @@ -2879,14 +2831,14 @@ (define-public mdbtools "0gwcpp9y09xhs21g7my2fs8ncb8i6ahlyixcx8jd3q97jbzj441l")))) (build-system gnu-build-system) (inputs - `(("glib" ,glib))) + (list glib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("txt2man" ,txt2man) - ("which" ,which))) + (list autoconf + automake + libtool + pkg-config + txt2man + which)) (home-page "http://mdbtools.sourceforge.net/") (synopsis "Read Microsoft Access databases") (description "MDB Tools is a set of tools and applications to read the @@ -2918,7 +2870,7 @@ (define-public python-lmdb #t)))) (build-system python-build-system) (inputs - `(("lmdb" ,lmdb))) + (list lmdb)) (arguments `(#:phases (modify-phases %standard-phases @@ -2958,19 +2910,19 @@ (define-public python-orator ;; does not contain setup.py. How to test? (arguments '(#:tests? #f)) (propagated-inputs - `(("python-backpack" ,python-backpack) - ("python-blinker" ,python-blinker) - ("python-cleo" ,python-cleo) - ("python-faker" ,python-faker) - ("python-inflection" ,python-inflection) - ("python-lazy-object-proxy" ,python-lazy-object-proxy) - ("python-pendulum" ,python-pendulum) - ("python-pyaml" ,python-pyaml) - ("python-pygments" ,python-pygments) - ("python-pyyaml" ,python-pyyaml) - ("python-simplejson" ,python-simplejson) - ("python-six" ,python-six) - ("python-wrapt" ,python-wrapt))) + (list python-backpack + python-blinker + python-cleo + python-faker + python-inflection + python-lazy-object-proxy + python-pendulum + python-pyaml + python-pygments + python-pyyaml + python-simplejson + python-six + python-wrapt)) (home-page "https://orator-orm.com/") (synopsis "ActiveRecord ORM for Python") (description @@ -3009,10 +2961,7 @@ (define-public virtuoso-ose '("libvirtuoso-t.a" "libvirtuoso-t.la")))))))) (inputs - `(("openssl" ,openssl) - ("net-tools" ,net-tools) - ("readline" ,readline) - ("zlib" ,zlib))) + (list openssl net-tools readline zlib)) (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/") (synopsis "Multi-model database system") (description "Virtuoso is a scalable cross-platform server that combines @@ -3035,11 +2984,10 @@ (define-public python-ccm "177dfxsmk3k4cih6fh6v8d91bh4nqx7ns6pc07w7m7i3cvdx3c8n")))) (build-system python-build-system) (propagated-inputs - `(("python-pyyaml" ,python-pyyaml) - ;; Not listed in setup.py, but used in ccmlib/node.py for full - ;; functionality - ("python-psutil" ,python-psutil) - ("python-six" ,python-six))) + (list python-pyyaml + ;; Not listed in setup.py, but used in ccmlib/node.py for full + ;; functionality + python-psutil python-six)) (home-page "https://github.com/pcmanus/ccm") (synopsis "Cassandra Cluster Manager for Apache Cassandra clusters on localhost") @@ -3064,7 +3012,7 @@ (define-public python2-pysqlite "1424gwq9sil2ffmnizk60q36vydkv8rxs6m7xs987kz8cdc37lqp")))) (build-system python-build-system) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:python ,python-2 ; incompatible with Python 3 #:tests? #f)) ; no test target @@ -3087,11 +3035,10 @@ (define-public python-sqlalchemy (base32 "031jbd0svrvwr3n52iibp9mkwsj9wicnck45yd26da5kmsfkas6p")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) ; for C extensions - ("python-pytest" ,python-pytest) - ("python-mock" ,python-mock))) ; for tests + (list python-cython ; for C extensions + python-pytest python-mock)) ; for tests (propagated-inputs - `(("python-greenlet" ,python-greenlet))) + (list python-greenlet)) (arguments `(#:phases (modify-phases %standard-phases @@ -3137,8 +3084,7 @@ (define-public python-sqlalchemy-stubs "1bppjmv7v7m0q8gwg791pgxbx4ay7mna0zq204pn9vw28kfxcrf6")))) (build-system python-build-system) (propagated-inputs - `(("python-mypy" ,python-mypy) - ("python-typing-extensions" ,python-typing-extensions))) + (list python-mypy python-typing-extensions)) (home-page "https://github.com/dropbox/sqlalchemy-stubs") (synopsis "SQLAlchemy stubs and mypy plugin") (description "This package contains type stubs and a mypy plugin to @@ -3166,14 +3112,10 @@ (define-public python-sqlalchemy-utils ;; (lambda _ ;; (zero? (system* "py.test" "sqlalchemy_utils" "tests"))))) (propagated-inputs - `(("python-six" ,python-six) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-six python-sqlalchemy)) (native-inputs - `(("python-dateutil" ,python-dateutil) - ("python-flexmock" ,python-flexmock) - ("python-psycopg2" ,python-psycopg2) - ("python-pytest" ,python-pytest) - ("python-pytz" ,python-pytz))) + (list python-dateutil python-flexmock python-psycopg2 python-pytest + python-pytz)) (home-page "https://github.com/kvesteri/sqlalchemy-utils") (synopsis "Various utility functions for SQLAlchemy") (description @@ -3219,11 +3161,9 @@ (define-public python-alchemy-mock (invoke "pytest" "-vv" "--doctest-modules" "alchemy_mock/")))))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) + (list python-mock python-pytest)) (propagated-inputs - `(("python-six" ,python-six) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-six python-sqlalchemy)) (synopsis "Mock helpers for SQLAlchemy") (description "This package provides mock helpers for SQLAlchemy that makes it easy @@ -3251,13 +3191,9 @@ (define-public python-alembic (lambda _ (invoke "pytest" "-vv")))))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-mock python-pytest-cov)) (propagated-inputs - `(("python-dateutil" ,python-dateutil) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-mako" ,python-mako) - ("python-editor" ,python-editor))) + (list python-dateutil python-sqlalchemy python-mako python-editor)) (home-page "https://bitbucket.org/zzzeek/alembic") (synopsis "Database migration tool for SQLAlchemy") (description @@ -3282,7 +3218,7 @@ (define-public python-pickleshare (lambda _ (invoke "pytest")))))) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/vivainio/pickleshare") (synopsis "Tiny key value database with concurrency support") (description @@ -3300,8 +3236,9 @@ (define-public python2-pickleshare (let ((pickleshare (package-with-python2 (strip-python2-variant python-pickleshare)))) (package (inherit pickleshare) - (propagated-inputs `(("python2-pathlib2" ,python2-pathlib2) - ,@(package-propagated-inputs pickleshare)))))) + (propagated-inputs (modify-inputs (package-propagated-inputs + pickleshare) + (prepend python2-pathlib2)))))) (define-public python-apsw (package @@ -3317,9 +3254,9 @@ (define-public python-apsw "0w8q73147hv77dlpqrx6h1gx03acc8xqhvdpfp6vkffdm0wmqd8p")))) (build-system python-build-system) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (inputs - `(("sqlite" ,sqlite))) + (list sqlite)) (arguments `(#:phases (modify-phases %standard-phases @@ -3369,9 +3306,9 @@ (define-public python-aiosqlite (format #t "test suite not run~%")) #t))))) (propagated-inputs - `(("python-typing-extensions" ,python-typing-extensions))) + (list python-typing-extensions)) (native-inputs - `(("python-aiounittest" ,python-aiounittest))) + (list python-aiounittest)) (home-page "https://github.com/jreese/aiosqlite") (synopsis "Asyncio bridge for sqlite3") @@ -3439,7 +3376,7 @@ (define-public python-psycopg2 ;; and a running postgresql database management service. `(#:tests? #f)) ; TODO re-enable after providing a test-db. (inputs - `(("postgresql" ,postgresql))) ; libpq + (list postgresql)) ; libpq (home-page "http://initd.org/psycopg/") (synopsis "Python PostgreSQL adapter") (description @@ -3471,10 +3408,10 @@ (define-public python-sadisplay (invoke "pytest" "-vv")) (format #t "test suite not run~%"))))))) (propagated-inputs - `(("python-sqlalchemy" ,python-sqlalchemy))) + (list python-sqlalchemy)) (native-inputs ;; For tests. - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://bitbucket.org/estin/sadisplay") (synopsis "SQLAlchemy schema displayer") (description "This package provides a program to build Entity @@ -3503,8 +3440,7 @@ (define-public yoyo-migrations ;; fails to connect to it. '(#:tests? #f)) (propagated-inputs - `(("python-sqlparse" ,python-sqlparse) - ("python-tabulate" ,python-tabulate))) + (list python-sqlparse python-tabulate)) (home-page "https://ollycope.com/software/yoyo/latest/") (synopsis "Database migrations with SQL") (description @@ -3578,9 +3514,7 @@ (define-public python-fakeredis ;; no tests `(#:tests? #f)) (propagated-inputs - `(("python-packaging" ,python-packaging) - ("python-redis" ,python-redis) - ("python-sortedcontainers" ,python-sortedcontainers))) + (list python-packaging python-redis python-sortedcontainers)) (home-page "https://github.com/jamesls/fakeredis") (synopsis "Fake implementation of redis API for testing purposes") (description @@ -3647,12 +3581,9 @@ (define-public python-rq (getenv "PATH"))) (invoke "pytest" "-vv"))))))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("redis" ,redis))) + (list python-mock python-pytest redis)) (propagated-inputs - `(("python-click" ,python-click) - ("python-redis" ,python-redis))) + (list python-click python-redis)) (home-page "https://python-rq.org/") (synopsis "Simple job queues for Python") (description @@ -3688,11 +3619,9 @@ (define-public python-rq-scheduler (which "env"))) (invoke "./run_tests.py")))))) (native-inputs - `(("redis" ,redis) - ("which" ,which))) + (list redis which)) (propagated-inputs - `(("python-croniter" ,python-croniter) - ("python-rq" ,python-rq))) + (list python-croniter python-rq)) (synopsis "Job scheduling capabilities for RQ (Redis Queue)") (description "This package provides job scheduling capabilities to @code{python-rq} @@ -3755,7 +3684,7 @@ (define-public python-sqlparse (string-append output sitedir)) (list python out)))))))))) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/andialbrecht/sqlparse") (synopsis "Non-validating SQL parser") (description "Sqlparse is a non-validating SQL parser for Python. It @@ -3794,7 +3723,7 @@ (define-public python-pypika "001pg36sw9a36zdd1kccbymcxndphjcjbbrsy6ri7ng8h4dgz549")))) (build-system python-build-system) (native-inputs - `(("python-parameterized" ,python-parameterized))) + (list python-parameterized)) (home-page "https://github.com/kayak/pypika") (synopsis "SQL query builder API for Python") (description @@ -3917,13 +3846,10 @@ (define-public apache-arrow ("xsimd" ,xsimd))) ;; These are all listed under Requires.private in arrow.pc (propagated-inputs - `(("apache-thrift" ,apache-thrift "lib") - ("lz4" ,lz4) - ("utf8proc" ,utf8proc) - ("zlib" ,zlib) - ("zstd" ,zstd "lib"))) + (list `(,apache-thrift "lib") lz4 utf8proc zlib + `(,zstd "lib"))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (outputs '("out" "lib" "include")) (home-page "https://arrow.apache.org/") (synopsis "Columnar in-memory analytics") @@ -4004,7 +3930,7 @@ (define-public python-crate "0ngmlvi320c5gsxab0s7qgq0ck4jdlcwvb6lbjhnfprafdp56vvx")))) (build-system python-build-system) (propagated-inputs - `(("python-urllib3" ,python-urllib3))) + (list python-urllib3)) (home-page "https://github.com/crate/crate-python") (synopsis "CrateDB Python client") (description @@ -4048,10 +3974,8 @@ (define-public libdbi-drivers "0m680h8cc4428xin4p733azysamzgzcmv4psjvraykrsaz6ymlj3")))) (build-system gnu-build-system) (native-inputs - `(;; For tests. - ("inetutils" ,inetutils) - ("glibc-locales" ,glibc-locales) - ("mariadb" ,mariadb))) + (list ;; For tests. + inetutils glibc-locales mariadb)) (inputs `(("libdbi" ,libdbi) ("mariadb:dev" ,mariadb "dev") @@ -4179,7 +4103,7 @@ (define-public python-tinydb ;; have a setup.py file (only pyproject). (arguments `(#:tests? #f)) (propagated-inputs - `(("python-typing-extensions" ,python-typing-extensions))) + (list python-typing-extensions)) (home-page "https://github.com/msiemens/tinydb") (synopsis "TinyDB is a lightweight document oriented database") (description diff --git a/gnu/packages/datamash.scm b/gnu/packages/datamash.scm index d0f4bdfbc0..51a35e0a1d 100644 --- a/gnu/packages/datamash.scm +++ b/gnu/packages/datamash.scm @@ -39,8 +39,8 @@ (define-public datamash (base32 "1cxdlhgz3wzjqlq8bgwad93fgqymk2abbldfzw1ffnhcp4mmjjjp")))) (native-inputs - `(("which" ,which) ;for tests - ("perl" ,perl))) ;for help2man + (list which ;for tests + perl)) ;for help2man (build-system gnu-build-system) (home-page "https://www.gnu.org/software/datamash/") (synopsis "Scriptable statistics and data calculation") diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm index e79fe76954..2b00137a3e 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -72,9 +72,7 @@ (define-public marisa (base32 "1pk6wmi28pa8srb4szybrwfn71jldb61c5vgxsiayxcyg1ya4qqh")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (home-page "https://github.com/s-yata/marisa-trie") (synopsis "Trie data structure C++ library") (description "@acronym{MARISA, Matching Algorithm with Recursively @@ -149,7 +147,7 @@ (define-public liburcu "085s437nig6bdiv9im4k4qwqbrbnc4qw9flqi16jlb493az0vcnb")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) ; for tests + (list perl)) ; for tests (home-page "https://liburcu.org/") (synopsis "User-space RCU data synchronisation library") (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data @@ -174,7 +172,7 @@ (define-public uthash (base32 "0k80bjbb6ss5wpmfmfji6xbyjm990hg9kcshwwnhdnh73vxkcd1m")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl))) + (list perl)) (arguments `(#:make-flags (list "CC=gcc") @@ -269,7 +267,7 @@ (define-public sdsl-lite out ,version))) #t)))))) (native-inputs - `(("libdivsufsort" ,libdivsufsort))) + (list libdivsufsort)) (home-page "https://github.com/simongog/sdsl-lite") (synopsis "Succinct data structure library") (description "The Succinct Data Structure Library (SDSL) is a powerful and @@ -346,7 +344,7 @@ (define-public robin-map "1li70vwsksva9c4yly90hjafgqfixi1g6d52qq9p6r60vqc4pkjj")))) (build-system cmake-build-system) (native-inputs - `(("boost" ,boost))) ; needed for tests + (list boost)) ; needed for tests (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm index 712149f173..8738eb36f2 100644 --- a/gnu/packages/dav.scm +++ b/gnu/packages/dav.scm @@ -53,17 +53,15 @@ (define-public radicale (base32 "1xlsvrmx6jhi71j6j8z9sli5vwxasivzjyqf8zq8r0l5p7350clf")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-flake8" ,python-pytest-flake8) - ("python-pytest-isort" ,python-pytest-isort) - ("python-pytest-runner" ,python-pytest-runner) - ("python-waitress" ,python-waitress))) + (list python-pytest + python-pytest-cov + python-pytest-flake8 + python-pytest-isort + python-pytest-runner + python-waitress)) (propagated-inputs - `(("python-dateutil" ,python-dateutil) - ("python-defusedxml" ,python-defusedxml) - ("python-passlib" ,python-passlib) - ("python-vobject" ,python-vobject))) + (list python-dateutil python-defusedxml python-passlib + python-vobject)) (synopsis "Basic CalDAV and CardDAV server") (description "Radicale is a CalDAV and CardDAV server for UNIX-like platforms. Calendars and address books are available for both local and remote @@ -88,12 +86,12 @@ (define-public xandikos (base32 "13ikmcja9p42azb5ccqj2bw98zybna6zlflj10hqy0kvbib70l94")))) (build-system python-build-system) (propagated-inputs - `(("python-aiohttp" ,python-aiohttp) - ("python-defusedxml" ,python-defusedxml) - ("python-dulwich" ,python-dulwich) - ("python-icalendar" ,python-icalendar) - ("python-jinja2" ,python-jinja2) - ("python-multidict" ,python-multidict))) + (list python-aiohttp + python-defusedxml + python-dulwich + python-icalendar + python-jinja2 + python-multidict)) (home-page "https://www.xandikos.org/") (synopsis "Lightweight CalDAV/CardDAV server") (description @@ -153,24 +151,22 @@ (define-public vdirsyncer "/share/man/man1")) #t))))) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm) - ("python-sphinx" ,python-sphinx) - ;; Required for testing - ("python-hypothesis" ,python-hypothesis) - ("python-pytest" ,python-pytest) - ("python-pytest-localserver" ,python-pytest-localserver) - ("python-pytest-subtesthack" ,python-pytest-subtesthack) - ("python-urllib3" ,python-urllib3) - ("python-wsgi-intercept" ,python-wsgi-intercept) - ("radicale" ,radicale))) + (list python-setuptools-scm + python-sphinx + ;; Required for testing + python-hypothesis + python-pytest + python-pytest-localserver + python-pytest-subtesthack + python-urllib3 + python-wsgi-intercept + radicale)) (inputs - `(;; XXX https://github.com/mitsuhiko/click/issues/200 - ("python-click" ,python-click-5))) + (list ;; XXX https://github.com/mitsuhiko/click/issues/200 + python-click-5)) (propagated-inputs - `(("python-atomicwrites" ,python-atomicwrites) - ("python-click-log" ,python-click-log) - ("python-click-threading" ,python-click-threading) - ("python-requests-toolbelt" ,python-requests-toolbelt))) + (list python-atomicwrites python-click-log python-click-threading + python-requests-toolbelt)) (synopsis "Synchronize calendars and contacts") (description "Vdirsyncer synchronizes your calendars and addressbooks between two storage locations. The most popular purpose is to diff --git a/gnu/packages/dc.scm b/gnu/packages/dc.scm index f22ac93723..41620ea6cf 100644 --- a/gnu/packages/dc.scm +++ b/gnu/packages/dc.scm @@ -43,14 +43,14 @@ (define-public ncdc (base32 "1bdgqd07f026qk6vpbxqsin536znd33931m3b4z44prlm9wd6pyi")))) (build-system gnu-build-system) (inputs - `(("bzip2" ,bzip2) - ("glib" ,glib) - ("gnutls" ,gnutls) - ("ncurses" ,ncurses) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list bzip2 + glib + gnutls + ncurses + sqlite + zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://dev.yorhel.nl/ncdc") (synopsis "Lightweight direct connect client with a friendly ncurses interface") diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index be2f8cc62b..66cb8e2fab 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -71,8 +71,7 @@ (define-public debian-archive-keyring (find-files "trusted.gpg" "\\.gpg$"))) #t))))) (native-inputs - `(("gnupg" ,gnupg) - ("jetring" ,jetring))) + (list gnupg jetring)) (home-page "https://packages.qa.debian.org/d/debian-archive-keyring.html") (synopsis "GnuPG archive keys of the Debian archive") (description @@ -136,7 +135,7 @@ (define-public debian-ports-archive-keyring (find-files "trusted.gpg" "\\.gpg$"))) #t))))) (native-inputs - `(("gnupg" ,gnupg))) + (list gnupg)) (home-page "https://tracker.debian.org/pkg/debian-ports-archive-keyring") (synopsis "GnuPG archive keys of the Debian ports archive") (description @@ -177,8 +176,7 @@ (define-public ubuntu-keyring (find-files "." "ubuntu-[am].*\\.gpg$"))) #t))) (native-inputs - `(("tar" ,tar) - ("gzip" ,gzip))) + (list tar gzip)) (home-page "https://launchpad.net/ubuntu/+source/ubuntu-keyring") (synopsis "GnuPG keys of the Ubuntu archive") (description @@ -259,7 +257,7 @@ (define-public debootstrap ("gnupg" ,gnupg) ("wget" ,wget))) (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "https://tracker.debian.org/pkg/debootstrap") (synopsis "Bootstrap a basic Debian system") (description "Debootstrap is used to create a Debian base system from @@ -328,8 +326,7 @@ (define-public apt-mirror "PREFIX=/") #:phases (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("wget" ,wget) - ("perl" ,perl))) + (list wget perl)) (home-page "http://apt-mirror.github.io/") (synopsis "Script for mirroring a Debian repository") (description @@ -379,12 +376,12 @@ (define-public dpkg ("pkg-config" ,pkg-config) ("perl-io-string" ,perl-io-string))) (inputs - `(("bzip2" ,bzip2) - ("libmd" ,libmd) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("xz" ,xz) - ("zlib" ,zlib))) + (list bzip2 + libmd + ncurses + perl + xz + zlib)) (home-page "https://wiki.debian.org/Teams/Dpkg") (synopsis "Debian package management system") (description "This package provides the low-level infrastructure for @@ -429,15 +426,14 @@ (define-public reprepro (string-append zsh "_reprepro")) #t)))))) (inputs - `(("bdb" ,bdb) - ("bzip2" ,bzip2) - ("gpgme" ,gpgme) - ("libarchive" ,libarchive) - ("xz" ,xz) - ("zlib" ,zlib))) + (list bdb + bzip2 + gpgme + libarchive + xz + zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (home-page "https://salsa.debian.org/brlink/reprepro") (synopsis "Debian package repository producer") (description "Reprepro is a tool to manage a repository of Debian packages diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index ffcbbe9eb4..81e27b1ddf 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -84,7 +84,7 @@ (define-public delta "184wh35pf2ddx97319s6sgkzpz48xxkbwzcjpycv009bm53lh61q")))) (build-system gnu-build-system) (inputs ;Installed programs are perl scripts - `(("perl" ,perl))) + (list perl)) (arguments `(#:phases (modify-phases %standard-phases @@ -127,7 +127,7 @@ (define-public c-reduce (sha256 (base32 "0qx0zq8jxzx2as2zf0740g7kvgq163ayn3041di4vwk77490y76v")))) (build-system gnu-build-system) - (native-inputs `(("flex" ,flex))) + (native-inputs (list flex)) (inputs `(("astyle" ,astyle) ("llvm" ,llvm) @@ -189,9 +189,7 @@ (define-public c-vise (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("flex" ,flex) - ("python-pytest" ,python-pytest) - ("python-pytest-flake8" ,python-pytest-flake8))) + (list flex python-pytest python-pytest-flake8)) (inputs `(("bash" ,bash-minimal) ; For wrap-program ("clang" ,clang) @@ -252,7 +250,7 @@ (define-public american-fuzzy-lop (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs - `(("qemu" ,qemu-for-american-fuzzy-lop))) + (list qemu-for-american-fuzzy-lop)) (arguments `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "DOC_PATH=$(PREFIX)/share/doc/" @@ -470,9 +468,7 @@ (define-public stress-make "0k55cy7x0hlc6rgpascl6ibhcfxaash3p9r9r8kwvbm3zag1rmac")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("go" ,go))) + (list autoconf automake go)) (inputs `(("make-source" ,(package-source gnu-make)))) (arguments @@ -572,17 +568,17 @@ (define-public scanmem `("GUIX_PYTHONPATH" ":" prefix (,python-path)))) #t))))) (native-inputs - `(("libtool" ,libtool) - ("python-wrapper" ,python-wrapper) - ("gobject-introspection" ,gobject-introspection) - ("gtk+" ,gtk+) - ("intltool" ,intltool) - ("automake" ,automake) - ("autoconf" ,autoconf))) + (list libtool + python-wrapper + gobject-introspection + gtk+ + intltool + automake + autoconf)) (inputs - `(("readline" ,readline))) + (list readline)) (propagated-inputs - `(("python-pygobject" ,python-pygobject))) + (list python-pygobject)) (home-page "https://github.com/scanmem/scanmem") (synopsis "Memory scanner") (description "Scanmem is a debugging utility designed to isolate the @@ -612,8 +608,8 @@ (define-public remake "0xlx2485y0israv2pfghmv74lxcv9i5y65agy69mif76yc4vfvif")) (patches (search-patches "remake-impure-dirs.patch")))) (inputs - `(("readline" ,readline) - ,@(package-inputs gnu-make))) + (modify-inputs (package-inputs gnu-make) + (prepend readline))) (home-page "http://bashdb.sourceforge.net/remake/") (description "Remake is an enhanced version of GNU Make that adds improved error reporting, better tracing, profiling, and a debugger.") @@ -665,14 +661,9 @@ (define-public rr (setenv "HOME" (getcwd)) #t))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("ninja" ,ninja) - ("which" ,which))) + (list pkg-config ninja which)) (inputs - `(("gdb" ,gdb) - ("capnproto" ,capnproto) - ("python" ,python) - ("python-pexpect" ,python-pexpect))) + (list gdb capnproto python python-pexpect)) (home-page "https://rr-project.org/") (synopsis "Record and reply debugging framework") (description @@ -741,8 +732,7 @@ (define-public libleak (let* ((out (assoc-ref outputs "out"))) (install-file "libleak.so" (string-append out "/lib")) #t)))))) - (inputs `(("libbacktrace" ,libbacktrace) - ("libwuya" ,libwuya))) + (inputs (list libbacktrace libwuya)) (home-page "https://github.com/WuBingzheng/libleak") (synopsis "Memory leaks detection tool") (description "The libleak tool detects memory leaks by hooking memory @@ -781,8 +771,7 @@ (define-public mspdebug "INSTALL=install" (string-append "PREFIX=" %output)))) (inputs - `(("libusb-compat" ,libusb-compat) - ("readline" ,readline))) + (list libusb-compat readline)) (synopsis "Debugging tool for MSP430 MCUs") (description "MspDebug supports FET430UIF, eZ430, RF2500 and Olimex MSP430-JTAG-TINY programmers, as well as many other compatible diff --git a/gnu/packages/dejagnu.scm b/gnu/packages/dejagnu.scm index 0dee89dfc1..08be5a8afd 100644 --- a/gnu/packages/dejagnu.scm +++ b/gnu/packages/dejagnu.scm @@ -38,7 +38,7 @@ (define-public dejagnu (base32 "0qfj2wd4qk1yn9yzam6g8nmyxfazcc0knjyyibycb2ainkhp21hd")))) (build-system gnu-build-system) - (inputs `(("expect" ,expect))) + (inputs (list expect)) (arguments '(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/dhall.scm b/gnu/packages/dhall.scm index d9ec1fbade..b406d89eb5 100644 --- a/gnu/packages/dhall.scm +++ b/gnu/packages/dhall.scm @@ -40,63 +40,63 @@ (define-public dhall (base32 "1by2d84fbckspczddl4npfsf89q6nprmbg0i5g8yr1psp0fpl4ab")))) (build-system haskell-build-system) (inputs - `(("ghc-aeson" ,ghc-aeson) - ("ghc-aeson-pretty" ,ghc-aeson-pretty) - ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-atomic-write" ,ghc-atomic-write-0.2.0.7) - ("ghc-case-insensitive" ,ghc-case-insensitive) - ("ghc-cborg" ,ghc-cborg) - ("ghc-cborg-json" ,ghc-cborg-json) - ("ghc-contravariant" ,ghc-contravariant) - ("ghc-data-fix" ,ghc-data-fix) - ("ghc-diff" ,ghc-diff) - ("ghc-dotgen" ,ghc-dotgen) - ("ghc-either" ,ghc-either) - ("ghc-exceptions" ,ghc-exceptions) - ("ghc-half" ,ghc-half) - ("ghc-hashable" ,ghc-hashable) - ("ghc-lens-family-core" ,ghc-lens-family-core) - ("ghc-megaparsec" ,ghc-megaparsec) - ("ghc-memory" ,ghc-memory) - ("ghc-mmorph" ,ghc-mmorph) - ("ghc-network-uri" ,ghc-network-uri) - ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-parsers" ,ghc-parsers) - ("ghc-parser-combinators" ,ghc-parser-combinators) - ("ghc-prettyprinter" ,ghc-prettyprinter) - ("ghc-prettyprinter-ansi-terminal" ,ghc-prettyprinter-ansi-terminal) - ("ghc-pretty-simple" ,ghc-pretty-simple) - ("ghc-profunctors" ,ghc-profunctors) - ("ghc-pretty-simple" ,ghc-pretty-simple) - ("ghc-repline" ,ghc-repline) - ("ghc-serialise" ,ghc-serialise) - ("ghc-scientific" ,ghc-scientific) - ("ghc-text-manipulate" ,ghc-text-manipulate) - ("ghc-th-lift-instances" ,ghc-th-lift-instances) - ("ghc-transformers-compat" ,ghc-transformers-compat) - ("ghc-unordered-containers" ,ghc-unordered-containers) - ("ghc-uri-encode" ,ghc-uri-encode) - ("ghc-vector" ,ghc-vector) - ("ghc-cryptonite" ,ghc-cryptonite) - ("ghc-http-types" ,ghc-http-types) - ("ghc-http-client" ,ghc-http-client) - ("ghc-http-client-tls" ,ghc-http-client-tls))) + (list ghc-aeson + ghc-aeson-pretty + ghc-ansi-terminal + ghc-atomic-write-0.2.0.7 + ghc-case-insensitive + ghc-cborg + ghc-cborg-json + ghc-contravariant + ghc-data-fix + ghc-diff + ghc-dotgen + ghc-either + ghc-exceptions + ghc-half + ghc-hashable + ghc-lens-family-core + ghc-megaparsec + ghc-memory + ghc-mmorph + ghc-network-uri + ghc-optparse-applicative + ghc-parsers + ghc-parser-combinators + ghc-prettyprinter + ghc-prettyprinter-ansi-terminal + ghc-pretty-simple + ghc-profunctors + ghc-pretty-simple + ghc-repline + ghc-serialise + ghc-scientific + ghc-text-manipulate + ghc-th-lift-instances + ghc-transformers-compat + ghc-unordered-containers + ghc-uri-encode + ghc-vector + ghc-cryptonite + ghc-http-types + ghc-http-client + ghc-http-client-tls)) (native-inputs - `(("ghc-foldl" ,ghc-foldl) - ("ghc-generic-random" ,ghc-generic-random-1.3.0.1) - ("ghc-quickcheck" ,ghc-quickcheck) - ("ghc-quickcheck-instances" ,ghc-quickcheck-instances) - ("ghc-semigroups" ,ghc-semigroups) - ("ghc-special-values" ,ghc-special-values) - ("ghc-spoon" ,ghc-spoon) - ("ghc-tasty" ,ghc-tasty) - ("ghc-tasty-expected-failure" ,ghc-tasty-expected-failure) - ("ghc-tasty-hunit" ,ghc-tasty-hunit) - ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck) - ("ghc-tasty-silver" ,ghc-tasty-silver) - ("ghc-turtle" ,ghc-turtle) - ("ghc-mockery" ,ghc-mockery) - ("ghc-doctest" ,ghc-doctest))) + (list ghc-foldl + ghc-generic-random-1.3.0.1 + ghc-quickcheck + ghc-quickcheck-instances + ghc-semigroups + ghc-special-values + ghc-spoon + ghc-tasty + ghc-tasty-expected-failure + ghc-tasty-hunit + ghc-tasty-quickcheck + ghc-tasty-silver + ghc-turtle + ghc-mockery + ghc-doctest)) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/dico.scm b/gnu/packages/dico.scm index fb97ee3d85..c7c1963726 100644 --- a/gnu/packages/dico.scm +++ b/gnu/packages/dico.scm @@ -65,7 +65,7 @@ (define-public dico (lambda _ ;; Test '71: append + dooffs + env' fails if $V is not 2. (invoke "make" "check" "V=2")))))) - (native-inputs `(("groff" ,groff))) + (native-inputs (list groff)) (inputs `(("m4" ,m4) ;used at run time ("pcre" ,pcre) diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm index 75f1b1bed4..f9d6e57877 100644 --- a/gnu/packages/dictionaries.scm +++ b/gnu/packages/dictionaries.scm @@ -100,9 +100,7 @@ (define-public vera "vera.texi" "--force" "--html" "-o" (string-append html "/vera.html")))) #:modules ((guix build utils)))) - (native-inputs `(("texinfo" ,texinfo) - ("tar" ,tar) - ("gzip" ,gzip))) + (native-inputs (list texinfo tar gzip)) (home-page "https://savannah.gnu.org/projects/vera/") (synopsis "List of acronyms") (description @@ -167,7 +165,7 @@ (define-public ding (base32 "0chjqs3z9zs1w3l7b5lsaj682rgnkf9kibcbzhggqqcn1pbvl5sq")))) (build-system gnu-build-system) - (inputs `(("tk" ,tk))) + (inputs (list tk)) (arguments `(#:phases (modify-phases %standard-phases @@ -290,9 +288,7 @@ (define-public translate-shell (guix build utils)) #:test-target "test")) (inputs - `(("curl" ,curl) - ("fribidi" ,fribidi) - ("rlwrap" ,rlwrap))) + (list curl fribidi rlwrap)) (native-inputs `(("emacs" ,emacs-minimal) ("util-linux" ,util-linux))) ; hexdump, for the test @@ -329,12 +325,9 @@ (define-public lttoolbox (lambda _ (invoke "autoreconf" "-vfi")))))) (inputs - `(("libxml2" ,libxml2))) + (list libxml2)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "https://wiki.apertium.org/wiki/Lttoolbox") (synopsis "Lexical processing toolbox") (description "Lttoolbox is a toolbox for lexical processing, morphological @@ -360,10 +353,7 @@ (define-public apertium (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) (inputs - `(("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("lttoolbox" ,lttoolbox) - ("pcre" ,pcre))) + (list libxml2 libxslt lttoolbox pcre)) (native-inputs `(("apertium-get" ,(origin @@ -435,10 +425,7 @@ (define-public sdcv `(("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config))) (inputs - `(("glib" ,glib) - ("ncurses" ,ncurses) - ("readline" ,readline) - ("zlib" ,zlib))) + (list glib ncurses readline zlib)) (home-page "https://dushistov.github.io/sdcv/") (synopsis "Console version of StarDict") (description "sdcv is simple text-based utility for work with dictionaries diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index f0197817a6..696270d506 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -140,14 +140,14 @@ (define-public diffoscope (let* ((out (assoc-ref outputs "out")) (man (string-append out "/share/man/man1"))) (install-file "doc/diffoscope.1" man))))))) - (inputs `(("rpm" ,rpm) ;for rpm-python - ("python-debian" ,python-debian) - ("python-libarchive-c" ,python-libarchive-c) - ("python-magic" ,python-magic) - ("python-tlsh" ,python-tlsh) - ("acl" ,acl) ;for getfacl - ("colordiff" ,colordiff) - ("xxd" ,xxd))) + (inputs (list rpm ;for rpm-python + python-debian + python-libarchive-c + python-magic + python-tlsh + acl ;for getfacl + colordiff + xxd)) (native-inputs `(("help2man" ,help2man) ;; Below are modules used for tests. ("binwalk" ,binwalk) @@ -243,10 +243,7 @@ (define-public reprotest (base32 "19lwsxq53isgfkvlxvxqqmbjfcim3lhcxwk7m9ddfjiynhq74949")))) (inputs - `(("python-debian" ,python-debian) - ("python-distro" ,python-distro) - ("python-libarchive-c" ,python-libarchive-c) - ("python-rstr" ,python-rstr))) + (list python-debian python-distro python-libarchive-c python-rstr)) (native-inputs `(("diffoscope" ,diffoscope) ("help2man" ,help2man) @@ -324,10 +321,9 @@ (define-public trydiffoscope (string-append share "/doc/" ,name "-" ,version))) #t))))) (propagated-inputs - `(("python-requests" ,python-requests))) + (list python-requests)) (native-inputs - `(("gzip" ,gzip) - ("python-docutils" ,python-docutils))) + (list gzip python-docutils)) (build-system python-build-system) (home-page "https://try.diffoscope.org") (synopsis "Client for remote diffoscope service") diff --git a/gnu/packages/direct-connect.scm b/gnu/packages/direct-connect.scm index b2e9776f94..87bf0a7c8a 100644 --- a/gnu/packages/direct-connect.scm +++ b/gnu/packages/direct-connect.scm @@ -50,16 +50,14 @@ (define-public linuxdcpp #:scons-flags (list (string-append "PREFIX=" %output)) #:tests? #f)) ; no tests (inputs - `(("boost" ,boost) - ("bzip2" ,bzip2) - ("gtk+" ,gtk+-2) - ("libglade" ,libglade) - ("libnotify" ,libnotify) - ("openssl" ,openssl))) + (list boost + bzip2 + gtk+-2 + libglade + libnotify + openssl)) (native-inputs - `(("bazaar" ,bazaar) - ("gettext-minimal" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list bazaar gettext-minimal pkg-config)) (home-page "https://launchpad.net/linuxdcpp/") (synopsis "Direct Connect client") (description "LinuxDC++ is a Direct Connect (DC) client. Direct Connect diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index a9880d7abb..d74d941ee0 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -141,7 +141,7 @@ (define-public bcache-tools "/share/man/man8")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("util-linux:lib" ,util-linux "lib"))) ; libblkid (home-page "https://bcache.evilpiepirate.org") @@ -209,15 +209,14 @@ (define-public udevil (("`which udevil 2>/dev/null`") "/run/setuid-programs/udevil")) #t))))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (inputs - `(("cifs-utils" ,cifs-utils) - ("curlftpfs" ,curlftpfs) - ("eudev" ,eudev) - ("fakeroot" ,fakeroot) - ("glib" ,glib) - ("sshfs" ,sshfs))) + (list cifs-utils + curlftpfs + eudev + fakeroot + glib + sshfs)) (synopsis "Device and file system manager") (description "udevil is a command line program that mounts and unmounts removable devices without a password, shows device info, and monitors device @@ -249,9 +248,8 @@ (define-public parted (("/usr/bin/python") (which "python"))) #t))))) (inputs - `(("lvm2" ,lvm2) - ("readline" ,readline) - ("util-linux" ,util-linux "lib"))) + (list lvm2 readline + `(,util-linux "lib"))) (native-inputs `(("gettext" ,gettext-minimal) @@ -335,8 +333,7 @@ (define-public gpart (substitute* "autogen.sh" (("\\./configure") ""))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (home-page "https://github.com/baruch/gpart") (synopsis "Guess and recover PC-style partition tables") (description @@ -424,7 +421,7 @@ (define-public ddrescue `(#:configure-flags (list (string-append "CXX=" ,(cxx-for-target))))) (home-page "https://www.gnu.org/software/ddrescue/ddrescue.html") (synopsis "Data recovery utility") - (native-inputs `(("lzip" ,lzip))) + (native-inputs (list lzip)) (description "GNU ddrescue is a fully automated data recovery tool. It copies data from one file to another, working to rescue data in case of read errors. The @@ -451,10 +448,9 @@ (define-public dosfstools #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "CC=" ,(cc-for-target))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ;; For tests. - ("xxd" ,xxd))) + (list autoconf automake + ;; For tests. + xxd)) (home-page "https://github.com/dosfstools/dosfstools") (synopsis "Utilities for making and checking MS-DOS FAT file systems") (description @@ -489,7 +485,7 @@ (define-public fatfsck/static ;; Add fsck.vfat symlink to match the Linux driver name. (symlink exe "fsck.vfat") #t))))) - (inputs `(("dosfstools" ,dosfstools/static))) + (inputs (list dosfstools/static)) (home-page (package-home-page dosfstools)) (synopsis "Statically linked fsck.fat from dosfstools") (description "This package provides a statically-linked @command{fsck.fat} @@ -570,17 +566,13 @@ (define-public gparted ;; as '/dev/disk/by-id' `(#:tests? #f)) (inputs - `(("util-linux" ,util-linux "lib") - ("parted" ,parted) - ("glib" ,glib) - ("gtkmm" ,gtkmm-3) - ("libxml2" ,libxml2))) + (list `(,util-linux "lib") parted glib gtkmm-3 libxml2)) (native-inputs - `(("intltool" ,intltool) - ("itstool" ,itstool) - ("lvm2" ,lvm2) ; for tests - ("yelp-tools" ,yelp-tools) - ("pkg-config" ,pkg-config))) + (list intltool + itstool + lvm2 ; for tests + yelp-tools + pkg-config)) (home-page "https://gparted.org/") (synopsis "Partition editor to graphically manage disk partitions") (description "GParted is a GNOME partition editor for creating, @@ -638,8 +630,7 @@ (define-public f3 (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "install-extra" make-flags)))))) (inputs - `(("eudev" ,eudev) - ("parted" ,parted))) + (list eudev parted)) (home-page "http://oss.digirati.com.br/f3/") (synopsis "Test real capacity of flash memory cards and such.") (description "F3 (Fight Flash Fraud or Fight Fake Flash) tests the full @@ -675,12 +666,11 @@ (define-public python-parted (invoke "python" "-m" "unittest" "discover" "-v") #t))))) (native-inputs - `(("e2fsprogs" ,e2fsprogs) - ("pkg-config" ,pkg-config))) + (list e2fsprogs pkg-config)) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (inputs - `(("parted" ,parted))) + (list parted)) (home-page "https://github.com/dcantrell/pyparted") (synopsis "Parted bindings for Python") (description "This package provides @code{parted} bindings for Python.") @@ -701,10 +691,9 @@ (define-public duperemove (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("glib" ,glib) - ("sqlite" ,sqlite))) + (list glib sqlite)) (arguments `(#:tests? #f ; no test suite #:phases @@ -744,12 +733,11 @@ (define-public ranger "0lfjrpv3z4h0knd3v94fijrw2zjba51mrp3mjqx2c98wr428l26f")))) (build-system python-build-system) (inputs - `(("w3m" ,w3m))) + (list w3m)) (native-inputs - `(("which" ,which) - - ;; For tests. - ("python-pytest" ,python-pytest))) + (list which + ;; For tests. + python-pytest)) (arguments '( ;; The 'test' target runs developer tools like pylint, which fail. #:test-target "test_pytest" @@ -791,9 +779,7 @@ (define-public volume-key "16rhfz6sjwxlmss1plb2wv2i3jq6wza02rmz1d2jrlnsq67p98vc")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("swig" ,swig) - ("python" ,python-3))) ; used to generate the Python bindings + (list pkg-config swig python-3)) ; used to generate the Python bindings (inputs `(("cryptsetup" ,cryptsetup) ("nss" ,nss) @@ -834,23 +820,20 @@ (define-public ndctl "1vi61bm9wyawklswh9mj9zdp28ar7r97qckwnhgiyila73fb3jx2")))) (build-system gnu-build-system) (native-inputs - `(("asciidoc" ,asciidoc) - ("automake" ,automake) - ("autoconf" ,autoconf) - ("bash-completion" ,bash-completion) - ("docbook-xsl" ,docbook-xsl) - ("libtool" ,libtool) - ("libxml2" ,libxml2) - ("pkg-config" ,pkg-config) - ("xmlto" ,xmlto) - ;; Required for offline docbook generation. - ("which" ,which))) + (list asciidoc + automake + autoconf + bash-completion + docbook-xsl + libtool + libxml2 + pkg-config + xmlto + ;; Required for offline docbook generation. + which)) (inputs - `(("eudev" ,eudev) - ("json-c" ,json-c) - ("keyutils" ,keyutils) - ("kmod" ,kmod) - ("util-linux" ,util-linux "lib"))) + (list eudev json-c keyutils kmod + `(,util-linux "lib"))) (arguments `(#:configure-flags (list "--disable-asciidoctor" ; use docbook-xsl instead @@ -890,8 +873,8 @@ (define-public dmraid (base32 "1n7vsqvh7y6yvil682q129d21yhb0cmvd5fvsbkza7ypd78inhlk")))) (build-system gnu-build-system) - (inputs `(("lvm2" ,lvm2))) - (native-inputs `(("which" ,which))) + (inputs (list lvm2)) + (native-inputs (list which)) (arguments `(#:tests? #f ; No tests. ;; Prevent a race condition where some target would attempt to link @@ -947,22 +930,22 @@ (define-public libblockdev ("python" ,python-wrapper) ("util-linux" ,util-linux))) (inputs - `(("btrfs-progs" ,btrfs-progs) - ("cryptsetup" ,cryptsetup) - ("dosfstools" ,dosfstools) - ("dmraid" ,dmraid) - ("eudev" ,eudev) - ("glib" ,glib) - ("kmod" ,kmod) - ("libbytesize" ,libbytesize) - ("libyaml" ,libyaml) - ("lvm2" ,lvm2) - ("mdadm" ,mdadm) - ("ndctl" ,ndctl) - ("nss" ,nss) - ("parted" ,parted) - ("volume-key" ,volume-key) - ("xfsprogs" ,xfsprogs))) + (list btrfs-progs + cryptsetup + dosfstools + dmraid + eudev + glib + kmod + libbytesize + libyaml + lvm2 + mdadm + ndctl + nss + parted + volume-key + xfsprogs)) (home-page "https://github.com/storaged-project/libblockdev") (synopsis "Library for manipulating block devices") (description @@ -1125,8 +1108,7 @@ (define-public xfe (("~/.config/xfe") xfe))) #t)))))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (inputs `(("bash" ,bash) ("coreutils" ,coreutils) @@ -1204,15 +1186,12 @@ (define-public memkind "0w5hws12l167mbr4n6a6fl0mhf8mci61fsn55lh2cxz33f7q8n2x")))) (build-system gnu-build-system) (inputs - `(;; memkind patched jemalloc to add je_arenalookupx, - ;; je_check_reallocatex--i.e. they forked jemalloc. - ;("jemalloc" ,jemalloc) - ("ndctl" ,ndctl) - ("numactl" ,numactl))) + (list ;; memkind patched jemalloc to add je_arenalookupx, + ;; je_check_reallocatex--i.e. they forked jemalloc. + ;("jemalloc" ,jemalloc) + ndctl numactl)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (arguments `(#:configure-flags (list (string-append "--docdir=" (assoc-ref %outputs "out") @@ -1296,10 +1275,9 @@ (define-public bmaptools (invoke "nosetests" "-v" "--exclude" "test_bmap_helpers")))))) (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + (list python-mock python-nose)) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (home-page "https://github.com/intel/bmap-tools") (synopsis "Create block map for a file or copy a file using block map") (description "Bmaptool is a tool for creating the block map (bmap) for a @@ -1340,15 +1318,9 @@ (define-public duc (doc (string-append out "/share/doc/" ,name "-" ,version))) (copy-recursively "examples" (string-append doc "/examples")))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (inputs - `(("cairo" ,cairo) - ("pango" ,pango) - ("tokyocabinet" ,tokyocabinet) - ("ncurses" ,ncurses))) + (list cairo pango tokyocabinet ncurses)) (home-page "http://duc.zevv.nl") (synopsis "Library and suite of tools for inspecting disk usage") (description "Duc maintains a database of accumulated sizes of diff --git a/gnu/packages/display-managers.scm b/gnu/packages/display-managers.scm index 1bfd85beae..86415bc0cf 100644 --- a/gnu/packages/display-managers.scm +++ b/gnu/packages/display-managers.scm @@ -74,28 +74,24 @@ (define-public sddm "0hcdysw8ibr66vk8i7v56l0v5ijvhlq67v4460mc2xf2910g2m72")))) (build-system qt-build-system) (native-inputs - `(("extra-cmake-modules" ,extra-cmake-modules) - ("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list extra-cmake-modules pkg-config qttools)) (inputs - `(("elogind" ,elogind) - ("glib" ,glib) - ("libxcb" ,libxcb) - ("libxkbcommon" ,libxkbcommon) - ("linux-pam" ,linux-pam) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - - ;; Some user-defined themes use QtQuick components internally. Adding - ;; QtQuick & co. here; they end up in QML2_IMPORT_PATH thanks to - ;; 'wrap-qt-program'. - ("qtgraphicaleffects" ,qtgraphicaleffects) - ("qtquickcontrols" ,qtquickcontrols) - ("qtquickcontrols2" ,qtquickcontrols2) - ("qtsvg" ,qtsvg) - - ("shadow" ,shadow) - ("wayland" ,wayland))) + (list elogind + glib + libxcb + libxkbcommon + linux-pam + qtbase-5 + qtdeclarative + ;; Some user-defined themes use QtQuick components internally. Adding + ;; QtQuick & co. here; they end up in QML2_IMPORT_PATH thanks to + ;; 'wrap-qt-program'. + qtgraphicaleffects + qtquickcontrols + qtquickcontrols2 + qtsvg + shadow + wayland)) (arguments `(#:configure-flags ,#~(list @@ -234,11 +230,11 @@ (define-public lightdm (unsetenv "LC_ALL") #t))))) (inputs - `(("audit" ,audit) - ("linux-pam" ,linux-pam) - ("shadow" ,shadow) ;for sbin/nologin - ("libgcrypt" ,libgcrypt) - ("libxcb" ,libxcb))) + (list audit + linux-pam + shadow ;for sbin/nologin + libgcrypt + libxcb)) (native-inputs `(("gobject-introspection" ,gobject-introspection) ("pkg-config" ,pkg-config) @@ -251,9 +247,7 @@ (define-public lightdm ("python-pygobject" ,python2-pygobject))) ;; Required by liblightdm-gobject-1.pc. (propagated-inputs - `(("glib" ,glib) - ("libx11" ,libx11) - ("libxklavier" ,libxklavier))) + (list glib libx11 libxklavier)) (home-page "https://www.freedesktop.org/wiki/Software/LightDM/") (synopsis "Lightweight display manager") (description "The Light Display Manager (LightDM) is a cross-desktop @@ -305,10 +299,7 @@ (define-public lightdm-gtk-greeter `("GIO_EXTRA_MODULES" ":" prefix (,gtk)))) #t))))) (native-inputs - `(("exo" ,exo) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("xfce4-dev-tools" ,xfce4-dev-tools))) + (list exo intltool pkg-config xfce4-dev-tools)) (inputs `(("bash" ,bash-minimal) ; for wrap-program ("lightdm" ,lightdm) @@ -353,7 +344,7 @@ (define-public slim ("libxmu" ,libxmu) ("xauth" ,xauth))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (arguments '(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/distributed.scm b/gnu/packages/distributed.scm index 868fc589a6..182be4aaf7 100644 --- a/gnu/packages/distributed.scm +++ b/gnu/packages/distributed.scm @@ -58,20 +58,17 @@ (define-public boinc-client "1p8y3mnf5yfhavhqxwf9v68prg1601h8q1pllm5z89zh661di3mj")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--disable-server"))) - (inputs `(("openssl" ,openssl) - ("curl" ,curl) - ("wxwidgets" ,wxwidgets) - ("gtk+" ,gtk+) - ("gdk-pixbuf" ,gdk-pixbuf) - ("libnotify" ,libnotify) - ("sqlite" ,sqlite) - ("python" ,python) - ("python-pyserial" ,python-pyserial))) + (inputs (list openssl + curl + wxwidgets + gtk+ + gdk-pixbuf + libnotify + sqlite + python + python-pyserial)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (synopsis "Help cutting-edge science research using your computer") (description "BOINC is a platform for high-throughput computing on a large scale (thousands or millions of computers). It can be used for volunteer diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 00a4e3f175..3aeba5b4a3 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -97,29 +97,27 @@ (define-public python-django (delete 'wrap)))) ;; TODO: Install extras/django_bash_completion. (native-inputs - `(("tzdata" ,tzdata-for-tests) - ;; Remaining packages are test requirements taken from - ;; tests/requirements/py3.txt - ("python-docutils" ,python-docutils) - ;; optional for tests: ("python-geoip2" ,python-geoip2) - ;; optional for tests: ("python-memcached" ,python-memcached) - ("python-numpy" ,python-numpy) - ("python-pillow" ,python-pillow) - ("python-pyyaml" ,python-pyyaml) - ;; optional for tests: ("python-selenium" ,python-selenium) - ("python-tblib" ,python-tblib))) + (list tzdata-for-tests + ;; Remaining packages are test requirements taken from + ;; tests/requirements/py3.txt + python-docutils + ;; optional for tests: ("python-geoip2" ,python-geoip2) + ;; optional for tests: ("python-memcached" ,python-memcached) + python-numpy + python-pillow + python-pyyaml + ;; optional for tests: ("python-selenium" ,python-selenium) + python-tblib)) (propagated-inputs - `(("python-asgiref" ,python-asgiref) - ("python-pytz" ,python-pytz) - ("python-sqlparse" ,python-sqlparse) - - ;; Optional dependencies. - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-bcrypt" ,python-bcrypt) - - ;; This input is not strictly required, but in practice many Django - ;; libraries need it for test suites and similar. - ("python-jinja2" ,python-jinja2))) + (list python-asgiref + python-pytz + python-sqlparse + ;; Optional dependencies. + python-argon2-cffi + python-bcrypt + ;; This input is not strictly required, but in practice many Django + ;; libraries need it for test suites and similar. + python-jinja2)) (home-page "https://www.djangoproject.com/") (synopsis "High-level Python Web framework") (description @@ -141,9 +139,9 @@ (define-public python-django-2.2 (base32 "171ll8m1wp684z1r0lz93l377jc6jyq63q5p7sqx8iqk6ypmxrmi")))) (native-inputs - `(;; 2.2 requires Selenium for the test suite. - ("python-selenium" ,python-selenium) - ,@(package-native-inputs python-django))))) + (modify-inputs (package-native-inputs python-django) + (prepend ;; 2.2 requires Selenium for the test suite. + python-selenium))))) (define-public python-django-extensions (package @@ -164,19 +162,16 @@ (define-public python-django-extensions (arguments '(#:tests? #f)) ;XXX: requires a Postgres or MySQL database (propagated-inputs - `(("python-six" ,python-six) - ("python-vobject" ,python-vobject) - ("python-werkzeug" ,python-werkzeug) - ("python-dateutil" ,python-dateutil) - ("python-django" ,python-django))) + (list python-six python-vobject python-werkzeug python-dateutil + python-django)) (native-inputs - `(("python-mock" ,python-mock) - ("python-factory-boy" ,python-factory-boy) - ("python-tox" ,python-tox) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-django" ,python-pytest-django) - ("python-shortuuid" , python-shortuuid))) + (list python-mock + python-factory-boy + python-tox + python-pytest + python-pytest-cov + python-pytest-django + python-shortuuid)) (home-page "https://github.com/django-extensions/django-extensions") (synopsis "Custom management extensions for Django") @@ -208,13 +203,9 @@ (define-public python-django-localflavor (getenv "GUIX_PYTHONPATH"))) (invoke "invoke" "test"))))))) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-invoke" ,python-invoke) - ("python-pytest-django" ,python-pytest-django) - ("which" ,which))) + (list python-coverage python-invoke python-pytest-django which)) (propagated-inputs - `(("python-django" ,python-django) - ("python-stdnum" ,python-stdnum))) + (list python-django python-stdnum)) (home-page "https://django-localflavor.readthedocs.io/en/latest/") (synopsis "Country-specific Django helpers") (description "Django-LocalFlavor is a collection of assorted pieces of code @@ -251,10 +242,9 @@ (define-public python-django-simple-math-captcha (lambda _ (invoke "python" "runtests.py")))))) (native-inputs - `(("python-mock" ,python-mock))) + (list python-mock)) (propagated-inputs - `(("python-django" ,python-django) - ("python-six" ,python-six))) + (list python-django python-six)) (synopsis "Easy-to-use math field/widget captcha for Django forms") (description "A multi-value-field that presents a human answerable question, @@ -277,7 +267,7 @@ (define-public python-django-classy-tags ;; FIXME: How to make the test templates available to Django? (arguments '(#:tests? #f)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/divio/django-classy-tags") (synopsis "Class based template tags for Django") (description @@ -306,11 +296,9 @@ (define-public python-django-taggit (lambda _ (invoke "python3" "-m" "django" "test" "--settings=tests.settings")))))) (propagated-inputs - `(("python-django" ,python-django) - ("python-isort" ,python-isort))) + (list python-django python-isort)) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-mock" ,python-mock))) + (list python-pytest python-mock)) (home-page "https://github.com/jazzband/django-taggit") (synopsis @@ -332,8 +320,7 @@ (define-public python-easy-thumbnails "14gzp5cv24z0qhxb7f7k7v9jgzpaj4n8yhjq83ynpx8183fs1rz4")))) (build-system python-build-system) (propagated-inputs - `(("python-django" ,python-django) - ("python-pillow" ,python-pillow))) + (list python-django python-pillow)) (home-page "https://github.com/SmileyChris/easy-thumbnails") (synopsis "Easy thumbnails for Django") (description @@ -376,12 +363,11 @@ (define-public python-pytest-django " and not test_urls_cache_is_cleared"))) (format #t "test suite not run~%"))))))) (native-inputs - `(("python-django" ,python-django) - ("python-setuptools-scm" ,python-setuptools-scm) - ;; For tests. - ("python-pytest-xdist" ,python-pytest-xdist-next))) + (list python-django python-setuptools-scm + ;; For tests. + python-pytest-xdist-next)) (propagated-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://pytest-django.readthedocs.org/") (synopsis "Django plugin for py.test") (description "Pytest-django is a plugin for py.test that provides a set of @@ -416,18 +402,18 @@ (define-public python-django-haystack (delete 'sanity-check)) #:tests? #f)) ; OSError: libgdal.so.27: cannot open shared object file (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (native-inputs - `(("gdal" ,gdal) - ("python-coverage" ,python-coverage) - ("python-dateutil" ,python-dateutil) - ("python-geopy" ,python-geopy) - ("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-requests" ,python-requests) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-pysolr" ,python-pysolr) - ("python-whoosh" ,python-whoosh))) + (list gdal + python-coverage + python-dateutil + python-geopy + python-mock + python-nose + python-requests + python-setuptools-scm + python-pysolr + python-whoosh)) (home-page "http://haystacksearch.org/") (synopsis "Pluggable search for Django") (description "Haystack provides modular search for Django. It features a @@ -454,10 +440,8 @@ (define-public python-django-filter (lambda _ (invoke "python" "runtests.py")))))) (native-inputs - `(("python-django" ,python-django) - ("python-djangorestframework" ,python-djangorestframework) - ("python-django-crispy-forms" ,python-django-crispy-forms) - ("python-mock" ,python-mock))) + (list python-django python-djangorestframework + python-django-crispy-forms python-mock)) (home-page "https://django-filter.readthedocs.io/en/latest/") (synopsis "Reusable Django application to filter querysets dynamically") (description @@ -488,13 +472,11 @@ (define-public python-django-allauth (invoke "django-admin" "test" "allauth.tests" "--pythonpath=.")))))) (propagated-inputs - `(("python-openid" ,python-openid) - ("python-requests" ,python-requests) - ("python-requests-oauthlib" ,python-requests-oauthlib))) + (list python-openid python-requests python-requests-oauthlib)) (native-inputs - `(("python-mock" ,python-mock))) + (list python-mock)) (inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/pennersr/django-allauth") (synopsis "Set of Django applications addressing authentication") (description @@ -519,11 +501,9 @@ (define-public python-django-debug-toolbar "1m1j2sx7q0blma0miswj3c8hrfi5q4y5cq2b816v8gagy89xgc57")))) (build-system python-build-system) (propagated-inputs - `(("python-sqlparse" ,python-sqlparse) - ("python-django" ,python-django))) + (list python-sqlparse python-django)) (native-inputs - `(("python-django-jinja" ,python-django-jinja) - ("python-html5lib" ,python-html5lib))) + (list python-django-jinja python-html5lib)) (arguments '(#:phases (modify-phases %standard-phases @@ -552,11 +532,8 @@ (define-public python-django-debug-toolbar-alchemy (build-system python-build-system) (arguments '(#:tests? #f)) ;XXX: 'make check' does "echo TODO" (propagated-inputs - `(("python-django" ,python-django) - ("python-django-debug-toolbar" ,python-django-debug-toolbar) - ("python-jsonplus" ,python-jsonplus) - ("python-six" ,python-six) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-django python-django-debug-toolbar python-jsonplus + python-six python-sqlalchemy)) (synopsis "Django Debug Toolbar panel for SQLAlchemy") (description "This package completely mimics the default Django Debug Toolbar SQL @@ -580,7 +557,7 @@ (define-public python-django-gravatar2 '(;; TODO: The django project for the tests is missing from the release. #:tests? #f)) (inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/twaddington/django-gravatar") (synopsis "Gravatar support for Django, improved version") (description @@ -600,10 +577,9 @@ (define-public python-django-assets "0fc6i77faxxv1gjlp06lv3kw64b5bhdiypaygfxh5djddgk83fwa")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (propagated-inputs - `(("python-django" ,python-django) - ("python-webassets" ,python-webassets))) + (list python-django python-webassets)) (home-page "https://github.com/miracle2k/django-assets") (synopsis "Asset management for Django") (description @@ -628,10 +604,7 @@ (define-public python-django-jinja "0p9pkn6jjzagpnvcrl9c2vjqamkms7ymvyhhmaqqqhrlv89qnzp7")))) (build-system python-build-system) (propagated-inputs - `(("python-django" ,python-django) - ("python-jinja2" ,python-jinja2) - ("python-pytz" ,python-pytz) - ("python-django-pipeline" ,python-django-pipeline))) + (list python-django python-jinja2 python-pytz python-django-pipeline)) (arguments '(;; TODO Tests currently fail due to issues with the configuration for ;; django-pipeline @@ -721,7 +694,7 @@ (define-public python-django-bulk-update ;; XXX: Tests require a Postgres database. `(#:tests? #f)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/aykut/django-bulk-update") (synopsis "Simple bulk update over Django ORM or with helper function") (description @@ -748,9 +721,9 @@ (define-public python-django-contact-form (invoke "coverage" "run" "--source" "contact_form" "runtests.py")))))) (native-inputs - `(("python-coverage" ,python-coverage))) + (list python-coverage)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/ubernostrum/django-contact-form") (synopsis "Contact form for Django") (description @@ -770,8 +743,7 @@ (define-public python-django-contrib-comments "0ccdiv784a5vnpfal36km4dyg12340rwhpr0riyy0k89wfnjn8yi")))) (build-system python-build-system) (propagated-inputs - `(("python-django" ,python-django) - ("python-six" ,python-six))) + (list python-django python-six)) (home-page "https://github.com/django/django-contrib-comments") (synopsis "Comments framework") (description @@ -808,10 +780,8 @@ (define-public python-django-pipeline (invoke "django-admin" "test" "tests" "--pythonpath=."))))))) (propagated-inputs - `(("python-css-html-js-minify" ,python-css-html-js-minify) - ("python-django" ,python-django) - ("python-slimit" ,python-slimit) - ("python-jsmin" ,python-jsmin))) + (list python-css-html-js-minify python-django python-slimit + python-jsmin)) (home-page "https://github.com/jazzband/django-pipeline") (synopsis "Asset packaging library for Django") @@ -841,14 +811,10 @@ (define-public python-django-redis (with-directory-excursion "tests" (invoke "python" "runtests.py"))))))) (native-inputs - `(("python-fakeredis" ,python-fakeredis) - ("python-hiredis" ,python-hiredis) - ("python-mock" ,python-mock) - ("python-msgpack" ,python-msgpack) - ("redis" ,redis))) + (list python-fakeredis python-hiredis python-mock python-msgpack + redis)) (propagated-inputs - `(("python-django" ,python-django) - ("python-redis" ,python-redis))) + (list python-django python-redis)) (home-page "https://github.com/niwibe/django-redis") (synopsis "Full featured redis cache backend for Django") (description @@ -876,13 +842,9 @@ (define-public python-django-rq "--settings=django_rq.tests.settings" "--pythonpath=.")))))) (native-inputs - `(("python-django-redis" ,python-django-redis) - ("python-mock" ,python-mock) - ("python-rq-scheduler" ,python-rq-scheduler) - ("redis" ,redis))) + (list python-django-redis python-mock python-rq-scheduler redis)) (propagated-inputs - `(("python-django" ,python-django) - ("python-rq" ,python-rq))) + (list python-django python-rq)) (home-page "https://github.com/ui/django-rq") (synopsis "Django integration with RQ") (description @@ -905,10 +867,8 @@ (define-public python-django-q ;; FIXME: Tests require disque, Redis, MongoDB, Docker. (arguments '(#:tests? #f)) (propagated-inputs - `(("python-arrow" ,python-arrow) - ("python-blessed" ,python-blessed) - ("python-django" ,python-django) - ("python-django-picklefield" ,python-django-picklefield))) + (list python-arrow python-blessed python-django + python-django-picklefield)) (home-page "https://django-q.readthedocs.io/") (synopsis "Multiprocessing distributed task queue for Django") (description @@ -935,7 +895,7 @@ (define-public python-django-sortedm2m "test" "--settings=test_project.settings" "--pythonpath=.")))))) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/jazzband/django-sortedm2m") (synopsis "Drop-in replacement for django's own ManyToManyField") (description @@ -962,7 +922,7 @@ (define-public python-django-appconf (setenv "DJANGO_SETTINGS_MODULE" "tests.test_settings") (invoke "django-admin" "test" "--pythonpath=.")))))) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/django-compressor/django-appconf") (synopsis "Handle configuration defaults of packaged Django apps") (description @@ -996,8 +956,7 @@ (define-public python-django-statici18n (setenv "DJANGO_SETTINGS_MODULE" "project.settings") (invoke "pytest" "-vv")))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-django" ,python-pytest-django))) + (list python-pytest python-pytest-django)) (propagated-inputs `(("python-django" ,python-django) ("django-appconf" ,python-django-appconf))) @@ -1027,7 +986,7 @@ (define-public python-django-tagging (setenv "DJANGO_SETTINGS_MODULE" "tagging.tests.settings") (invoke "django-admin" "test" "--pythonpath=.")))))) (inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://github.com/Fantomas42/django-tagging") (synopsis "Generic tagging application for Django") (description "This package provides a generic tagging application for @@ -1065,10 +1024,9 @@ (define-public python-djangorestframework (invoke "python" "runtests.py" "--nolint") (format #t "test suite not run~%"))))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-django" ,python-pytest-django))) + (list python-pytest python-pytest-django)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "https://www.django-rest-framework.org") (synopsis "Toolkit for building Web APIs with Django") (description @@ -1090,9 +1048,7 @@ (define-public python-django-sekizai (build-system python-build-system) (arguments '(#:tests? #f)) ; Tests not included with release. (propagated-inputs - `(("python-django" ,python-django) - ("python-django-classy-tags" ,python-django-classy-tags) - ("python-six" ,python-six))) + (list python-django python-django-classy-tags python-six)) (home-page "https://github.com/divio/django-sekizai") (synopsis "Template blocks for Django projects") (description "Sekizai means blocks in Japanese, and that is what this app @@ -1121,7 +1077,7 @@ (define-public python-django-crispy-forms '(;; No included tests #:tests? #f)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (home-page "http://github.com/maraujop/django-crispy-forms") (synopsis "Tool to control Django forms without custom templates") @@ -1156,15 +1112,10 @@ (define-public python-django-compressor ;; https://github.com/django-compressor/django-compressor/issues/998 #:tests? #f)) (propagated-inputs - `(("python-django-appconf" ,python-django-appconf) - ("python-rcssmin" ,python-rcssmin) - ("python-rjsmin" ,python-rjsmin))) + (list python-django-appconf python-rcssmin python-rjsmin)) (native-inputs - `(("python-beautifulsoup4" ,python-beautifulsoup4) - ("python-brotli" ,python-brotli) - ("python-csscompressor" ,python-csscompressor) - ("python-django-sekizai" ,python-django-sekizai) - ("python-mock" ,python-mock))) + (list python-beautifulsoup4 python-brotli python-csscompressor + python-django-sekizai python-mock)) (home-page "https://django-compressor.readthedocs.io/en/latest/") (synopsis "Compress linked and inline JavaScript or CSS into single cached files") @@ -1195,9 +1146,9 @@ (define-public python-django-override-storage (lambda _ (invoke "python" "runtests.py")))))) (native-inputs - `(("python-mock" ,python-mock))) + (list python-mock)) (propagated-inputs - `(("python-django" ,python-django))) + (list python-django)) (synopsis "Django test helpers to manage file storage side effects") (description "This project provides tools to help reduce the side effects of using @@ -1228,11 +1179,9 @@ (define-public python-django-auth-ldap (invoke "python" "-m" "django" "test" "--settings" "tests.settings"))))))) (native-inputs - `(("openldap" ,openldap) - ("python-mock" ,python-mock))) + (list openldap python-mock)) (propagated-inputs - `(("python-django" ,python-django) - ("python-ldap" ,python-ldap))) + (list python-django python-ldap)) (home-page "https://github.com/django-auth-ldap/django-auth-ldap") (synopsis "Django LDAP authentication backend") (description @@ -1256,10 +1205,7 @@ (define-public python-django-logging-json ;; Importing this module requires a Django project. (delete 'sanity-check)))) (propagated-inputs - `(("python-certifi" ,python-certifi) - ("python-django" ,python-django) - ("python-elasticsearch" ,python-elasticsearch) - ("python-six" ,python-six))) + (list python-certifi python-django python-elasticsearch python-six)) (home-page "https://github.com/cipriantarta/django-logging") (synopsis "Log requests/responses in various formats") (description @@ -1281,10 +1227,7 @@ (define-public python-django-netfields (build-system python-build-system) (arguments '(#:tests? #f)) ;XXX: Requires a running PostgreSQL server (propagated-inputs - `(("python-django" ,python-django) - ("python-netaddr" ,python-netaddr) - ("python-psycopg2" ,python-psycopg2) - ("python-six" ,python-six))) + (list python-django python-netaddr python-psycopg2 python-six)) (home-page "https://github.com/jimfunk/django-postgresql-netfields") (synopsis "PostgreSQL netfields implementation for Django") (description @@ -1324,9 +1267,7 @@ (define-public python-django-url-filter "tests/" "url_filter/")) (format #t "test suite not run~%"))))))) (propagated-inputs - `(("python-cached-property" ,python-cached-property) - ("python-django" ,python-django) - ("python-six" ,python-six))) + (list python-cached-property python-django python-six)) (synopsis "Filter data via human-friendly URLs") (description "The main goal of Django URL Filter is to provide an easy URL interface @@ -1350,9 +1291,7 @@ (define-public python-django-svg-image-form-field (base32 "131m545khn8l20j4x2bvlvz36dlbnhj9pc98i2dw72s3bw8pgws0")))) (build-system python-build-system) (propagated-inputs - `(("python-defusedxml" ,python-defusedxml) - ("python-django" ,python-django) - ("python-pillow" ,python-pillow))) + (list python-defusedxml python-django python-pillow)) (home-page "https://github.com/artrey/django-svg-image-form-field") (synopsis "Form field to validate SVG and other images") (description "This form field allows users to provide SVG images for diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm index a4cd4da2ed..07c77f318e 100644 --- a/gnu/packages/djvu.scm +++ b/gnu/packages/djvu.scm @@ -71,13 +71,9 @@ (define-public djvulibre (build-system gnu-build-system) (native-inputs ;; The 3.5.28 release tarball isn't bootstrapped. - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("libjpeg-turbo" ,libjpeg-turbo) - ("libtiff" ,libtiff) - ("zlib" ,zlib))) + (list libjpeg-turbo libtiff zlib)) (arguments `(#:phases (modify-phases %standard-phases @@ -109,17 +105,9 @@ (define-public djview (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list autoconf automake libtool pkg-config qttools)) (inputs - `(("djvulibre" ,djvulibre) - ("glib" ,glib) - ("libxt" ,libxt) - ("libtiff" ,libtiff) - ("qtbase" ,qtbase-5))) + (list djvulibre glib libxt libtiff qtbase-5)) (arguments `(#:phases (modify-phases %standard-phases @@ -213,12 +201,12 @@ (define-public djvu2pdf (base32 "0v2ax30m7j1yi4m02nzn9rc4sn4vzqh5vywdh96r64j4pwvn5s5g")))) (build-system gnu-build-system) (inputs - `(("djvulibre" ,djvulibre) - ("gawk" ,gawk) - ("ghostscript" ,ghostscript) - ("grep" ,grep) - ("ncurses" ,ncurses) - ("which" ,which))) + (list djvulibre + gawk + ghostscript + grep + ncurses + which)) (arguments `(#:tests? #f ; No test suite #:phases @@ -277,9 +265,7 @@ (define-public minidjvu (native-inputs `(("gettext" ,gettext-minimal))) (inputs - `(("libjpeg-turbo" ,libjpeg-turbo) - ("libtiff" ,libtiff) - ("zlib" ,zlib))) + (list libjpeg-turbo libtiff zlib)) (arguments '(#:configure-flags '("--disable-static") #:parallel-build? #f @@ -318,10 +304,8 @@ (define-public djvusmooth (base32 "0z403cklvxzz0qaczgv83ax0nknrd9h8micp04j9kjfdxk2sgval")))) (build-system python-build-system) (inputs - `(("djvulibre" ,djvulibre) - ("python2-djvulibre" ,python2-djvulibre) - ("python2-subprocess32" ,python2-subprocess32) - ("python2-wxpython" ,python2-wxpython))) + (list djvulibre python2-djvulibre python2-subprocess32 + python2-wxpython)) (arguments `(#:python ,python-2 #:phases @@ -360,7 +344,7 @@ (define-public didjvu (base32 "0xyrnk8d2khi7q1zr28gjkjq6frz4mkb5jdl8821yzf12k7c8pbv")))) (build-system gnu-build-system) (native-inputs - `(("python2-nose" ,python2-nose))) + (list python2-nose)) (inputs `(("djvulibre" ,djvulibre) ("minidjvu" ,minidjvu) @@ -427,9 +411,7 @@ (define-public ocrodjvu (base32 "09w9rqr7z2jd5kwp178zz2yrsc82mxs7gksipg92znxzgzhmw2ng")))) (build-system gnu-build-system) (native-inputs - `(("libxml2" ,libxml2) - ("python2-nose" ,python2-nose) - ("python2-pillow" ,python2-pillow))) + (list libxml2 python2-nose python2-pillow)) (inputs `(("djvulibre" ,djvulibre) ("ocrad" ,ocrad) diff --git a/gnu/packages/dlang.scm b/gnu/packages/dlang.scm index c4cf1d9665..403fcbbd6b 100644 --- a/gnu/packages/dlang.scm +++ b/gnu/packages/dlang.scm @@ -75,7 +75,7 @@ (define-public rdmd (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "rdmd" bin))))))) (native-inputs - `(("ldc" ,ldc))) + (list ldc)) (home-page "https://github.com/D-Programming-Language/tools/") (synopsis "Specialized equivalent to 'make' for the D language") (description @@ -448,9 +448,9 @@ (define-public dub (install-file "bin/dub" bin) #t)))))) (inputs - `(("curl" ,curl))) + (list curl)) (native-inputs - `(("ldc" ,ldc))) + (list ldc)) (home-page "https://code.dlang.org/getting_started") (synopsis "Package and build manager for D projects") (description diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 63bf66647c..dae3b27ee2 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -127,10 +127,7 @@ (define-public cloudflare-cli ":")))) #t))))) (inputs - `(("bash-minimal" ,bash-minimal) - ("curl" ,curl) - ("grep" ,grep) - ("json.sh" ,json.sh))) + (list bash-minimal curl grep json.sh)) (synopsis "CLI to edit Cloudflare DNS records") (description @@ -213,9 +210,7 @@ (define-public ldns ("python" ,python-wrapper) ("swig" ,swig))) (inputs - `(("libpcap" ,libpcap) - ("nss-certs" ,nss-certs) - ("openssl" ,openssl))) + (list libpcap nss-certs openssl)) (synopsis "DNS library that facilitates DNS tool programming") (description "LDNS aims to simplify DNS programming, it supports recent RFCs like the DNSSEC documents, and allows developers to easily create @@ -342,9 +337,9 @@ (define-public dnsmasq "027b0ycw8h8yvvkq46vnr7dv8iqn5srm4kr7hm7sq110kvy2rm98")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("dbus" ,dbus))) + (list dbus)) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure)) @@ -388,16 +383,15 @@ (define-public isc-bind (outputs `("out" "utils")) (inputs ;; It would be nice to add GeoIP and gssapi once there are packages. - `(("libcap" ,libcap) - ("libuv" ,libuv) - ("libxml2" ,libxml2) - ("openssl" ,openssl) - ("p11-kit" ,p11-kit) - ("python" ,python) - ("python-ply" ,python-ply))) + (list libcap + libuv + libxml2 + openssl + p11-kit + python + python-ply)) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list perl pkg-config)) (arguments `(#:configure-flags (list (string-append "--with-pkcs11=" @@ -490,13 +484,9 @@ (define-public dnscrypt-proxy ;; The system version is still favored and referenced. (invoke "autoreconf" "-vif")))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("automake" ,automake) - ("autoconf" ,autoconf) - ("libtool" ,libtool))) + (list pkg-config automake autoconf libtool)) (inputs - `(("libltdl" ,libltdl) - ("libsodium" ,libsodium))) + (list libltdl libsodium)) (home-page "https://www.dnscrypt.org/") (synopsis "Securely send DNS requests to a remote server") (description @@ -535,10 +525,9 @@ (define-public dnscrypt-wrapper (lambda _ (invoke "make" "configure")))))) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (inputs - `(("libevent" ,libevent) - ("libsodium" ,libsodium))) + (list libevent libsodium)) (home-page "https://github.com/Cofyc/dnscrypt-wrapper") (synopsis "Server-side dnscrypt proxy") (description @@ -575,10 +564,7 @@ (define-public libasr (string-append out "/share/man/man3")) #t)))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "https://www.opensmtpd.org") (synopsis "Asynchronous resolver library by the OpenBSD project") (description @@ -640,8 +626,7 @@ (define-public nsd (string-append doc "/examples/" file-name))))))) #:tests? #f)) ; no tests (inputs - `(("libevent" ,libevent) - ("openssl" ,openssl))) + (list libevent openssl)) (home-page "https://www.nlnetlabs.nl/projects/nsd/about/") (synopsis "Authoritative DNS name server") (description "@dfn{NSD}, short for Name Server Daemon, is an authoritative @@ -692,7 +677,7 @@ (define-public rbldnsd (install-file "rbldnsd" sbin) (install-file "rbldnsd.8" man8))))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs ;; For running the test suite. Python 3 is not yet supported by a release: ;; see . @@ -728,15 +713,14 @@ (define-public unbound (build-system gnu-build-system) (outputs '("out" "python")) (native-inputs - `(("flex" ,flex) - ("swig" ,swig))) + (list flex swig)) (inputs - `(("expat" ,expat) - ("libevent" ,libevent) - ("nghttp2" ,nghttp2 "lib") - ("protobuf" ,protobuf) - ("python-wrapper" ,python-wrapper) - ("openssl" ,openssl))) + (list expat + libevent + `(,nghttp2 "lib") + protobuf + python-wrapper + openssl)) (arguments `(#:configure-flags (list "--disable-static" ; save space and non-determinism in libunbound.a @@ -889,9 +873,9 @@ (define-public yadifa (base32 "1mwy6sfnlaslx26f3kpj9alh8i8y8bf1nbnsdd5j04hjsbavd07p"))))) (build-system gnu-build-system) (native-inputs - `(("which" ,which))) + (list which)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (arguments `(#:phases (modify-phases %standard-phases @@ -1018,13 +1002,13 @@ (define-public knot (rename-file (string-append out "/share/man/man1") (string-append tools "/share/man/man1")))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("python-sphinx" ,python-sphinx) - ("ragel" ,ragel) - ("texinfo" ,texinfo))) + (list autoconf + automake + libtool + pkg-config + python-sphinx + ragel + texinfo)) (inputs `(("fstrm" ,fstrm) ("gnutls" ,gnutls) @@ -1115,14 +1099,14 @@ (define-public knot-resolver `("LUA_CPATH" ";" prefix ,(map lua-cpath lua-*))) #t)))))) (native-inputs - `(("cmocka" ,cmocka) ; for unit tests - ("doxygen" ,doxygen) - ("protobuf-c" ,protobuf-c) - ("pkg-config" ,pkg-config) - ("python-breathe" ,python-breathe) - ("python-sphinx" ,python-sphinx) - ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme) - ("texinfo" ,texinfo))) + (list cmocka ; for unit tests + doxygen + protobuf-c + pkg-config + python-breathe + python-sphinx + python-sphinx-rtd-theme + texinfo)) (inputs `(("fstrm" ,fstrm) ("gnutls" ,gnutls) @@ -1159,14 +1143,13 @@ (define-public ddclient (base32 "0hf377g4j9r9sac75xp17nk2h58mazswz4vkg4g2gl2yyhvzq91w")))) (build-system trivial-build-system) ; no Makefile.PL (native-inputs - `(("bash" ,bash) - ("perl" ,perl))) + (list bash perl)) (inputs - `(("inetutils" ,inetutils) ; logger - ("net-tools" ,net-tools) - ("perl-data-validate-ip" ,perl-data-validate-ip) - ("perl-digest-sha1" ,perl-digest-sha1) - ("perl-io-socket-ssl" ,perl-io-socket-ssl))) + (list inetutils ; logger + net-tools + perl-data-validate-ip + perl-digest-sha1 + perl-io-socket-ssl)) (arguments `(#:modules ((guix build utils)) #:builder @@ -1264,12 +1247,9 @@ (define-public hnsd (arguments '(#:configure-flags '("--disable-static"))) ;no need for libhsk.a (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("unbound" ,unbound) - ("libuv" ,libuv))) + (list unbound libuv)) (home-page "https://www.handshake.org/") (synopsis "Resolver daemon for the Handshake naming protocol") (description @@ -1431,7 +1411,7 @@ (define-public openresolv PATH=~a/bin:$PATH" coreutils))))))))) (inputs - `(("coreutils-minimal" ,coreutils-minimal))) + (list coreutils-minimal)) (home-page "https://roy.marples.name/projects/openresolv/") (synopsis "Resolvconf POSIX compliant implementation, a middleman for resolv.conf") (description "openresolv is an implementation of @command{resolvconf}, the diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm index 1a1f963821..cb1a0d4d5e 100644 --- a/gnu/packages/docbook.scm +++ b/gnu/packages/docbook.scm @@ -78,7 +78,7 @@ (define-public docbook-xml-5 (string-append "uri=\"file://" dtd "/"))) #t))))) - (native-inputs `(("unzip" ,unzip))) + (native-inputs (list unzip)) (home-page "https://docbook.org") (synopsis "DocBook XML DTDs for document authoring") (description @@ -221,9 +221,8 @@ (define name-version name-version "/"))) #t)) #:modules ((guix build utils)))) - (native-inputs `(("bzip2" ,bzip2) - ("xz" ,xz) ;needed for repacked tarballs - ("tar" ,tar))) + (native-inputs (list bzip2 xz ;needed for repacked tarballs + tar)) (home-page "https://docbook.org") (synopsis "DocBook XSL style sheets for document authoring") (description @@ -317,10 +316,9 @@ (define-public docbook-dsssl ;; The doc output contains 1.4 MiB of HTML documentation. (symlink docbook-dsssl-doc doc))))) (inputs - `(("docbook-dsssl-doc" ,docbook-dsssl-doc))) + (list docbook-dsssl-doc)) (native-inputs - `(("bzip2" ,bzip2) - ("tar" ,tar))) + (list bzip2 tar)) (home-page "https://docbook.org/") (synopsis "DSSSL style sheets for DocBook") (description "This package provides DSSSL style sheets for DocBook.") @@ -398,9 +396,9 @@ (define-public docbook-sgml (("(.*ISO 8879.*)\"iso-(.*)\\.gml\"" _ head name) (string-append head "\"" iso-entities-dir "/ISO" name "\""))))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (inputs - `(("iso-8879-entities" ,iso-8879-entities))) + (list iso-8879-entities)) (home-page "https://docbook.org") (synopsis "DocBook SGML style sheets for document authoring") (description "This package provides SGML style sheets for DocBook.") @@ -591,13 +589,13 @@ (define-public docbook-utils ;; Propagated for convenience. All these tools are used at run time to ;; provide the complete functionality of the docbook-utils commands. (propagated-inputs - `(("texlive-jadetex" ,texlive-jadetex) - ("docbook-sgml" ,docbook-sgml-3.1) - ("docbook-dsssl" ,docbook-dsssl) - ("openjade" ,openjade) - ("opensp" ,opensp) - ("lynx" ,lynx) - ("perl-sgmls" ,perl-sgmls))) + (list texlive-jadetex + docbook-sgml-3.1 + docbook-dsssl + openjade + opensp + lynx + perl-sgmls)) (home-page "https://packages.debian.org/sid/docbook-utils") (synopsis "DocBook converter to other formats") (description "The docbook-utils package is a collection of utilities diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 472c5eb957..cdf62f5e9a 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -69,13 +69,10 @@ (define-public python-docker ;; TODO: Tests require a running Docker daemon. (arguments '(#:tests? #f)) (inputs - `(("python-requests" ,python-requests) - ("python-six" ,python-six) - ("python-urllib3" ,python-urllib3))) + (list python-requests python-six python-urllib3)) (propagated-inputs - `(("python-docker-pycreds" ,python-docker-pycreds) - ("python-paramiko" ,python-paramiko) ;adds SSH support - ("python-websocket-client" ,python-websocket-client))) + (list python-docker-pycreds python-paramiko ;adds SSH support + python-websocket-client)) (home-page "https://github.com/docker/docker-py/") (synopsis "Python client for Docker") (description "Docker-Py is a Python client for the Docker container @@ -95,7 +92,7 @@ (define-public python-dockerpty "1kjn64wx23jmr8dcc6g7bwlmrhfmxr77gh6iphqsl39sayfxdab9")))) (build-system python-build-system) (native-inputs - `(("python-six" ,python-six))) + (list python-six)) (home-page "https://github.com/d11wtq/dockerpty") (synopsis "Python library to use the pseudo-TTY of a Docker container") (description "Docker PTY provides the functionality needed to operate the @@ -118,18 +115,18 @@ (define-public docker-compose ;; TODO: Tests require running Docker daemon. (arguments '(#:tests? #f)) (inputs - `(("python-cached-property" ,python-cached-property) - ("python-distro" ,python-distro) - ("python-docker" ,python-docker) - ("python-dockerpty" ,python-dockerpty) - ("python-docopt" ,python-docopt) - ("python-dotenv" ,python-dotenv) - ("python-jsonschema" ,python-jsonschema) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-six" ,python-six) - ("python-texttable" ,python-texttable) - ("python-websocket-client" ,python-websocket-client))) + (list python-cached-property + python-distro + python-docker + python-dockerpty + python-docopt + python-dotenv + python-jsonschema + python-pyyaml + python-requests + python-six + python-texttable + python-websocket-client)) (home-page "https://www.docker.com/") (synopsis "Multi-container orchestration for Docker") (description "Docker Compose is a tool for defining and running @@ -161,11 +158,9 @@ (define-public python-docker-pycreds (("2.4.1") ,(package-version python-flake8))) #t))))) (native-inputs - `(("python-flake8" ,python-flake8) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov))) + (list python-flake8 python-pytest python-pytest-cov)) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (home-page "https://github.com/shin-/dockerpy-creds") (synopsis "Python bindings for the Docker credentials store API") @@ -233,14 +228,9 @@ (define-public containerd (apply invoke "make" (string-append "DESTDIR=" out) "install" ',make-flags))))))))) (inputs - `(("btrfs-progs" ,btrfs-progs) - ("libseccomp" ,libseccomp) - ("pigz" ,pigz) - ("runc" ,runc) - ("util-linux" ,util-linux))) + (list btrfs-progs libseccomp pigz runc util-linux)) (native-inputs - `(("go" ,go) - ("pkg-config" ,pkg-config))) + (list go pkg-config)) (synopsis "Docker container runtime") (description "This package provides the container daemon for Docker. It includes image transfer and storage, container execution and supervision, @@ -594,10 +584,8 @@ (define-public docker ("xfsprogs" ,xfsprogs) ("xz" ,xz))) (native-inputs - `(("eudev" ,eudev) ; TODO: Should be propagated by lvm2 (.pc -> .pc) - ("go" ,go) - ("gotestsum" ,gotestsum) - ("pkg-config" ,pkg-config))) + (list eudev ; TODO: Should be propagated by lvm2 (.pc -> .pc) + go gotestsum pkg-config)) (synopsis "Docker container component library, and daemon") (description "This package provides a framework to assemble specialized container systems. It includes components for orchestration, image @@ -668,9 +656,7 @@ (define-public docker-cli (install-file "build/docker" out-bin) #t)))))) (native-inputs - `(("go" ,go) - ("libltdl" ,libltdl) - ("pkg-config" ,pkg-config))) + (list go libltdl pkg-config)) (synopsis "Command line interface to Docker") (description "This package provides a command line interface to Docker.") (home-page "https://www.docker.com/") diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm index 4313af387e..c1a8c43363 100644 --- a/gnu/packages/documentation.scm +++ b/gnu/packages/documentation.scm @@ -93,7 +93,7 @@ (define-public latex2html (assoc-ref outputs "out"))) #t))))) (inputs - `(("perl" ,perl))) + (list perl)) (synopsis "LaTeX documents to HTML") (description "LaTeX2HTML is a utility that converts LaTeX documents to web pages in HTML.") @@ -160,13 +160,9 @@ (define-public asciidoc "/xml/dtd/docbook/docbookx.dtd"))) #t))))) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (inputs - `(("python" ,python) - ("docbook-xml" ,docbook-xml) - ("docbook-xsl" ,docbook-xsl) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt))) + (list python docbook-xml docbook-xsl libxml2 libxslt)) (home-page "https://asciidoc.org/") (synopsis "Text-based document generation system") (description @@ -199,10 +195,8 @@ (define-public doxygen "1lcif1qi20gf04qyjrx7x367669g17vz2ilgi4cmamp1whdsxbk7")))) (build-system cmake-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("libxml2" ,libxml2) ;provides xmllint for the tests - ("python" ,python))) ;for creating the documentation + (list bison flex libxml2 ;provides xmllint for the tests + python)) ;for creating the documentation (inputs `(("bash" ,bash-minimal))) (arguments @@ -281,13 +275,11 @@ (define-public scrollkeeper (assoc-ref %build-inputs "docbook-xml") "/xml/dtd/docbook/catalog.xml")))) (inputs - `(("perl" ,perl) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ;; The configure script checks for either version 4.2 or 4.1.2. - ("docbook-xml" ,docbook-xml-4.2))) + (list perl libxml2 libxslt + ;; The configure script checks for either version 4.2 or 4.1.2. + docbook-xml-4.2)) (native-inputs - `(("intltool" ,intltool))) + (list intltool)) (home-page "http://scrollkeeper.sourceforge.net/") (synopsis "Open Documentation Cataloging Project") (description "ScrollKeeper is a cataloging system for documentation on open @@ -329,8 +321,7 @@ (define-public zeal `("QTWEBENGINEPROCESS_PATH" = (,qt-process-path))) #t)))))) (native-inputs - `(("extra-cmake-modules" ,extra-cmake-modules) - ("pkg-config" ,pkg-config))) + (list extra-cmake-modules pkg-config)) (inputs `(("libarchive" ,libarchive) ("sqlite" ,sqlite) diff --git a/gnu/packages/dunst.scm b/gnu/packages/dunst.scm index 2449620891..998470e411 100644 --- a/gnu/packages/dunst.scm +++ b/gnu/packages/dunst.scm @@ -63,22 +63,21 @@ (define-public dunst #:phases (modify-phases %standard-phases (delete 'configure)))) (native-inputs - `(("pkg-config" ,pkg-config) - ("perl" ,perl) ; for pod2man - ("which" ,which))) + (list pkg-config perl ; for pod2man + which)) (inputs - `(("dbus" ,dbus) - ("librsvg" ,librsvg) ; for svg support - ("glib" ,glib) - ("cairo" ,cairo) - ("pango" ,pango) - ("libnotify" ,libnotify) ; for dunstify - ("libx11" ,libx11) - ("libxscrnsaver" ,libxscrnsaver) - ("libxinerama" ,libxinerama) - ("libxrandr" ,libxrandr) - ("libxdg-basedir" ,libxdg-basedir) - ("wayland" ,wayland))) ; for wayland support + (list dbus + librsvg ; for svg support + glib + cairo + pango + libnotify ; for dunstify + libx11 + libxscrnsaver + libxinerama + libxrandr + libxdg-basedir + wayland)) ; for wayland support (home-page "https://dunst-project.org/") (synopsis "Customizable and lightweight notification daemon") (description diff --git a/gnu/packages/dvtm.scm b/gnu/packages/dvtm.scm index 8515c5d06b..8c39bb7c03 100644 --- a/gnu/packages/dvtm.scm +++ b/gnu/packages/dvtm.scm @@ -41,7 +41,7 @@ (define-public dvtm #:phases (modify-phases %standard-phases (delete 'configure) (delete 'check)))) ; no test suite - (inputs `(("ncurses" ,ncurses))) + (inputs (list ncurses)) (synopsis "Tiling window management for the console") (description "dvtm brings the concept of tiling window management, popularized by X11-window managers like dwm, to the console. As a console diff --git a/gnu/packages/easyrpg.scm b/gnu/packages/easyrpg.scm index 2350efdb79..007e7ce5bc 100644 --- a/gnu/packages/easyrpg.scm +++ b/gnu/packages/easyrpg.scm @@ -51,7 +51,7 @@ (define-public liblcf "0n2k4brd264jg9p6918x7dnb2iimpzjh8q3v1fws58450xbgnkqc")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (propagated-inputs ;; Required by 'liblcf.pc'. `(("expat" ,expat) @@ -91,23 +91,23 @@ (define-public easyrpg-player (list (string-append "--with-bash-completion-dir=" %output "/etc/bash_completion.d/")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("freetype" ,freetype) - ("harfbuzz" ,harfbuzz) - ("liblcf" ,liblcf) - ("libpng" ,libpng) - ("libsndfile" ,libsndfile) - ("libvorbis" ,libvorbis) - ("libxmp" ,libxmp) - ("mpg123" ,mpg123) - ("opusfile" ,opusfile) - ("pixman" ,pixman) - ("sdl2-mixer" ,sdl2-mixer) - ("sdl2" ,sdl2) - ("speexdsp" ,speexdsp) - ("wildmidi" ,wildmidi) - ("zlib" ,zlib))) + (list freetype + harfbuzz + liblcf + libpng + libsndfile + libvorbis + libxmp + mpg123 + opusfile + pixman + sdl2-mixer + sdl2 + speexdsp + wildmidi + zlib)) (home-page "https://easyrpg.org/") (synopsis "Play RPG Maker 2000 and 2003 games") (description diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index deb001862c..393b439b5c 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -110,7 +110,7 @@ (define-public python-pychm "0wpn9ijlsmrpyiwg3drmgz4dms1i1i347adgqw37bkrh3vn6yq16")))) (build-system python-build-system) (inputs - `(("chmlib" ,chmlib))) + (list chmlib)) (home-page "https://github.com/dottedmag/pychm") (synopsis "Handle CHM files") (description "This package provides a Python module for interacting @@ -150,11 +150,11 @@ (define-public calibre "calibre-remove-test-unrar.patch")))) (build-system python-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("qtbase" ,qtbase-5) ; for qmake - ("python-flake8" ,python-flake8) - ("python-pyqt-builder" ,python-pyqt-builder) - ("xdg-utils" ,xdg-utils))) + (list pkg-config + qtbase-5 ; for qmake + python-flake8 + python-pyqt-builder + xdg-utils)) (inputs `(("fontconfig" ,fontconfig) ("font-liberation" ,font-liberation) @@ -368,10 +368,9 @@ (define-public ebook-tools `(#:tests? #f)) ; No 'test' target (build-system cmake-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("libzip" ,libzip) - ("libxml2" ,libxml2))) + (list libzip libxml2)) (home-page "http://ebook-tools.sourceforge.net") (synopsis "Tools and library for dealing with various ebook file formats") (description "This package provides command-line tools and a library for @@ -408,7 +407,7 @@ (define-public inkbox (lambda* (#:key make-flags #:allow-other-keys) (apply invoke (cons "qmake" make-flags))))))) (native-inputs - `(("qtbase" ,qtbase-5))) + (list qtbase-5)) (home-page "https://alpinekobox.ddns.net/InkBox/inkbox/") (synopsis "EBook reader") (description "This package provides InkBox eBook reader.") @@ -567,26 +566,26 @@ (define-public cozy ("pkg-config" ,pkg-config) ("python" ,python-wrapper))) (inputs - `(("file" ,file) - ("granite" ,granite) - ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gst-libav" ,gst-libav) - ("gst-plugins-bad" ,gst-plugins-bad) - ("gst-plugins-good" ,gst-plugins-good) - ("gst-plugins-ugly" ,gst-plugins-ugly) - ("gtk+" ,gtk+) - ("libdazzle" ,libdazzle) - ("libgee" ,libgee) - ("libhandy" ,libhandy) - ("python-distro" ,python-distro) - ("python-gst" ,python-gst) - ("python-mutagen" ,python-mutagen) - ("python-packaging" ,python-packaging) - ("python-peewee" ,python-peewee) - ("python-pycairo" ,python-pycairo) - ("python-pygobject" ,python-pygobject) - ("python-pytz" ,python-pytz) - ("python-requests" ,python-requests))) + (list file + granite + gsettings-desktop-schemas + gst-libav + gst-plugins-bad + gst-plugins-good + gst-plugins-ugly + gtk+ + libdazzle + libgee + libhandy + python-distro + python-gst + python-mutagen + python-packaging + python-peewee + python-pycairo + python-pygobject + python-pytz + python-requests)) (home-page "https://cozy.geigi.de/") (synopsis "Modern audiobook player using GTK+") (description @@ -625,10 +624,9 @@ (define-public xchm "0b12ym7cn65wy268kbksyhakicwb053c8xfn76q2dawrvbras9dj")))) (build-system gnu-build-system) (inputs - `(("wxwidgets" ,wxwidgets) - ("chmlib" ,chmlib))) + (list wxwidgets chmlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/rzvncj/xCHM") (synopsis "CHM file viewer") (description "xCHM is a graphical CHM file viewer. It is a frontend to @@ -650,12 +648,9 @@ (define-public libmobi "0yps72cm609xn2k7alflkdhp9kgr1w7zzyxjygz0n1kqrdcplihh")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (inputs - `(("zlib" ,zlib) - ("libxml2" ,libxml2))) + (list zlib libxml2)) (home-page "https://github.com/bfabiszewski/libmobi/") (synopsis "C library for handling MOBI formats") (description "Libmobi is a C library for handling MOBI ebook diff --git a/gnu/packages/ed.scm b/gnu/packages/ed.scm index accc461e9b..a42ba40102 100644 --- a/gnu/packages/ed.scm +++ b/gnu/packages/ed.scm @@ -37,7 +37,7 @@ (define-public ed (base32 "0m2yrkfjjraakxr98nsiakqrn351h99n706x9asgmdi57j43kpki")))) (build-system gnu-build-system) - (native-inputs `(("lzip" ,lzip))) + (native-inputs (list lzip)) (arguments '(#:configure-flags '("CC=gcc") #:phases diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 739acb6453..8d08355694 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -241,8 +241,7 @@ (define-public gotypist (with-directory-excursion bin (rename-file "v1" "gotypist")))))))) (native-inputs - `(("go-github-com-gizak-termui" ,go-github-com-gizak-termui) - ("go-github-com-stretchr-testify" ,go-github-com-stretchr-testify))) + (list go-github-com-gizak-termui go-github-com-stretchr-testify)) (home-page "https://github.com/KappaDistributive/gotypist") (synopsis "Simple typing trainer for text terminals") (description @@ -297,8 +296,7 @@ (define-public tipp10 ;; Recreate Makefile (invoke "qmake"))))))) (inputs - `(("qtbase" ,qtbase-5) - ("qtmultimedia" ,qtmultimedia))) + (list qtbase-5 qtmultimedia)) (home-page "https://www.tipp10.com/") (synopsis "Touch typing tutor") (description "Tipp10 is a touch typing tutor. The ingenious thing about @@ -428,9 +426,9 @@ (define-public toutenclic out))) #t)))))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (inputs - `(("python-pyqt" ,python-pyqt))) + (list python-pyqt)) (synopsis "School tools for physically disabled children") (description "ToutEnClic is intended to facilitate the schooling of physically disabled children in ordinary schools. It is both @@ -563,8 +561,7 @@ (define-public omnitux #t)))) (build-system python-build-system) (inputs - `(("python2-pygame" ,python2-pygame) - ("python2-pygtk" ,python2-pygtk))) + (list python2-pygame python2-pygtk)) (arguments `(#:tests? #f ;no test #:python ,python-2 @@ -672,7 +669,7 @@ (define-public fet (replace 'configure (lambda _ (invoke "qmake" "fet.pro")))))) (inputs - `(("qtbase" ,qtbase))) + (list qtbase)) (home-page "https://www.lalescu.ro/liviu/fet/") (synopsis "Timetabling software") (description @@ -698,14 +695,9 @@ (define-public klavaro (base32 "0z6c3lqikk50mkz3ipm93l48qj7b98lxyip8y6ndg9y9k0z0n878")))) (build-system gnu-build-system) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list intltool pkg-config)) (inputs - `(("cairo" ,cairo) - ("curl" ,curl) - ("gtk+" ,gtk+) - ("gtkdatabox" ,gtkdatabox) - ("pango" ,pango))) + (list cairo curl gtk+ gtkdatabox pango)) (home-page "https://klavaro.sourceforge.io/en/index.html") (synopsis "Touch typing tutor") (description @@ -726,32 +718,30 @@ (define-public ktouch (base32 "10lm2p8w26c9n6lhvw3301myfss0dq7hl7rawzb3hsy1lqvmvdib")))) (build-system qt-build-system) (native-inputs - `(("extra-cmake-modules" ,extra-cmake-modules) - ("kdoctools" ,kdoctools) - ("pkg-config" ,pkg-config))) + (list extra-cmake-modules kdoctools pkg-config)) (inputs - `(("kcmutils" ,kcmutils) - ("kcompletion" ,kcompletion) - ("kconfig" ,kconfig) - ("kconfigwidgets" ,kconfigwidgets) - ("kcoreaddons" ,kcoreaddons) - ("kdeclarative" ,kdeclarative) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("kitemviews" ,kitemviews) - ("kqtquickcharts" ,kqtquickcharts) - ("ktextwidgets" ,ktextwidgets) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kwindowsystem" ,kwindowsystem) - ("kxmlgui" ,kxmlgui) - ("libxcb" ,libxcb) - ("libxkbfile" ,libxkbfile) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - ("qtgraphicaleffects" ,qtgraphicaleffects) - ("qtquickcontrols2" ,qtquickcontrols2) - ("qtx11extras" ,qtx11extras) - ("qtxmlpatterns" ,qtxmlpatterns))) + (list kcmutils + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kdeclarative + ki18n + kiconthemes + kitemviews + kqtquickcharts + ktextwidgets + kwidgetsaddons + kwindowsystem + kxmlgui + libxcb + libxkbfile + qtbase-5 + qtdeclarative + qtgraphicaleffects + qtquickcontrols2 + qtx11extras + qtxmlpatterns)) (home-page "https://edu.kde.org/ktouch/") (synopsis "Touch typing tutor") (description @@ -784,8 +774,7 @@ (define-public kanatest `(("gettext" ,gettext-minimal) ; for msgfmt ("pkg-config" ,pkg-config))) (inputs - `(("libxml2" ,libxml2) - ("gtk+" ,gtk+))) + (list libxml2 gtk+)) (home-page "https://kanatest.sourceforge.io/") (synopsis "Hiragana and Katakana simple flashcard tool") (description "Kanatest is a Japanese kana (Hiragana and Katakana) simple @@ -866,7 +855,7 @@ (define-public anki (find-files bin "."))) #t))))) (native-inputs - `(("xdg-utils" ,xdg-utils))) + (list xdg-utils)) (inputs `(("lame" ,lame) ("mpv" ,mpv) @@ -946,7 +935,7 @@ (define-public t4k-common "/share/fonts/truetype"))) #t))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("font-andika" ,font-sil-andika) ("libpng" ,libpng) @@ -1004,7 +993,7 @@ (define-public tuxmath "tuxmath\\.(png|ico|svg)$")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs `(("librsvg" ,librsvg) ("libxml2" ,libxml2) @@ -1038,9 +1027,9 @@ (define-public libeb "0psbdzirazfnn02hp3gsx7xxss9f1brv4ywp6a15ihvggjki1rxb")))) (build-system gnu-build-system) (native-inputs ; Required for building docs - `(("perl" ,perl))) + (list perl)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (synopsis "C library for accessing Japanese CD-ROM books") (description "The EB library is a library for accessing CD-ROM books, which are a common way to distribute electronic dictionaries in @@ -1067,16 +1056,16 @@ (define-public qolibri (arguments '(#:tests? #f)) ; no test target (native-inputs - `(("qttools", qttools))) + (list qttools)) (inputs - `(("libeb" ,libeb) - ("qtbase" ,qtbase-5) - ("qtmultimedia" ,qtmultimedia) - ("qtquickcontrols2" ,qtquickcontrols2) - ("qtdeclarative" ,qtdeclarative) - ("qtwebchannel" ,qtwebchannel) - ("qtwebengine" ,qtwebengine) - ("zlib" ,zlib))) + (list libeb + qtbase-5 + qtmultimedia + qtquickcontrols2 + qtdeclarative + qtwebchannel + qtwebengine + zlib)) (synopsis "EPWING dictionary reader") (description "qolibri is a dictionary viewer for the EPWING dictionary format. Most monolingual Japanese dictionaries can only be found in the @@ -1100,16 +1089,14 @@ (define-public mdk (arguments `(#:configure-flags (list "--enable-gui=yes" "-with-readline=yes"))) (native-inputs - `(("flex" ,flex) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list flex intltool pkg-config)) (inputs - `(("glib" ,glib) - ("gtk+" ,gtk+) - ("libglade" ,libglade) - ("ncurses" ,ncurses) - ("pango" ,pango) - ("readline" ,readline))) + (list glib + gtk+ + libglade + ncurses + pango + readline)) (home-page "https://www.gnu.org/software/mdk/manual/") (synopsis "Virtual development environment for Knuth's MIX") (description diff --git a/gnu/packages/efi.scm b/gnu/packages/efi.scm index 8bbd873435..4625538d26 100644 --- a/gnu/packages/efi.scm +++ b/gnu/packages/efi.scm @@ -143,12 +143,12 @@ (define-public sbsigntools (setenv "CC" "gcc") #t))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("bash" ,bash) - ("help2man" ,help2man) - ("pkg-config" ,pkg-config) - ("util-linux" ,util-linux))) ; getopt + (list autoconf + automake + bash + help2man + pkg-config + util-linux)) ; getopt (inputs `(("gnu-efi" ,gnu-efi) ("libuuid" ,util-linux "lib") @@ -202,13 +202,9 @@ (define-public efitools #t)) (delete 'configure)))) (native-inputs - `(("help2man" ,help2man) - ("perl" ,perl) - ("perl-file-slurp" ,perl-file-slurp) - ("sbsigntools" ,sbsigntools))) + (list help2man perl perl-file-slurp sbsigntools)) (inputs - `(("gnu-efi" ,gnu-efi) - ("openssl" ,openssl))) + (list gnu-efi openssl)) (synopsis "EFI tools (key management, variable management)") (description "This package provides EFI tools for EFI key management and EFI variable management.") @@ -257,7 +253,7 @@ (define-public efilinux "/libexec")) #t))))) (inputs - `(("gnu-efi" ,gnu-efi))) + (list gnu-efi)) (synopsis "Minimal Linux loader for UEFI") (description "This package provides a minimal Linux loader as an UEFI program.") diff --git a/gnu/packages/electronics.scm b/gnu/packages/electronics.scm index 0e985c9750..3f4409764f 100644 --- a/gnu/packages/electronics.scm +++ b/gnu/packages/electronics.scm @@ -94,14 +94,10 @@ (define-public libsigrokdecode "/share/doc/libsigrokdecode")) #t))))) (native-inputs - `(("check" ,check-0.14) - ("doxygen" ,doxygen) - ("graphviz" ,graphviz) - ("pkg-config" ,pkg-config))) + (list check-0.14 doxygen graphviz pkg-config)) ;; libsigrokdecode.pc lists "python" in Requires.private, and "glib" in Requires. (propagated-inputs - `(("glib" ,glib) - ("python" ,python))) + (list glib python)) (build-system gnu-build-system) (home-page "https://www.sigrok.org/wiki/Libsigrokdecode") (synopsis "Library providing (streaming) protocol decoding functionality") @@ -192,23 +188,19 @@ (define-public libsigrok (find-files input-dir "."))) #t))))) (native-inputs - `(("doxygen" ,doxygen) - ("graphviz" ,graphviz) - ("sigrok-firmware-fx2lafw" ,sigrok-firmware-fx2lafw) - ("pkg-config" ,pkg-config))) + (list doxygen graphviz sigrok-firmware-fx2lafw pkg-config)) (inputs - `(("python" ,python) - ("zlib" ,zlib))) + (list python zlib)) ;; libsigrokcxx.pc lists "glibmm" in Requires ;; libsigrok.pc lists "libserialport", "libusb", "libftdi" and "libzip" in ;; Requires.private and "glib" in Requires (propagated-inputs - `(("glib" ,glib) - ("glibmm" ,glibmm) - ("libserialport" ,libserialport) - ("libusb" ,libusb) - ("libftdi" ,libftdi) - ("libzip" ,libzip))) + (list glib + glibmm + libserialport + libusb + libftdi + libzip)) (build-system gnu-build-system) (home-page "https://www.sigrok.org/wiki/Libsigrok") (synopsis "Library which provides the basic hardware access drivers for logic @@ -231,11 +223,9 @@ (define-public sigrok-cli (base32 "1f0a2k8qdcin0pqiqq5ni4khzsnv61l21v1dfdjzayw96qzl9l3i")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("glib" ,glib) - ("libsigrok" ,libsigrok) - ("libsigrokdecode" ,libsigrokdecode))) + (list glib libsigrok libsigrokdecode)) (build-system gnu-build-system) (home-page "https://sigrok.org/wiki/Sigrok-cli") (synopsis "Command-line frontend for sigrok") @@ -269,16 +259,15 @@ (define-public pulseview (rmdir "doc")) #t)))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("qttools" ,qttools))) + (list pkg-config qttools)) (inputs - `(("boost" ,boost) - ("glib" ,glib) - ("glibmm" ,glibmm) - ("libsigrok" ,libsigrok) - ("libsigrokdecode" ,libsigrokdecode) - ("qtbase" ,qtbase-5) - ("qtsvg" ,qtsvg))) + (list boost + glib + glibmm + libsigrok + libsigrokdecode + qtbase-5 + qtsvg)) (home-page "https://www.sigrok.org/wiki/PulseView") (synopsis "Qt based logic analyzer, oscilloscope and MSO GUI for sigrok") (description "PulseView is a Qt based logic analyzer, oscilloscope and MSO GUI @@ -319,14 +308,9 @@ (define-public xoscope "0a5ycfc1qdmibvagc82r2mhv2i99m6pndy5i6ixas3j2297g6pgq")))) (build-system gnu-build-system) (native-inputs - `(("m4" ,m4) - ("pkg-config" ,pkg-config))) + (list m4 pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("comedilib" ,comedilib) - ("fftw" ,fftw) - ("gtk+" ,gtk+) - ("gtkdatabox" ,gtkdatabox))) + (list alsa-lib comedilib fftw gtk+ gtkdatabox)) (synopsis "Digital oscilloscope") (description "Xoscope is a digital oscilloscope that can acquire signals from ALSA, ESD, and COMEDI sources. This package currently does not include diff --git a/gnu/packages/elf.scm b/gnu/packages/elf.scm index 2bc1d00048..d4f75c9726 100644 --- a/gnu/packages/elf.scm +++ b/gnu/packages/elf.scm @@ -100,8 +100,8 @@ (define-public elfutils (("run-backtrace-native.sh") "")) #t))))) - (native-inputs `(("m4" ,m4))) - (inputs `(("zlib" ,zlib))) + (native-inputs (list m4)) + (inputs (list zlib)) (home-page "https://source