aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/disk.scm
diff options
context:
space:
mode:
authorTobias Geerinckx-Rice <me@tobias.gr>2023-02-12 01:00:00 +0100
committerTobias Geerinckx-Rice <me@tobias.gr>2023-02-19 01:00:01 +0100
commit1e6ddceb8318d413745ca1c9d91fde01b1e0364b (patch)
tree4563ba325496be1950bdb302af8eb895fb5bddb8 /gnu/packages/disk.scm
parentc756c62cfdba8d4079be1ba9e370779b850f16b6 (diff)
downloadguix-1e6ddceb8318d413745ca1c9d91fde01b1e0364b.tar.gz
guix-1e6ddceb8318d413745ca1c9d91fde01b1e0364b.zip
gnu: Use HTTPS package home pages wherever possible.
* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS. * gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise. * gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]: Likewise. * gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise. * gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise. * gnu/packages/astronomy.scm (casacore, sextractor, libnova) (xplanet)[home-page]: Likewise. * gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao) (freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms) (libmodplug, libxmp, xmp, sox, drc, gsm, gnaural) (streamripper)[home-page]: Likewise. * gnu/packages/authentication.scm (pamtester)[home-page]: Likewise. * gnu/packages/backup.scm (grsync)[home-page]: Likewise. * gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma) (r-plgem)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1) (bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard) (java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools) (snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip) (libsbml)[home-page]: Likewise. * gnu/packages/build-tools.scm (tup)[home-page]: Likewise. * gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools) (cd-discid)[home-page]: Likewise. * gnu/packages/check.scm (cunit, python-nose) (python-pyhamcrest)[home-page]: Likewise. * gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise. * gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise. * gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise. * gnu/packages/compression.scm (p7zip)[home-page]: Likewise. * gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial) (r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook) (r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags) (r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm) (r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet) (r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde) (r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels) (r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom) (r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat) (r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]: Likewise. * gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13) (rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20) (rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20) (rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20) (rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise. * gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise. * gnu/packages/curl.scm (curlpp)[home-page]: Likewise. * gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger) (libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers) (soci)[home-page]: Likewise. * gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise. * gnu/packages/debug.scm (remake)[home-page]: Likewise. * gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise. * gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise. * gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise. * gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise. * gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise. * gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise. * gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise. * gnu/packages/electronics.scm (xoscope)[home-page]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu) (emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel) (emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc) (emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap) (emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+) (emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise. * gnu/packages/embedded.scm (sdcc)[home-page]: Likewise. * gnu/packages/engineering.scm (asco, libngspice, libspnav) (openctm)[home-page]: Likewise. * gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise. * gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]: Likewise. * gnu/packages/finance.scm (gbonds)[home-page]: Likewise. * gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]: Likewise. * gnu/packages/fltk.scm (ntk)[home-page]: Likewise. * gnu/packages/fonts.scm (font-terminus, font-tex-gyre) (font-comic-neue)[home-page]: Likewise. * gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]: Likewise. * gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave) (python-myhdl)[home-page]: Likewise. * gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise. * gnu/packages/ftp.scm (weex)[home-page]: Likewise. * gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc) (eureka, plib)[home-page]: Likewise. * gnu/packages/games.scm (abe, alex4, armagetronad, barony) (foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally) (cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki) (quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks) (flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise. * gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise. * gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise. * gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish) (workrave)[home-page]: Likewise. * gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise. * gnu/packages/graph.scm (mscgen)[home-page]: Likewise. * gnu/packages/graphics.scm (assimp, alembic, ctl, agg) (opencsg)[home-page]: Likewise. * gnu/packages/graphviz.scm (gts)[home-page]: Likewise. * gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise. * gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise. * gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise. * gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise. * gnu/packages/haskell-web.scm (ghc-http-client-restricted) (ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg) (ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats) (ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints) (ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon) (ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards) (ghc-template-haskell, ghc-boot-th, ghc-binary-orphans) (ghc-postgresql-simple)[home-page]: Likewise. * gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise. * gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise. * gnu/packages/image-processing.scm (mia)[home-page]: Likewise. * gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr) (qiv)[home-page]: Likewise. * gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib) (sng, mtpaint)[home-page]: Likewise. * gnu/packages/java-xml.scm (java-simple-xml, java-jaxp) (java-apache-xml-commons-resolver)[home-page]: Likewise. * gnu/packages/java.scm (java-cisd-base, java-cisd-args4j) (java-hamcrest-core, java-jsr305, java-eclipse-osgi) (java-eclipse-equinox-common, java-eclipse-core-jobs) (java-eclipse-equinox-registry, java-eclipse-equinox-app) (java-eclipse-equinox-preferences, java-eclipse-core-contenttype) (java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq) (java-cdi-api)[home-page]: Likewise. * gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise. * gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]: Likewise. * gnu/packages/kde-internet.scm (kget)[home-page]: Likewise. * gnu/packages/kde-systemtools.scm (dolphin-plugins) (konsole)[home-page]: Likewise. * gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise. * gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise. * gnu/packages/lego.scm (nqc)[home-page]: Likewise. * gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise. * gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise. * gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise. * gnu/packages/libffi.scm (libffi)[home-page]: Likewise. * gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]: Likewise. * gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise. * gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools) (kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise. * gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser) (sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore) (sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell) (sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise. * gnu/packages/lisp.scm (lush2)[home-page]: Likewise. * gnu/packages/logging.scm (log4cpp)[home-page]: Likewise. * gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise. * gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]: Likewise. * gnu/packages/mail.scm (muchsync, procmail, sendmail) (opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise. * gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise. * gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh) (metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3) (frama-c)[home-page]: Likewise. * gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]: Likewise. * gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise. * gnu/packages/monitoring.scm (python-whisper, python-carbon) (hostscope)[home-page]: Likewise. * gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321) (lame)[home-page]: Likewise. * gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise. * gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol) (portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot) (schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2) (shiru-lv2)[home-page]: Likewise. * gnu/packages/ncurses.scm (stfl)[home-page]: Likewise. * gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird) (tunctl, traceroute)[home-page]: Likewise. * gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise. * gnu/packages/ntp.scm (openntpd)[home-page]: Likewise. * gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib) (ocaml-graph, cubicle)[home-page]: Likewise. * gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise. * gnu/packages/package-management.scm (xstow, modules)[home-page]: Likewise. * gnu/packages/parallel.scm (xjobs)[home-page]: Likewise. * gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]: Likewise. * gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]: Likewise. * gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]: Likewise. * gnu/packages/plan9.scm (drawterm)[home-page]: Likewise. * gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]: Likewise. * gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise. * gnu/packages/profiling.scm (otf2)[home-page]: Likewise. * gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise. * gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise. * gnu/packages/python-web.scm (python-cssutils) (python-translationstring)[home-page]: Likewise. * gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml) (python-docutils, python-pexpect, python-importlib-resources) (python-simplegeneric, python-urwid, python-xlrd, python-xlwt) (python-pyasn1, python-pythondialog, python-tftpy, python-random2) (python-arcp, python-pyopengl, python-sortedcollections) (python-sortedcontainers, python-yapsy, python-pydispatcher) (python-posix-ipc)[home-page]: Likewise. * gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise. * gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise. * gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise. * gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise. * gnu/packages/regex.scm (tre)[home-page]: Likewise. * gnu/packages/rsync.scm (librsync)[home-page]: Likewise. * gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox) (ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise. * gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise. * gnu/packages/screen.scm (dtach)[home-page]: Likewise. * gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise. * gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise. * gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise. * gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]: Likewise. * gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise. * gnu/packages/speech.scm (espeak)[home-page]: Likewise. * gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise. * gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice) (r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable) (python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm) (r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]: Likewise. * gnu/packages/swig.scm (swig)[home-page]: Likewise. * gnu/packages/task-management.scm (wtime)[home-page]: Likewise. * gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise. * gnu/packages/terminals.scm (libtermkey, mlterm, libvterm) (libvterm)[home-page]: Likewise. * gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs) (texlive-csplain, biber, texmaker)[home-page]: Likewise. * gnu/packages/text-editors.scm (joe)[home-page]: Likewise. * gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise. * gnu/packages/tv.scm (tvtime)[home-page]: Likewise. * gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise. * gnu/packages/upnp.scm (libupnp)[home-page]: Likewise. * gnu/packages/version-control.scm (cvs)[home-page]: Likewise. * gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib) (liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl) (dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise. * gnu/packages/virtualization.scm (bochs)[home-page]: Likewise. * gnu/packages/w3m.scm (w3m)[home-page]: Likewise. * gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi) (tidy-html, htmlcxx)[home-page]: Likewise. * gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise. * gnu/packages/wv.scm (wv)[home-page]: Likewise. * gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise. * gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise. * gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise. * gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c) (opensp)[home-page]: Likewise. * gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
Diffstat (limited to 'gnu/packages/disk.scm')
-rw-r--r--gnu/packages/disk.scm6
1 files changed, 3 insertions, 3 deletions
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index f9fe9c5989..6fc69a8a63 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -527,7 +527,7 @@ and a @command{fsck.vfat} compatibility symlink for use in an initrd.")
(sha256
(base32 "1gmdxr36allrgap2j4dv238d8awkj327ww0jjwpjwrpbvfpyzjf4"))))
(build-system gnu-build-system)
- (home-page "http://sg.danny.cz/sg/sdparm.html")
+ (home-page "https://sg.danny.cz/sg/sdparm.html")
(synopsis "Provide access to SCSI device parameters")
(description
"Sdparm reads and modifies SCSI device parameters. These devices can be
@@ -562,7 +562,7 @@ and unloading removable media and some other housekeeping functions.")
(string-append "manprefix=")
(string-append "DESTDIR="
(assoc-ref %outputs "out")))))
- (home-page "http://idle3-tools.sourceforge.net")
+ (home-page "https://idle3-tools.sourceforge.net")
(synopsis "Change or disable Western Digital hard drives' Idle3 timer")
(description
"Idle3-tools provides a utility to get, set, or disable the Idle3 timer
@@ -1448,7 +1448,7 @@ reliably with @code{bmaptool} than with traditional tools, like @code{dd} or
(list autoconf automake libtool pkg-config))
(inputs
(list cairo pango tokyocabinet ncurses))
- (home-page "http://duc.zevv.nl")
+ (home-page "https://duc.zevv.nl")
(synopsis "Library and suite of tools for inspecting disk usage")
(description "Duc maintains a database of accumulated sizes of
directories of the file system, and allows you to query this database with
ref='/guix/diff/gnu/packages/music.scm?id=72e886328c14c832b2ed71c400069b63852ee18d'>gnu/packages/music.scm15
-rw-r--r--gnu/packages/parallel.scm4
-rw-r--r--gnu/packages/password-utils.scm5
-rw-r--r--gnu/packages/patches/hplip-usb-timeout.patch24
-rw-r--r--gnu/packages/patches/online-judge-tools.patch62
-rw-r--r--gnu/packages/patches/python-online-judge-api-client-tests.patch429
-rw-r--r--gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch97
-rw-r--r--gnu/packages/patches/python-pycrypto-time-clock.patch23
-rw-r--r--gnu/packages/pdf.scm10
-rw-r--r--gnu/packages/python-check.scm20
-rw-r--r--gnu/packages/python-science.scm31
-rw-r--r--gnu/packages/python-xyz.scm224
-rw-r--r--gnu/packages/radio.scm4
-rw-r--r--gnu/packages/rust-apps.scm58
-rw-r--r--gnu/packages/sdl.scm27
-rw-r--r--gnu/packages/sphinx.scm46
-rw-r--r--gnu/packages/statistics.scm105
-rw-r--r--gnu/packages/syncthing.scm4
-rw-r--r--gnu/packages/telephony.scm6
-rw-r--r--gnu/packages/terminals.scm42
-rw-r--r--gnu/packages/tls.scm15
-rw-r--r--gnu/packages/tor.scm4
-rw-r--r--gnu/packages/upnp.scm56
-rw-r--r--gnu/packages/video.scm75
-rw-r--r--gnu/packages/vim.scm4
-rw-r--r--gnu/packages/web-browsers.scm4
-rw-r--r--gnu/packages/web.scm35
-rw-r--r--gnu/packages/wine.scm5
-rw-r--r--gnu/packages/wm.scm9
-rw-r--r--gnu/services/admin.scm24
-rw-r--r--gnu/system/file-systems.scm2
-rw-r--r--gnu/system/vm.scm6
-rw-r--r--guix/build-system/go.scm11
-rw-r--r--guix/build-system/r.scm2
-rw-r--r--guix/channels.scm3
-rw-r--r--guix/grafts.scm43
-rw-r--r--guix/import/cran.scm4
-rw-r--r--guix/packages.scm7
-rw-r--r--guix/profiles.scm49
-rw-r--r--guix/scripts/environment.scm35
-rw-r--r--guix/utils.scm7
-rw-r--r--po/doc/guix-cookbook.de.po3901
-rw-r--r--po/doc/guix-cookbook.fr.po3120
-rw-r--r--po/doc/guix-manual.de.po30903
-rw-r--r--po/doc/guix-manual.fr.po30786
-rw-r--r--po/doc/guix-manual.zh_CN.po31747
-rw-r--r--po/guix/es.po11
-rw-r--r--po/guix/it.po13
-rw-r--r--po/guix/zh_CN.po82
-rw-r--r--po/packages/zh_CN.po15
-rw-r--r--tests/grafts.scm50
-rw-r--r--tests/guix-environment-container.sh2
-rw-r--r--tests/guix-pack.sh4
-rw-r--r--tests/profiles.scm24
-rw-r--r--tests/transformations.scm5
101 files changed, 59900 insertions, 49795 deletions
diff --git a/doc/contributing.texi b/doc/contributing.texi
index ac7f8d2e0f..30876447d4 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -1666,7 +1666,7 @@ relies on the @file{etc/teams.scm} script, which can also be invoked
manually if you do not use the preferred @command{git send-email}
command to submit patches. To list the available actions of the script,
you can invoke it via the @command{etc/teams.scm help} command. For
-more information regarding teams, see @xref{Teams}.
+more information regarding teams, @pxref{Teams}.
@unnumberedsubsubsec Multiple Patches
@anchor{Multiple Patches}
diff --git a/doc/guix-cookbook.texi b/doc/guix-cookbook.texi
index 712c131a51..3d86fca396 100644
--- a/doc/guix-cookbook.texi
+++ b/doc/guix-cookbook.texi
@@ -3714,7 +3714,7 @@ reference.
@section Guix Profiles in Practice
Guix provides a very useful feature that may be quite foreign to newcomers:
-@emph{profiles}. They are a way to group package installations together and all users
+@dfn{profiles}. They are a way to group package installations together and all users
on the same system are free to use as many profiles as they want.
Whether you're a developer or not, you may find that multiple profiles bring you
@@ -3722,6 +3722,16 @@ great power and flexibility. While they shift the paradigm somewhat compared to
@emph{traditional package managers}, they are very convenient to use once you've
understood how to set them up.
+@quotation Note
+This section is an opinionated guide on the use of multiple profiles.
+It predates @command{guix shell} and its fast profile cache
+(@pxref{Invoking guix shell,,, guix, GNU Guix Reference Manual}).
+
+In many cases, you may find that using @command{guix shell} to set up
+the environment you need, when you need it, is less work that
+maintaining a dedicated profile. Your call!
+@end quotation
+
If you are familiar with Python's @samp{virtualenv}, you can think of a profile as a
kind of universal @samp{virtualenv} that can hold any kind of software whatsoever, not
just Python software. Furthermore, profiles are self-sufficient: they capture
@@ -3977,7 +3987,9 @@ without having to specify the path to a profile.
@node The benefits of manifests
@subsection The benefits of manifests
-Manifests are a convenient way to keep your package lists around and, say,
+Manifests let you @dfn{declare} the set of packages you'd like to have
+in a profile (@pxref{Writing Manifests,,, guix, GNU Guix Reference Manual}).
+They are a convenient way to keep your package lists around and, say,
to synchronize them across multiple machines using a version control system.
A common complaint about manifests is that they can be slow to install when they
@@ -4034,29 +4046,12 @@ profiles, they are not strictly equivalent: profiles have the side effect that
they ``pin'' packages in the store, which prevents them from being
garbage-collected (@pxref{Invoking guix gc,,, guix, GNU Guix Reference Manual})
and ensures that they will still be available at any point in
-the future.
-
-Let's take an example:
-
-@enumerate
-@item
-We have an environment for hacking on a project for which there isn't a Guix
-package yet. We build the environment using a manifest, and then run @code{guix
- environment -m manifest.scm}. So far so good.
+the future. The @command{guix shell} command also protects
+recently-used profiles from garbage collection; profiles that have not
+been used for a while may be garbage-collected though, along with the
+packages they refer to.
-@item
-Many weeks pass and we have run a couple of @code{guix pull} in the mean time.
-Maybe a dependency from our manifest has been updated; or we may have run
-@code{guix gc} and some packages needed by our manifest have been
-garbage-collected.
-
-@item
-Eventually, we set to work on that project again, so we run @code{guix shell
- -m manifest.scm}. But now we have to wait for Guix to build and install
-stuff!
-@end enumerate
-
-Ideally, we could spare the rebuild time. And indeed we can, all we need is to
+To be 100% sure that a given profile will never be collected,
install the manifest to a profile and use @code{GUIX_PROFILE=/the/profile;
. "$GUIX_PROFILE"/etc/profile} as explained above: this guarantees that our
hacking environment will be available at all times.
@@ -4071,16 +4066,18 @@ To reproduce a profile bit-for-bit, we need two pieces of information:
@itemize
@item
-a manifest,
+a manifest (@pxref{Writing Manifests,,, guix, GNU Guix Reference Manual});
@item
-a Guix channel specification.
+a Guix channel specification (@pxref{Replicating Guix,,, guix, GNU Guix
+Reference Manual}).
@end itemize
Indeed, manifests alone might not be enough: different Guix versions (or
different channels) can produce different outputs for a given manifest.
You can output the Guix channel specification with @samp{guix describe
---format=channels}.
+--format=channels} (@pxref{Invoking guix describe,,, guix, GNU Guix
+Reference Manual}).
Save this to a file, say @samp{channel-specs.scm}.
On another computer, you can use the channel specification file and the manifest
@@ -4331,7 +4328,7 @@ guix build -f guix.scm --target=x86_64-w64-mingw32
@end lisp
You can also use @dfn{package transformations} to test package variants
-(@pxref{Package Transformations,,, guix, GNU Guix Reference Manual}):
+(@pxref{Package Transformation Options,,, guix, GNU Guix Reference Manual}):
@example
# What if we built with Clang instead of GCC?
diff --git a/doc/guix.texi b/doc/guix.texi
index c67404a007..61892866af 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -185,7 +185,6 @@ Weblate} (@pxref{Translating Guix}).
* Introduction:: What is Guix about?
* Installation:: Installing Guix.
* System Installation:: Installing the whole operating system.
-* System Troubleshooting Tips:: When things don't go as planned.
* Getting Started:: Your first steps.
* Package Management:: Package installation, upgrade, etc.
* Channels:: Customizing the package collection.
@@ -194,6 +193,7 @@ Weblate} (@pxref{Translating Guix}).
* Utilities:: Package management commands.
* Foreign Architectures:: Build for foreign architectures.
* System Configuration:: Configuring the operating system.
+* System Troubleshooting Tips:: When things don't go as planned.
* Home Configuration:: Configuring the home environment.
* Documentation:: Browsing software user manuals.
* Platforms:: Defining platforms.
@@ -251,10 +251,6 @@ Manual Installation
* Keyboard Layout and Networking and Partitioning:: Initial setup.
* Proceeding with the Installation:: Installing.
-System Troubleshooting Tips
-
-* Chrooting into an existing system::
-
Package Management
* Features:: How Guix will make your life brighter.
@@ -427,6 +423,10 @@ Defining Services
* Shepherd Services:: A particular type of service.
* Complex Configurations:: Defining bindings for complex configurations.
+System Troubleshooting Tips
+
+* Chrooting into an existing system::
+
Home Configuration
* Declaring the Home Environment:: Customizing your Home.
@@ -2978,123 +2978,6 @@ guix system image --system=armhf-linux -e '((@@ (gnu system install) os-with-u-b
@code{A20-OLinuXino-Lime2} is the name of the board. If you specify an invalid
board, a list of possible boards will be printed.
-@c *********************************************************************
-@cindex troubleshooting, guix system
-@cindex guix system troubleshooting
-@node System Troubleshooting Tips
-@chapter System Troubleshooting Tips
-
-Guix System allows rebooting into a previous generation should the last
-one be malfunctioning, which makes it quite robust against being broken
-irreversibly. This feature depends on GRUB being correctly functioning
-though, which means that if for whatever reasons your GRUB installation
-becomes corrupted during a system reconfiguration, you may not be able
-to easily boot into a previous generation. A technique that can be used
-in this case is to @i{chroot} into your broken system and reconfigure it
-from there. Such technique is explained below.
-
-@cindex chroot, guix system
-@cindex chrooting, guix system
-@cindex repairing GRUB, via chroot
-@menu
-* Chrooting into an existing system::
-@end menu
-
-@node Chrooting into an existing system
-@section Chrooting into an existing system
-
-This section details how to @i{chroot} to an already installed Guix
-System with the aim of reconfiguring it, for example to fix a broken
-GRUB installation. The process is similar to how it would be done on
-other GNU/Linux systems, but there are some Guix System particularities
-such as the daemon and profiles that make it worthy of explaining here.
-
-@enumerate
-@item
-Obtain a bootable image of Guix System. It is recommended the latest
-development snapshot so the kernel and the tools used are at least as as
-new as those of your installed system; it can be retrieved from the
-@url{https://ci.guix.gnu.org/search/latest/ISO-9660?query=spec:images+status:success+system:x86_64-linux+image.iso,
-https://ci.guix.gnu.org} URL. Follow the @pxref{USB Stick and DVD
-Installation} section for copying it to a bootable media.
-
-@item
-Boot the image, and proceed with the graphical text-based installer
-until your network is configured. Alternatively, you could configure
-the network manually by following the
-@ref{manual-installation-networking} section. If you get the error
-@samp{RTNETLINK answers: Operation not possible due to RF-kill}, try
-@samp{rfkill list} followed by @samp{rfkill unblock 0}, where @samp{0}
-is your device identifier (ID).
-
-@item
-Switch to a virtual console (tty) if you haven't already by pressing
-simultaneously the @kbd{Control + Alt + F4} keys. Mount your file
-system at @file{/mnt}. Assuming your root partition is
-@file{/dev/sda2}, you would do:
-
-@example sh
-mount /dev/sda2 /mnt
-@end example
-
-@item
-Mount special block devices and Linux-specific directories:
-
-@example sh
-mount --rbind /proc /mnt/proc
-mount --rbind /sys /mnt/sys
-mount --rbind /dev /mnt/dev
-@end example
-
-If your system is EFI-based, you must also mount the ESP partition.
-Assuming it is @file{/dev/sda1}, you can do so with:
-
-@example sh
-mount /dev/sda1 /mnt/boot/efi
-@end example
-
-@item
-Enter your system via chroot:
-
-@example sh
-chroot /mnt /bin/sh
-@end example
-
-@item
-Source the system profile as well as your @var{user} profile to setup
-the environment, where @var{user} is the user name used for the Guix
-System you are attempting to repair:
-
-@example sh
-source /var/guix/profiles/system/profile/etc/profile
-source /home/@var{user}/.guix-profile/etc/profile
-@end example
-
-To ensure you are working with the Guix revision you normally would as
-your normal user, also source your current Guix profile:
-
-@example sh
-source /home/@var{user}/.config/guix/current/etc/profile
-@end example
-
-@item
-Start a minimal @command{guix-daemon} in the background:
-
-@example sh
-guix-daemon --build-users-group=guixbuild --disable-chroot &
-@end example
-
-@item
-Edit your Guix System configuration if needed, then reconfigure with:
-
-@example sh
-guix system reconfigure your-config.scm
-@end example
-
-@item
-Finally, you should be good to reboot the system to test your fix.
-
-@end enumerate
@c *********************************************************************
@node Getting Started
@@ -3191,6 +3074,10 @@ deleting old generations, collecting garbage, and other nifty features
that will come in handy as you become more familiar with Guix. If you
are a developer, @pxref{Development} for additional tools. And if
you're curious, @pxref{Features}, to peek under the hood.
+
+You can also manage the configuration of your entire @dfn{home
+environment}---your user ``dot files'', services, and packages---using
+Guix Home. @xref{Home Configuration}, to learn more about it!
@end quotation
Once you've installed a set of packages, you will want to periodically
@@ -43148,6 +43035,124 @@ is-married = true
@end example
+@c *********************************************************************
+@cindex troubleshooting, Guix System
+@cindex guix system troubleshooting
+@node System Troubleshooting Tips
+@chapter System Troubleshooting Tips
+
+Guix System allows rebooting into a previous generation should the last
+one be malfunctioning, which makes it quite robust against being broken
+irreversibly. This feature depends on GRUB being correctly functioning
+though, which means that if for whatever reasons your GRUB installation
+becomes corrupted during a system reconfiguration, you may not be able
+to easily boot into a previous generation. A technique that can be used
+in this case is to @i{chroot} into your broken system and reconfigure it
+from there. Such technique is explained below.
+
+@cindex chroot, guix system
+@cindex chrooting, guix system
+@cindex repairing GRUB, via chroot
+@menu
+* Chrooting into an existing system::
+@end menu
+
+@node Chrooting into an existing system
+@section Chrooting into an existing system
+
+This section details how to @i{chroot} to an already installed Guix
+System with the aim of reconfiguring it, for example to fix a broken
+GRUB installation. The process is similar to how it would be done on
+other GNU/Linux systems, but there are some Guix System particularities
+such as the daemon and profiles that make it worthy of explaining here.
+
+@enumerate
+@item
+Obtain a bootable image of Guix System. It is recommended the latest
+development snapshot so the kernel and the tools used are at least as as
+new as those of your installed system; it can be retrieved from the
+@url{https://ci.guix.gnu.org/search/latest/ISO-9660?query=spec:images+status:success+system:x86_64-linux+image.iso,
+https://ci.guix.gnu.org} URL. Follow the @pxref{USB Stick and DVD
+Installation} section for copying it to a bootable media.
+
+@item
+Boot the image, and proceed with the graphical text-based installer
+until your network is configured. Alternatively, you could configure
+the network manually by following the
+@ref{manual-installation-networking} section. If you get the error
+@samp{RTNETLINK answers: Operation not possible due to RF-kill}, try
+@samp{rfkill list} followed by @samp{rfkill unblock 0}, where @samp{0}
+is your device identifier (ID).
+
+@item
+Switch to a virtual console (tty) if you haven't already by pressing
+simultaneously the @kbd{Control + Alt + F4} keys. Mount your file
+system at @file{/mnt}. Assuming your root partition is
+@file{/dev/sda2}, you would do:
+
+@example sh
+mount /dev/sda2 /mnt
+@end example
+
+@item
+Mount special block devices and Linux-specific directories:
+
+@example sh
+mount --rbind /proc /mnt/proc
+mount --rbind /sys /mnt/sys
+mount --rbind /dev /mnt/dev
+@end example
+
+If your system is EFI-based, you must also mount the ESP partition.
+Assuming it is @file{/dev/sda1}, you can do so with:
+
+@example sh
+mount /dev/sda1 /mnt/boot/efi
+@end example
+
+@item
+Enter your system via chroot:
+
+@example sh
+chroot /mnt /bin/sh
+@end example
+
+@item
+Source the system profile as well as your @var{user} profile to setup
+the environment, where @var{user} is the user name used for the Guix
+System you are attempting to repair:
+
+@example sh
+source /var/guix/profiles/system/profile/etc/profile
+source /home/@var{user}/.guix-profile/etc/profile
+@end example
+
+To ensure you are working with the Guix revision you normally would as
+your normal user, also source your current Guix profile:
+
+@example sh
+source /home/@var{user}/.config/guix/current/etc/profile
+@end example
+
+@item
+Start a minimal @command{guix-daemon} in the background:
+
+@example sh
+guix-daemon --build-users-group=guixbuild --disable-chroot &
+@end example
+
+@item
+Edit your Guix System configuration if needed, then reconfigure with:
+
+@example sh
+guix system reconfigure your-config.scm
+@end example
+
+@item
+Finally, you should be good to reboot the system to test your fix.
+
+@end enumerate
+
@node Home Configuration
@chapter Home Configuration
@cindex home configuration
@@ -43163,12 +43168,6 @@ command (@pxref{Invoking guix home}).
@c Maybe later, it will be possible to make home configuration a part of
@c system configuration to make everything managed by guix system.
-@quotation Note
-The functionality described in this section is still under development
-and is subject to change. Get in touch with us on
-@email{guix-devel@@gnu.org}!
-@end quotation
-
The user's home environment usually consists of three basic parts:
software, configuration, and state. Software in mainstream distros are
usually installed system-wide, but with GNU Guix most software packages
diff --git a/etc/teams.scm b/etc/teams.scm
index f3d4c73132..2f920a5876 100755
--- a/etc/teams.scm
+++ b/etc/teams.scm
@@ -1,4 +1,5 @@
#!/bin/sh
+# -*- mode: scheme; -*-
# Extra care is taken here to ensure this script can run in most environments,
# since it is invoked by 'git send-email'.
pre_inst_env_maybe=
@@ -522,6 +523,12 @@ GLib/GIO, GTK, GStreamer and Webkit."
#:scope (list "gnu/packages/lxqt.scm"
"gnu/packages/qt.scm")))
+(define-team audio
+ (team 'audio
+ #:name "Audio team"
+ #:description "Audio related packages."
+ #:scope (list "gnu/packages/audio.scm")))
+
(define-member (person "Eric Bavier"
"bavier@posteo.net")
@@ -651,6 +658,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
"me@bonfacemunyoki.com")
python lisp)
+(define-member (person "Gabriel Wicki"
+ "gabriel@erlikon.ch")
+ audio)
+
(define (find-team name)
(or (hash-ref %teams (string->symbol name))
diff --git a/gnu/bootloader.scm b/gnu/bootloader.scm
index 2c36d8c6cf..ba06de7618 100644
--- a/gnu/bootloader.scm
+++ b/gnu/bootloader.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2017 David Craven <david@craven.ch>
;;; Copyright © 2017, 2020, 2022 Mathieu Othacehe <othacehe@gnu.org>
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2019, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2021, 2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2022 Josselin Poiret <dev@jpoiret.xyz>
;;; Copyright © 2022 Reza Alizadeh Majd <r.majd@pantherx.org>
@@ -335,7 +335,7 @@ FILES may contain file like objects produced by procedures like plain-file,
local-file, etc., or package contents produced with file-append.
HOOKS lists additional hook functions to modify the profile."
- (define (efi-bootloader-profile-hook manifest)
+ (define* (efi-bootloader-profile-hook manifest #:optional system)
(define build
(with-imported-modules '((guix build utils))
#~(begin
@@ -383,6 +383,7 @@ HOOKS lists additional hook functions to modify the profile."
(gexp->derivation "efi-bootloader-profile"
build
+ #:system system
#:local-build? #t
#:substitutable? #f
#:properties
diff --git a/gnu/home/services.scm b/gnu/home/services.scm
index 282fed74c1..44f585aff5 100644
--- a/gnu/home/services.scm
+++ b/gnu/home/services.scm
@@ -435,7 +435,10 @@ activation.")))
;; after complete logout/reboot.
(if (file-exists? xdg-runtime-dir)
(when (claim-first-run flag-file-path)
- (begin #$@gexps)) ;GEXPS can be empty, hence 'begin'
+ ;; GEXPS can be empty, hence 'begin *unspecified*'. Having just
+ ;; 'begin' without '*unspecified*' leads to
+ ;; "Syntax error: ... sequence of zero expressions in form (begin)"
+ (begin *unspecified* #$@gexps))
;; TRANSLATORS: 'on-first-login' is the name of a service and
;; shouldn't be translated
(warning (G_ "XDG_RUNTIME_DIR doesn't exists, on-first-login script
diff --git a/gnu/local.mk b/gnu/local.mk
index 27ff79f0f6..254804d055 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -61,6 +61,7 @@
# Copyright © 2023 Andy Tai <atai@atai.org>
# Copyright © 2023 B. Wilson <elaexuotee@wilsonb.com>
# Copyright © 2023 Bruno Victal <mirai@makinata.eu>
+# Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
#
# This file is part of GNU Guix.
#
@@ -1409,6 +1410,7 @@ dist_patch_DATA = \
%D%/packages/patches/heimdal-CVE-2022-45142.patch \
%D%/packages/patches/helm-fix-gcc-9-build.patch \
%D%/packages/patches/highlight-gui-data-dir.patch \
+ %D%/packages/patches/hplip-usb-timeout.patch \
%D%/packages/patches/http-parser-CVE-2020-8287.patch \
%D%/packages/patches/htslib-for-stringtie.patch \
%D%/packages/patches/hubbub-sort-entities.patch \
@@ -1710,6 +1712,7 @@ dist_patch_DATA = \
%D%/packages/patches/omake-fix-non-determinism.patch \
%D%/packages/patches/oneko-remove-nonfree-characters.patch \
%D%/packages/patches/onionshare-cli-async-mode.patch \
+ %D%/packages/patches/online-judge-tools.patch \
%D%/packages/patches/onnx-optimizer-system-library.patch \
%D%/packages/patches/onnx-use-system-googletest.patch \
%D%/packages/patches/onnx-shared-libraries.patch \
@@ -1869,6 +1872,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-fixtures-remove-monkeypatch-test.patch \
%D%/packages/patches/python-hiredis-fix-header.patch \
%D%/packages/patches/python-hiredis-use-system-hiredis.patch \
+ %D%/packages/patches/python-online-judge-api-client-tests.patch \
%D%/packages/patches/python-pdoc3-tests.patch \
%D%/packages/patches/python-peachpy-determinism.patch \
%D%/packages/patches/python-pep8-stdlib-tokenize-compat.patch \
@@ -1882,8 +1886,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-parso-unit-tests-in-3.10.patch \
%D%/packages/patches/python-packaging-test-arch.patch \
%D%/packages/patches/python-paste-remove-timing-test.patch \
- %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \
- %D%/packages/patches/python-pycrypto-time-clock.patch \
%D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \
%D%/packages/patches/python-pyan3-fix-positional-arguments.patch \
%D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 8f72b0eeae..afbcf7fda6 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -406,7 +406,7 @@ interface and is based on GNU Guile.")
(define-public swineherd
(package
(name "swineherd")
- (version "0.0.1")
+ (version "0.0.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -415,7 +415,7 @@ interface and is based on GNU Guile.")
(file-name (git-file-name name version))
(sha256
(base32
- "18nk0sy5s0dm2rhxnrrn8g0m098b110mxnnxa2vnl1dnvfdzszw8"))))
+ "0il1ikaj478n7xs4vqgawbshvmwq3nd0gp235mwqvmf4knra6j3g"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--localstatedir=/var")
@@ -2835,13 +2835,13 @@ specified directories.")
(define-public ansible-core
(package
(name "ansible-core")
- (version "2.14.4")
+ (version "2.15.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ansible-core" version))
(sha256
- (base32 "057g87smxcn6zc558xk4zr6ga4q8clmkyxghn5gx60a94sy61clh"))))
+ (base32 "00hnwjk4dxgxbz4xlza2wqx20yks5xr7074hzlzsyja3ip5kkicc"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build python-build-system)
@@ -2911,14 +2911,6 @@ test_context)" all)
(when tests?
;; Otherwise Ansible fails to create its config directory.
(setenv "HOME" "/tmp")
- ;; This test module messes up with sys.path and causes many
- ;; test failures.
- (delete-file "test/units/_vendor/test_vendor.py")
- ;; The test fails when run in the container, for reasons
- ;; unknown.
- (delete-file "test/units/utils/test_display.py")
- ;; This test fail for reasons unknown.
- (delete-file "test/units/cli/test_adhoc.py")
;; These tests fail in the container; it appears that the
;; mocking of the absolute file names such as /usr/bin/svcs do
;; not work as intended there.
@@ -2933,7 +2925,7 @@ test_command_nonexisting.py")
;; does some extra environment setup. Taken from
;; https://raw.githubusercontent.com/ansible/ansible/\
;; devel/test/utils/shippable/shippable.sh.
- (invoke "ansible-test" "units" "-v"
+ (invoke "./bin/ansible-test" "units" "-v"
"--num-workers" (number->string
(parallel-job-count)))))))))
(native-inputs
@@ -2954,7 +2946,7 @@ test_command_nonexisting.py")
python-jinja2
python-pyyaml
python-packaging ;for version number parsing
- python-resolvelib-0.5))
+ python-resolvelib))
(home-page "https://www.ansible.com/")
(synopsis "Radically simple IT automation")
(description "Ansible aims to be a radically simple IT automation system.
@@ -2981,13 +2973,13 @@ provides the following commands:
(define-public ansible
(package
(name "ansible")
- (version "7.4.0")
+ (version "8.5.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ansible" version))
(sha256
- (base32 "142barhwz0wx5kn74xi0bfl21iwq2yq3jp14kxajsg9nggndcr09"))))
+ (base32 "0bazj5h12wraf30bb2schzwk553y20n9vh45km4b5kgmvadm0z1j"))))
(build-system python-build-system)
(propagated-inputs (list ansible-core))
;; The Ansible collections are found by ansible-core via the Python search
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index c061184aee..c0fe75ddfd 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -936,7 +936,7 @@ algorithms from the FORTRAN library MINPACK.")
(define-public symengine
(package
(name "symengine")
- (version "0.10.1")
+ (version "0.11.1")
(source
(origin
(method git-fetch)
@@ -945,7 +945,7 @@ algorithms from the FORTRAN library MINPACK.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0qy5w5msq0zy7drbhdy0vx451zglha8jm5s4zzmvmsja5yyv8fx9"))))
+ (base32 "105rnnf33vx2n03wwv4962az7bfzgsn1gx6a6wyakmyrfdkb07jc"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 764a674a6d..908c3ada3a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -493,6 +493,60 @@ in FITS files.")
(license (license:non-copyleft "file://License.txt"
"See License.txt in the distribution."))))
+(define-public python-aplpy
+ (package
+ (name "python-aplpy")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "aplpy" version))
+ (sha256
+ (base32 "0ph9jhv4q4i4z6nkqr6hjw9148kdlnayxsn83qgv5dqn0h3nc9r8"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-astropy
+ python-matplotlib
+ python-numpy
+ python-pillow
+ python-pyavm
+ python-pyregion
+ python-reproject
+ python-scikit-image
+ python-shapely))
+ (native-inputs
+ (list python-pytest-astropy
+ python-pytest-mpl
+ python-semantic-version))
+ (home-page "http://aplpy.github.io")
+ (synopsis "Astronomical Plotting Library in Python")
+ (description
+ "@acronym{APLpy, the Astronomical Plotting Library in Python} is a Python
+module aimed at producing publication-quality plots of astronomical imaging data
+in FITS format. The module uses @code{matplotlib}, a powerful and interactive
+plotting package. It is capable of creating output files in several graphical
+formats, including EPS, PDF, PS, PNG, and SVG.
+
+Main features:
+@itemize
+@item Make plots interactively or using scripts
+@item Show grayscale, colorscale, and 3-color RGB images of FITS files
+@item Generate co-aligned FITS cubes to make 3-color RGB images
+@item Make plots from FITS files with arbitrary WCS (e.g. position-velocity)
+@item Slice multi-dimensional FITS cubes
+@item Overlay any number of contour sets
+@item Overlay markers with fully customizable symbols
+@item Plot customizable shapes like circles, ellipses, and rectangles
+@item Overlay ds9 region files
+@item Overlay coordinate grids
+@item Show colorbars, scalebars, and beams
+@item Customize the appearance of labels and ticks
+@item Hide, show, and remove different contour and marker layers
+@item Pan, zoom, and save any view as a full publication-quality plot
+@item Save plots as EPS, PDF, PS, PNG, and SVG
+@end itemize")
+ (license license:expat)))
+
(define-public python-astroml
(package
(name "python-astroml")
@@ -2166,6 +2220,29 @@ cases for which diffractive rather than geometric optics is the topic of
interest, and which require portability between platforms or ease of scripting.")
(license license:bsd-3)))
+(define-public python-pyavm
+ (package
+ (name "python-pyavm")
+ (version "0.9.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "PyAVM" version))
+ (sha256
+ (base32 "0vgjqvddq4a5lnmg8msm7fwqs3r6fc748xzvnhyvc387h0z8pdxk"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-astropy python-numpy))
+ (native-inputs
+ (list python-pillow python-pytest python-setuptools-scm))
+ (home-page "https://astrofrog.github.io/pyavm/")
+ (synopsis "Simple pure-python AVM meta-data handling")
+ (description
+ "PyAVM is a module to represent, read, and write metadata following the
+@acronym{AVM, Astronomy Visualization Metadata} standard provided by
+@url{https://www.virtualastronomy.org/avm_metadata.php, vamp} project.")
+ (license license:expat)))
+
(define-public python-pyvo
(package
(name "python-pyvo")
@@ -2455,6 +2532,60 @@ positions of the sun: dawn, sunrise, solar noon, sunset, dusk, solar
elevation, solar azimuth, rahukaalam, and the phases of the moon.")
(license license:asl2.0)))
+(define-public python-spectral-cube
+ (package
+ (name "python-spectral-cube")
+ (version "0.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "spectral-cube" version))
+ (sha256
+ (base32 "10q76rsgf9w4j7y68mfa870bpxf06m6kqvivj4340jmgnsrfy1zg"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-astropy
+ python-aplpy
+ python-casa-formats-io
+ python-dask
+ python-distributed
+ python-fsspec
+ ;; python-glue-core ; Not packed http://glueviz.org/, optional.
+ python-joblib
+ python-matplotlib
+ python-numpy
+ python-radio-beam
+ python-reproject
+ python-scipy
+ python-six
+ ;; python-yt ; Not packed https://yt-project.org/, optional.
+ python-zarr))
+ (native-inputs
+ (list ;; XXX: Introduce cycle with pvextractor, listed as extra requiremnts
+ ;; in [noviz] option.
+ ;; python-pvextractor
+ python-pytest-astropy
+ python-regions
+ python-semantic-version
+ python-setuptools-scm))
+ (home-page "https://spectral-cube.readthedocs.io/en/latest/")
+ (synopsis "Library for reading and analyzing astrophysical spectral data cubes")
+ (description
+ "The spectral-cube package provides an easy way to read, manipulate,
+analyze, and write data cubes with two positional dimensions and one spectral
+dimension, optionally with Stokes parameters.
+
+It provides the following main features:
+@itemize
+@item A uniform interface to spectral cubes, robust to the wide range of conventions
+of axis order, spatial projections, and spectral units that exist in the wild.
+@item Easy extraction of cube sub-regions using physical coordinates.
+@item Ability to easily create, combine, and apply masks to datasets.
+@item Basic summary statistic methods like moments and array aggregates.
+@item Designed to work with datasets too large to load into memory.
+@end itemize")
+ (license license:bsd-3)))
+
(define-public python-spherical-geometry
(package
(name "python-spherical-geometry")
@@ -3471,6 +3602,46 @@ astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
N-Chilada and RAMSES AMR outputs.")
(license license:gpl3+)))
+(define-public python-pyregion
+ (package
+ (name "python-pyregion")
+ (version "2.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyregion" version))
+ (sha256
+ (base32 "0l7qb7r8fnv46mdih4m5b8jaxixgpw6m7v37dpikjkblgh0vigaw"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (propagated-inputs
+ (list python-astropy python-numpy python-pyparsing))
+ (native-inputs
+ (list python-cython
+ python-pytest
+ python-pytest-astropy-header
+ python-setuptools-scm))
+ (home-page "https://github.com/astropy/pyregion")
+ (synopsis "Python parser for ds9 region files")
+ (description
+ "@code{pyregion} is a python module to parse ds9 region files. It also
+supports ciao region files.
+Features:
+@itemize
+@item ds9 and ciao region files.
+@item (physical, WCS) coordinate conversion to the image coordinate.
+@item convert regions to matplotlib patches.
+@item convert regions to spatial filter (i.e., generate mask images)
+@end itemize")
+ (license license:expat)))
+
(define-public python-pysynphot
(package
(name "python-pysynphot")
@@ -3955,6 +4126,40 @@ format, which are used by ASDF to serialize and deserialize data for the Nancy
Grace Roman Space Telescope.")
(license license:bsd-3)))
+(define-public python-radio-beam
+ (package
+ (name "python-radio-beam")
+ (version "0.3.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "radio-beam" version))
+ (sha256
+ (base32 "19c6gmm1wvyp5nn1yfbzl428rkysdq273j2yaarxpivv7cwj7qjk"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-astropy
+ python-matplotlib
+ python-numpy
+ python-scipy
+ python-six))
+ (native-inputs (list python-pytest-astropy python-setuptools-scm))
+ (home-page "https://radio-beam.readthedocs.io/en/latest/")
+ (synopsis "Operations for radio astronomy beams with Astropy")
+ (description
+ "Radio Beam is a simple toolkit for reading beam information from FITS
+headers and manipulating beams.
+Some example applications include:
+@itemize
+@item Convolution and deconvolution
+@item Unit conversion (Jy to/from K)
+@item Handle sets of beams for spectral cubes with varying resolution between
+channels
+@item Find the smallest common beam from a set of beams
+@item Add the beam shape to a matplotlib plot
+@end itemize")
+ (license license:bsd-3)))
+
(define-public python-roman-datamodels
(package
(name "python-roman-datamodels")
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3ff0b1127..b15a856fb9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -68,6 +68,59 @@
;;; Annotations
+(define-public r-hpo-db
+ (package
+ (name "r-hpo-db")
+ (version "0.99.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HPO.db" version
+ 'annotation))
+ (sha256
+ (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was"))))
+ (properties `((upstream-name . "HPO.db")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'avoid-internet-access
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((cache (string-append #$output "/share/HPO.db/cache"))
+ (file (string-append cache "/118333")))
+ (mkdir-p cache)
+ (copy-file #$(this-package-native-input "HPO.sqlite") file)
+ (substitute* "R/zzz.R"
+ (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
+ (string-append
+ "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
+ (("dbfile <- ah.*" m)
+ (string-append
+ "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
+ file "\";} else { " m " }\n")))))))))
+ (propagated-inputs
+ (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("HPO.sqlite"
+ ,(origin
+ (method url-fetch)
+ (uri "https://annotationhub.bioconductor.org/fetch/118333")
+ (file-name "HPO.sqlite")
+ (sha256
+ (base32 "1wwdwf27iil0p41183qgygh2ifphhmlljjkgjm2h8sr25qycf0md"))))))
+ (home-page "https://bioconductor.org/packages/HPO.db")
+ (synopsis
+ "Annotation maps describing the entire Human Phenotype Ontology")
+ (description
+ "Human Phenotype Ontology (HPO) was developed to create a consistent
+description of gene products with disease perspectives, and is essential for
+supporting functional genomics in disease context. Accurate disease
+descriptions can discover new relationships between genes and disease, and new
+functions for previous uncharacteried genes and alleles.")
+ (license license:artistic2.0)))
+
(define-public r-mafh5-gnomad-v3-1-2-grch38
(package
(name "r-mafh5-gnomad-v3-1-2-grch38")
@@ -98,6 +151,65 @@ It retrieves this data from the Genome Aggregation Database
(@code{gnomAD} version 3.1.2) for the human genome version GRCh38.")
(license license:artistic2.0)))
+(define-public r-mpo-db
+ (package
+ (name "r-mpo-db")
+ (version "0.99.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MPO.db" version
+ 'annotation))
+ (sha256
+ (base32 "0x1rcikg189akbd71yh0p02482km9hry6i69s2srdf5mlgqficvl"))))
+ (properties `((upstream-name . "MPO.db")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'avoid-internet-access
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((cache (string-append #$output "/share/MPO.db/cache"))
+ (file (string-append cache "/118299")))
+ (mkdir-p cache)
+ (copy-file #$(this-package-native-input "MPO.sqlite") file)
+ (substitute* "R/zzz.R"
+ (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
+ (string-append
+ "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
+ (("dbfile <- ah.*" m)
+ (string-append
+ "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
+ file "\";} else { " m " }\n")))))))))
+ (propagated-inputs
+ (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("MPO.sqlite"
+ ,(origin
+ (method url-fetch)
+ (uri "https://annotationhub.bioconductor.org/fetch/118299")
+ (file-name "MPO.sqlite")
+ (sha256
+ (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0"))))))
+ (home-page "https://github.com/YuLab-SMU/MPO.db")
+ (synopsis "set of annotation maps describing the Mouse Phenotype Ontology")
+ (description
+ "This is the human disease ontology R package HDO.db, which provides the
+semantic relationship between human diseases. Relying on the DOSE and
+GO@code{SemSim} packages, this package can carry out disease enrichment and
+semantic similarity analyses. Many biological studies are achieved through
+mouse models, and a large number of data indicate the association between
+genotypes and phenotypes or diseases. The study of model organisms can be
+transformed into useful knowledge about normal human biology and disease to
+facilitate treatment and early screening for diseases. Organism-specific
+genotype-phenotypic associations can be applied to cross-species phenotypic
+studies to clarify previously unknown phenotypic connections in other species.
+Using the same principle to diseases can identify genetic associations and
+even help to identify disease associations that are not obvious.")
+ (license license:artistic2.0)))
+
(define-public r-org-eck12-eg-db
(package
(name "r-org-eck12-eg-db")
@@ -1841,6 +1953,40 @@ LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
files for various search engines.")
(license license:gpl2+)))
+(define-public r-msexperiment
+ (package
+ (name "r-msexperiment")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MsExperiment" version))
+ (sha256
+ (base32 "06m0i60zh3xjqmsz6dpp0il833xzdfj0fm6xbhl7kmicvfrcnyfg"))))
+ (properties `((upstream-name . "MsExperiment")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-iranges
+ r-protgenerics
+ r-qfeatures
+ r-s4vectors
+ r-spectra
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/RforMassSpectrometry/MsExperiment")
+ (synopsis "Infrastructure for Mass Spectrometry experiments")
+ (description
+ "This package provides infrastructure to store and manage all aspects
+related to a complete proteomics or metabolomics mass spectrometry (MS)
+experiment. The @code{MsExperiment} package provides light-weight and
+flexible containers for MS experiments building on the new MS infrastructure
+provided by the Spectra, QFeatures and related packages. Along with raw data
+representations, links to original data files and sample annotations,
+additional metadata or annotations can also be stored within the
+@code{MsExperiment} container. To guarantee maximum flexibility only minimal
+constraints are put on the type and content of the data within the
+containers.")
+ (license license:artistic2.0)))
+
(define-public r-msigdb
(package
(name "r-msigdb")
@@ -2135,13 +2281,13 @@ and @code{Sailfish}. Alevin example output is also included.")
(define-public r-abarray
(package
(name "r-abarray")
- (version "1.68.0")
+ (version "1.70.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ABarray" version))
(sha256
(base32
- "0vrsyx06acdkb3hq350zdnx3bqzz43grf1w8n0pmxlcr2dncchv9"))))
+ "0p9q2x6n6n1d4w2hfbhhj54qflc6rf1w1qm9p2zqv9fcrm3g153v"))))
(properties `((upstream-name . "ABarray")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-multtest))
@@ -2161,13 +2307,13 @@ into folders according to the analysis settings used.")
(define-public r-absseq
(package
(name "r-absseq")
- (version "1.54.0")
+ (version "1.56.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ABSSeq" version))
(sha256
(base32
- "1my2slp88qpb15qidjd646hlslvn8brv6i553h21c4c76jzxzsiz"))))
+ "0y8j66yargvipwxg2ffcs62idk5q5r8vracfldbd1x5rgq7lf6nq"))))
(properties `((upstream-name . "ABSSeq")))
(build-system r-build-system)
(propagated-inputs (list r-limma r-locfit))
@@ -2190,13 +2336,13 @@ ranking by fold-change and visualization.")
(define-public r-adacgh2
(package
(name "r-adacgh2")
- (version "2.40.0")
+ (version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ADaCGH2" version))
(sha256
- (base32 "1mmckrxhv23kl3g4d3n4hfdm97sfg2k36khzy9i6d73g7c033hsv"))))
+ (base32 "0lzgn4zqckv37jsgd1azvshblb38khrlcncm98g74qhkswqj5wx3"))))
(properties `((upstream-name . "ADaCGH2")))
(build-system r-build-system)
(arguments
@@ -2232,13 +2378,13 @@ storing data.")
(define-public r-adam
(package
(name "r-adam")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ADAM" version))
(sha256
(base32
- "1hy7xdf6v2fqggvc9rdl90gn0l6vfbmvb23c61i8q45s3qsaxksp"))))
+ "0gz3mpkj1q4j7w08ylfzclpa6saxsz7wyp0cldllhxpcj9lxljs5"))))
(properties `((upstream-name . "ADAM")))
(build-system r-build-system)
(propagated-inputs (list r-dplyr
@@ -2267,13 +2413,13 @@ functionally associated genes} (GFAG).")
(define-public r-adamgui
(package
(name "r-adamgui")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ADAMgui" version))
(sha256
(base32
- "0jc0sbmmc98z75x73ns3qwcvklvx73wqla87cki8sls6ywa8w93j"))))
+ "10m5dplkzxsxm7dxcmybihv81yflm3f7q6fmgb1dvwr8lsn1dm03"))))
(properties `((upstream-name . "ADAMgui")))
(build-system r-build-system)
(propagated-inputs
@@ -2315,13 +2461,13 @@ the @code{GFAGpathUi} function.")
(define-public r-adimpute
(package
(name "r-adimpute")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ADImpute" version))
(sha256
(base32
- "0a3r4bkf6g28lgsq21077ag9ba6zrfv6yflawx9fg73zdx4266jp"))))
+ "0299yyin2j8577db2w6mrxmsq68cjlzwyh7z1wvhbj0n1p75r871"))))
(properties `((upstream-name . "ADImpute")))
(build-system r-build-system)
(propagated-inputs
@@ -2364,13 +2510,13 @@ results from different methods into an ensemble.")
(define-public r-adsplit
(package
(name "r-adsplit")
- (version "1.70.0")
+ (version "1.72.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "adSplit" version))
(sha256
(base32
- "0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z"))))
+ "0av0kji4r788cn5808g13svqpydq6xk4d2awpzpsckz7xbjyx0ya"))))
(properties `((upstream-name . "adSplit")))
(build-system r-build-system)
(propagated-inputs
@@ -2392,13 +2538,13 @@ the supporting gene set is determined.")
(define-public r-affixcan
(package
(name "r-affixcan")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AffiXcan" version))
(sha256
(base32
- "0nf5dkidar6zp5rvpd7i19gdb7mnam9rmca3z3anxi0pdnalwc9d"))))
+ "1f508sz5vsmmmvp2mcyd2l4hislg2xhnn11xxva010l3i7by8c2r"))))
(properties `((upstream-name . "AffiXcan")))
(build-system r-build-system)
(propagated-inputs
@@ -2420,13 +2566,13 @@ expression values are known.")
(define-public r-affyilm
(package
(name "r-affyilm")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyILM" version))
(sha256
- (base32 "02g0bg21ms0gmq6dvdcj91b0p47ppqcfvgj73y0mbdx6prrmcagx"))))
+ (base32 "1sbgc787gvcnpjhm0hv80rsms679wlvphq2ch7s28zdlaa2vz7sv"))))
(properties `((upstream-name . "affyILM")))
(build-system r-build-system)
(propagated-inputs
@@ -2447,13 +2593,13 @@ concentrations on behal of the Langmuir model.")
(define-public r-affylmgui
(package
(name "r-affylmgui")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affylmGUI" version))
(sha256
- (base32 "1m1gvz313h4x080889b05fjq60wn57dxlgq03qkwy65scl3x2fcn"))))
+ (base32 "1431zmh9van9605lh0i96as48zih17s3cfhjw94v37rswfq09fkg"))))
(properties `((upstream-name . "affylmGUI")))
(build-system r-build-system)
(propagated-inputs
@@ -2479,13 +2625,13 @@ limma packages.")
(define-public r-affyplm
(package
(name "r-affyplm")
- (version "1.76.1")
+ (version "1.78.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyPLM" version))
(sha256
- (base32 "1660nn4541f2k5qpzxkkkf9h92ndzqr0j1jpzh4czs466766kn8y"))))
+ (base32 "0l7rfwj1bdkk9vd5j0zby2ijpapmd5k0s6l84zy4ld47vabxyaa6"))))
(properties `((upstream-name . "affyPLM")))
(build-system r-build-system)
(inputs (list zlib))
@@ -2510,13 +2656,13 @@ also provided.")
(define-public r-affyrnadegradation
(package
(name "r-affyrnadegradation")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AffyRNADegradation" version))
(sha256
(base32
- "14s3kvxcc3qj931bf5ya088flijmn5z89hps3di98kkdsl3w6d4g"))))
+ "0i7929cyqvbx81v1d629g53480m48cbdpxfv0k6lwjfzf4yvazhf"))))
(properties `((upstream-name . "AffyRNADegradation")))
(build-system r-build-system)
(propagated-inputs (list r-affy))
@@ -2535,13 +2681,13 @@ of samples that are affected by RNA degradation.")
(define-public r-agdex
(package
(name "r-agdex")
- (version "1.48.0")
+ (version "1.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AGDEX" version))
(sha256
(base32
- "0p9qmwhi4ik24m51cvgxnny4yfqv4v0rvra16bj5d3w9bw9yf3an"))))
+ "06z74p3khw3r8dnwrpyyikq3ifcdvffxgfwcic9j8vc9s8pf921s"))))
(properties `((upstream-name . "AGDEX")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-gseabase))
@@ -2562,13 +2708,13 @@ experiment.")
(define-public r-aggregatebiovar
(package
(name "r-aggregatebiovar")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "aggregateBioVar" version))
(sha256
(base32
- "0g7n6dj1scad833y2182946hn3yh4jad20wvw9ic8gmqb438vihj"))))
+ "1i04hhncz9lhjp730gyknd8v7zakz1whc2a5pw3pn37h8k9mq5la"))))
(properties `((upstream-name . "aggregateBioVar")))
(build-system r-build-system)
(propagated-inputs
@@ -2596,13 +2742,13 @@ bulk RNA-seq tools.")
(define-public r-agilp
(package
(name "r-agilp")
- (version "3.32.0")
+ (version "3.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "agilp" version))
(sha256
(base32
- "0rm646iqc8hf8vfk0pdg064hm9k4k371bp1q4k7z2l16zhs8a07r"))))
+ "0xbbcmnbnj7y3a1wndv6zhqhrwdpdj6207wh4n0qz794akciw84a"))))
(properties `((upstream-name . "agilp")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/agilp")
@@ -2618,13 +2764,13 @@ but which also provides utilities which may be useful for other platforms.")
(define-public r-adductomicsr
(package
(name "r-adductomicsr")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "adductomicsR" version))
(sha256
(base32
- "17cm65n2awbwmk5i8h1n30abk6pww42ngcy9m24dxz1qdbnvx5fn"))))
+ "0fb670gxzl5aq6vmb5d2l04r0408gxrqs06k1a3b3pzkdbd7qxwm"))))
(properties `((upstream-name . "adductomicsR")))
(build-system r-build-system)
(propagated-inputs
@@ -2693,13 +2839,13 @@ objects are used so that other packages could be used as well.")
(define-public r-aims
(package
(name "r-aims")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AIMS" version))
(sha256
(base32
- "1mbwv70ypkb3x086css94m89wq9pqzd23i7nar1844vbqpw3j83q"))))
+ "0fmzyd8vypcfadqfa8w11mxr12h4a9shgiqpi2n2y150fvhlqf6c"))))
(properties `((upstream-name . "AIMS")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-e1071))
@@ -2717,13 +2863,13 @@ well as on dataset of gene expression data.")
(define-public r-airpart
(package
(name "r-airpart")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "airpart" version))
(sha256
(base32
- "024vcxf23irlysc8srqii3zqhhldpwdcj0i4zzhz18x3bdy9cbj0"))))
+ "1bdlg078nlpibbn3y1cbkglhlm440crx3alzhv9k0psv6arg2kqb"))))
(properties `((upstream-name . "airpart")))
(build-system r-build-system)
(propagated-inputs
@@ -2764,13 +2910,13 @@ datasets.")
(define-public r-amountain
(package
(name "r-amountain")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AMOUNTAIN" version))
(sha256
(base32
- "12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj"))))
+ "1c65vn2k3hzzymik9ia7nk32sf0hr83q27yzf561a1hgv3m67d65"))))
(properties `((upstream-name . "AMOUNTAIN")))
(build-system r-build-system)
(inputs (list gsl))
@@ -2788,13 +2934,13 @@ in multi-layer WGCN using a continuous optimization approach.")
(define-public r-amplican
(package
(name "r-amplican")
- (version "1.22.1")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "amplican" version))
(sha256
(base32
- "1bws4awpjvswzj53zwn9x5ra76ngpqn2h8hlr6y0x7j9wwwqldc7"))))
+ "0xsw6226yyyl5zgmcyfim6dxj04zrpzbd1288l0hysq1s3b1yslw"))))
(properties `((upstream-name . "amplican")))
(build-system r-build-system)
(propagated-inputs
@@ -2835,13 +2981,13 @@ problems.")
(define-public r-amaretto
(package
(name "r-amaretto")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AMARETTO" version))
(sha256
(base32
- "1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f"))))
+ "1h0ci2sak2x5dhcshmgk4hy53ggjvrz3kaj61m47w5fjkj0lz79s"))))
(properties `((upstream-name . "AMARETTO")))
(build-system r-build-system)
(propagated-inputs
@@ -2887,13 +3033,13 @@ canonical cancer pathways.")
(define-public r-anaquin
(package
(name "r-anaquin")
- (version "2.24.0")
+ (version "2.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Anaquin" version))
(sha256
(base32
- "0f2xc0pm7ld72fnmqirr0q2a5xfh12cag6s2yysblslh9ajyzcmw"))))
+ "1f2xf1i9l1s7433mvqjsralpm77qg0m73dw1rq9jsxbpk1f502ld"))))
(properties `((upstream-name . "Anaquin")))
(build-system r-build-system)
(propagated-inputs
@@ -2917,13 +3063,13 @@ analysis, modelling, and visualization of spike-in controls.")
(define-public r-ancombc
(package
(name "r-ancombc")
- (version "2.2.2")
+ (version "2.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ANCOMBC" version))
(sha256
(base32
- "0jws3wqgwc0gnp7smc0lsqfw9jbcik36pl7vz9a8ndgwpp9c8653"))))
+ "1m63k1b9xh5mv4zb5m9nlrdcqkh2h477x1zyfk8j89idcvk9jil7"))))
(properties `((upstream-name . "ANCOMBC")))
(build-system r-build-system)
(propagated-inputs
@@ -3025,13 +3171,13 @@ to understand their data better and discover new insights.")
(define-public r-annotationhubdata
(package
(name "r-annotationhubdata")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHubData" version))
(sha256
- (base32 "109gi5cs82j135q00wg9dfx0z5m9bs1kc7s246ym13ik43z0h3qq"))))
+ (base32 "0jkz65z7l9vaxid6vpsr4rdavarkayfrgkybzhwf9va82jsnkd3z"))))
(properties `((upstream-name . "AnnotationHubData")))
(build-system r-build-system)
(arguments
@@ -3076,13 +3222,13 @@ for use in Bioconductor’s AnnotationHub.")
(define-public r-anvil
(package
(name "r-anvil")
- (version "1.12.4")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnVIL" version))
(sha256
(base32
- "05wgrr16vaqb7982j7nyri6rrhx90ljgxc37afhw190wc5dj07n0"))))
+ "0syd1m992i2xqw2djw6s07zwwvrzvd0aksix1cbhx9plpswd2245"))))
(properties `((upstream-name . "AnVIL")))
(build-system r-build-system)
(propagated-inputs
@@ -3117,19 +3263,22 @@ to transform JSON responses to formats more amenable to manipulation in R.")
(define-public r-aldex2
(package
(name "r-aldex2")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ALDEx2" version))
(sha256
(base32
- "0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8"))))
+ "0wchlw9dprw7vkw26h26ypx06xv2j0cxbidw61pcqaxmrrh14dhz"))))
(properties `((upstream-name . "ALDEx2")))
(build-system r-build-system)
(propagated-inputs
(list r-biocparallel
+ r-directlabels
r-genomicranges
r-iranges
+ r-lattice
+ r-latticeextra
r-multtest
r-rfast
r-s4vectors
@@ -3158,13 +3307,13 @@ paired or unpaired study designs.")
(define-public r-alevinqc
(package
(name "r-alevinqc")
- (version "1.16.1")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "alevinQC" version))
(sha256
(base32
- "137bvqyh1cqmhf9x3xl6n1dv0380lpcr2nxhd60b7zqiw4p14i5a"))))
+ "0lhbh9xgkbrad9fqvxl4c6y0f2kgibn6sinp8znysk5m9z0ngpwp"))))
(properties `((upstream-name . "alevinQC")))
(build-system r-build-system)
(propagated-inputs
@@ -3192,13 +3341,13 @@ generated as HTML or PDF files, or as Shiny applications.")
(define-public r-alphabeta
(package
(name "r-alphabeta")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AlphaBeta" version))
(sha256
(base32
- "11431d453xszzjyxr10npnblhlrfw8hl5jgabpxla7cj77w02wnr"))))
+ "0zja8mysw0ljkvk6vqdx4c9wpf45zs64iyazh90mlf6xhbrvqfvq"))))
(properties `((upstream-name . "AlphaBeta")))
(build-system r-build-system)
(propagated-inputs
@@ -3272,13 +3421,13 @@ data.")
(define-public r-alpsnmr
(package
(name "r-alpsnmr")
- (version "4.2.0")
+ (version "4.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AlpsNMR" version))
(sha256
(base32
- "0rp82y7163pjbl7n6fyywh4l0sgzn1z8kp83v0kg7xk3810mj9sm"))))
+ "0141kayx20mm8skqr2210bpl76ra560ik7gf71iar03r3izcfczq"))))
(properties `((upstream-name . "AlpsNMR")))
(build-system r-build-system)
(propagated-inputs
@@ -3326,13 +3475,13 @@ data. Efficient plotting with 1-D data is also available. Basic reading of
(define-public r-altcdfenvs
(package
(name "r-altcdfenvs")
- (version "2.62.0")
+ (version "2.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "altcdfenvs" version))
(sha256
(base32
- "1jpimj195rdw86pp623ylrmcxkxmn8qmc84vsw9prnf3gdz3q18b"))))
+ "17kgiqa5dbfp74jrm565wlx9sj4ydbds2y8ahs7dikvdvm725qsn"))))
(properties `((upstream-name . "altcdfenvs")))
(build-system r-build-system)
(propagated-inputs
@@ -3357,37 +3506,37 @@ create an alternative mapping from sequences.")
(define-public r-aneufinder
(package
(name "r-aneufinder")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AneuFinder" version))
(sha256
(base32
- "1l33yb20pynkvlla1dmgbwjhnhxh067fci0ciryxmbzqwq2sn1kc"))))
+ "0x7v60j1c1g12qlqxgshpmbnwzjbmlnkrfh60wl43inr0wyllq1l"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
(propagated-inputs
- (list r-genomicranges
- r-aneufinderdata
+ (list r-aneufinderdata
+ r-bamsignals
+ r-biocgenerics
+ r-biostrings
+ r-cowplot
+ r-dnacopy
+ r-doparallel
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-genomicranges
r-ggdendro
+ r-ggplot2
r-ggrepel
+ r-iranges
r-mclust
- r-cowplot))
+ r-reshape2
+ r-rsamtools
+ r-s4vectors))
(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
@@ -3426,13 +3575,13 @@ network fusion.")
(define-public r-annmap
(package
(name "r-annmap")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "annmap" version))
(sha256
(base32
- "0gilb8yxba1cqi678w9xkq77m8lf3k8dqcldh68cll61xsgihl1v"))))
+ "1gf0qdhj4ijgb6b67fh94zx084k5r87la3d7vc0qxs413rvr4mj8"))))
(properties `((upstream-name . "annmap")))
(build-system r-build-system)
(propagated-inputs
@@ -3460,13 +3609,13 @@ Functions to plot gene architecture and BAM file data are also provided.")
(define-public r-antiprofiles
(package
(name "r-antiprofiles")
- (version "1.40.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "antiProfiles" version))
(sha256
(base32
- "0ix0r36fs6vr0gyryi1j15pcc0hvpynsg9505w95dsn3p4fdnhg8"))))
+ "14lzyq08gnm9r99xwaqh50sz0dwzhmiyyylkg239dlbw80zmv404"))))
(properties `((upstream-name . "antiProfiles")))
(build-system r-build-system)
(propagated-inputs
@@ -3486,13 +3635,13 @@ tumor samples from healthy controls.")
(define-public r-arrayexpress
(package
(name "r-arrayexpress")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ArrayExpress" version))
(sha256
(base32
- "1ib33fw379sakk084csa3pwcc3wvba38ily6mmv2ax1wh16i0pfz"))))
+ "0cnb6r6rqbz5qph32aa1mghr0w2rhl6znyiblj0cbkv45mx2k4jr"))))
(properties `((upstream-name . "ArrayExpress")))
(build-system r-build-system)
(propagated-inputs
@@ -3513,13 +3662,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
(define-public r-arrayqualitymetrics
(package
(name "r-arrayqualitymetrics")
- (version "3.56.0")
+ (version "3.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "arrayQualityMetrics" version))
(sha256
(base32
- "06plgmgla7hvryqfcid4y35s24r50s39d9f8sjchwbxqciwy72wj"))))
+ "1k80ih7r3hf48r9rp9dl2wl8m17620dqr4fch49kdsq97hm5q5dm"))))
(properties `((upstream-name . "arrayQualityMetrics")))
(build-system r-build-system)
(propagated-inputs (list r-affy
@@ -3551,13 +3700,13 @@ supported.")
(define-public r-arraymvout
(package
(name "r-arraymvout")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "arrayMvout" version))
(sha256
- (base32 "1wdqcfa0h070lky4m2h5k4wg8lg7014y0gk95gip5zags29zjwqb"))))
+ (base32 "0z3ksx0yigan5aiq7vsdx78khlrcdxa4yd5b46rfn83gsrjbxzhz"))))
(properties `((upstream-name . "arrayMvout")))
(build-system r-build-system)
(arguments
@@ -3587,13 +3736,13 @@ fixed Type I error rate.")
(define-public r-arrayquality
(package
(name "r-arrayquality")
- (version "1.78.0")
+ (version "1.80.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "arrayQuality" version))
(sha256
- (base32 "0lq59y4pi13z4v1i1ah78xlchxy34x1lplsh0n42wlk88rk0rqxd"))))
+ (base32 "1bm46zf5c1i7fd848bqajv3agl05b93xsvam7034033ypyx6bf1z"))))
(properties `((upstream-name . "arrayQuality")))
(build-system r-build-system)
(propagated-inputs
@@ -3612,13 +3761,13 @@ quality assessment.")
(define-public r-asafe
(package
(name "r-asafe")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASAFE" version))
(sha256
(base32
- "05xw42552x7by63psb05hvjraax66flg94i331ca61zx107q7fai"))))
+ "13pn2s59npp8lhc2sk9sa7dq8fy6jlq22c71n3rcjgxrrh690nb8"))))
(properties `((upstream-name . "ASAFE")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -3635,13 +3784,13 @@ pairs.")
(define-public r-aseb
(package
(name "r-aseb")
- (version "1.44.0")
+ (version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASEB" version))
(sha256
(base32
- "1dq6b5rg9iw6hdjmd7g0w64z7cxm52yg1cjyv355qs064dx26nph"))))
+ "1hiapxdbp1fg6wk62s31nkv9mkxzvd23hn3zhmf9n0nvqfhi7bdf"))))
(properties `((upstream-name . "ASEB")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/ASEB")
@@ -3662,13 +3811,13 @@ RNAs.")
(define-public r-asgsca
(package
(name "r-asgsca")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASGSCA" version))
(sha256
(base32
- "0vb37rvrb08qvv0i2k9jnqpajzpj044ww05w3kq1kypbby0c84zs"))))
+ "13nk19rccrp0xl1s5gjwydpl1ayc7zc2izjrij9iz7fh2r79gn7f"))))
(properties `((upstream-name . "ASGSCA")))
(build-system r-build-system)
(propagated-inputs (list r-mass r-matrix))
@@ -3685,13 +3834,13 @@ model as latent variables.")
(define-public r-asics
(package
(name "r-asics")
- (version "2.16.0")
+ (version "2.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASICS" version))
(sha256
(base32
- "0svl9wnfn9z88j1yyl30b1f3d14h01x4cga8q04x530723xnjws7"))))
+ "10wlmnlpn6ji256fp81rhsm2rsbsqsbvbjqqpw9vib11cwpam9wd"))))
(properties `((upstream-name . "ASICS")))
(build-system r-build-system)
(propagated-inputs
@@ -3719,13 +3868,13 @@ the spectra of the library with a sparse penalty.")
(define-public r-aspli
(package
(name "r-aspli")
- (version "2.10.0")
+ (version "2.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASpli" version))
(sha256
(base32
- "0462hf7anpmmqq4585kmjilw1q229r38lijbxq8xg0f3m8xvr1ga"))))
+ "0rj103vvff2c20r018491i71393x0idq22ri4zg3qibx2accd7jy"))))
(properties `((upstream-name . "ASpli")))
(build-system r-build-system)
(propagated-inputs
@@ -3767,13 +3916,13 @@ that might arise in splicing patterns.")
(define-public r-assessorf
(package
(name "r-assessorf")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AssessORF" version))
(sha256
(base32
- "16nv6sh7z3l6ff3a7zrixkc04mhrak38q045xlirgljkcragz1c5"))))
+ "0v64d3nmvcj6bz8zplyqzslm7kz6j3y0nl316h76g094hify64lk"))))
(properties `((upstream-name . "AssessORF")))
(build-system r-build-system)
(propagated-inputs
@@ -3796,13 +3945,13 @@ start codons as the forms of evidence.")
(define-public r-asset
(package
(name "r-asset")
- (version "2.18.0")
+ (version "2.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ASSET" version))
(sha256
(base32
- "1vksbfd4wd2xcc0nl3wp53vm0jyqy97p0hqps2aml04745vkg023"))))
+ "0mm15i59vsnz8zh2d10xnab3a6kq08hwd3pzm3r12g4wcrdsxfxc"))))
(properties `((upstream-name . "ASSET")))
(build-system r-build-system)
(propagated-inputs (list r-mass r-msm r-rmeta))
@@ -3823,13 +3972,13 @@ variant.")
(define-public r-atena
(package
(name "r-atena")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "atena" version))
(sha256
(base32
- "1057mkxrjfnqhb1mydhd7vlb1s8h7n4zc4cl063gw4sgj6mw99ij"))))
+ "1qfgy76d65hbx32fw1yf20n1vavylcafb9fgqqp02r455vk3xzng"))))
(properties `((upstream-name . "atena")))
(build-system r-build-system)
(propagated-inputs
@@ -3864,13 +4013,13 @@ transcripts in an integrated manner.")
(define-public r-atsnp
(package
(name "r-atsnp")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "atSNP" version))
(sha256
(base32
- "14j8lbry4wpn8izch1nra5npg4qsh49ql4bf21jvvr3gl3qa1g7l"))))
+ "1nksx6al1cr6apknvrabi3gdbr7m61ms81nmkq4qykx5aysmp8mv"))))
(properties `((upstream-name . "atSNP")))
(build-system r-build-system)
(propagated-inputs
@@ -3897,13 +4046,13 @@ SNP-led changes in motif matches.")
(define-public r-attract
(package
(name "r-attract")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "attract" version))
(sha256
(base32
- "1lb6npxm5f82z8278v6fh7k5w8d4z73881iplm3ashc27wiw6sz3"))))
+ "0lk8gfbccrxly7gn629497sxz0mj3m9wcwdahqv1m7l6fjnf5563"))))
(properties `((upstream-name . "attract")))
(build-system r-build-system)
(propagated-inputs
@@ -3928,13 +4077,13 @@ transcriptionally-coordinated changes in gene expression.")
(define-public r-awfisher
(package
(name "r-awfisher")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AWFisher" version))
(sha256
(base32
- "1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x"))))
+ "10c5qi040z2w46k7qdcd2yap11mzllllrbr0nx7gd9gfzwlx089s"))))
(properties `((upstream-name . "AWFisher")))
(build-system r-build-system)
(propagated-inputs
@@ -3952,13 +4101,13 @@ meta-pattern.")
(define-public r-awst
(package
(name "r-awst")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "awst" version))
(sha256
(base32
- "0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji"))))
+ "0hry7ynv69hqbwyhlsilf1f9w8yadidbn2ckm5dx9mnb5ihgkyvj"))))
(properties `((upstream-name . "awst")))
(build-system r-build-system)
(propagated-inputs (list r-summarizedexperiment))
@@ -3979,13 +4128,13 @@ artifacts.")
(define-public r-baalchip
(package
(name "r-baalchip")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BaalChIP" version))
(sha256
(base32
- "0bp8p7cn59iv08cf4yw9xl1f83dcr6v1kqvggxjals8y4gmls9nz"))))
+ "0d08mp12lw4qdy7w7i474ywcy2zgv940nc44w0gbb9h9dfl22crv"))))
(properties `((upstream-name . "BaalChIP")))
(build-system r-build-system)
(inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
@@ -4019,13 +4168,13 @@ alleles, a known phenotypical feature of cancer samples.")
(define-public r-basespacer
(package
(name "r-basespacer")
- (version "1.44.0")
+ (version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BaseSpaceR" version))
(sha256
(base32
- "15aqf2s51gl6gcnv24170v9hlq1vgya58qh1f5vjmark7j2k8vvm"))))
+ "1ldsgrhxb1nm8xj7mws461apjknp9c2bhq3738f63i2qj9g25j4g"))))
(properties `((upstream-name . "BaseSpaceR")))
(build-system r-build-system)
(propagated-inputs (list r-rcurl r-rjsonio))
@@ -4066,13 +4215,13 @@ you will have to normalize your data beforehand.")
(define-public r-bader
(package
(name "r-bader")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BADER" version))
(sha256
(base32
- "0g3yvgrarpdcxpvjrxg0gbdcagknh80cr0xyzinzpmiiz0rywmzc"))))
+ "0zmf7a7lwsnk9gcg48vmzdvfmzhvnbawwg77pb4gy3cw9sjdz5ym"))))
(properties `((upstream-name . "BADER")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BADER")
@@ -4090,13 +4239,13 @@ can be used for further down-stream analyses such as gene set enrichment.")
(define-public r-badregionfinder
(package
(name "r-badregionfinder")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BadRegionFinder" version))
(sha256
(base32
- "04bzb3i461gwkq9ygkjljpjk32c3arqr08hfzxyig1sarrryzl3q"))))
+ "17smlghl8s667n6cjx64mqli9drmv0pkq51mhjlyjy2v019im7l9"))))
(properties `((upstream-name . "BadRegionFinder")))
(build-system r-build-system)
(propagated-inputs
@@ -4117,13 +4266,13 @@ Various visual and textual types of output are available.")
(define-public r-bambu
(package
(name "r-bambu")
- (version "3.2.6")
+ (version "3.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "bambu" version))
(sha256
(base32
- "0h7ps32vbcn4hjpfb343nn8b50zq9my0k61847fi69vc4siwcx5k"))))
+ "02pcab8jfwlx4y00yky63anba61bb1h884m0f6ajvasfpgl30w6i"))))
(properties `((upstream-name . "bambu")))
(build-system r-build-system)
(propagated-inputs
@@ -4160,13 +4309,13 @@ usage.")
(define-public r-bandits
(package
(name "r-bandits")
- (version "1.16.1")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BANDITS" version))
(sha256
(base32
- "04l6iy0sij7zhzswhxjzir3xmrjnp6aapp0a93xp01xiv2sgdzni"))))
+ "1xdyi61scfay5l5v7c40wjjl83kcvagvypxnfvsws4avh08x3ni3"))))
(properties `((upstream-name . "BANDITS")))
(build-system r-build-system)
(propagated-inputs
@@ -4198,13 +4347,13 @@ the posterior densities for the average relative abundance of transcripts.")
(define-public r-banocc
(package
(name "r-banocc")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "banocc" version))
(sha256
(base32
- "0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y"))))
+ "0y6mizkbx3s2x6465g53q87q0sixxrxhjvjmvwiilhirxf4x7hgp"))))
(properties `((upstream-name . "banocc")))
(build-system r-build-system)
(propagated-inputs
@@ -4226,13 +4375,13 @@ estimates for each correlation element.")
(define-public r-barcodetrackr
(package
(name "r-barcodetrackr")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "barcodetrackR" version))
(sha256
(base32
- "155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8"))))
+ "1w5p6dqagf3g27ymqsxdim0qhnwm11rrs3nnpp4mj8jcxm8wjsh9"))))
(properties `((upstream-name . "barcodetrackR")))
(build-system r-build-system)
(propagated-inputs
@@ -4268,14 +4417,14 @@ retrieval analyses, or similar technologies.")
(define-public r-biocversion
(package
(name "r-biocversion")
- (version "3.17.1")
+ (version "3.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocVersion" version))
(sha256
(base32
- "0n29adnb62agp9li8rmn68z653d2m41iy9zjz75h43a05drlgp33"))))
+ "07zcf19gcbki2d18xgyrdzp3vn90cz2ww45p8ra4lc1mif5gy0c3"))))
(properties `((upstream-name . "BiocVersion")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -4288,13 +4437,13 @@ of Bioconductor.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.46.0")
+ (version "0.48.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "19kwpis282i8x31xlh8nc3z6vvn23p3wpx7wmrqhclf8ymq61c7z"))))
+ "0av525j9l0y3kjdy5wl6s35sh4nsabmdclq3687l5258kmq2dq8k"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@@ -4308,13 +4457,13 @@ packages.")
(define-public r-breakpointr
(package
(name "r-breakpointr")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "breakpointR" version))
(sha256
(base32
- "001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n"))))
+ "1jhgimybc2ib201k6vs5nfyi1whpkkzn7nj562yhz74208fx793a"))))
(properties `((upstream-name . "breakpointR")))
(build-system r-build-system)
(propagated-inputs
@@ -4342,13 +4491,13 @@ export of Strand-seq data.")
(define-public r-cardelino
(package
(name "r-cardelino")
- (version "1.2.0")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cardelino" version))
(sha256
(base32
- "0ivhqd3da23iy2qklk2nljkjjr943m9r2y1q51fphld33izmv64v"))))
+ "0y4d3db01jwahz01hx3dswc4gg0x5k7325v4n1illgw3ddj2mvgn"))))
(properties `((upstream-name . "cardelino")))
(build-system r-build-system)
(propagated-inputs (list r-combinat
@@ -4380,20 +4529,20 @@ stochastic dropout events as well as systematic allelic imbalance is used.")
(define-public r-cellid
(package
(name "r-cellid")
- (version "1.8.1")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CelliD" version))
(sha256
(base32
- "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03"))))
+ "1x4kp8i204rqas2bgg4qanwdncafilymlpvxvfyv39zpdji91yv5"))))
(properties `((upstream-name . "CelliD")))
(build-system r-build-system)
(propagated-inputs
- (list r-data-table
- r-biocparallel
+ (list r-biocparallel
+ r-data-table
r-fastmatch
- r-fgsea
+ r-fgsea
r-ggplot2
r-glue
r-irlba
@@ -4404,13 +4553,14 @@ stochastic dropout events as well as systematic allelic imbalance is used.")
r-rcpparmadillo
r-reticulate
r-rtsne
+ r-scater
r-seurat
+ r-singlecellexperiment
r-stringr
- r-tictoc
- r-singlecellexperiment
r-summarizedexperiment
+ r-tictoc
r-umap))
- (native-inputs (list r-knitr r-scater))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/CelliD")
(synopsis
"Single cell gene signature extraction using multiple correspondence analysis")
@@ -4422,24 +4572,69 @@ omics protocols. The package can also be used to explore functional pathways
enrichment in single cell data.")
(license license:gpl3)))
+(define-public r-coregx
+ (package
+ (name "r-coregx")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CoreGx" version))
+ (sha256
+ (base32 "0ffbi5afw759mi5r657h67hdh9yr5jrzvl3aigp960jzb5542105"))))
+ (properties `((upstream-name . "CoreGx")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-bench
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-bumpymatrix
+ r-checkmate
+ r-crayon
+ r-data-table
+ r-glue
+ r-lsa
+ r-matrixgenerics
+ r-multiassayexperiment
+ r-piano
+ r-rlang
+ r-s4vectors
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/CoreGx")
+ (synopsis
+ "Classes and functions to serve as the basis for other Gx packages")
+ (description
+ "This package provides a collection of functions and classes which serve
+as the foundation for packages such as PharmacoGx and RadioGx. It was created
+to abstract shared functionality to increase ease of maintainability and
+reduce code repetition in current and future Gx suite programs. Major
+features include a @code{CoreSet} class, from which RadioSet and PharmacoSet
+are derived, along with get and set methods for each respective slot.
+Additional functions related to fitting and plotting dose response curves,
+quantifying statistical correlation and calculating @acronym{AUC, area under
+the curve} or @acronym{SF, survival fraction} are included.")
+ (license license:gpl3+)))
+
(define-public r-coverageview
(package
(name "r-coverageview")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
- "1ci07y75nvvv1mxy23v6jp5xb6n023fvlqh9il5lsdqwyfl5nz9s"))))
+ "1sj1vr84nsbygkh5mmp7zm21zzk4zcw3bwcvcazmy54zs553blpf"))))
(build-system r-build-system)
(propagated-inputs
- (list r-s4vectors
- r-iranges
+ (list r-genomicalignments
r-genomicranges
- r-genomicalignments
+ r-iranges
+ r-rsamtools
r-rtracklayer
- r-rsamtools))
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/CoverageView/")
(synopsis "Coverage visualization package for R")
(description "This package provides a framework for the visualization of
@@ -4452,13 +4647,13 @@ how the coverage distributed across the genome.")
(define-public r-cummerbund
(package
(name "r-cummerbund")
- (version "2.42.0")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
- "1xin1azby96xxp4yyd4wc3rfcjc2g9p01ksfd89bk2vxcclccqxn"))))
+ "1a5x3jzagd1a385yk1brs4say02r0l21qqjak4cl6fsv8ihhy05s"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -4482,13 +4677,13 @@ used visualizations.")
(define-public r-dama
(package
(name "r-dama")
- (version "1.72.0")
+ (version "1.74.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "daMA" version))
(sha256
(base32
- "0z4y57hna312pkhkchair8calm7wl40rx8lcm8i6h1789hba063d"))))
+ "1ckk8h6adylaxq6bh14ym9vvrrhsfglnaigqz16v96vsj8q9i336"))))
(properties `((upstream-name . "daMA")))
(build-system r-build-system)
(propagated-inputs (list r-mass))
@@ -4504,13 +4699,13 @@ factorial microarray data.")
(define-public r-damefinder
(package
(name "r-damefinder")
- (version "1.12.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DAMEfinder" version))
(sha256
(base32
- "0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd"))))
+ "0mbm884dm30b4fwf3qr1w96j18dxdmr2bn11dw83hh0wrbhp8njm"))))
(properties `((upstream-name . "DAMEfinder")))
(build-system r-build-system)
(propagated-inputs
@@ -4545,14 +4740,14 @@ offers nice visualization of methyl-circle plots.")
(define-public r-dearseq
(package
(name "r-dearseq")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dearseq" version))
(sha256
(base32
- "12ld1f3892ag1a3lmkwjlkk6pd79ibykg8jrmddx2x33k23cv67g"))))
+ "1ldxw457zsfphm6izxz2kvxy3719gszhxb8mymx8njg6islljy27"))))
(build-system r-build-system)
(propagated-inputs
(list r-compquadform
@@ -4584,13 +4779,13 @@ set analyses, and can deal with repeated or longitudinal data.")
(define-public r-debcam
(package
(name "r-debcam")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "debCAM" version))
(sha256
(base32
- "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh"))
+ "1swqqrlwin2i2qq46qyfziblbfsfyd5hf6w39hygp7fdkpic14b7"))
(snippet
'(for-each delete-file
'("inst/java/CornerDetect.jar"
@@ -4599,9 +4794,6 @@ set analyses, and can deal with repeated or longitudinal data.")
(build-system r-build-system)
(arguments
(list
- ;; XXX: since the upgrade to R 4.3.0 this package takes too long to be
- ;; loaded.
- #:tests? #false
#:configure-flags '(list "--fake")
#:modules
'((guix build r-build-system)
@@ -4629,7 +4821,7 @@ set analyses, and can deal with repeated or longitudinal data.")
(add-after 'install 'strip-jar-timestamps
(assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
(inputs
- (list (list icedtea "jdk")
+ (list (list openjdk11 "jdk")
java-pj))
(propagated-inputs
(list r-apcluster
@@ -4661,13 +4853,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.")
(define-public r-decipher
(package
(name "r-decipher")
- (version "2.28.0")
+ (version "2.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DECIPHER" version))
(sha256
(base32
- "16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n"))))
+ "1ri8ldx3dqcpfvn3mz0022f77zi6ki04mh27qp132bbrjkj6zl79"))))
(build-system r-build-system)
(propagated-inputs
(list r-biostrings
@@ -4760,13 +4952,13 @@ mechanism based on the shared signatures.")
(define-public r-decomptumor2sig
(package
(name "r-decomptumor2sig")
- (version "2.16.0")
+ (version "2.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "decompTumor2Sig" version))
(sha256
(base32
- "028sczy1d108i05ymr1wpj6jdrcds476wbmmc7rzzflzyg4aix75"))))
+ "13vwrg82zprb9h72azdqd0rkm5k2xm4mw7viawbzwkkqvg6azsdj"))))
(properties `((upstream-name . "decompTumor2Sig")))
(build-system r-build-system)
(inputs (list perl)) ;script/extractSpecColumns.pl
@@ -4803,13 +4995,13 @@ of the signatures to the mutation load of the tumor.")
(define-public r-deconrnaseq
(package
(name "r-deconrnaseq")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DeconRNASeq" version))
(sha256
(base32
- "0bmkyci31p7g097i8fvc0s1fz47hv6vp5rcfqqkvclm86wfkkmkc"))))
+ "1k5xrx97w9g0jfvjzawyfsqyz2fj9r463nj849djxgmcw8vp53vg"))))
(properties `((upstream-name . "DeconRNASeq")))
(build-system r-build-system)
(propagated-inputs
@@ -4830,13 +5022,13 @@ single expression profiles.")
(define-public r-decontam
(package
(name "r-decontam")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "decontam" version))
(sha256
(base32
- "08niwixy4m6gqmazisxzbbla9nsxicpa685jy3r6knapwaznvcb2"))))
+ "0m4zd6qxsrp7w9a8psg8xcrviim6plwgwn4rgdxy8ag0c442fsvk"))))
(properties `((upstream-name . "decontam")))
(build-system r-build-system)
(propagated-inputs
@@ -4856,13 +5048,13 @@ negative control samples.")
(define-public r-deconvr
(package
(name "r-deconvr")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "deconvR" version))
(sha256
(base32
- "1r5js5prwy1libnf1g1a4pdi15pj216bb8ajhzii3symn5r0cdj9"))))
+ "0pl4nwaf8swwz9nl2ynf9mm38d0x223gpz89qrj03yihxszy2n13"))))
(properties `((upstream-name . "deconvR")))
(build-system r-build-system)
(propagated-inputs
@@ -4901,13 +5093,13 @@ make mapping WGBS data to their probe IDs easier.")
(define-public r-decoupler
(package
(name "r-decoupler")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "decoupleR" version))
(sha256
- (base32 "012d76jwgg6fwfjc00zdws59y6jbj0grzd4lgjrqs2afp2ycmh9s"))))
+ (base32 "1vnlrkza33nb80qf810yfz66m3j84p8chhfdxak5lvpciqwx7dh9"))))
(properties `((upstream-name . "decoupleR")))
(build-system r-build-system)
(propagated-inputs
@@ -4942,13 +5134,13 @@ targeted by a kinase.")
(define-public r-deepsnv
(package
(name "r-deepsnv")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "deepSNV" version))
(sha256
(base32
- "11cnyy3hyn8akhmax25293mx2blcs8ba5vfax6mx6hjhb577hkwb"))))
+ "16dkjqy9ba5v8nikaxdjcz7rr60dg46sfsgrjjlp82rf3256bf8r"))))
(properties `((upstream-name . "deepSNV")))
(build-system r-build-system)
(propagated-inputs
@@ -4978,13 +5170,13 @@ bases such as COSMIC.")
(define-public r-degreport
(package
(name "r-degreport")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DEGreport" version))
(sha256
(base32
- "15xm1l2qgsyzaw820a1fq5qdzh5pj4dmr1hx6s6b6wm2p02cvvai"))
+ "1ska9fh1bzdqd9pi67vqgx0vz4wz2r5kzmh73fb9zh9m0gnjjr23"))
(snippet
'(delete-file "docs/jquery.sticky-kit.min.js"))))
(properties `((upstream-name . "DEGreport")))
@@ -5049,13 +5241,13 @@ fold changes mean and variability for each selected gene.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.26.7")
+ (version "0.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha"))))
+ "0mf30vdns64mpm11zcz9qx6nh5clr6krjvcmr7dqv2xg5ig0a1f7"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
@@ -5065,7 +5257,8 @@ fold changes mean and variability for each selected gene.")
r-matrix
r-matrixgenerics
r-s4arrays
- r-s4vectors))
+ r-s4vectors
+ r-sparsearray))
(native-inputs
(list r-knitr))
(home-page "https://bioconductor.org/packages/DelayedArray")
@@ -5083,17 +5276,21 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-densvis
(package
(name "r-densvis")
- (version "1.10.3")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "densvis" version))
(sha256
(base32
- "1nkii02bj49z9qm3rj8lzwpz7dllrsa5zf7dn5ffcczyxr3b1ap9"))))
+ "164pyy5l69qhdgqkxjginapvfjy0rjx4p6m83cijz6jbz6kf6gks"))))
(properties `((upstream-name . "densvis")))
(build-system r-build-system)
- (propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp
- r-reticulate))
+ (propagated-inputs (list r-assertthat
+ r-basilisk
+ r-irlba
+ r-rcpp
+ r-reticulate
+ r-rtsne))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/densvis")
(synopsis
@@ -5114,13 +5311,13 @@ heterogeneity in the original high-dimensional space.")
(define-public r-derfinder
(package
(name "r-derfinder")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "derfinder" version))
(sha256
(base32
- "1gb65hk26ffn0njsgwgk43z9i9bcvx89pz5m9x951c2a07c1xrcw"))))
+ "0rj3szlpbxiwj3rajmr6ccnbs1mkcskql12iip8zgswmhz76rxh1"))))
(properties `((upstream-name . "derfinder")))
(build-system r-build-system)
(propagated-inputs (list r-annotationdbi
@@ -5160,13 +5357,13 @@ The DER Finder approach can also be used to identify differentially bounded
(define-public r-derfinderhelper
(package
(name "r-derfinderhelper")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "derfinderHelper" version))
(sha256
- (base32 "0ww4lvwmm8rf44wgksg98bqh7zlm503c4gc8dwilb1w0dz2k7qll"))))
+ (base32 "01vq8xnszxqhijranzaciapw8mcn6px0jhx9zb9lyqhsvaffjh5r"))))
(properties `((upstream-name . "derfinderHelper")))
(build-system r-build-system)
(propagated-inputs
@@ -5226,13 +5423,13 @@ possibly confounded by SNPs and cross-hybridisation. It includes
(define-public r-drimseq
(package
(name "r-drimseq")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DRIMSeq" version))
(sha256
- (base32 "1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98"))))
+ (base32 "1nf044cfqywfnglm081xbppamva87z2j2xz0f51z8mra11apj6i6"))))
(properties `((upstream-name . "DRIMSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -5261,13 +5458,13 @@ results.")
(define-public r-dropletutils
(package
(name "r-dropletutils")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DropletUtils" version))
(sha256
- (base32 "09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y"))))
+ (base32 "0bnxk72a0ygh4nqwyjzzi79zc4md8pwk0pr6jn43in0wdk054wf6"))))
(properties `((upstream-name . "DropletUtils")))
(build-system r-build-system)
(propagated-inputs
@@ -5331,13 +5528,13 @@ Beta-Binomial distributions.")
(define-public r-dyndoc
(package
(name "r-dyndoc")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DynDoc" version))
(sha256
(base32
- "16cb4pby6ja0xy8ygbgr6zfbyp4agyhlds5sayc5ryq50vafykah"))))
+ "0d2axaszy7rpi47yg4vhd1z70m53nx40znapgg5pq6ahrx7if5f1"))))
(properties `((upstream-name . "DynDoc")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/DynDoc")
@@ -5350,13 +5547,13 @@ dynamic documents and vignettes.")
(define-public r-bluster
(package
(name "r-bluster")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "bluster" version))
(sha256
(base32
- "15f103lpl686730vl8g69fhki9iq2ncgr5dm6qm2xc9bq9vh65s9"))))
+ "16zkv567d39258syhfb215y04sq3pnfjh9pgbp5z85hcfpz4qmhc"))))
(properties `((upstream-name . "bluster")))
(build-system r-build-system)
(propagated-inputs
@@ -5380,21 +5577,21 @@ and evaluate clustering results.")
(define-public r-ideoviz
(package
(name "r-ideoviz")
- (version "1.36.0")
+ (version "1.37.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
- "1za1cxf734mar9hbvqrijdg61g0jag9jdzmi8p8ka62xbikxqa3s"))))
+ "1bhari5ghag5f5dlrgm79hckbh0bamd9567z04qi0spnfr97wf3s"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
- r-iranges
+ r-genomeinfodb
r-genomicranges
+ r-iranges
r-rcolorbrewer
- r-rtracklayer
- r-genomeinfodb))
+ r-rtracklayer))
(home-page "https://bioconductor.org/packages/IdeoViz/")
(synopsis "Plots data along a chromosomal ideogram")
(description "This package provides functions to plot data associated with
@@ -5404,14 +5601,14 @@ arbitrary genomic intervals along chromosomal ideogram.")
(define-public r-infercnv
(package
(name "r-infercnv")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "infercnv" version))
(sha256
(base32
- "19fk4pzhwj9pfh4vg943xb4cdfpq65ax75d61w1mm3f71gg56z5g"))))
+ "1yxg04644yqy3wbqbsf4hcvvimkk8z60xizpy4rc48i3hxjm7nbf"))))
(properties `((upstream-name . "infercnv")))
(build-system r-build-system)
(inputs (list python))
@@ -5443,8 +5640,8 @@ arbitrary genomic intervals along chromosomal ideogram.")
r-rcolorbrewer
r-reshape2
r-rjags
- r-singlecellexperiment
r-seurat
+ r-singlecellexperiment
r-summarizedexperiment
r-tidyr))
(native-inputs (list r-knitr))
@@ -5464,13 +5661,13 @@ over-abundant or less-abundant as compared to that of normal cells.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.34.1")
+ (version "2.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z"))))
+ "0rhh82hrsm32bdjamfah84p7zi8fvr4shyq2rdjfxzdp9qy5rh2q"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -5492,13 +5689,13 @@ possible.")
(define-public r-isoformswitchanalyzer
(package
(name "r-isoformswitchanalyzer")
- (version "2.0.1")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
(sha256
- (base32 "1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf"))))
+ (base32 "1yin2jv06g3jrzadq6yjcr14jz1zzwyxipzna5csgr013dkkrl8h"))))
(properties `((upstream-name . "IsoformSwitchAnalyzeR")))
(build-system r-build-system)
(propagated-inputs
@@ -5573,13 +5770,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).")
(define-public r-italics
(package
(name "r-italics")
- (version "2.60.0")
+ (version "2.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ITALICS" version))
(sha256
- (base32 "09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08"))))
+ (base32 "0zk9n94nqw6vpw908ka32zppxwqkki9krzxib06y1nic3bri3w9i"))))
(properties `((upstream-name . "ITALICS")))
(build-system r-build-system)
(propagated-inputs
@@ -5708,13 +5905,13 @@ mapping.")
(define-public r-nebulosa
(package
(name "r-nebulosa")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Nebulosa" version))
(sha256
(base32
- "0lqm9mfmaxdhhs9di2kjg2rixng78lrrikyp7blmpyqk4c41j3nh"))))
+ "0kzkdwxrhl7plbcbqr58gnadhhbhx2811ian0s4kds14y4mxl26c"))))
(properties `((upstream-name . "Nebulosa")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2
@@ -5784,14 +5981,14 @@ performing parallel computations on multicore machines.")
(define-public r-affy
(package
(name "r-affy")
- (version "1.78.2")
+ (version "1.80.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affy" version))
(sha256
(base32
- "0zsr87zsw5rp5rgdiv1bbsi6fx6b7qzlgjirzczky6fmf4dqwgnm"))))
+ "0lsvcv7nprmsh62d0r2v44a5n915crvv1cbj9ba6fdggj7wp8zyk"))))
(build-system r-build-system)
(propagated-inputs
(list r-affyio
@@ -5812,14 +6009,14 @@ analysis.")
(define-public r-affycomp
(package
(name "r-affycomp")
- (version "1.76.1")
+ (version "1.78.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycomp" version))
(sha256
(base32
- "0wccj8q8sl0zc68nr5qf1qih8awqf1h6bwi5hq9d7r59p4g4r9n1"))))
+ "0818mgwny9hznw7lawrvmk11nwy0wxgjnlkf083vv3js4aq31gfp"))))
(properties `((upstream-name . "affycomp")))
(build-system r-build-system)
(propagated-inputs (list r-biobase))
@@ -5878,14 +6075,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
(define-public r-affycontam
(package
(name "r-affycontam")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyContam" version))
(sha256
(base32
- "07a6kd51rlj433yxmyd2j8nl8qn1hw8wv3mk270dp8xxlk613y3p"))))
+ "1jxp4qacclfl07ig8dfwy5gpnsqrfqnjbci1a7znc7acqg0kv0zv"))))
(properties `((upstream-name . "affyContam")))
(build-system r-build-system)
(propagated-inputs
@@ -5943,14 +6140,14 @@ to streamline the more common analyses that a Biostatistician might see.")
(define-public r-affyio
(package
(name "r-affyio")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyio" version))
(sha256
(base32
- "1r1c0iwix0n8r433x4bv8hvzhkablc4xkdgg2b1fk4ijhd1iwf3c"))))
+ "01shv7936cb5yynxkdssczl752ayv2rx4qkrkddqhi5smksw13z9"))))
(build-system r-build-system)
(propagated-inputs
(list r-zlibbioc))
@@ -5967,14 +6164,14 @@ CDF file formats.")
(define-public r-affxparser
(package
(name "r-affxparser")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affxparser" version))
(sha256
(base32
- "0n86my3bzy3g7xn60kizs5ym5m016zrkg7dv96kx246mrnv0ax8y"))))
+ "18qjdsgkmdhwv2c4sbixp7fn69sbjdipn363jnms95dksdj2xvr9"))))
(properties `((upstream-name . "affxparser")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -5995,14 +6192,14 @@ structure.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.78.0")
+ (version "1.80.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "1104r6jdy3nza8329xmq428ljfbfi2xwkd92sw519g0yqryh09vy"))))
+ "10mdlbgbvdj967bih6wpvxmy91r10p8frhgcwv8mhv4g94ardasd"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -6022,13 +6219,13 @@ microarrays.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.62.2")
+ (version "1.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0vprm84k79pfnkkg9vf3gyb1nhzmin5lp5375rsaj6fnzbd46dw9"))))
+ "0nyw3x5ivq969p2w788zi4pp0pwjv5hhpjpl5lyfzhak9ydylgh6"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -6052,13 +6249,13 @@ annotation data packages using SQLite data storage.")
(define-public r-annotationfilter
(package
(name "r-annotationfilter")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationFilter" version))
(sha256
(base32
- "10jkxjmsshrr08c397qvkgrcfwzvrbd2hci1nal4vd5mm77f9cl9"))))
+ "0cd2vcnx0pn5wba3x5q32vddjjp7fvix7yd7jrwv07a2fkv9c4p5"))))
(properties
`((upstream-name . "AnnotationFilter")))
(build-system r-build-system)
@@ -6077,14 +6274,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.42.2")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "0b4dmjv7y50c1rn76wlhnlz93kidvg1byj72vq2s11kdzyq3pmss"))))
+ "0dbbg0wvk1ndv20d5j80waaz0z1bsp7y2k2m17jly4ax2hc5frc9"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@@ -6109,14 +6306,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "3.8.0")
+ (version "3.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "0ri8qj5j10bhprkb810c2hl5sl944kpb8rf5lab6nxykzgyz73v0"))))
+ "1mx3vip1rx5lq0vnkxpmkyksnq4vygmww85vxq3spr0fah1pwnkr"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
@@ -6150,14 +6347,14 @@ by the user, helping with quick and reproducible access.")
(define-public r-aroma-light
(package
(name "r-aroma-light")
- (version "3.30.0")
+ (version "3.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "aroma.light" version))
(sha256
(base32
- "118yqvbj4ad2b2bik0zi3ir15kxh9fbdi9qqyk52isvcdbv6069p"))))
+ "1i6rml0slfsf01a3sphyzrxp2z759psq5bv9cfy5dxx44fnav8b8"))))
(properties `((upstream-name . "aroma.light")))
(build-system r-build-system)
(propagated-inputs
@@ -6174,14 +6371,14 @@ classes.")
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk"))))
+ "1qv2gydn8awrkbhdrgxm8zxpicphqc29rwzkj3vyaa9glmnx2y34"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
@@ -6204,13 +6401,13 @@ paired-end data.")
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.60.0")
+ (version "2.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "1xjs5nxr3dffllp599hf0cx71a2czqmhf7zj2sp6rz06kcxib905"))))
+ "0znkawzr3hgbp2dkdk30ziqa6ylbq2nf0xmz4vi089cw9763lxgg"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
@@ -6227,13 +6424,13 @@ on Bioconductor or which replace R functions.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.56.1")
+ (version "2.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0jqv2mv4ridi5lffva20a5s479bzpxhblyymricb17fd400rag8f"))))
+ "1m6c6m9z0d1k6s2q0ikd78ahcq72gzqnhlprdn0xvkjxrgh1i2lf"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -6267,13 +6464,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biomartr
(package
(name "r-biomartr")
- (version "1.0.5")
+ (version "1.0.6")
(source (origin
(method url-fetch)
(uri (cran-uri "biomartr" version))
(sha256
(base32
- "14nw44dkyrfw43dc4zwsnvkrmdhsl131m9w1wa80j3qkbhyaypfl"))))
+ "06wd8s2cssw58xp9d078fc7iycpxryccnclrk3gnh757j1h0vzim"))))
(properties `((upstream-name . "biomartr")))
(build-system r-build-system)
(propagated-inputs
@@ -6312,13 +6509,13 @@ only one command.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.34.2")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "0j0yi0g0zri0liy9xm2j3k848smhib5mmkvwcw6281iwnpn7yypq"))))
+ "19h80qf0zdxfg3pkcwwywh9gg0ymv92n51qpimnw4c3w5iaszy6b"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -6363,13 +6560,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.68.1")
+ (version "2.70.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "13cnjbq2iykv83ycb4151d7yys21s3v15fc72v3s02m1i92lqyq4"))))
+ "198y36yfkncsp4sw00ij8cal45al67f9nx84bbszhygaq0jh504y"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -6380,6 +6577,7 @@ objects.")
r-iranges
r-s4vectors
r-xvector))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/Biostrings")
(synopsis "String objects and algorithms for biological sequences")
(description
@@ -6391,14 +6589,14 @@ biological sequences or sets of sequences.")
(define-public r-biovizbase
(package
(name "r-biovizbase")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biovizBase" version))
(sha256
(base32
- "0na37f2nfavgxd2xhprfb6bv68zm2h6glbkffspc3gsnw1q5h6da"))))
+ "01hli49aq1fjjgpk465znq1ki0qi7nxg71pqg18fz6nblg3ny9z5"))))
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
@@ -6433,18 +6631,19 @@ effort and encourages consistency.")
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.68.0")
+ (version "1.70.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "0fx2mkzyhbn8iayw14nr913wd4xhp76b1zjb85akrxaab2dm4zz8"))))
+ "1bdrh1kp7ihnlyvgdvwdzly69l9zy5rr09gizm0l59zy4kh59nih"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
+ r-biocio
r-biostrings
r-genomeinfodb
r-genomicranges
@@ -6464,14 +6663,14 @@ genome data packages and support for efficient SNP representation.")
(define-public r-category
(package
(name "r-category")
- (version "2.66.0")
+ (version "2.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "1wjf6xbnys7nv8z4xrzck1wk5xifkdni672kigs0aqdxqj8d80f5"))))
+ "19qyxqky1gsrjylmc2h0sndbqlk2ibrps7123gqwn19p8kg4nhf0"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
@@ -6479,12 +6678,12 @@ genome data packages and support for efficient SNP representation.")
r-annotationdbi
r-biobase
r-biocgenerics
+ r-dbi
r-genefilter
r-graph
r-gseabase
r-matrix
- r-rbgl
- r-dbi))
+ r-rbgl))
(home-page "https://bioconductor.org/packages/Category")
(synopsis "Category analysis")
(description
@@ -6557,13 +6756,13 @@ regions and to highlight copy number alterations.")
(define-public r-chipseeker
(package
(name "r-chipseeker")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChIPseeker" version))
(sha256
(base32
- "0nngygci1g8bb3rsica348zi59hskr6hf8319csia6cman89gvqm"))))
+ "0bx85y5888w85miif73y0yd9j4kdmjn1cfck1xshnqnsrh7p3m50"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -6572,18 +6771,17 @@ regions and to highlight copy number alterations.")
r-aplot
r-biocgenerics
r-boot
+ r-dplyr
r-enrichplot
- r-iranges
r-genomeinfodb
- r-genomicranges
r-genomicfeatures
+ r-genomicranges
r-ggplot2
r-gplots
r-gtools
- r-dplyr
- r-plotrix
- r-dplyr
+ r-iranges
r-magrittr
+ r-plotrix
r-rtracklayer
r-s4vectors
r-tibble
@@ -6605,14 +6803,14 @@ annotation, distance to TSS, and overlap of peaks or genes.")
(define-public r-chipseq
(package
(name "r-chipseq")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chipseq" version))
(sha256
(base32
- "0q83c4dm9qbdxlh4cbdzp357fn4sa16d7dqb4s65650pcnjg3a48"))))
+ "1fw99xnll4jwdmp49jh59zxcbp3qs2850pjdg403sv4cg1bgfdyi"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
@@ -6632,14 +6830,14 @@ experiments.")
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "08jpbw7qns736zq1fwk9lyr4qm7rgzzw3hksv59zwb1458a79pzy"))))
+ "0zzp0kci5daffpyv56advdcs05pz3nmjn07bmm7r3hwpk0nr3fcf"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
@@ -6794,14 +6992,14 @@ distribution.")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.40.2")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0rb6b2aqn3an5ria4yjasjr7aldr5606rkc4yw275x9ddii22djg"))))
+ "1mz7v0vcl741zjvj63mk48hhbq6sk2fl2dwn9y1a6hr8fb79vy1a"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
@@ -6812,6 +7010,7 @@ distribution.")
r-ggplot2
r-iranges
r-locfit
+ r-matrixgenerics
r-matrixstats
r-rcpp
r-rcpparmadillo
@@ -6831,14 +7030,14 @@ distribution.")
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "0z4i3lsaziq3hprk64akx7jl6b757kmd8k6gv5pn36pavc6x1a0g"))))
+ "1q59agaidf0nkq599iz54a253sjxzillj39za86ihfj5xws24f8w"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6876,13 +7075,13 @@ exploration of the results.")
(define-public r-diffcyt
(package
(name "r-diffcyt")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "diffcyt" version))
(sha256
- (base32 "1vsn9z06vmfw6741x7dri3d9wh4rqhzak9r506y3c3h2gjjwilv1"))))
+ (base32 "1k3gzzgda29m2v7v8hqw7c2s8z778p0plqxag443lhsxcm6izcxi"))))
(properties `((upstream-name . "diffcyt")))
(build-system r-build-system)
(propagated-inputs
@@ -6914,14 +7113,14 @@ adapted from transcriptomics.")
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DirichletMultinomial" version))
(sha256
(base32
- "1vslg6hp498ar4l1b8rdxscz5wj1xci866j8975wr378lnymb942"))))
+ "1rvic3acrf4qdag423f8xa6bnqrqr31vj7k4l7a5kzf1fjm359wy"))))
(properties
`((upstream-name . "DirichletMultinomial")))
(build-system r-build-system)
@@ -6941,13 +7140,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-dittoseq
(package
(name "r-dittoseq")
- (version "1.12.1")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "dittoSeq" version))
(sha256
(base32
- "0gpgmy1yqgxvxiyrinxnn78w68w81ldqyhzwz3yxj2brlld6ycd1"))))
+ "17ks6bbhv8iw8grzlkibgqmwggrqp5hikg1p49m4a6b6bayillv2"))))
(properties `((upstream-name . "dittoSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6985,14 +7184,14 @@ code{dittoColors()}.")
(define-public r-edaseq
(package
(name "r-edaseq")
- (version "2.34.0")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EDASeq" version))
(sha256
(base32
- "0gf4k02b5qywrg5rpg6hs9gyzcdlpw36ndgz3ca19plicair4mih"))))
+ "0xvi5mynkf1n74bn2k6gxmyhp1piwzsljd37biibdfzy14r1ir08"))))
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
@@ -7025,17 +7224,18 @@ global-scaling and full-quantile normalization.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.42.4")
+ (version "4.0.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1lyn017jqgn6d987zrk0kp2p2nw3mxf8zjspk31pky532p9pkhs3"))))
+ "0vjydwjazl7br0hvshy7jip3z6w73bif9vaky20im5rv40pqnchh"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(list r-limma r-locfit r-rcpp))
+ (native-inputs (list r-knitr))
(home-page "https://bioinf.wehi.edu.au/edgeR")
(synopsis "EdgeR does empirical analysis of digital gene expression data")
(description "This package can do differential expression analysis of
@@ -7050,13 +7250,13 @@ CAGE.")
(define-public r-enhancedvolcano
(package
(name "r-enhancedvolcano")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "EnhancedVolcano" version))
(sha256
(base32
- "1mcyhgdvfmkkh0rlhf51an7j1zi96lqdhifki2aqmlx0lqvg4qxq"))))
+ "097w3957m47m03iy8xc1m7pdgm3qy0kzqbllic8pd79qglrla802"))))
(properties `((upstream-name . "EnhancedVolcano")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2 r-ggrepel))
@@ -7078,13 +7278,13 @@ parameter configurations.")
(define-public r-enmix
(package
(name "r-enmix")
- (version "1.36.0")
+ (version "1.38.01")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ENmix" version))
(sha256
(base32
- "1cwj45rnb6ra1bnd0plkjfvfsix25xr51yh6rwrfj524c35r70w1"))))
+ "1wh9lri9dp3904c2n6562z7p9gqx39dmag55imx8zrqnayxamc03"))))
(properties `((upstream-name . "ENmix")))
(build-system r-build-system)
(propagated-inputs
@@ -7101,9 +7301,9 @@ parameter configurations.")
r-illuminaio
r-impute
r-iranges
+ r-irlba
r-matrixstats
r-minfi
- r-preprocesscore
r-quadprog
r-rpmm
r-s4vectors
@@ -7120,14 +7320,14 @@ visualization of Illumina DNA methylation array data.")
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.24.1")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "1x73lln0rlnypl8iia54srl3wrazs94f8rspmjsaqsxwknkym319"))))
+ "010fp03x1splddxmhpxlfv1i3paqgbcxm7l9z2lmm6zfixhb158a"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -7165,18 +7365,19 @@ chromosome region or transcript models of lincRNA genes.")
(define-public r-fastseg
(package
(name "r-fastseg")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fastseg" version))
(sha256
(base32
- "0gygyf1xq1z6vzand43n965p366zh0k3rv58gnyqa81whj4dvcq3"))))
+ "10g9mdh7nzdz2b1k5gg5hk35lpapcnbs3p3z17k15aq040lpm236"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase r-biocgenerics r-genomicranges r-iranges
r-s4vectors))
+ (native-inputs (list r-knitr))
(home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
(synopsis "Fast segmentation algorithm for genetic sequencing data")
(description
@@ -7192,14 +7393,14 @@ microarrays or GRanges for sequencing data.")
(define-public r-gage
(package
(name "r-gage")
- (version "2.50.0")
+ (version "2.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "16wx2w70i12420022xz2zx8pizzyxb7z1pcmqn515cs89f1qcnli"))))
+ "0bm5hvy3cdcm46527w45mnnnk95qm28xzdk1m53615gh55ix4iy8"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi r-go-db r-graph r-keggrest))
@@ -7220,14 +7421,14 @@ analysis using other methods.")
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.82.1")
+ (version "1.84.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "1wpg8banz6s6smycfqf9hqryp4kf2gs069s7npyvpq53wy0kxyny"))))
+ "0q80z872d3z1jy69b53qxzvmshf5zx4qssmp4gj7fwdpfxj9qqjw"))))
(build-system r-build-system)
(native-inputs
(list gfortran r-knitr))
@@ -7244,16 +7445,16 @@ high-throughput sequencing experiments.")
(define-public r-geneoverlap
(package
(name "r-geneoverlap")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GeneOverlap" version))
(sha256
(base32
- "1bimsayaf68j15im591r6rbvydhbmiqcp1pphd5zzg6hzp6va927"))))
+ "074d3inz8sh8xxjliisa0p99rgy6r9fg9ljaka5bf1waxwpknzpw"))))
(build-system r-build-system)
(propagated-inputs
- (list r-rcolorbrewer r-gplots))
+ (list r-gplots r-rcolorbrewer))
(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
@@ -7263,13 +7464,13 @@ and visualize the results.")
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "0y6a2qxxp5mnkllcq46j00069z22ixnrbkd15s007a35lhkibz21"))))
+ "1vbpx187m5d5g307f4jiwyy1sw4jgj1s18622y3a458ixv540zkc"))))
(build-system r-build-system)
(propagated-inputs
(list r-biostrings
@@ -7310,13 +7511,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.36.4")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0wwh72sj894m3awk4g2zmkkwqafdjyxzsr49vnd1fiyz909hw02a"))))
+ "1a82xx1ijmfxk6d4pjqy45cdrnf75yrs7l7l64brl5d5dif45s42"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -7336,13 +7537,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1irzcz9s97gqbyj9j71wxv2ikdfd8g14296fg33w2ykfdm80nzf0"))))
+ "06xa3dcdk6jprvpyvr3pfbv6qv8xrqw2n6rrfp8q8qizx3ifj431"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@@ -7369,13 +7570,13 @@ alignments.")
(define-public r-genomicdatacommons
(package
(name "r-genomicdatacommons")
- (version "1.24.3")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicDataCommons" version))
(sha256
(base32
- "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38"))))
+ "1inikcczkhav6h6a46ix9ixkf7b1n8rf766m5hmhmx09sspzsm5w"))))
(properties `((upstream-name . "GenomicDataCommons")))
(build-system r-build-system)
(propagated-inputs (list r-dplyr
@@ -7401,13 +7602,13 @@ Commons RESTful service.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.52.2")
+ (version "1.54.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0givyx77gvx24wgq180jsb2q1b8g4j49rs6bxdmd0l04a87hm9cr"))))
+ "1b2rx16l7zd4lisqssbkcwi534s7m7h1w6k72km6c835x2cdxfs4"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -7445,14 +7646,14 @@ extracting the desired features in a convenient format.")
(define-public r-genomicfiles
(package
(name "r-genomicfiles")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFiles" version))
(sha256
(base32
- "0nxz8lvpmyllgs1ksgbha8qqs4fhppkg5casppnas9x47dj4bxph"))))
+ "1kvys60hhb0ndjvjdanfgciq3jc42iag8r0a199gv6w5bjaxp6wm"))))
(properties `((upstream-name . "GenomicFiles")))
(build-system r-build-system)
(propagated-inputs
@@ -7480,13 +7681,13 @@ provide added flexibility for data combination and manipulation.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.52.0")
+ (version "1.54.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "0vbr8nqn4pk0w3wx94q4f44psy6lxgx4b7p8hp0vf46flwggj2lj"))))
+ "1vrs3r8dyhhwj0s3vwvr168s84x5hj10lnpg1xf5c2kbj26bdv0w"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
@@ -7507,13 +7708,13 @@ manipulating genomic intervals and variables defined along a genome.")
(define-public r-glad
(package
(name "r-glad")
- (version "2.64.0")
+ (version "2.66.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GLAD" version))
(sha256
(base32
- "0fi7wwn0ai4bwy8wgwl4dh3fbl6zhrkcy662dc1fcnk5i7rnv3y5"))))
+ "04wyzn56crz7sa453qj07p90vvg8nwrqz54m9ms9vf9z8adpck51"))))
(properties `((upstream-name . "GLAD")))
(build-system r-build-system)
(inputs (list gsl))
@@ -7531,13 +7732,13 @@ regions identified.")
(define-public r-globalancova
(package
(name "r-globalancova")
- (version "4.18.0")
+ (version "4.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GlobalAncova" version))
(sha256
(base32
- "1fld18rmi6rqm2nr549a4740w1iq3mf5df67v9ba6h42r4abs1ar"))))
+ "0j1ma04zjsvf668idms8hx1vnw3sh5yy8fbhwscyk1qbfy708cfh"))))
(properties `((upstream-name . "GlobalAncova")))
(build-system r-build-system)
(propagated-inputs (list r-annotate
@@ -7563,13 +7764,13 @@ linear models via the extra sum of squares principle.")
(define-public r-globaltest
(package
(name "r-globaltest")
- (version "5.54.0")
+ (version "5.56.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "globaltest" version))
(sha256
(base32
- "0jjhhg4vi44xqlvmcd80m30m93qyd4c79i7m9jn5hz3mw211xaig"))))
+ "14kcsx1gynl0fijq67qb5zvfxn4yqj8809p7535y455rd0vddp5r"))))
(properties `((upstream-name . "globaltest")))
(build-system r-build-system)
(propagated-inputs
@@ -7587,14 +7788,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.")
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.66.0")
+ (version "2.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "1jjcjc1zp42l3gw36rr84al07ghih0cjx4p8gn8rlmv1jsz6kp1h"))))
+ "1v10ss1gf4a3qp6hbwa2f0la9sgiwhszg4c45qd6gv0dja2v30fs"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
@@ -7605,8 +7806,8 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.")
r-category
r-go-db
r-graph
- r-rgraphviz
- r-rbgl))
+ r-rbgl
+ r-rgraphviz))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/GOstats")
(synopsis "Tools for manipulating GO and microarrays")
@@ -7619,14 +7820,14 @@ testing and other simple calculations.")
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "0xfcgvsglcwkwsb1azmp4n4hx95fxnjk7rlwggb1f5rjw440qjnh"))))
+ "1y7z3627shskwss8bzjz1xm02rv4s7cdi91v1xqdsbdayjkrh1nb"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
@@ -7648,13 +7849,13 @@ Enrichment Analysis} (GSEA).")
(define-public r-gsva
(package
(name "r-gsva")
- (version "1.48.3")
+ (version "1.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GSVA" version))
(sha256
(base32
- "0ljfw65ray9ks8g55bfzn0c1w4412y4a7996zddywn5qj5pkjkfb"))))
+ "01w5j7fmi3hsfd282kcn4v41mi58z2yfhapff2zgf9swdfps4m6z"))))
(properties `((upstream-name . "GSVA")))
(build-system r-build-system)
(propagated-inputs (list r-biobase
@@ -7688,13 +7889,13 @@ manner.")
(define-public r-harshlight
(package
(name "r-harshlight")
- (version "1.72.0")
+ (version "1.74.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Harshlight" version))
(sha256
(base32
- "1rg3gx42a68jqbdmbqx7lh97y0rird1lci7146hnxa4svj827d5p"))))
+ "1djs95l04b3qrqcb7jkzhfmxzbsn2riyydz8p2lmilg6z9rkdqx7"))))
(properties `((upstream-name . "Harshlight")))
(build-system r-build-system)
(propagated-inputs
@@ -7715,14 +7916,14 @@ matrix to solve the memory problem.")
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "1sg0mjada72a13xh3k6xsiaff7xj4mp76r6i8iab8nfkvng07p4i"))))
+ "19jdy0q3larl5lxjzqlnyynq9rya56fyvf1yx9pwsyag1c148z08"))))
(build-system r-build-system)
(arguments
(list
@@ -7747,19 +7948,120 @@ matrix to solve the memory problem.")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-r3cseq
+ (package
+ (name "r-r3cseq")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "r3Cseq" version))
+ (sha256
+ (base32 "1llkfcy13h0c973703jmpgp2n6xxfsizb9iw1wxzgkbp1v0iy268"))))
+ (properties `((upstream-name . "r3Cseq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biostrings
+ r-data-table
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-qvalue
+ r-rcolorbrewer
+ r-rsamtools
+ r-rtracklayer
+ r-sqldf
+ r-vgam))
+ (home-page "http://r3cseq.genereg.net/Site/index.html")
+ (synopsis
+ "Analysis of Chromosome conformation capture and Next-generation sequencing")
+ (description
+ "This package is used for the analysis of long-range chromatin
+interactions from 3C-seq assay.")
+ (license license:gpl3)))
+
+(define-public r-r4rna
+ (package
+ (name "r-r4rna")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "R4RNA" version))
+ (sha256
+ (base32 "1qmr1s7z2f126wkwxjpr9fvak4i7mzgvfflkycgavbdqshn1rk6l"))))
+ (properties `((upstream-name . "R4RNA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biostrings))
+ (home-page "https://www.e-rna.org/r-chie/")
+ (synopsis "RNA visualization and analysis")
+ (description
+ "This package provides a package for RNA basepair analysis, including the
+visualization of basepairs as arc diagrams for easy comparison and annotation of
+sequence and structure. Arc diagrams can additionally be projected onto
+multiple sequence alignments to assess basepair conservation and covariation,
+with numerical methods for computing statistics for each.")
+ (license license:gpl3)))
+
+(define-public r-radiogx
+ (package
+ (name "r-radiogx")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RadioGx" version))
+ (sha256
+ (base32 "0ykmvva5h1y7x9bxhqqfc18car9nasy06v1jjban7dlm95dl8nmk"))))
+ (properties `((upstream-name . "RadioGx")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-assertthat
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-catools
+ r-coregx
+ r-data-table
+ r-downloader
+ r-magicaxis
+ r-matrixstats
+ r-rcolorbrewer
+ r-reshape2
+ r-s4vectors
+ r-scales
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/RadioGx")
+ (synopsis "Analysis of large-scale radio-genomic data")
+ (description
+ "This package is a computational tool box for radio-genomic analysis
+which integrates radio-response data, radio-biological modelling and
+comprehensive cell line annotations for hundreds of cancer cell lines. The
+@code{RadioSet} class enables creation and manipulation of standardized
+datasets including information about cancer cells lines, radio-response assays
+and dose-response indicators. Included methods allow fitting and plotting
+dose-response data using established radio-biological models along with
+quality control to validate results. Additional functions related to fitting
+and plotting dose response curves, quantifying statistical correlation and
+calculating @acronym{AUC, area under the curve} or @acronym{SF, survival
+fraction} are included.")
+ (license license:gpl3)))
+
(define-public r-raggedexperiment
(package
(name "r-raggedexperiment")
- (version "1.24.2")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RaggedExperiment" version))
(sha256
(base32
- "0aa886mmk1c5h1i3xnk4niq4ylrawpsn2f62hwmfj5dsyl8a36ka"))))
+ "07wx2icvxgrds1w7cx9pn99z6rzk2ih938j8g1laxmgx9sya74v6"))))
(properties `((upstream-name . "RaggedExperiment")))
(build-system r-build-system)
- (propagated-inputs (list r-biocgenerics
+ (propagated-inputs (list r-biocbaseutils
+ r-biocgenerics
r-genomeinfodb
r-genomicranges
r-iranges
@@ -7783,13 +8085,13 @@ rectangular dataset.")
(define-public r-rdisop
(package
(name "r-rdisop")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rdisop" version))
(sha256
(base32
- "02mj02sa9qxc6678irx7g3yzab4sa5sf4jkdjzsi9i6519xd7sa4"))))
+ "1jz063hsrrbrqqx8p5yknagw19hsw51arck591h95dckncxd0006"))))
(properties `((upstream-name . "Rdisop")))
(build-system r-build-system)
(propagated-inputs (list r-rcpp))
@@ -7805,14 +8107,14 @@ be calculated to search in MS peak lists.")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "1p8imns26knh21r254n7i9xvy8xzz3zizx0kq4si7cdaf2b4xayi"))))
+ "1h0hzs4f4mmnpi436dgib9lakljacznkyyssy7c4mdd419431aq2"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -7834,13 +8136,13 @@ of other R packages who wish to make use of HTSlib.")
(define-public r-impute
(package
(name "r-impute")
- (version "1.74.1")
+ (version "1.76.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "0nz8ggzk2g5w20yyhp6av6hy69kbmg3ncfpq9ppmq6p5a0msx92l"))))
+ "0q7mnx99ndna1r2r0v7jc3w8ly8qw33flwbgkcvrfhk6dzvbn4pl"))))
(native-inputs
(list gfortran))
(build-system r-build-system)
@@ -7851,16 +8153,17 @@ of other R packages who wish to make use of HTSlib.")
microarray data, using nearest neighbor averaging.")
(license license:gpl2+)))
+;; TODO: check javascript
(define-public r-interactivedisplay
(package
(name "r-interactivedisplay")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "interactiveDisplay" version))
(sha256
(base32
- "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl"))
+ "0w81c5kc48gjavln50ysgr3vaf8s4fb6632ckzb1q225j9ik2gia"))
(snippet
'(for-each delete-file
'("inst/www/js/jquery.js"
@@ -7897,9 +8200,7 @@ microarray data, using nearest neighbor averaging.")
(propagated-inputs
(list r-annotationdbi
r-biocgenerics
- r-biocmanager
r-category
- r-dt
r-ggplot2
r-gridsvg
r-interactivedisplaybase
@@ -7907,7 +8208,6 @@ microarray data, using nearest neighbor averaging.")
r-rcolorbrewer
r-reshape2
r-shiny
- r-zlibbioc
r-xml))
(native-inputs
`(("esbuild" ,esbuild)
@@ -7938,14 +8238,14 @@ visualizations and interfaces for working with Bioconductor data.")
(define-public r-interactivedisplaybase
(package
(name "r-interactivedisplaybase")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "interactiveDisplayBase" version))
(sha256
(base32
- "1p3lwk8g14srkhl3x3i0v2d9071251ldy9964mii11k1bp2g08am"))))
+ "14cw90qlp8y4k0fs7xim8qvhzwbb8sn334mc72fkxg1h4bs8bxjw"))))
(properties
`((upstream-name . "interactiveDisplayBase")))
(build-system r-build-system)
@@ -7963,14 +8263,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.40.1")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "13pbw5nlkjwplliv2pdwazv2idfjklvw0ykx5ja8rchvzs5f1vk4"))))
+ "05fc1i1bcdvvy4mr4m2cdqxd3jrj1rxkxy7c43yrliv5dlikyb07"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
@@ -7987,13 +8287,13 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-lea
(package
(name "r-lea")
- (version "3.12.2")
+ (version "3.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "LEA" version))
(sha256
(base32
- "1kxrrl8pxhaipmzsw8gs4gs8g8xbp8169z9f7bcpgrfapnawafm9"))))
+ "1rhlrcp9rzf64rkabgk3gd8jqdg8ldwpkxvpfb6g49bgpkg1h6b1"))))
(properties `((upstream-name . "LEA")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -8018,13 +8318,13 @@ scale with the dimensions of large data sets.")
(define-public r-lfa
(package
(name "r-lfa")
- (version "2.0.11")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lfa" version))
(sha256
- (base32 "0x169fxwlccsqwj1bpviaky3hfr0zdwsdrlgfvrb4j6j95qfgnns"))))
+ (base32 "1xrwvw7227znd1h7426k8l86197yc24b4v608issh5fqglmhljns"))))
(properties `((upstream-name . "lfa")))
(build-system r-build-system)
(propagated-inputs (list r-corpcor r-rspectra))
@@ -8039,14 +8339,16 @@ Binomial data via estimation of latent structure in the natural parameter.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.56.2")
+ (version "3.58.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0miyba9frn1p4pkclzpr0bfazsk0br2jgpwpwwh773d3103hkn0r"))))
+ "01byjnhhjyxk9x871rk8bgqq6lkp1a6dylqbdphpzp88b1jf2f9m"))))
(build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (propagated-inputs (list r-statmod))
(home-page "https://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(description "This package can be used for the analysis of gene expression
@@ -8058,13 +8360,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-maaslin2
(package
(name "r-maaslin2")
- (version "1.14.1")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Maaslin2" version))
(sha256
- (base32 "06mb72hbzihdficv73yqbb2m86bkw78w3vbw1rm98n0npxq2fch6"))))
+ (base32 "1d95dv46b36ncwb7zdn0wvshg4v73qjfs3hij0jmbkkxvf2il9iq"))))
(properties `((upstream-name . "Maaslin2")))
(build-system r-build-system)
(propagated-inputs
@@ -8106,13 +8408,13 @@ of data exploration, normalization, and transformation methods.")
(define-public r-made4
(package
(name "r-made4")
- (version "1.74.0")
+ (version "1.76.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "made4" version))
(sha256
(base32
- "1233l5160msxp85vm2h0j3k073vv5d9wj55709x4s657fi9la6ij"))))
+ "03fhiszlmjh8nvz3gppf45r9kpcjrdb601ar17c4f2aygjpkf0cg"))))
(properties `((upstream-name . "made4")))
(build-system r-build-system)
(propagated-inputs
@@ -8135,13 +8437,13 @@ datasets (coinertia analysis).")
(define-public r-makecdfenv
(package
(name "r-makecdfenv")
- (version "1.76.0")
+ (version "1.78.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "makecdfenv" version))
(sha256
(base32
- "1a6kngwmc7nvzlgpnhdv4j180847gjh4i3dshld0pcvy3b6bjv8r"))))
+ "0mggcw0390i1y2wn4k8570gjmbsx6hbipi8fkhz2zj9icsx89x1l"))))
(properties `((upstream-name . "makecdfenv")))
(build-system r-build-system)
(inputs (list zlib))
@@ -8162,13 +8464,13 @@ package that automatically loads that environment.")
(define-public r-manor
(package
(name "r-manor")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MANOR" version))
(sha256
- (base32 "0ili9xy7vvw17mz44lxadv1vkf3ahpks2l34qa9yfccpalwhzriw"))))
+ (base32 "10zf6c1vx6cp4wg6axpmbpxk2hlmf6mga7rdh765fznwb71r4h0x"))))
(properties `((upstream-name . "MANOR")))
(build-system r-build-system)
(propagated-inputs (list r-glad))
@@ -8185,13 +8487,13 @@ experiments.")
(define-public r-maser
(package
(name "r-maser")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "maser" version))
(sha256
(base32
- "1ma5d1i56gw8hm2pgvzzvmdd1cm2xb42rgf5lb6sf4v47yzlyb9f"))))
+ "0h7x1fyfvnjc30w9ydbnlqijz58q2kcxv4yy784rf4adsrdhwh45"))))
(properties `((upstream-name . "maser")))
(build-system r-build-system)
(propagated-inputs
@@ -8217,13 +8519,13 @@ and visualizaton of alternative splicing events generated by rMATS.")
(define-public r-mdqc
(package
(name "r-mdqc")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mdqc" version))
(sha256
- (base32 "0y35z9sw3h77a5g4ah0fxrk5xh7irdw9z0y2jhh6dp0xxcqh6i0k"))))
+ (base32 "0q6ig9qdf2s9329wysrvgh13yq5c7n76as2c3mahqm78xb0mpplf"))))
(properties `((upstream-name . "mdqc")))
(build-system r-build-system)
(propagated-inputs
@@ -8239,16 +8541,42 @@ array against the quality of the other arrays. Then, arrays with unusually
high distances can be flagged as potentially low-quality.")
(license license:lgpl2.0+)))
+(define-public r-metabocoreutils
+ (package
+ (name "r-metabocoreutils")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MetaboCoreUtils" version))
+ (sha256
+ (base32 "0bs24dwqlm8isp231jds51l7v16q0gjli1qmhjxyva3qmi5yb4dl"))))
+ (properties `((upstream-name . "MetaboCoreUtils")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-mscoreutils))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils")
+ (synopsis "Core utils for Metabolomics data")
+ (description
+ "@code{MetaboCoreUtils} defines metabolomics-related core functionality
+provided as low-level functions to allow a data structure-independent usage
+across various R packages. This includes functions to calculate between
+ion (adduct) and compound mass-to-charge ratios and masses or functions to
+work with chemical formulas. The package provides also a set of adduct
+definitions and information on some commercially available internal standard
+mixes commonly used in MS experiments.")
+ (license license:artistic2.0)))
+
(define-public r-metagenomeseq
(package
(name "r-metagenomeseq")
- (version "1.42.0")
+ (version "1.43.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "metagenomeSeq" version))
(sha256
- (base32 "0293c531l0sjz8qxy7nrajfl081v9df0af9242017msbvyszq6wk"))))
+ (base32 "1m19qkwrbfr4yhbr1izfjka3brn1qasqql6alczv55l5h52m4s4b"))))
(properties `((upstream-name . "metagenomeSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -8276,13 +8604,13 @@ correlations.")
(define-public r-metaneighbor
(package
(name "r-metaneighbor")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MetaNeighbor" version))
(sha256
(base32
- "151ip70la12kj80c0airi1yyjbj69gnkshd6kfk88wsvq7s179id"))))
+ "0y8nk9jq0z48phg13mf6hsfg8l54w6z6b67g0k1c9gmsb7aqq04d"))))
(properties `((upstream-name . "MetaNeighbor")))
(build-system r-build-system)
(propagated-inputs
@@ -8312,13 +8640,13 @@ profiles than cells of different types.")
(define-public r-methylkit
(package
(name "r-methylkit")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
- "1qi4gwlxsxr4cgs8s12qybrs89vr79xwd7n9in1af3hyn0swikn1"))))
+ "0y45wa45kblm2g3nylvybvyfc34sjlynhsz3dirhs1favb83sdiv"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
@@ -8359,13 +8687,13 @@ TAB-Seq.")
(define-public r-mfuzz
(package
(name "r-mfuzz")
- (version "2.60.0")
+ (version "2.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Mfuzz" version))
(sha256
(base32
- "0rfna5ycwkx4xb2gv1wpfn7f7nz6f79w5nlkb7719l5730d81wnz"))))
+ "0v2l3fi9331lxfam6az265rfk52g4n75hh4rg12ykhp86ihplzpf"))))
(properties `((upstream-name . "Mfuzz")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-e1071 r-tkwidgets))
@@ -8379,13 +8707,13 @@ time-series data (including a graphical user interface).")
(define-public r-mmuphin
(package
(name "r-mmuphin")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MMUPHin" version))
(sha256
- (base32 "14cn1mg9ffhzy1vgschl2h0wzah3c1g67q367f2m050a3z2i2ndy"))
+ (base32 "0lhvsx5yjvqh5d3h860sv8cf3h73nrzvljpkqrd9ks0irc4gcm6d"))
;; Delete generated files.
(snippet
'(for-each delete-file
@@ -8474,14 +8802,14 @@ throughput genetic sequencing data sets using regression methods.")
(define-public r-muscat
(package
(name "r-muscat")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "muscat" version))
(sha256
(base32
- "1jcy07m8ywpgsmwkq6s7zj32w7gvxqj52j562irv2h2q429awdxk"))))
+ "0vasr9rwnfjxbb3y2saq7gqzis5xyamgvns2rlywdxv1jm0nr8y3"))))
(properties `((upstream-name . "muscat")))
(build-system r-build-system)
(propagated-inputs
@@ -8524,14 +8852,14 @@ platform that mimics both single and multi-sample scRNA-seq data.")
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "3.10.0")
+ (version "3.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h"))))
+ "19ya4ax6pa727hdn0118l9pwa9dxgh89dz54mm66dawxga3jhar4"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -8570,13 +8898,13 @@ in SNV base substitution data.")
(define-public r-msa
(package
(name "r-msa")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "msa" version))
(sha256
(base32
- "08fg4y8rmkvilsx2hxqwxa90p2wqrl4iyndp7wfjicvplmaxp708"))))
+ "1csa8j64xrfr6kdnndr3876bplclca9wf6ydy9kg97xsjq7gz8q5"))))
(properties `((upstream-name . "msa")))
(build-system r-build-system)
(propagated-inputs
@@ -8601,14 +8929,14 @@ package TeXshade.")
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.26.0")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g"))))
+ "0dway94j3k2dq5p8lqzj49ql85xrxxxgmlgppqg0h8k56xqrmf5i"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
@@ -8646,14 +8974,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc"))))
+ "1hmfh7v7p5d741x2wh1njqwkmfmf3xmwkqy88kalrcjzrdwfpv9b"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(arguments
@@ -8674,8 +9002,8 @@ of mass spectrometry based proteomics data.")
r-foreach
r-ggplot2
r-iterators
- r-msnbase
r-msmstests
+ r-msnbase
r-mzid
r-mzr
r-protgenerics
@@ -8703,14 +9031,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(define-public r-mzid
(package
(name "r-mzid")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzID" version))
(sha256
(base32
- "0grl7798vnpxb6nw98zj0lbvsrhkjfsyn0y15bi4v7vhyhkk26xm"))))
+ "1rgkd9iv0lxj1zxh96sifwa312ivw5kl5jw82ma4fmapr4iqhzsh"))))
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
@@ -8734,14 +9062,14 @@ specific parser.")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.34.1")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "1jsna4xwyph1gg72wwqlpavb65g5nc3db1vmcs1qcw1mdgasdjhk"))
+ "0z6ckp69syrdzhp6n4n399k2lar3w4n2d1ji2f90951c4ds6hkh8"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "src/boost"))))
@@ -8854,14 +9182,14 @@ Gao et al in Nature Biotechnology 2022}.")
(define-public r-organism-dplyr
(package
(name "r-organism-dplyr")
- (version "1.28.0")
+ (version "1.30.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Organism.dplyr" version))
(sha256
(base32
- "0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p"))))
+ "1s55fiqgxrdznn43qhm5yv9gp8d1msr2f39wxih0b5bm4wxhkq45"))))
(properties `((upstream-name . "Organism.dplyr")))
(build-system r-build-system)
(propagated-inputs
@@ -8893,14 +9221,14 @@ functionality of the @code{TxDb} packages (e.g.,
(define-public r-organismdbi
(package
(name "r-organismdbi")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OrganismDbi" version))
(sha256
(base32
- "1pw3qd6n0xf7vq3x73612bndcqhwrqkpi29f6crazdzjcy3fivlb"))))
+ "0g75y21lqmwsh28nx99zp2gxr6rhlhbw76f66qx5hrh6bm2zpm7j"))))
(properties `((upstream-name . "OrganismDbi")))
(build-system r-build-system)
(propagated-inputs
@@ -8926,13 +9254,13 @@ the fact that each of these packages implements a select methods.")
(define-public r-oscope
(package
(name "r-oscope")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Oscope" version))
(sha256
(base32
- "055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v"))))
+ "1li2l9mdq2q0580a7qzvfid5n15v62fr9ys87j42k3l2w5a26smf"))))
(properties `((upstream-name . "Oscope")))
(build-system r-build-system)
(propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat))
@@ -8952,14 +9280,14 @@ insertion module to recover the base cycle order for each oscillator group.")
(define-public r-pcaexplorer
(package
(name "r-pcaexplorer")
- (version "2.26.1")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pcaExplorer" version))
(sha256
(base32
- "04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx"))))
+ "0ihc9jqjy0nl4pfgcxczfdf973nb99325agk73y0222ad1mpkc07"))))
(properties `((upstream-name . "pcaExplorer")))
(build-system r-build-system)
(propagated-inputs
@@ -9007,14 +9335,14 @@ application encapsulates the whole analysis.")
(define-public r-pcamethods
(package
(name "r-pcamethods")
- (version "1.92.0")
+ (version "1.94.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pcaMethods" version))
(sha256
(base32
- "14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6"))))
+ "1asm4iafdzm98iv2j9sxvn5y9ss2p679cx7gwjipq8mf1d7bzfp0"))))
(properties `((upstream-name . "pcaMethods")))
(build-system r-build-system)
(propagated-inputs
@@ -9034,13 +9362,13 @@ structure (pcaRes) to provide a common interface to the PCA results.")
(define-public r-pfamanalyzer
(package
(name "r-pfamanalyzer")
- (version "1.0.1")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "pfamAnalyzeR" version))
(sha256
(base32
- "0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy"))))
+ "0qxxp7kfwbb9q471mgwc4bd8dmyid56ddyzw2jlg4gb1wcq9py67"))))
(properties `((upstream-name . "pfamAnalyzeR")))
(build-system r-build-system)
(propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble))
@@ -9054,6 +9382,43 @@ isotypes. This R package enables the identification and classification of such
domain isotypes from pfam data.")
(license license:expat)))
+(define-public r-piano
+ (package
+ (name "r-piano")
+ (version "2.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "piano" version))
+ (sha256
+ (base32 "0rw55ig3pbvi2kyg10rx60ldcncsd4gki2h1zpr1nhmqg3fv0l5y"))))
+ (properties `((upstream-name . "piano")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biobase
+ r-biocgenerics
+ r-dt
+ r-fgsea
+ r-gplots
+ r-htmlwidgets
+ r-igraph
+ r-marray
+ r-relations
+ r-scales
+ r-shiny
+ r-shinydashboard
+ r-shinyjs
+ r-visnetwork))
+ (native-inputs (list r-knitr))
+ (home-page "https://varemo.github.io/piano/")
+ (synopsis "Platform for integrative analysis of omics data")
+ (description
+ "Piano performs gene set analysis using various statistical methods, from
+different gene level statistics and a wide range of gene-set collections. The
+package contains functions for combining the results of multiple runs of gene
+set analyses.")
+ (license license:gpl2+)))
+
;; This is a CRAN package, but it depends on a Bioconductor package:
;; r-aroma-light, r-dnacopy..
(define-public r-pscbs
@@ -9099,14 +9464,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
(define-public r-protgenerics
(package
(name "r-protgenerics")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ProtGenerics" version))
(sha256
(base32
- "0fgsb47qrvrl4y3yr094mas22rai5h5yl9mciadd6zcpamp2p01i"))))
+ "1gjva76nxa9nzzmc9hya3bq7hswfmjd768v21f6m3gyygxvl581m"))))
(properties `((upstream-name . "ProtGenerics")))
(build-system r-build-system)
(home-page "https://github.com/lgatto/ProtGenerics")
@@ -9119,14 +9484,14 @@ proteomics packages.")
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.76.0")
+ (version "1.78.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "0y6ghiwraw3whs57i31qnvlvqlbl9143wxv2yg48rp7qxipxvn6s"))))
+ "0hxhl1l6qdi355w5y7fdq8vlba2pknfizggkgr2fp8f1f3zqh494"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs
@@ -9142,13 +9507,13 @@ the graph algorithms contained in the Boost library.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.26.0")
+ (version "1.28.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "073fhbh0pzyca90q2irbaiwj21sci8jf9ksflx9pm9fr1giy37i4"))))
+ "19ildsck3g8v4w0g2f473sb8hyhn4avprdi78fim0prva5f9nqnv"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@@ -9174,9 +9539,9 @@ the graph algorithms contained in the Boost library.")
r-plotrix
r-proxy
r-ranger
+ r-rmarkdown
r-rsqlite
r-rtracklayer
- r-rmarkdown
r-s4vectors
pandoc))
(native-inputs
@@ -9192,14 +9557,14 @@ library implementing most of the pipeline's features.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "0grlqga9d6mch9l487fdll65wi0m2kpq2097igfhx185i8jvwsz1"))))
+ "1qcgbj7d2fngs3p9a9apnj14x35kc651fy3m0651dnqrxz8j5yij"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -9306,16 +9671,16 @@ browser.")
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.44.0")
+ (version "2.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0"))))
+ "1csf5nrg2nkdwh8cz26idz6wrhj7bgnfh559mzlpdj4licnf1ymc"))))
(build-system r-build-system)
(propagated-inputs
- (list r-rhdf5filters r-rhdf5lib))
+ (list r-rhdf5filters r-rhdf5lib r-s4vectors))
(native-inputs
(list r-knitr))
(home-page "https://bioconductor.org/packages/rhdf5")
@@ -9333,42 +9698,26 @@ the available RAM.")
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5filters" version))
(sha256
(base32
- "1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m"))))
+ "1appjnggyljrn77nvv9adkwxplbrrlgkrrd1bf2b5r0nsa505hdc"))))
(properties `((upstream-name . "rhdf5filters")))
(build-system r-build-system)
(arguments
(list
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'use-system-libraries
- (lambda _
- (substitute* "src/blosc/Makefile.in"
- (("libblosc.a: blosc") "libwhatever.a:")
- (("libblosc.a")
- (string-append #$(this-package-input "c-blosc")
- "/lib/libblosc.so"))
- (("../zstd/libzstd.a") "-lzstd"))
- (substitute* "src/bzip2/Makefile"
- (("libH5Zbz2.so: bzip2-1.0.8/libbz2.a") "libH5Zbz2.so:")
- (("./bzip2-1.0.8/libbz2.a") "-lbz2"))
- (substitute* "src/zstd/Makefile"
- (("libH5Zzstd.so: libzstd.a") "libH5Zzstd.so:")
- (("libzstd.a") "-lzstd"))
- (substitute* "src/vbz/Makefile"
- (("../zstd/libzstd.a") "-lzstd")))))))
+ #:configure-flags
+ '(list "--without-bundled-libs")))
(propagated-inputs
(list r-rhdf5lib))
(inputs
(list bzip2 c-blosc zlib (list zstd "lib")))
(native-inputs
- (list r-biocstyle r-knitr r-rmarkdown))
+ (list r-knitr))
(home-page "https://github.com/grimbough/rhdf5filters")
(synopsis "HDF5 compression filters")
(description
@@ -9379,13 +9728,13 @@ HDF5 datasets.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "2.16.0")
+ (version "2.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "18kh6vmyjmv7zklqr5ifpfixjwldxgwj550c69mqfkk7m0zk52cl"))))
+ "0bcapiwdzv7rqgs4hmw7hq290r3pz5vvhg4apxard0yybq83na1g"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@@ -9408,7 +9757,8 @@ HDF5 datasets.")
r-iranges
r-rhtslib
r-s4vectors
- r-xvector))
+ r-xvector
+ r-zlibbioc))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
(synopsis "Interface to samtools, bcftools, and tabix")
@@ -9445,13 +9795,13 @@ tab-delimited (tabix) files.")
(define-public r-rtcga
(package
(name "r-rtcga")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RTCGA" version))
(sha256
(base32
- "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25"))))
+ "1lzdwkisvzj1wyx3wx4ll1c2j9ww3xz8kpbngmpf8cdrw4h3jrg1"))))
(properties `((upstream-name . "RTCGA")))
(build-system r-build-system)
(propagated-inputs (list r-assertthat
@@ -9490,13 +9840,13 @@ transforms TCGA data to tidy form which is convenient to use.")
(define-public r-rtcgatoolbox
(package
(name "r-rtcgatoolbox")
- (version "2.30.0")
+ (version "2.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RTCGAToolbox" version))
(sha256
(base32
- "03p5rgjzc1265q60jkvk92vhcib5wdnv6bz997r70q9c39y03wm5"))))
+ "1a38b30nsg2bnlnijf4aa4rn4db2y4v86awfbf6a6qzqwlzknrcq"))))
(properties `((upstream-name . "RTCGAToolbox")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
@@ -9506,7 +9856,6 @@ transforms TCGA data to tidy form which is convenient to use.")
r-genomicranges
r-httr
r-raggedexperiment
- r-rcircos
r-rcurl
r-rjsonio
r-rvest
@@ -9530,13 +9879,13 @@ pre-processed data.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.60.1")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8"))))
+ "1jxhv2fq62lz0j6kbwq43c8ggk14ccsjg0xgfqjqy941dj9ig0n2"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -9609,13 +9958,13 @@ differential expression analysis, RNAseq data and related problems.")
(define-public r-saturn
(package
(name "r-saturn")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "satuRn" version))
(sha256
(base32
- "0frm7iblxkc8ajcdqrfgsvf4krn6x8cr3mx7fnzq06xij0mqm3sj"))))
+ "12bivj0cnp38apwi3jqmil8bwsfa96cjp5f132a5raacd2z87gqf"))))
(properties `((upstream-name . "satuRn")))
(build-system r-build-system)
(propagated-inputs (list r-biocparallel
@@ -9643,13 +9992,13 @@ transcripts in groups of interest.")
(define-public r-scannotatr
(package
(name "r-scannotatr")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scAnnotatR" version))
(sha256
- (base32 "0mxq2dknrhgj1487kfshkayx963c7qdgxwmlh9fbfr0lwc7gljfn"))))
+ (base32 "13wrxxdwphngi0f9vxakykk54bqngw8g38w6wkk96999lzb3p57p"))))
(properties `((upstream-name . "scAnnotatR")))
(build-system r-build-system)
(propagated-inputs
@@ -9680,13 +10029,13 @@ cell types based on specific research needs.")
(define-public r-scdblfinder
(package
(name "r-scdblfinder")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scDblFinder" version))
(sha256
- (base32 "0lvacrgfj9i8mwlcv5ykxs69hd3bm6bvr6fsddxffsr7cckpn31w"))))
+ (base32 "1f3n1m6fjx965wm2jllzk51ssj92ifxb4bln4vwk25qxd3g0bna8"))))
(properties `((upstream-name . "scDblFinder")))
(build-system r-build-system)
(propagated-inputs
@@ -9762,13 +10111,13 @@ method applicable to massive single-cell datasets (>10,000 cells).")
(define-public r-scmap
(package
(name "r-scmap")
- (version "1.22.3")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scmap" version))
(sha256
- (base32 "06i3r7zybwcgnak9ml2jaz7fy70zjqdh28v03ckaqhvck49kdqdm"))))
+ (base32 "1sd5ixs8fbiqqp1p4p505l1f0lncmagkhzh4xrk8wrca6db6k6d8"))))
(properties `((upstream-name . "scmap")))
(build-system r-build-system)
(propagated-inputs
@@ -9804,13 +10153,13 @@ different experiment.")
(define-public r-scry
(package
(name "r-scry")
- (version "1.12.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scry" version))
(sha256
(base32
- "0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz"))))
+ "0hbdsjsn0jl0dr2ly5vx0wb4bnz7nl15kkypryywjvis9rdasjj3"))))
(properties `((upstream-name . "scry")))
(build-system r-build-system)
(propagated-inputs
@@ -9835,13 +10184,13 @@ single-cell RNA-seq.")
(define-public r-seqarray
(package
(name "r-seqarray")
- (version "1.40.1")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SeqArray" version))
(sha256
(base32
- "1771vk23psjavvi1nf2z8i2xawygdh4amawlijnskci8y9w4x5dm"))))
+ "0zs60yh3x6kgy6izn11d400vw59ww2w6bmhg6fw5ijinknyr3ixc"))))
(properties `((upstream-name . "SeqArray")))
(build-system r-build-system)
(propagated-inputs (list r-biostrings
@@ -9865,14 +10214,14 @@ data access using the R programming language.")
(define-public r-seqlogo
(package
(name "r-seqlogo")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqLogo" version))
(sha256
(base32
- "0727yrmm194gskrcpmq4fh0qmi6dnp70gx627psrpvzlk6vlcl8k"))))
+ "106359wn4v0m53b33x4zjsyjsj4j8h7bnvd1whamsig982h6szp2"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(native-inputs
@@ -9888,13 +10237,13 @@ Stephens (1990).")
(define-public r-seqpattern
(package
(name "r-seqpattern")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "seqPattern" version))
(sha256
(base32
- "033hss67dxi6fbvn6ya7vc61f60m20hwms9kmdia0icyp8nv2yil"))))
+ "0rs9dy540d4agp7fc8glbrcnly4s6qcxqsq4yv8y555bbdld6dv0"))))
(properties
`((upstream-name . "seqPattern")))
(build-system r-build-system)
@@ -9911,13 +10260,13 @@ reference point and sorted by a user defined feature.")
(define-public r-sesame
(package
(name "r-sesame")
- (version "1.18.4")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "sesame" version))
(sha256
(base32
- "1il33ygys6y72l8p3fhx301q16w9kylfy6w92b64n8gqkn6dmsmn"))))
+ "0yh4mrsj3pqhjkrq5dwmcpcqwixs0pmjy7dfa3cr0mf52fgzcvmr"))))
(properties `((upstream-name . "sesame")))
(build-system r-build-system)
(propagated-inputs (list r-biocfilecache
@@ -9953,13 +10302,13 @@ and advanced quality control routines.")
(define-public r-shinymethyl
(package
(name "r-shinymethyl")
- (version "1.36.1")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "shinyMethyl" version))
(sha256
(base32
- "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck"))))
+ "1gkj15q1rxvsdzbsp3gkk02kvvx0kq4wsqycf3ln1bszb9688jw6"))))
(properties `((upstream-name . "shinyMethyl")))
(build-system r-build-system)
(propagated-inputs
@@ -9981,14 +10330,14 @@ methylation array data. Both the 450k and EPIC array are supported.")
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0wpr3ksr7j5yk6m1zaa47dwdgznajsz8as4p9vf7schaqvhq1wc4"))))
+ "0fgiszb5qhplppfngpi4s33sx62ff5sdhd6n31a3b6l7fnlvk51m"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@@ -10001,11 +10350,11 @@ methylation array data. Both the 450k and EPIC array are supported.")
r-genomeinfodb
r-genomicalignments
r-genomicranges
- r-rhtslib
r-hwriter
r-iranges
r-lattice
r-latticeextra
+ r-rhtslib
r-rsamtools
r-s4vectors
r-xvector
@@ -10024,14 +10373,14 @@ ungapped alignment formats.")
(define-public r-simplifyenrichment
(package
(name "r-simplifyenrichment")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "simplifyEnrichment" version))
(sha256
(base32
- "1vs57j361fbwv7vaybs71vc208qn76djmbmakhwwcvxwrx77jp5f"))))
+ "0qhrlhf881mi2v0n0y410c0bf2cm3imrlglq8argnw86n9xj51pw"))))
(properties
`((upstream-name . "simplifyEnrichment")))
(build-system r-build-system)
@@ -10065,13 +10414,13 @@ and comparing the clusterings.")
(define-public r-singscore
(package
(name "r-singscore")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "singscore" version))
(sha256
(base32
- "1s1kyvkbfgwskf0hi4b44c2yx256rjp1yk9ijpld9qlm7z7pi67q"))))
+ "0hafzbhbik1512pisjvnnzmy8pl2shrgra6l06kpvsrczkqlmi04"))))
(properties `((upstream-name . "singscore")))
(build-system r-build-system)
(propagated-inputs (list r-biobase
@@ -10103,13 +10452,13 @@ level.")
(define-public r-tcgautils
(package
(name "r-tcgautils")
- (version "1.20.4")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TCGAutils" version))
(sha256
(base32
- "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q"))))
+ "0r79iiqv7q83wz5w3lm271dn3jdrkggmvjdyj1wnjsih1n2viy7d"))))
(properties `((upstream-name . "TCGAutils")))
(build-system r-build-system)
(propagated-inputs (list r-annotationdbi
@@ -10142,13 +10491,13 @@ identifier translation via the GDC API.")
(define-public r-tkwidgets
(package
(name "r-tkwidgets")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tkWidgets" version))
(sha256
(base32
- "1xp0gdfrhhfzfww4ig3y90f7334y24rhzrmlxmm4wav8slvcran2"))))
+ "11a8rflmga2d63l5nzdlbkyfnzsf20dzg2sy6qr143hg9sjzqrrj"))))
(properties `((upstream-name . "tkWidgets")))
(build-system r-build-system)
(propagated-inputs (list r-dyndoc r-widgettools))
@@ -10158,16 +10507,17 @@ identifier translation via the GDC API.")
"This package implements widgets to provide user interfaces.")
(license license:artistic2.0)))
+;; TODO: check javascript
(define-public r-trackviewer
(package
(name "r-trackviewer")
- (version "1.36.2")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "trackViewer" version))
(sha256
(base32
- "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))
+ "15agkyqx6gl5zzdxra5nl0czd4j7mw456r587w039l9hzwznwbr8"))
(snippet
'(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
(properties `((upstream-name . "trackViewer")))
@@ -10227,13 +10577,13 @@ methylation data.")
(define-public r-transcriptr
(package
(name "r-transcriptr")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "transcriptR" version))
(sha256
- (base32 "0i38zs33drzk9szy2mdfs9ff9c3ccjgiyyynrrsinrx0szc8l22r"))))
+ (base32 "1lbla2syljpmgdf7da7vl1260fy54xs3hk6m2gjpark0dka0kqbh"))))
(properties `((upstream-name . "transcriptR")))
(build-system r-build-system)
(propagated-inputs
@@ -10277,14 +10627,14 @@ able to deal also with novel and case specific events.")
(define-public r-trajectoryutils
(package
(name "r-trajectoryutils")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TrajectoryUtils" version))
(sha256
(base32
- "1q3c226fskl45gq28xj2w5paz2s9n9kxm0bkkgg0329w399cs09k"))))
+ "0pqdl0v16q90ffxla34rp07mq0if1q9izpbimfnq0rx7633mk95v"))))
(properties
`((upstream-name . "TrajectoryUtils")))
(build-system r-build-system)
@@ -10304,13 +10654,13 @@ structures to hold pseudotime inference results.")
(define-public r-scds
(package
(name "r-scds")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scds" version))
(sha256
(base32
- "059gahl679if8xsfgpxmi3h9fiagb6v08rd6rs7yv96s3pb8qywn"))))
+ "0cmzvc1m29ijhzs2p407bhhxfqbflzsnrk7nq0jshjyw6v6pkfn0"))))
(properties `((upstream-name . "scds")))
(build-system r-build-system)
(propagated-inputs (list r-dplyr
@@ -10332,13 +10682,13 @@ scRNA-seq data computationally.")
(define-public r-slingshot
(package
(name "r-slingshot")
- (version "2.8.0")
+ (version "2.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "slingshot" version))
(sha256
(base32
- "1xr17rg8nfpcvdwa19qrcaqffkz048l5lkqlm6gw0abm8bg2k8x7"))))
+ "0q3j0jpc4mnmjb3xha5cmfhk1qdr1jiz7kdghznk4zqxn4bchc1d"))))
(build-system r-build-system)
(propagated-inputs
(list r-igraph
@@ -10404,19 +10754,20 @@ tools either included in speaq or available elsewhere on CRAN.")
(define-public r-spectra
(package
(name "r-spectra")
- (version "1.10.3")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Spectra" version))
(sha256
(base32
- "1fx6xkl29frfk8bzz5jvr1cn0hjyi46ck23izb1cypiag4lsrf8v"))))
+ "07zs9x5fzxzwicjc5x29sv33yidmq1ar70ss91py094zbw9i63qy"))))
(properties `((upstream-name . "Spectra")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
r-biocparallel
r-fs
r-iranges
+ r-metabocoreutils
r-mscoreutils
r-protgenerics
r-s4vectors))
@@ -10435,13 +10786,13 @@ data sets ensuring a small memory footprint.")
(define-public r-stager
(package
(name "r-stager")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "stageR" version))
(sha256
- (base32 "0advih0g2g5w8bx9f21chz8a66f4v84qn3p5skxi084pp142v5ms"))))
+ (base32 "064hvx8qyw5hdhihwl9k0jqhg6saz4ng2m37d2ipr5pz9v8adspb"))))
(properties `((upstream-name . "stageR")))
(build-system r-build-system)
(propagated-inputs (list r-summarizedexperiment))
@@ -10458,13 +10809,13 @@ Biology at
(define-public r-stringdb
(package
(name "r-stringdb")
- (version "2.12.1")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "STRINGdb" version))
(sha256
- (base32 "1c0m9k3gjmj160k8xyj2r60lpx4qgp7xibljfg8ljxr33f8aqyaz"))))
+ (base32 "1ffn73sx0qbzbh8cjil9r159g0fjnvi6y8rlbg6nf7p3zx3aya54"))))
(properties `((upstream-name . "STRINGdb")))
(build-system r-build-system)
(propagated-inputs
@@ -10491,13 +10842,13 @@ that integrates the various evidences.")
(define-public r-structuralvariantannotation
(package
(name "r-structuralvariantannotation")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "StructuralVariantAnnotation" version))
(sha256
- (base32 "0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb"))))
+ (base32 "1h3l3xbxwf2w2dl0qz72v68h5g77zhd2rr0g86l2dhn67mhy8ml2"))))
(build-system r-build-system)
(propagated-inputs
(list r-assertthat
@@ -10528,13 +10879,13 @@ involving two separate genomic loci encoded as GRanges objects.")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.30.2")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "05dy57fi43rpq9bhbsc4apa62xki99r84098pbvi3rjmac811425"))))
+ "1949k2658drmcrrr7v6748b40g2qym39n0ch50jxf0xmmlb1r04z"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -10563,13 +10914,13 @@ samples.")
(define-public r-survcomp
(package
(name "r-survcomp")
- (version "1.50.0")
+ (version "1.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "survcomp" version))
(sha256
(base32
- "1va0ijx3qk3rjhzaflygfwlzn5a670y833qly8in8p5r3al9bdj6"))))
+ "18a81vv88xj3frkdy5l6w2fc4xzr1k6vgbz4j4marlmh6mz6skin"))))
(properties `((upstream-name . "survcomp")))
(build-system r-build-system)
(propagated-inputs (list r-bootstrap
@@ -10590,22 +10941,22 @@ of risk prediction (survival) models.")
(define-public r-sva
(package
(name "r-sva")
- (version "3.48.0")
+ (version "3.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sva" version))
(sha256
(base32
- "1f6ia57fn2sn7c2zdfswvj9kx8xayssrgf5q6hrr9nrxc0jq19g3"))))
+ "0p4zgw1pi5vnaqxn6jmvhpy0h5hnnqp41n0k2v0chhqgqxgn67x1"))))
(build-system r-build-system)
(propagated-inputs
- (list r-edger
+ (list r-biocparallel
+ r-edger
r-genefilter
- r-mgcv
- r-biocparallel
+ r-limma
r-matrixstats
- r-limma))
+ r-mgcv))
(home-page "https://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
@@ -10621,14 +10972,14 @@ unmodeled, or latent sources of noise.")
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "2.6.3")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "068rikfq32awhvj0abl30bghv5k2z4zlfkbxpmsdapxhmdzhgnba"))))
+ "01amqib9ahrf19xpy4ivlsss82zyp3w7fbgwrwp53zfbg0cninga"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
@@ -10664,21 +11015,21 @@ annotation infrastructure.")
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.52.0")
+ (version "2.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "0avjjvih387qhw8n4vjz4jq66q7sicgacsw53b85lq2c6ppib662"))))
+ "1sznyx11kzw8d8zg5ynl9sp6m0daf2yw3f2b24maxbpr1xkif9nx"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
- r-dbi
r-biobase
r-biocgenerics
+ r-dbi
r-go-db
r-graph
r-lattice
@@ -10697,13 +11048,13 @@ dependencies between GO terms can be implemented and applied.")
(define-public r-tximport
(package
(name "r-tximport")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tximport" version))
(sha256
(base32
- "0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1"))))
+ "0m6avd815xcv3py5sym083pdccvd4crdyyc7sfpxccnksgchyrf2"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -10756,15 +11107,16 @@ R, enabling interactive analysis and visualization of genome-scale data.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm"))))
+ "1r1cyimr5l5jzgxvmrm3vq8mvz3f1klfdwy9mz31xvnvgjacr58p"))))
(properties
`((upstream-name . "VariantAnnotation")))
+ (build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
r-biobase
@@ -10777,14 +11129,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
r-genomicranges
r-iranges
r-matrixgenerics
- r-summarizedexperiment
r-rhtslib
r-rsamtools
r-rtracklayer
r-s4vectors
+ r-summarizedexperiment
r-xvector
r-zlibbioc))
- (build-system r-build-system)
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/VariantAnnotation")
(synopsis "Package for annotation of genetic variants")
(description "This R package can annotate variants, compute amino acid
@@ -10794,14 +11146,14 @@ coding changes and predict coding outcomes.")
(define-public r-vsn
(package
(name "r-vsn")
- (version "3.68.0")
+ (version "3.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "vsn" version))
(sha256
(base32
- "0i6c0wyhj0gcq0mw13zyk60cza2baq4yrj1n2dzqgsqkmhm5lfla"))))
+ "0li0yxf8m34xpmrgv5vciy8zdsbfdlajl9cmnxr4g4nmarik2bkh"))))
(build-system r-build-system)
(propagated-inputs
(list r-affy r-biobase r-ggplot2 r-lattice r-limma))
@@ -10863,13 +11215,13 @@ inference.")
(define-public r-xina
(package
(name "r-xina")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "XINA" version))
(sha256
- (base32 "1byk8xgn9rwfbi677b99ysxi4a9n58fr3hbnwjzhnziy2n2cd703"))))
+ (base32 "1cnw2zbjfs8qcgqrx557g00m59h5pldcx788v9r4gn2f70rx7vx3"))))
(properties `((upstream-name . "XINA")))
(build-system r-build-system)
(propagated-inputs
@@ -10899,13 +11251,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
(define-public r-xmapbridge
(package
(name "r-xmapbridge")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xmapbridge" version))
(sha256
- (base32 "09pskmhjymqvhk26mk5yy1k195v536a2qp4k6xdd67xhf5ag260i"))))
+ (base32 "0pby2h8m12xlngpk33dvh3nkrpgqi4f2mb7g9jafyiv3sl8pjd19"))))
(properties `((upstream-name . "xmapbridge")))
(build-system r-build-system)
(home-page "https://git.bioconductor.org/packages/xmapbridge")
@@ -10926,13 +11278,13 @@ describing each of the graphs.")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.40.0")
+ (version "0.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2"))))
+ "0h03imdl0pyy714kmddsdnsv69bd8kr7bhi9wq9z18y8ahg5cqx1"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
@@ -10949,7 +11301,7 @@ describing each of the graphs.")
(inputs
(list zlib))
(propagated-inputs
- (list r-biocgenerics r-iranges r-s4vectors))
+ (list r-biocgenerics r-iranges r-s4vectors r-zlibbioc))
(home-page "https://bioconductor.org/packages/XVector")
(synopsis "Representation and manpulation of external sequences")
(description
@@ -10960,13 +11312,13 @@ describing each of the graphs.")
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "zlibbioc" version))
(sha256
(base32
- "0x3d5kihckqnfjkc7dxk6mc194vwwr03jfjx2qh15g5494gfmm53"))))
+ "043xwgw3yclxnxlfl7fdwf7qf7fajzvqdv34qxnngxj9wpgha3gv"))))
(properties
`((upstream-name . "zlibbioc")))
(build-system r-build-system)
@@ -10979,13 +11331,13 @@ libraries for systems that do not have these available via other means.")
(define-public r-zellkonverter
(package
(name "r-zellkonverter")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zellkonverter" version))
(sha256
- (base32 "1p89i2dfwcgrdchdnxrywp3jjjn5jjs5bisrx5kav26yh2pyx1wk"))))
+ (base32 "02q9icblcnh0l7vah29mnhcczw8w0gpgd57v19gy7222nrqpcd9m"))))
(properties `((upstream-name . "zellkonverter")))
(build-system r-build-system)
(propagated-inputs
@@ -11011,14 +11363,14 @@ saving AnnData objects to disk.")
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.78.0")
+ (version "1.80.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "03x90l7rvxk0z03p5immqbyyhiygi3mkik636al1cjdcxl9dr5f8"))))
+ "0zvb84jlsvmr2dvwyy4xjqv353qrxpls0v2vz0nmj1q4m7lrpl1k"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotate
@@ -11027,6 +11379,8 @@ saving AnnData objects to disk.")
r-biocgenerics
r-lattice
r-rcolorbrewer))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/geneplotter")
(synopsis "Graphics functions for genomic data")
(description
@@ -11036,14 +11390,14 @@ saving AnnData objects to disk.")
(define-public r-oligoclasses
(package
(name "r-oligoclasses")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligoClasses" version))
(sha256
(base32
- "0i745q2kx7rdfbkz3cwzzp1m4diny25mc301vy0sh4z5lpi5mdm8"))))
+ "1gdvjvyjfpvvrqyj9rq1l4dnq00hr8vr8knnlb9gnjk21sbcf1d7"))))
(properties `((upstream-name . "oligoClasses")))
(build-system r-build-system)
(propagated-inputs
@@ -11071,14 +11425,14 @@ packages.")
(define-public r-oligo
(package
(name "r-oligo")
- (version "1.64.1")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligo" version))
(sha256
(base32
- "0gs26h0hm8xlv3aayz4w0vwmw15x5602g02728spsm3n0qra3b1j"))))
+ "0pqn5qslynylx235wknwj71a6j7xf5i6pb7wjm00jwrdbqwvdlp6"))))
(properties `((upstream-name . "oligo")))
(build-system r-build-system)
(inputs (list zlib))
@@ -11107,13 +11461,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
(define-public r-qfeatures
(package
(name "r-qfeatures")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QFeatures" version))
(sha256
(base32
- "1xnmd14nf4cqbfxkjsl6af312k7l27ars5g8qdnljylkn8kq276z"))))
+ "1g744fpb6g690bjbjs4v2899wwv6qc7n5cyq977pm8f3wln0m7mx"))))
(properties `((upstream-name . "QFeatures")))
(build-system r-build-system)
(propagated-inputs (list r-annotationfilter
@@ -11142,13 +11496,13 @@ proteins) in a coherent and tractable format.")
(define-public r-quantsmooth
(package
(name "r-quantsmooth")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "quantsmooth" version))
(sha256
- (base32 "05lja0viz5jgc7g3b8qfhd1x596vczid0dz8278qpl4zwv9i17vx"))))
+ (base32 "050nnwhxk3ld615f6ij4cc3d6wzrrxykvv02fr20fg5gzdj0z08a"))))
(properties `((upstream-name . "quantsmooth")))
(build-system r-build-system)
(propagated-inputs (list r-quantreg))
@@ -11169,14 +11523,14 @@ on the location of the probe, and other useful tools.")
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.32.0")
+ (version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "1552390pf3wrrir6c9xshgll69a33fhbdnh2cvpnznma1ag490ki"))))
+ "10v5khnrs1fa84d430zy52f9466rwb1byaw1l3c9nivbhmaxhvyi"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-reshape2))
@@ -11224,13 +11578,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
(define-public r-apcomplex
(package
(name "r-apcomplex")
- (version "2.66.0")
+ (version "2.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "apComplex" version))
(sha256
- (base32 "057p1bsqqw3r49bsx78prqc4jha468bfx50gpl62giix0cfs007f"))))
+ (base32 "1y3c3358y7ynn5lj2gcy9ll2gxnnlv689pj0bgr2gsnhbss1kw1r"))))
(properties `((upstream-name . "apComplex")))
(build-system r-build-system)
(propagated-inputs
@@ -11249,13 +11603,13 @@ spectrometry} data.")
(define-public r-apeglm
(package
(name "r-apeglm")
- (version "1.22.1")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "apeglm" version))
(sha256
(base32
- "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7"))))
+ "0cj9yzmh9w3fk3rxmk2k5j55r42mmz9znszmr4l160mr23alkzx4"))))
(properties `((upstream-name . "apeglm")))
(build-system r-build-system)
(propagated-inputs
@@ -11276,13 +11630,13 @@ posterior for individual coefficients.")
(define-public r-greylistchip
(package
(name "r-greylistchip")
- (version "1.32.1")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GreyListChIP" version))
(sha256
(base32
- "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm"))))
+ "1k974cvfbkl8ffn7k2la843bv2pf33cr5f6fahiiy24d68lxwifr"))))
(properties `((upstream-name . "GreyListChIP")))
(build-system r-build-system)
(propagated-inputs
@@ -11303,14 +11657,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.10.1")
+ (version "3.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "12frl2wfvfz4gpq4fjsmglqyqfxdk3zjbhqkc78rzylbw37xx3bf"))))
+ "1nlcx4fl1cpcg38cn9p55f75bv6pcg6h2jv4z94g2b7g1gwjd686"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
@@ -11381,13 +11735,13 @@ processing to visualization and annotation.")
(define-public r-mbecs
(package
(name "r-mbecs")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MBECS" version))
(sha256
- (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz"))))
+ (base32 "1j7vb26n2fnf5fkk8hfz552yx91g4zg719alhg4hg2vvjd1qx2l1"))))
(properties `((upstream-name . "MBECS")))
(build-system r-build-system)
(arguments
@@ -11406,7 +11760,6 @@ processing to visualization and annotation.")
r-lme4
r-lmertest
r-magrittr
- r-markdown
r-matrix
r-pheatmap
r-phyloseq
@@ -11432,13 +11785,13 @@ before and after correcting for batch effects.")
(define-public r-mbkmeans
(package
(name "r-mbkmeans")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "mbkmeans" version))
(sha256
(base32
- "0c48ycgba1m10p1w2qz9r7yxw15nqzlz8fp44d6lbrvj3svmgjwi"))))
+ "1x7azijfs28iz2w40b9hnpgwh4jxgihl8cj6h91b2wgz79sq649l"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -11464,13 +11817,13 @@ large datasets, including support for on-disk data representation.")
(define-public r-multibac
(package
(name "r-multibac")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiBaC" version))
(sha256
- (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i"))))
+ (base32 "1mwfibakrxgs3r572bqqqmzq7ys6cs0bpn0wfrcb08ww2197xc4j"))))
(properties `((upstream-name . "MultiBaC")))
(build-system r-build-system)
(propagated-inputs
@@ -11494,17 +11847,17 @@ the batches considered.")
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.56.0")
+ (version "2.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "19c6l8pkyp0m2zdzhr81cnmx5lqf501sap9h6ig5iiv66sf2ysmz"))))
+ "0s8x2rg2xp6awg2cikybgxrxpi9f91jah7dskk5dnfkazd20di4j"))))
(build-system r-build-system)
(propagated-inputs
- (list r-survival r-biocgenerics r-biobase r-mass))
+ (list r-biobase r-biocgenerics r-mass r-survival))
(home-page "https://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
@@ -11529,13 +11882,13 @@ expressed genes in DNA microarray experiments.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "184izzxc8bpagcac8wqinjp8kmf9zpvjibl0g32nnr64kp9f4rsn"))))
+ "0p7g7ykpkngbs3h1dsackfy93l8lvc301lr64ffsiaw60gllcx01"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics))
@@ -11572,13 +11925,13 @@ fitting of some classes of graphical Markov models.")
(define-public r-ggtreeextra
(package
(name "r-ggtreeextra")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ggtreeExtra" version))
(sha256
(base32
- "19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr"))))
+ "0q8k81mq5q9fym4zyrkzapgyww23lkxpkyj2s9r1y0ciclk90zdc"))))
(properties `((upstream-name . "ggtreeExtra")))
(build-system r-build-system)
(propagated-inputs (list r-cli
@@ -11672,13 +12025,13 @@ a given recall, F-score for single and multiple classes are available.")
(define-public r-pepsnmr
(package
(name "r-pepsnmr")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "PepsNMR" version))
(sha256
(base32
- "17rbadvay3kbp4r6p023yww4biw9cl359q200ciygr7d2ffcas85"))))
+ "013jw9l7r87j4bmpjrvq5qn91kp44wj5vd68cl5axbqhjg7fq4ww"))))
(properties `((upstream-name . "PepsNMR")))
(build-system r-build-system)
(propagated-inputs
@@ -11728,14 +12081,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.34.1")
+ (version "3.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "0y9qskkdkl2vdbn66md4xisny0i7g2biasylp357vrkv41d3al6l"))))
+ "012hhakhk81qk1hi4igfa4vji678gmyvdxi05z9mdsx721lwwy2i"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -11782,13 +12135,13 @@ enrichedGO (addGeneIDs).")
(define-public r-matrixgenerics
(package
(name "r-matrixgenerics")
- (version "1.12.3")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MatrixGenerics" version))
(sha256
(base32
- "07hrafzn3787vprdwdk3cfyhi8df7hjvxg9vq7ad8raqzb37lqil"))))
+ "14x5jib5xh2006lg96v3b9n2pnbjcbsd5igqybqsv0c53rk9394d"))))
(properties
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
@@ -11809,12 +12162,12 @@ incompatibilities.")
(define-public r-marray
(package
(name "r-marray")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "1z8fx47ng1av8nfpk0i7wpb8k8lsrn66k613p36mbh19m5fx05ks"))))
+ (base32 "1gj4mdbni5fk2z3zrk2cnhy610ihhhwjb9l1crglkklwxhkqlkvd"))))
(build-system r-build-system)
(propagated-inputs
(list r-limma))
@@ -11828,12 +12181,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "1r050acahvfp2ib88sy9xj4yjzy2d8h73hndi1s075h0zv12mjj7"))))
+ (base32 "1iw03gq1kvmn9a6h0kw389l9i7h99fbxcsag9f3gkfznjv0vp5k4"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@@ -11847,16 +12200,16 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.62.0")
+ (version "2.64.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "02d8j0al062k33h6n3ihn7kwbqp3pjwg9zzbr45ay1m1jm6bappi"))))
+ (base32 "1x2zfr40bm42zd1bljwpbz3cz1q23a3yy1g277lwsp78gxbn3zly"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
- (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
+ (list r-biobase r-cghbase r-dnacopy r-impute 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
@@ -11866,12 +12219,12 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "0lcf5zkv44s7xsa2svxia7inv6iz2k1kilfj5zcq80r339pj3vx4"))))
+ (base32 "1n2qngqqw3hfv1yscksnpg8wslc85dlvaqw1hz2qvsxf1gcq2mks"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
@@ -11898,14 +12251,14 @@ respectively.")
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.31.0")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh"))))
+ "1b5vvzl0kkm6kb03vr6m6sdlr3azpc24933a7ayxkiffmf2wbi0g"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
@@ -11922,14 +12275,14 @@ more complex hypotheses) via empirical Bayesian methods.")
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "1v27bqik5cgcvs1kb67s52r56v6fakvmi81iybvvvbxvcn1dmy9r"))))
+ "061d2z1rrcyad6cf19si14ab9a3dxdi17sfbkx3vx8kdsfs3djy9"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
@@ -11956,14 +12309,14 @@ datasets.")
(define-public r-riboprofiling
(package
(name "r-riboprofiling")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
- "0qgzq82v4glkc0krk81zj9z71cnrvflsf1w45r9zmaw6bq45rfqd"))))
+ "1bd37ypxsj9p94p2851hhc9ind59b5pkg1lyalha1nfw5gf8iay3"))))
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
@@ -11997,14 +12350,14 @@ assessment, principal component analysis on codon coverage.")
(define-public r-riboseqr
(package
(name "r-riboseqr")
- (version "1.32.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
- "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"))))
+ "1cigbp3pc70ipja9mmprkrs91723r1zwgxbzyp87n5mb0i4q8xqh"))))
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
@@ -12025,14 +12378,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
(define-public r-interactionset
(package
(name "r-interactionset")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
- "1vs3mqf3x8zk7p83jkv41kag1bmn5zxrr3j1ldqk6wxsl77h55c5"))))
+ "0mpgxcwhb734pyn6bj93xknb704yrjkprxpa7kqwl24rbqyjydqs"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
@@ -12059,14 +12412,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0qhb2mm5nynnw0cj5da0i6hb1bz7cyns0gp7xy0wscmfyh2wahbv"))))
+ "13rnxig22agykzv3q7wm4wr9c5aw56q6q1zv8m5g5ngjcssy8l4c"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -12100,14 +12453,14 @@ information and producing various plots and statistics.")
(define-public r-ctc
(package
(name "r-ctc")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
- "0ph22v1an2havnh9sm7hms0q2pq4fjad2cm4dffiy3344cv70sn1"))))
+ "10a83rr0qhnzdhvlbyn0y690hxnl8q86z47dpimr6sq41w463im3"))))
(build-system r-build-system)
(propagated-inputs (list r-amap))
(home-page "https://bioconductor.org/packages/ctc/")
@@ -12120,14 +12473,14 @@ trees and clusters to other programs.")
(define-public r-goseq
(package
(name "r-goseq")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
- "1r13n64s9fbx951yaa4mpna71vynbkjz78irk96yzh2x2zzxpjvx"))))
+ "0waw5hhxh8yab8fqw9gnd3l39s6wkmp8690rhs4llarpqz6ssrhk"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -12146,14 +12499,14 @@ defined categories which are over/under represented in RNA-seq data.")
(define-public r-glimma
(package
(name "r-glimma")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
- "0171wizl516chzzwnbc2z2bf5sk4a491fcs4yhq5ycqaqpjmbg35"))
+ "0pkh15jjjb83pq7d49yzwb2gyc95x4rww78qnzpdrzhycgmcapii"))
(modules '((guix build utils)))
(snippet
'(with-directory-excursion "inst/htmlwidgets/lib/"
@@ -12231,13 +12584,13 @@ information.")
(define-public r-glmgampoi
(package
(name "r-glmgampoi")
- (version "1.12.2")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "glmGamPoi" version))
(sha256
(base32
- "0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7"))))
+ "1qc3f1spzkcjk95b07jpxgrjiwmlamwwx6mlhml4lgzy5qby7dpw"))))
(properties `((upstream-name . "glmGamPoi")))
(build-system r-build-system)
(propagated-inputs
@@ -12267,14 +12620,14 @@ experiments.")
(define-public r-rots
(package
(name "r-rots")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
- "0b2fl4wn696ia2kxihc6088ncnvd87ffq40bz58qi1bhq6krcmwv"))))
+ "1zd5w3mq0vjs3ivdb23x6d28sqq0dsfv13d64k1yijr4vdk3wvp6"))))
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
@@ -12290,14 +12643,14 @@ in omics data.")
(define-public r-plgem
(package
(name "r-plgem")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "plgem" version))
(sha256
(base32
- "1kzrscaqsrsvdq2c9g93l7bjmv1s5p1l3cbrz6skkqls9h4gsw08"))))
+ "0s5hia3xvddi0gaawcr5zsh34v6sh2zdi5gsjis8ar2g2p7agqgg"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase r-mass))
@@ -12314,13 +12667,13 @@ genes or proteins in these datasets.")
(define-public r-plyranges
(package
(name "r-plyranges")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "plyranges" version))
(sha256
(base32
- "1qv8snpcxpg16v5ji7sq3bnmgrgghz9h4mh246mcnnxfhi44b6nv"))))
+ "1z4pc9slbd6ji3c6g9flxhvvf0anjmywrlnjblv1mpgsh88avp7w"))))
(properties `((upstream-name . "plyranges")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
@@ -12348,14 +12701,14 @@ accessiblity for new Bioconductor users is hopefully increased.")
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.30.0")
+ (version "1.31.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "1nyfl78fjj956bk1xf32k3jdqhlffx6grbl7vajn48q5ldsx8kcx"))))
+ "0c7bw9cnav41vals2scv2gh5mj5nx2mgzagdb8g99sprdqv5924n"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@@ -12394,14 +12747,14 @@ modeling the rates that determines changes in mature mRNA levels.")
(define-public r-dnabarcodes
(package
(name "r-dnabarcodes")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
- "1jys0lj92zkqa3bb22fg35q5y8ij5pqhy3yvzg8zc8bjpzdvrg3a"))))
+ "12x4k55kshvwyzl83zkgkp0ylryr8wd3kz44ngp60k4pkwhkl9h9"))))
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
@@ -12421,14 +12774,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
(define-public r-ruvseq
(package
(name "r-ruvseq")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
- "0kxaaqf6py7kfndgpd0faxv6g610zj16pyvn9b4x9s3b22ib06j1"))))
+ "04byggwsvmqrl77268smbas0wax460cdshmp4v5iqc5fghl7n0p2"))))
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -12446,14 +12799,14 @@ samples.")
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd"))))
+ "0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
@@ -12474,14 +12827,14 @@ achieved for all methods using the BiocParallel framework.")
(define-public r-scaledmatrix
(package
(name "r-scaledmatrix")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ScaledMatrix" version))
(sha256
(base32
- "0xhw77w28r3agv0hw7fjpn1fp2p9bz7kdzwzx7gsa8411nffmd4d"))))
+ "1aigca0s8cmi46458pl9p9vwlkrmqawbgi0xmbwslz646x2s2h4a"))))
(properties `((upstream-name . "ScaledMatrix")))
(build-system r-build-system)
(propagated-inputs
@@ -12500,19 +12853,18 @@ multiplication.")
(define-public r-treeio
(package
(name "r-treeio")
- (version "1.24.3")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "treeio" version))
(sha256
(base32
- "0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif"))))
+ "1kvzdryw74r74gwxddsrng81ww49p3s7hgxn8ggl0p8fvz3sfgir"))))
(properties `((upstream-name . "treeio")))
(build-system r-build-system)
(propagated-inputs
(list r-ape
- r-cli
r-dplyr
r-jsonlite
r-magrittr
@@ -12533,13 +12885,13 @@ platform for merging tree with associated data and converting file formats.")
(define-public r-treesummarizedexperiment
(package
(name "r-treesummarizedexperiment")
- (version "2.8.0")
+ (version "2.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TreeSummarizedExperiment" version))
(sha256
(base32
- "1grnz82a7l5dpwssc24yxhllqdcvza2gc4h4cc6zxjcdg5r4l1ra"))))
+ "1yvqixlivapasx0ircfhmc8ckr7sw86d9vfvnqj97p4r667x6z6g"))))
(properties `((upstream-name . "TreeSummarizedExperiment")))
(build-system r-build-system)
(propagated-inputs
@@ -12566,14 +12918,14 @@ data.")
(define-public r-ggtree
(package
(name "r-ggtree")
- (version "3.8.2")
+ (version "3.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggtree" version))
(sha256
(base32
- "0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja"))))
+ "12w2l1q0c5aznd5fls04wvgsmjidqhr1kkqj4gajz1abj9f49cqf"))))
(properties `((upstream-name . "ggtree")))
(build-system r-build-system)
(propagated-inputs
@@ -12604,14 +12956,14 @@ data.")
(define-public r-metapod
(package
(name "r-metapod")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "metapod" version))
(sha256
(base32
- "0lr2sgbgdbqq626nsm3vyhghs8nalg5cxycr4cwsqh9nqrmip3wa"))))
+ "1nhxwj6gwc3hqji7icp1q6n0hj1gnvv1y5zhd2myhm7kj3sic2qc"))))
(properties `((upstream-name . "metapod")))
(build-system r-build-system)
(propagated-inputs
@@ -12633,14 +12985,14 @@ missing values and weighting where appropriate.")
(define-public r-biocsingular
(package
(name "r-biocsingular")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9"))))
+ "0z1p02329wk2x058ij42q5pyvp0vhsihaxmizgzcj4sww6i28j33"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
@@ -12668,14 +13020,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
(define-public r-destiny
(package
(name "r-destiny")
- (version "3.14.0")
+ (version "3.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
- "0hc85dq68h7dy5jcflpjj05231ny7na9i4lksfsw89jhmxgzhacd"))))
+ "06xwyqlsas98lxmd0qw5ysjwbk397kyapd5jq5pzjrynsj4r9xn6"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -12733,14 +13085,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
(define-public r-chipexoqual
(package
(name "r-chipexoqual")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPexoQual" version))
(sha256
(base32
- "1iysqs2k0xxiwd48ymahf6rywwj9ingjcfmnhx9d1x6w2h00v7lz"))))
+ "04dhkm8cq87x3c9f114z6q1pcw77xgs33rmhgzk4ajzxywhklq4j"))))
(properties `((upstream-name . "ChIPexoQual")))
(build-system r-build-system)
(propagated-inputs
@@ -12793,14 +13145,14 @@ penalized least squares regression method.")
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.74.1")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "1bj87ksvch5cm5zxwgfiiql0j94pvzbpn59wp6bacyip65z7w3ax"))))
+ "0hyjin75v8l2a8qymsd6rjb8m7svv2q07s6z1dllqag09wja1yfz"))))
(properties `((upstream-name . "DNAcopy")))
(build-system r-build-system)
(native-inputs (list gfortran))
@@ -12891,18 +13243,23 @@ and regression inferences from RNA-sequencing data.")
(define-public r-ebseq
(package
(name "r-ebseq")
- (version "1.40.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBSeq" version))
(sha256
(base32
- "0y23k607f61csj2ciaqnl8pzsjisqlcnnhlasv36446n8f3silx5"))))
+ "07x9fh8akgiixsv1xddkvs2q8xxfsibas01kdx0kw6wak3nihn4w"))))
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
- (list r-blockmodeling r-gplots r-testthat))
+ (list r-bh
+ r-blockmodeling
+ r-gplots
+ r-rcpp
+ r-rcppeigen
+ r-testthat))
(home-page "https://bioconductor.org/packages/EBSeq")
(synopsis "Differential expression analysis of RNA-seq data")
(description
@@ -12913,13 +13270,13 @@ gene and isoform level using RNA-seq data")
(define-public r-karyoploter
(package
(name "r-karyoploter")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
- "1nqcm2jlazm8wsa4p6a59m1j8y1qdwg0w3kii4dqnkann3q2q68x"))))
+ "0jr9lp250s9066hh40vxb6c6yhdd8yrnk0zklwylkf3jpbdgl621"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -12951,14 +13308,14 @@ coordinates.")
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lpsymphony" version))
(sha256
(base32
- "08b4d7k5qx19bpg12pw89ckk8x6r2n28qjdxbmy1cxn6dcgzhijd"))))
+ "1946wlw9zvyxdd99rs2rliks54ff5dkibavxd48aj7cqjsjh6b7g"))))
(build-system r-build-system)
(arguments
(list
@@ -12973,7 +13330,7 @@ coordinates.")
(inputs
(list zlib))
(native-inputs
- (list gfortran pkg-config 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
@@ -12990,14 +13347,14 @@ to install interface to SYMPHONY.")
(define-public r-ihw
(package
(name "r-ihw")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IHW" version))
(sha256
(base32
- "0i4yahgkrg9rnc0xldm026k6bd1bn5nkgkaf6kpyyday41rxzyq8"))))
+ "1pix38lg9snw0jdihh8sifnmckyw1lniwp95r93ca524g6swfc8b"))))
(properties `((upstream-name . "IHW")))
(build-system r-build-system)
(propagated-inputs
@@ -13019,14 +13376,14 @@ independent of the p-value under the null hypothesis.")
(define-public r-icobra
(package
(name "r-icobra")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iCOBRA" version))
(sha256
(base32
- "120bcakhhl6xqsfclzgmn7rcxmld289bjl6j7nrli7aiq5ilz8h4"))))
+ "1f0j10wha60vv592vsnv2pcqwz7g2fkld8pnar9rpwwb7qd0wcnf"))))
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
@@ -13056,14 +13413,14 @@ interactive exploration of results.")
(define-public r-residualmatrix
(package
(name "r-residualmatrix")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ResidualMatrix" version))
(sha256
(base32
- "1yay0i0nh2ax35ayqlpnmq0839syl5991hacyrbv3li3gqjc9qqv"))))
+ "06py71xbygfwq55kawh2x340idrf5mmxmnsz5m6lph2ka086dc5v"))))
(properties
`((upstream-name . "ResidualMatrix")))
(build-system r-build-system)
@@ -13085,14 +13442,14 @@ multiplication and calculation of row/column sums or means.")
(define-public r-batchelor
(package
(name "r-batchelor")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "batchelor" version))
(sha256
(base32
- "1cswij2mdjsdh99rmyh68wscg6h7cs0cff69gnki4gzzjfxy8x3f"))))
+ "1d5zik3bhz26ky2kpxd9kdzs9ff696qqys5gl8qwmmp8qym520l2"))))
(properties `((upstream-name . "batchelor")))
(build-system r-build-system)
(propagated-inputs
@@ -13128,14 +13485,14 @@ the numbers of cells across batches.")
(define-public r-mast
(package
(name "r-mast")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MAST" version))
(sha256
(base32
- "0vm7v2anbrci6mcans9y9svd6xjm4waf2kny3rz0cjgsasw60ycx"))
+ "17iycxxp6jb56ra21546kh2zlrm8by2vrlvsxvx8xmbpk32fb4lp"))
(snippet
'(delete-file "docs/jquery.sticky-kit.min.js"))))
(properties `((upstream-name . "MAST")))
@@ -13185,14 +13542,14 @@ single cell assay data.")
(define-public r-monocle
(package
(name "r-monocle")
- (version "2.28.0")
+ (version "2.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "monocle" version))
(sha256
(base32
- "05pix638s4hkig2i048m5jjhvw6cqr2b5qvfkk14i64p9kpifmqj"))))
+ "0i1qnmiaf3gf8955nlqzd81xzg4siliq154k699jmsz0fyyykia1"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -13276,13 +13633,13 @@ several functions from the R igraph package.")
(define-public r-sangerseqr
(package
(name "r-sangerseqr")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "sangerseqR" version))
(sha256
(base32
- "0hhq5zsx4srd9ndr370m44f80qdlrqafjv1838wf65gzijffhfqb"))))
+ "1vggjvxfmmm2gcyfay22wahkib15i164ic148jdps36pxapl6hi3"))))
(properties `((upstream-name . "sangerseqR")))
(build-system r-build-system)
(propagated-inputs (list r-biostrings r-shiny r-stringr))
@@ -13392,14 +13749,14 @@ user-defined and/or data-driven sets of hypotheses.")
(define-public r-noiseq
(package
(name "r-noiseq")
- (version "2.44.0")
+ (version "2.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "NOISeq" version))
(sha256
(base32
- "0cxhy4yrww6bh4z603389fikhix8rhfy04ylhm74fdmdng4jblg6"))))
+ "0qs0sc47n3p9wmf5cmc39cb30i8pbsyizhr29b3ld197pi1ba5wb"))))
(properties `((upstream-name . "NOISeq")))
(build-system r-build-system)
(propagated-inputs
@@ -13418,14 +13775,14 @@ assumptions.")
(define-public r-scdd
(package
(name "r-scdd")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scDD" version))
(sha256
(base32
- "1ndb1zcbdy00xkfx18slrm5bnld9ci5scysc37clhsq2lq5xb25z"))))
+ "15hzsq8ckw8v8ccz30kia9qr1iymmcszc9z31g5arrx1y816zgbq"))))
(properties `((upstream-name . "scDD")))
(build-system r-build-system)
(propagated-inputs
@@ -13456,14 +13813,14 @@ distributions.")
(define-public r-scone
(package
(name "r-scone")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scone" version))
(sha256
(base32
- "0v3rd2h0n52qz9kqxa3l49rjfssfk252dy7j2nvi34y85win2p1w"))))
+ "1y0blhh75hb60h9jmvz2naqfzky4zgw5gn81fbj74jfph9y712lp"))))
(build-system r-build-system)
(propagated-inputs
(list r-aroma-light
@@ -13500,14 +13857,14 @@ high-throughput analyses.")
(define-public r-geoquery
(package
(name "r-geoquery")
- (version "2.68.0")
+ (version "2.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GEOquery" version))
(sha256
(base32
- "1xyrfj8b7j2wdjlbmwhx1c0hfbvr7l7jxyw2v64fbw8604zprv4s"))))
+ "1xjfh9lx2cfwzkk61pdarajsa86nzhy3dz7r4zws20pz4xkhwv87"))))
(properties `((upstream-name . "GEOquery")))
(build-system r-build-system)
(propagated-inputs
@@ -13535,14 +13892,14 @@ the bridge between GEO and BioConductor.")
(define-public r-illuminaio
(package
(name "r-illuminaio")
- (version "0.42.0")
+ (version "0.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "illuminaio" version))
(sha256
(base32
- "190i3b9qmh26bic1lzi54mw4p1nrg57qijl1pg6b29w3i6srq692"))))
+ "15i47b995dqh0dlg60lss5vgj31as3cwhb2z5fqbnknx3lj7s6rl"))))
(build-system r-build-system)
(propagated-inputs
(list r-base64))
@@ -13556,14 +13913,14 @@ files, including IDAT.")
(define-public r-siggenes
(package
(name "r-siggenes")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "siggenes" version))
(sha256
(base32
- "0h5asj2w4xgfj9xapjawmxldnhq789py39drlr8illyhcczkzkbz"))))
+ "0jzxwg28ih1i0f7hal99g60zply0g613b4wrjsbv738cmlsai2kc"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase r-multtest r-scrime))
@@ -13580,14 +13937,14 @@ Bayes Analyses of Microarrays} (EBAM).")
(define-public r-bumphunter
(package
(name "r-bumphunter")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bumphunter" version))
(sha256
(base32
- "1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18"))))
+ "0vnm0m9abf8478f7lair58vw1v4mxj8sbmrxcpf8622ygf2na4qc"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -13614,13 +13971,13 @@ studies.")
(define-public r-bumpymatrix
(package
(name "r-bumpymatrix")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BumpyMatrix" version))
(sha256
(base32
- "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i"))))
+ "0ic87fjxwb39nmys09zb6k3ghcx8mmmj9pifljs10449i2lgzl2r"))))
(properties `((upstream-name . "BumpyMatrix")))
(build-system r-build-system)
(propagated-inputs (list r-iranges r-matrix r-s4vectors))
@@ -13640,13 +13997,13 @@ data in a format that is compatible with two-dimensional containers like the
(define-public r-mia
(package
(name "r-mia")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "mia" version))
(sha256
(base32
- "1p78yacx0cgihva7m2n3vnll5w4b47vl98hy12pq9rnmhk6r591z"))))
+ "044spfxsf7xijnbh0933cwdkycmg05zsfqhbx5pkfajysh6w5cxp"))))
(properties `((upstream-name . "mia")))
(build-system r-build-system)
(propagated-inputs
@@ -13654,6 +14011,7 @@ data in a format that is compatible with two-dimensional containers like the
r-biocgenerics
r-biocparallel
r-biostrings
+ r-bluster
r-decipher
r-decontam
r-delayedarray
@@ -13662,6 +14020,7 @@ data in a format that is compatible with two-dimensional containers like the
r-dplyr
r-iranges
r-mass
+ r-matrixgenerics
r-multiassayexperiment
r-rlang
r-s4vectors
@@ -13688,13 +14047,13 @@ summarization.")
(define-public r-microbiome
(package
(name "r-microbiome")
- (version "1.22.0")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "microbiome" version))
(sha256
(base32
- "120wyjv2r9cbjgxbp70nzf249hai8cqn59gcbgwnazynfy5ih1w8"))))
+ "0xmkwf7v89nwlpjrzqxv87lbsn6za99v7f0yxkgzfk5n6fadrf05"))))
(properties `((upstream-name . "microbiome")))
(build-system r-build-system)
(propagated-inputs
@@ -13759,13 +14118,13 @@ experiments.")
(define-public r-milor
(package
(name "r-milor")
- (version "1.8.1")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "miloR" version))
(sha256
(base32
- "073s239aqkixsrarqxfv4nmpcj025k32nhql63qaxrkrvvdd34di"))))
+ "1hnvw9x0xwjb0br4yvzkzn73nvm8p3j3wmcw8jrid105j0fz6vcj"))))
(properties `((upstream-name . "miloR")))
(build-system r-build-system)
(propagated-inputs
@@ -13807,14 +14166,14 @@ model.")
(define-public r-minfi
(package
(name "r-minfi")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "minfi" version))
(sha256
(base32
- "18b9yg9hnnm1saaiprm2hj86aajjwm1zwvpj0yadfa3s811pw4nq"))))
+ "13lldzj68vmmmrp5fi2rfxbchbivaa1scq56hl0v9mxxicw72a0x"))))
(build-system r-build-system)
(propagated-inputs
(list r-beanplot
@@ -13858,13 +14217,13 @@ methylation arrays.")
(define-public r-missmethyl
(package
(name "r-missmethyl")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "missMethyl" version))
(sha256
(base32
- "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h"))))
+ "1nv4rm5pbx0s7m5zak3jzmwz4pkf8ghkj0ckdcsnmw3k364ny856"))))
(properties `((upstream-name . "missMethyl")))
(build-system r-build-system)
(propagated-inputs
@@ -13908,14 +14267,14 @@ into account multi-gene associated probes.")
(define-public r-methylumi
(package
(name "r-methylumi")
- (version "2.46.0")
+ (version "2.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "methylumi" version))
(sha256
(base32
- "1aa0pwjyp2p9a4mx4n4qw88ndgrj56p669yzdkd7hxhc3x55nzlf"))))
+ "1vracrvy56kk3hc9midxdaxhad2zf1lspn0zzxjjbsyzx3r0ip0n"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotate
@@ -13955,13 +14314,13 @@ and Infinium HD arrays are also included.")
(define-public r-lefser
(package
(name "r-lefser")
- (version "1.10.1")
+ (version "1.11.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "lefser" version))
(sha256
(base32
- "1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4"))))
+ "1fnccnjllgxf51dlmcvv0r66xs0wvfxrj66qrqisqd99hrpxhws2"))))
(properties `((upstream-name . "lefser")))
(build-system r-build-system)
(propagated-inputs
@@ -13979,14 +14338,14 @@ to find biomarkers of groups and sub-groups.")
(define-public r-lumi
(package
(name "r-lumi")
- (version "2.52.0")
+ (version "2.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lumi" version))
(sha256
(base32
- "1lxxqr7x9jdjrsj5j95jb0dbd7p208vifxw3j4s4140zh1ppxnpj"))))
+ "0iwkag84w1sc703jcdfx0h799hlchdiqvlps8g8lwmil5b0xlsw5"))))
(build-system r-build-system)
(propagated-inputs
(list r-affy
@@ -14018,14 +14377,14 @@ especially Illumina Infinium methylation microarrays.")
(define-public r-linnorm
(package
(name "r-linnorm")
- (version "2.24.1")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Linnorm" version))
(sha256
(base32
- "1sqkmjah2lxahnvwv04a970za2b8kzvmxnb41k9xrnvj0akigc2d"))))
+ "1ax5zmby8zw0mgxjd8yhlk4ai0s03zq59qwzqgv8zqlms8yjpvs2"))))
(properties `((upstream-name . "Linnorm")))
(build-system r-build-system)
(propagated-inputs
@@ -14079,14 +14438,14 @@ evaluation of DEG analysis methods.")
(define-public r-ioniser
(package
(name "r-ioniser")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IONiseR" version))
(sha256
(base32
- "1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0"))))
+ "1y595hq40kpsasp74wsbf3ngd2rrriqg65z9y4svcwdygj03pgrz"))))
(properties `((upstream-name . "IONiseR")))
(build-system r-build-system)
(propagated-inputs
@@ -14146,14 +14505,14 @@ are standardized and usable by the accompanying mutossGUI package.")
(define-public r-metap
(package
(name "r-metap")
- (version "1.8")
+ (version "1.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "metap" version))
(sha256
(base32
- "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
+ "1w4mv7vb94d4pkllvabz9az8sbrbfhigxw4is3j0jzi1pnlyc8kg"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice
@@ -14175,13 +14534,13 @@ published results; and a routine for graphical display.")
(define-public r-tradeseq
(package
(name "r-tradeseq")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tradeSeq" version))
(sha256
(base32
- "14b90x9h34mhbc4sdpzkygrrswf84pi1ddwpzxhvlvr9gs443xqs"))))
+ "06k0jib20nq7zqc5vbgag8v1lbadjlg0idh5jwn5bcjc74dx15vj"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -14244,14 +14603,14 @@ peak definition in combination with known profile characteristics.")
(define-public r-varianttools
(package
(name "r-varianttools")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantTools" version))
(sha256
(base32
- "1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47"))))
+ "1ibg4cdpbv4ph3y4r90j8zfwr1cy1z33p4bazhzyi2zv3xa1nrq6"))))
(properties `((upstream-name . "VariantTools")))
(build-system r-build-system)
(propagated-inputs
@@ -14284,14 +14643,14 @@ gmapR.")
(define-public r-heatplus
(package
(name "r-heatplus")
- (version "3.8.0")
+ (version "3.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
- "031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx"))))
+ "1vs7x4dc2vrfi2wi300bjr2hl1wwp4v27sgzycr6qv6x2nx9i5xq"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
@@ -14309,18 +14668,18 @@ information about samples and features can be added to the plot.")
(define-public r-gosemsim
(package
(name "r-gosemsim")
- (version "2.26.1")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOSemSim" version))
(sha256
(base32
- "15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9"))))
+ "10jhjzgf10w9cmr97qzc3mqvgvgx9h7pqk7zkkqwhg7anv6wa788"))))
(properties `((upstream-name . "GOSemSim")))
(build-system r-build-system)
(propagated-inputs
- (list r-annotationdbi r-go-db r-rcpp))
+ (list r-annotationdbi r-go-db r-rcpp r-rlang))
(native-inputs
(list r-knitr))
(home-page "https://guangchuangyu.github.io/software/GOSemSim")
@@ -14336,14 +14695,14 @@ sets of GO terms, gene products and gene clusters.")
(define-public r-anota
(package
(name "r-anota")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "anota" version))
(sha256
(base32
- "0ic12p1qyfrmh3l1wv7s9yi8sr84crj4nksmcx0lybb6rak9gy0x"))))
+ "1b1r7jwilwvl89fw3rqascyhy8wnm8y81lnx85pwjk55ld56jlb1"))))
(build-system r-build-system)
(propagated-inputs
(list r-multtest r-qvalue))
@@ -14366,13 +14725,13 @@ the data set is suitable for such analysis.")
(define-public r-anota2seq
(package
(name "r-anota2seq")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "anota2seq" version))
(sha256
- (base32 "0pmk45276bl3qppzxlp4jpc8bsvdpca8nzrdl6c4n9r3xhzfpyq0"))))
+ (base32 "0kyxwhj5vq5z4v3x3hfb9ks3h37axqskyj9rzyj2bzsy2yk9hajn"))))
(properties `((upstream-name . "anota2seq")))
(build-system r-build-system)
(propagated-inputs
@@ -14399,38 +14758,16 @@ mRNA levels or buffering, a mechanism regulating translational efficiency so
that protein levels remain constant despite fluctuating total mRNA levels.")
(license license:gpl3)))
-(define-public r-sigpathway
- (package
- (name "r-sigpathway")
- (version "1.66.2")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "sigPathway" version))
- (sha256
- (base32
- "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy"))))
- (properties `((upstream-name . "sigPathway")))
- (build-system r-build-system)
- (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
- (synopsis "Pathway analysis")
- (description
- "This package is used to conduct pathway analysis by calculating the NT_k
-and NE_k statistics in a statistical framework for determining whether a
-specified group of genes for a pathway has a coordinated association with a
-phenotype of interest.")
- (license license:gpl2)))
-
(define-public r-fcscan
(package
(name "r-fcscan")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fcScan" version))
(sha256
- (base32 "071sylwwj27bk39pkn5a29r7bmfpmyaixkkg7dqcdq230c1dsrps"))))
+ (base32 "0hhad9vg43j0yz8fp2w7qdhvdy77yr7anv0fi170042x3piq1q7r"))))
(properties `((upstream-name . "fcScan")))
(build-system r-build-system)
(propagated-inputs
@@ -14457,14 +14794,14 @@ presence of additional sites within the allowed window size.")
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "0chnrwiwk31crrx4am1yrbxjdqd3jycgjgczqzj7lxaa9v7lvm7z"))))
+ "0sykd4ingpw41615hbr3vw9yd1ks225hdb5qxnhbk4m4wxj814ql"))))
(build-system r-build-system)
(propagated-inputs
(list r-bh
@@ -14490,14 +14827,14 @@ to multiple hypothesis correction.")
(define-public r-dose
(package
(name "r-dose")
- (version "3.26.1")
+ (version "3.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DOSE" version))
(sha256
(base32
- "1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx"))))
+ "1xirazskw2d0fllyf27jvsm69amcil1znx81m9d613vl03dpwswy"))))
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
@@ -14507,6 +14844,8 @@ to multiple hypothesis correction.")
r-ggplot2
r-gosemsim
r-hdo-db
+ r-hpo-db
+ r-mpo-db
r-qvalue
r-reshape2))
(native-inputs
@@ -14525,13 +14864,13 @@ data.")
(define-public r-enrichedheatmap
(package
(name "r-enrichedheatmap")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "EnrichedHeatmap" version))
(sha256
(base32
- "18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya"))))
+ "0j87x26qimsx4gi311bm1g9bldwq9r4z3aflxf8p91zlavjbv8zp"))))
(properties `((upstream-name . "EnrichedHeatmap")))
(build-system r-build-system)
(propagated-inputs (list r-circlize
@@ -14557,14 +14896,14 @@ correspondance between different data sources.")
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.20.3")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "11hgxs42wvirv6b9ywr2jb51s67k4r0pm21dkvm7xjbsbarlkhmh"))))
+ "05ps96adbn4h8i0mqflzm1h6chjlrmfz6hx393232bhb995jfllx"))))
(build-system r-build-system)
(propagated-inputs
(list r-aplot
@@ -14625,14 +14964,14 @@ attempts to assess their statistical significance.")
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
- (version "4.8.3")
+ (version "4.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3"))))
+ "1vlrybyczfci5qnw50k0y2j2853r2p1ff5bpj35rdca4ja0iqh2q"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
@@ -14645,6 +14984,8 @@ attempts to assess their statistical significance.")
r-go-db
r-gosemsim
r-gson
+ r-httr
+ r-igraph
r-magrittr
r-plyr
r-qvalue
@@ -14663,13 +15004,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
(define-public r-clusterexperiment
(package
(name "r-clusterexperiment")
- (version "2.20.0")
+ (version "2.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "clusterExperiment" version))
(sha256
(base32
- "0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706"))))
+ "1qnxrdpp75m342q4chwaig413l52giz1h7nd4p9y4b472dqx9hh4"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -14709,14 +15050,14 @@ expression data sets.")
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.80.0")
+ (version "1.82.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "1s5b27n01crfzrpshhiv6g0q0qf0dip1gw4nkrkg5sh5x9dsikq6"))))
+ "0aga7xhx5d1xp09n2im7yqi9y1b3v22l554hi35ahg2lwwvxjiw1"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
@@ -14753,14 +15094,14 @@ data in R and Bioconductor containers.")
(define-public r-annaffy
(package
(name "r-annaffy")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annaffy" version))
(sha256
(base32
- "0jy3qk31lb11bixncb2w2hw1ibvik31bfi2l5vyq5wjyxndfyax6"))))
+ "1mdv0x9lnr0bm96h5f9104nqg2j6cjqvp5prrxx10j0d6464vmkw"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -14785,14 +15126,14 @@ It allows searching of biological metadata using various criteria.")
(define-public r-a4core
(package
(name "r-a4core")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Core" version))
(sha256
(base32
- "14q9q3dxnmmm491af53hd0dwwqiz47xxrwy05axh85x4fh01j3xx"))))
+ "0iismcsnkyb7m4dwmxw5pyvscj2bhp6zw9hpdb2ff91viynbknq1"))))
(properties `((upstream-name . "a4Core")))
(build-system r-build-system)
(propagated-inputs
@@ -14809,14 +15150,14 @@ arrays.")
(define-public r-a4classif
(package
(name "r-a4classif")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Classif" version))
(sha256
(base32
- "1z5xypz5jvb06pk71x6953iirhh1w1mggm0pxqibg0ag9lx2zzmv"))))
+ "1wxkyqyhb3mj04kmaisd09dapywjpc081ihaig5rs04k611ddvhi"))))
(properties `((upstream-name . "a4Classif")))
(build-system r-build-system)
(propagated-inputs
@@ -14839,14 +15180,14 @@ Affymetrix arrays.")
(define-public r-a4preproc
(package
(name "r-a4preproc")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Preproc" version))
(sha256
(base32
- "1dxh0zbv4z4gqnwbv7yn247gx7cqv68vb43p6f98c2kyqilfpjg9"))))
+ "19nf3bc0gdwixif50f3bs47a1kw1w1lir1dz4l8zqdp3h8gfmj60"))))
(properties `((upstream-name . "a4Preproc")))
(build-system r-build-system)
(propagated-inputs
@@ -14863,14 +15204,14 @@ is used for preprocessing the arrays.")
(define-public r-a4reporting
(package
(name "r-a4reporting")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Reporting" version))
(sha256
(base32
- "0lx7fx2vlpq3c347gx842qlcvnzl0r25i5a55l0qbf8rb5liq2yv"))))
+ "16lgbwsgwp77x9a8c3hr1aqhp36skzz72xhbzm0a7w3kagmd8gn6"))))
(properties `((upstream-name . "a4Reporting")))
(build-system r-build-system)
(propagated-inputs
@@ -14887,14 +15228,14 @@ provides reporting features.")
(define-public r-a4base
(package
(name "r-a4base")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Base" version))
(sha256
(base32
- "01c8rps321820b0pchfqv8shglb26rys7hqkwygpzzx3jj310v8x"))))
+ "0hin5lpwa7cxa862jh3y7d8kq3q9bv76ri08b27jxzyr5p7xwcr2"))))
(properties `((upstream-name . "a4Base")))
(build-system r-build-system)
(propagated-inputs
@@ -14918,14 +15259,14 @@ Affymetrix arrays.")
(define-public r-a4
(package
(name "r-a4")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4" version))
(sha256
(base32
- "0n49scwwmg51gcakbc0bfjcy1lcpdxg974l11yk35kj0bg9ynpgi"))))
+ "1hdqnipg326z2k7vs6sc1brc9lvvhmr2l6cjp4f9a205g4q7r9rr"))))
(build-system r-build-system)
(propagated-inputs
(list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
@@ -14939,14 +15280,14 @@ Affymetrix arrays.")
(define-public r-abseqr
(package
(name "r-abseqr")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "abseqR" version))
(sha256
(base32
- "05kcwmv3d59lrdnpi82701biwawnnpfvpwr170xdi3hfdff6g59c"))))
+ "0s865nahgm0by2nvjydkjlhkj2sxmrvcrhw7rmm46ld4g10xsrc8"))))
(properties `((upstream-name . "abseqR")))
(build-system r-build-system)
(inputs
@@ -14987,14 +15328,14 @@ further downstream analysis on its output.")
(define-public r-bacon
(package
(name "r-bacon")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bacon" version))
(sha256
(base32
- "1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293"))))
+ "065b4xf5i1bx08494nm3r497bs47s5vf99l2g37nlpvxf7pypvrz"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocparallel r-ellipse r-ggplot2))
@@ -15012,14 +15353,14 @@ fitting a three-component normal mixture on z-scores.")
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.48.0")
+ (version "2.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "08li2wql2zhg06z0rjws9qcnv3ishgnpc6k8xyjcf7yfyg7qpk1d"))))
+ "14jcsqb56vn67hjmcjjnwswzbilsarkk8kblc715c7da72q7fzpn"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
@@ -15066,12 +15407,12 @@ distributions, modules and filter motifs.")
(define-public r-motifdb
(package
(name "r-motifdb")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MotifDb" version))
(sha256
- (base32 "18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw"))))
+ (base32 "1z72f5f3sh2ak6zjcfc6j6rblkllmdkli0kb57nwxg2j5hrys3xr"))))
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
@@ -15093,12 +15434,12 @@ frequency matrices from nine public sources, for multiple organisms.")
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
- (version "2.14.2")
+ (version "2.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
- (base32 "13fv0rkyb32grswlgzd3zr35p9xpibj2iq62sr23if4w6z5nbml2"))))
+ (base32 "02i3hkffhhsbzmn97mv8wc2px5caq9xnp45z0l53dp1jxbmms1h0"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
@@ -15143,40 +15484,29 @@ Bioconductor.")
(define-public r-motifstack
(package
(name "r-motifstack")
- (version "1.44.1")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifStack" version))
(sha256
(base32
- "1g46cxn1h3cqr0yrj6ancshzygiqr9finf1vmmig3h9g0ijgr5lz"))
+ "10hmqwkysifd59as9zx00p3gj595lwj30ywn9pqb1920q6f5mx2i"))
(snippet
'(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
(properties `((upstream-name . "motifStack")))
(build-system r-build-system)
(arguments
(list
- #:modules '((guix build utils)
- (guix build r-build-system)
- (srfi srfi-1))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/htmlwidgets/lib/d3"
- (call-with-values
- (lambda ()
- (unzip2
- `((,(assoc-ref inputs "_")
- "d3.v4.min.js"))))
- (lambda (sources targets)
- (for-each (lambda (source target)
- (format #true "Processing ~a --> ~a~%"
- source target)
- (invoke "esbuild" source "--minify"
- (string-append "--outfile=" target)))
- sources targets)))))))))
+ (let ((source (assoc-ref inputs "_"))
+ (target "d3.v4.min.js"))
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
(propagated-inputs
(list r-ade4
r-biostrings
@@ -15206,14 +15536,14 @@ type and symbol colors.")
(define-public r-genomicscores
(package
(name "r-genomicscores")
- (version "2.12.0")
+ (version "2.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicScores" version))
(sha256
(base32
- "1z8h9sbr6xqwbsfisr33qdxg0xdrw8r4vvxl1pf4x8vv08zw0vx6"))))
+ "1plpmi1sb9vv03480njf3awnc7i19f9iaxi3j6bvjzpi6zmw40dq"))))
(properties `((upstream-name . "GenomicScores")))
(build-system r-build-system)
(propagated-inputs
@@ -15244,14 +15574,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "0mcrkmirss484d2mskikyjdz5cmbhdk52yxkffz9g8g5m9lkq5xk"))))
+ "1b53rkhyqnyh5vangh3hy4yccx1yackwbv1pxdimbp840ji6d122"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -15291,14 +15621,14 @@ footprints.")
(define-public r-gofuncr
(package
(name "r-gofuncr")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOfuncR" version))
(sha256
(base32
- "05509xf768x8asqadjj5s50m0yqnklrxi28bmqd22cn6cbmahszw"))))
+ "1baa3aabkhmwq66xkzf4jk5nz85kkx1ks0mqc91s2ra9916wj6cd"))))
(properties `((upstream-name . "GOfuncR")))
(build-system r-build-system)
(propagated-inputs
@@ -15396,14 +15726,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
(define-public r-annotationtools
(package
(name "r-annotationtools")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotationTools" version))
(sha256
(base32
- "0dwbh2h2mp8gy0kwqmkri3q2glnzcj8cn83j1qyh7lk15anc33g8"))))
+ "0g086rj06k3wac24zx66dw1yc1bzv25bmlbjbpcpgdcmyjb1i8sf"))))
(properties
`((upstream-name . "annotationTools")))
(build-system r-build-system)
@@ -15421,14 +15751,14 @@ text files).")
(define-public r-allelicimbalance
(package
(name "r-allelicimbalance")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AllelicImbalance" version))
(sha256
(base32
- "1ms3x3x2gvhgllff3nwawg5jlpmgx6dhwll0dghklnv3lssbx4c7"))))
+ "0p7l856a46zzla8brsg901pmh5738j63h7h7rn3da94ny8k417mf"))))
(properties
`((upstream-name . "AllelicImbalance")))
(build-system r-build-system)
@@ -15464,14 +15794,14 @@ investigation using RNA-seq data.")
(define-public r-aucell
(package
(name "r-aucell")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AUCell" version))
(sha256
(base32
- "1zqjmg8nxxj30lxppl685ihynbz44vw7qm3kwjq6cp83c5556hz9"))))
+ "1d1icbq8i7mwsc7lv9pn4r0vs7azx1lwng5p3ghnray1ygqclbi0"))))
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
@@ -15505,14 +15835,14 @@ needed.")
(define-public r-ebimage
(package
(name "r-ebimage")
- (version "4.42.0")
+ (version "4.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBImage" version))
(sha256
(base32
- "0z0ajmy1zx7mqcjm2ibyk2qg3cj00kl76padyksbdbmwdncxs8yb"))))
+ "0jdi5cn4v5ll43xb3l6sy062snd5p9n2nrryc5aqd2ki18mdmghy"))))
(properties `((upstream-name . "EBImage")))
(build-system r-build-system)
(propagated-inputs
@@ -15544,14 +15874,14 @@ visualization with image data.")
(define-public r-yamss
(package
(name "r-yamss")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yamss" version))
(sha256
(base32
- "0kjlp62s2393jdwp0crizsgp4iqagbgnd3hdl9vpbr9qrjxg4s7m"))))
+ "16rdy35wmydcx322pf9j7l7z2mzgrksg1whr8i8xdmdqfnqz3xyb"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
@@ -15577,14 +15907,14 @@ analysis.")
(define-public r-gtrellis
(package
(name "r-gtrellis")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gtrellis" version))
(sha256
(base32
- "1kk7ysscq8xdbn35b20s8sn8gl93sy0c718fmvr1yrhiqaxq5alr"))))
+ "022wn0l2wfizlz6d5plkphjsjbmxw2wcvxrzr4vanczjzzyxv5c5"))))
(build-system r-build-system)
(propagated-inputs
(list r-circlize r-genomicranges r-getoptlong r-iranges))
@@ -15603,14 +15933,14 @@ genomic categories and to add self-defined graphics in the plot.")
(define-public r-somaticsignatures
(package
(name "r-somaticsignatures")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SomaticSignatures" version))
(sha256
(base32
- "075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s"))))
+ "0s9kjjh1n4a55ycjvcw8ymjcclcj8b35aygx4x1k5af1hf3f7wyb"))))
(properties
`((upstream-name . "SomaticSignatures")))
(build-system r-build-system)
@@ -15642,14 +15972,14 @@ decomposition algorithms.")
(define-public r-yapsa
(package
(name "r-yapsa")
- (version "1.26.8")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "YAPSA" version))
(sha256
(base32
- "16rr2bkni3jx5qskr5fz5lvf23d03xgd3m4068mnd3n9r23hpb4p"))))
+ "07dxhaywad9ivkrc454hhizfw6a5yvarrc5fp5za2jgsznv408wl"))))
(properties `((upstream-name . "YAPSA")))
(build-system r-build-system)
(propagated-inputs
@@ -15691,14 +16021,14 @@ provided.")
(define-public r-gcrma
(package
(name "r-gcrma")
- (version "2.72.0")
+ (version "2.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gcrma" version))
(sha256
(base32
- "0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p"))))
+ "07ina8w8p5bm382v452i2wpmv90gvgli393lsgp7xy0h9in7h6yg"))))
(build-system r-build-system)
(propagated-inputs
(list r-affy
@@ -15773,14 +16103,14 @@ chips with the MAQC reference datasets.")
(define-public r-quantro
(package
(name "r-quantro")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "quantro" version))
(sha256
(base32
- "08m94q65c11isbkx9xljm2bx2aq2rml1bqh5i1cg81xg2ilm9h6a"))))
+ "032qxwgldl1hbgsgb5q3fi7nfg1nx3k0yppqkvim5cif613m1nzq"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -15806,14 +16136,14 @@ groups.")
(define-public r-yarn
(package
(name "r-yarn")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yarn" version))
(sha256
(base32
- "0ddfl4jp0n8sb665hcpsij959fl28rj22n1h61wp2374kpc0fwfj"))))
+ "12d806pyiks5xbvxng4pxn0xqvgs4c526gp2pp2qhdxw0w2m29rj"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -15843,14 +16173,14 @@ large RNA-seq experiments.")
(define-public r-roar
(package
(name "r-roar")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "roar" version))
(sha256
(base32
- "0p5q6nyp8d0gl95rd89xrs08gv87m1q6d0x4ws2b6sd4gc1nw2ny"))))
+ "0pibk6zdqlbm0rxnb95pd94v6lbg67rwmjnpfxizq7wv36pw6kdr"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
@@ -15911,14 +16241,14 @@ genes.")
(define-public r-massspecwavelet
(package
(name "r-massspecwavelet")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MassSpecWavelet" version))
(sha256
(base32
- "1nc1imxia71sxxvi77f91yhwxza2l8kk1d7zkp5680xzw6yd6ajr"))))
+ "044rz2xsz2v8i9ha20hxn2cwf7wa74p5f25jql8ancp6r3gim9sy"))))
(properties
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
@@ -15935,14 +16265,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.22.0")
+ (version "4.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "112g2lpi074cr8g09cqwjbcwv9aw4djr7ashxpnxjycd3ayc0j3v"))))
+ "10bvxww489mb4bl5v9ma6klyg359zb9ady5rl95q1mkp54hahdw8"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -15952,16 +16282,19 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
r-lattice
r-massspecwavelet
r-mscoreutils
+ r-msexperiment
r-msfeatures
r-msnbase
r-multtest
r-mzr
r-plyr
+ r-progress
r-protgenerics
r-rann
r-rcolorbrewer
r-robustbase
r-s4vectors
+ r-spectra
r-summarizedexperiment))
(native-inputs
(list r-knitr))
@@ -15977,13 +16310,13 @@ data for high-throughput, untargeted analyte profiling.")
(define-public r-wppi
(package
(name "r-wppi")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "wppi" version))
(sha256
(base32
- "06y4pq8msjzwrw1jgyj9yskgpfhvcz54qcsv0h14bakhyrwk00pg"))))
+ "04wg645c0gww8mq3vg70gqlwm12dmqxmvk704zvmxcpifhrvpn2b"))))
(properties `((upstream-name . "wppi")))
(build-system r-build-system)
;; This is necessary because omnipathr attempts to write a configuration
@@ -16018,14 +16351,14 @@ scores and a path search algorithm.")
(define-public r-wrench
(package
(name "r-wrench")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Wrench" version))
(sha256
(base32
- "18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h"))))
+ "11g6a2315hllf197ssccybhv6i7p48n7bv2amzpgxs7bs7qg3k9d"))))
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
@@ -16042,14 +16375,14 @@ that arising from 16s metagenomic surveys.")
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "15gbs10bi1alxxbxaj4h3hzfgck4nxygy896y34x81w1rn7in3vp"))))
+ "1gq0hxmnnis0g1y6hiphz02dmk3pfjz874xb2bxqw49z7387fwm8"))))
(build-system r-build-system)
(propagated-inputs
(list r-assertthat
@@ -16076,14 +16409,14 @@ visualization of exonic read coverage.")
(define-public r-widgettools
(package
(name "r-widgettools")
- (version "1.78.0")
+ (version "1.80.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "widgetTools" version))
(sha256
(base32
- "03bvh2jk97jj40z35q5n1is2wxrs4dggw08ndyywy4pzx1diqdc4"))))
+ "1zkc275sb1qbban7sghqziv3xkg7wjdpghddklv451n7j282k6w1"))))
(properties `((upstream-name . "widgetTools")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/widgetTools/")
@@ -16097,14 +16430,14 @@ widgets in R.")
(define-public r-webbioc
(package
(name "r-webbioc")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "webbioc" version))
(sha256
(base32
- "0z2sixzs0rwdwdhxs5mqzghgiw4g64l8p9ag5lw289bzs4c4kqnd"))))
+ "1ca41q7hxy6p8kvc3qbjplvn40k4jwhf0mb03njifry4xi1xipgy"))))
(build-system r-build-system)
(inputs
(list netpbm perl))
@@ -16129,14 +16462,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
(define-public r-zinbwave
(package
(name "r-zinbwave")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zinbwave" version))
(sha256
(base32
- "1bmxbzpgmwama42a3vi1n0sic166v5zs0kl9mhmrh0rrx0nv303k"))))
+ "1lp8x9grc07kaz9iy7yc45mk708g9dplsl86fq0ip8rs51c8f31i"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocparallel
@@ -16162,14 +16495,14 @@ the data.")
(define-public r-zfpkm
(package
(name "r-zfpkm")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zFPKM" version))
(sha256
(base32
- "1fkzyq282xafyapgi5xi1c2dmfkyikqvf622pycjs80fas38044h"))))
+ "18pnzc51r7l1ypnhavl83r3gy7l91qnqzvl6771zid04g99pk844"))))
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
@@ -16187,14 +16520,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
(define-public r-rbowtie2
(package
(name "r-rbowtie2")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie2" version))
(sha256
(base32
- "11h4irhi0pxd0l378im455amqfamqypyl0ri2cs8nk1lg184ridr"))))
+ "0dx1psk6f27p1kiw4qwj1nf55gpqgisibzipvlnn5m9q3q8g70gv"))))
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
(propagated-inputs
@@ -16214,14 +16547,14 @@ rapid adapter trimming, identification, and read merging.")
(define-public r-progeny
(package
(name "r-progeny")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "progeny" version))
(sha256
(base32
- "047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7"))))
+ "1plgwi2fmx7bh648fqpzzfqnh84fsgnn5jfcbdf9yia6zzigicql"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -16246,14 +16579,14 @@ expression\".")
(define-public r-arrmnormalization
(package
(name "r-arrmnormalization")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ARRmNormalization" version))
(sha256
(base32
- "001nwl605prg942vmnbb1rwjwgpscpjs27ssic3h10rlmpb65yzp"))))
+ "1fd1pfw2ggqb0k2npvibfy8liix57m01cxfxp10shvfbzjjy4wjm"))))
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
@@ -16269,14 +16602,14 @@ Infinium HumanMethylation 450k assay.")
(define-public r-biocfilecache
(package
(name "r-biocfilecache")
- (version "2.8.0")
+ (version "2.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocFileCache" version))
(sha256
(base32
- "1qk1n50arlk0mfkv9p3zl3lqbapzfkjdbadv51hsp4h9lyaw9sbg"))))
+ "044kh1rfgb608y2v4wzbzddirhw5crj3k6i28wr78qgnzqc89mdm"))))
(properties `((upstream-name . "BiocFileCache")))
(build-system r-build-system)
(propagated-inputs
@@ -16301,14 +16634,14 @@ and data files used across sessions.")
(define-public r-iclusterplus
(package
(name "r-iclusterplus")
- (version "1.36.1")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iClusterPlus" version))
(sha256
(base32
- "1lbkmin9pkk9yzpmwrfyniyqnwmp0wcgiirq8prmzi5mvndl6wm3"))))
+ "0p56w6431jg921416dkyiykccvr7alq6x6r1gcx5d9hkcpyncks1"))))
(properties `((upstream-name . "iClusterPlus")))
(build-system r-build-system)
(native-inputs (list gfortran))
@@ -16331,14 +16664,14 @@ Gaussian distributions.")
(define-public r-rbowtie
(package
(name "r-rbowtie")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie" version))
(sha256
(base32
- "1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7"))))
+ "1arwr8gisc5g9bwxlachf3lvxpd2767ahnwdf2p1lidwpfism8l8"))))
(properties `((upstream-name . "Rbowtie")))
(build-system r-build-system)
(arguments
@@ -16367,14 +16700,14 @@ alignment tool.")
(define-public r-sgseq
(package
(name "r-sgseq")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SGSeq" version))
(sha256
(base32
- "0qsmy85400in2xvw3bnzjnk8ni3lipqjc81npk3fmvbp6cb85njq"))))
+ "1h44r0frrw54s9nqa539ifg270ggmm634gj9cyhn4z7nhxxh134c"))))
(properties `((upstream-name . "SGSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -16410,14 +16743,14 @@ interpretation.")
(define-public r-rhisat2
(package
(name "r-rhisat2")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhisat2" version))
(sha256
(base32
- "1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy"))))
+ "1pxlpwqzbdii0b1swy9vcq905934yfmyqwfx2j3f7n5n4dgglc2q"))))
(properties `((upstream-name . "Rhisat2")))
(build-system r-build-system)
(arguments
@@ -16448,14 +16781,14 @@ index.")
(define-public r-quasr
(package
(name "r-quasr")
- (version "1.40.1")
+ (version "1.42.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "QuasR" version))
(sha256
(base32
- "08vns1wbgpxw1x6djp84f9hl3gqaybbw9917ghfzk0x3ijpvggbg"))))
+ "0695pjvp742qn629kxly4a9crbg6vakdx1ygnyshprjsz6xz2vnn"))))
(properties `((upstream-name . "QuasR")))
(build-system r-build-system)
(propagated-inputs
@@ -16490,14 +16823,14 @@ quantification of genomic regions of interest.")
(define-public r-rqc
(package
(name "r-rqc")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rqc" version))
(sha256
(base32
- "15w5bmcl7h3fz6qhdqz4qc3qkg3pxcmzapg4mnnckzmyg8kh0i4l"))))
+ "0hrhfgv0b9ycw2vmzkpmrv9m9jvvq1n6asnxnrgvzlz81xak84ic"))))
(properties `((upstream-name . "Rqc")))
(build-system r-build-system)
(propagated-inputs
@@ -16533,14 +16866,14 @@ graphics.")
(define-public r-birewire
(package
(name "r-birewire")
- (version "3.32.0")
+ (version "3.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiRewire" version))
(sha256
(base32
- "1741raw1834093y5zhgx9jywfgz0wl0idlkynvab2c8vi40kc9a8"))))
+ "1h5pmd38b9zpbz1nngmk1s0cag4z0vx93yi2n7r85nca9z02cxad"))))
(properties `((upstream-name . "BiRewire")))
(build-system r-build-system)
(propagated-inputs
@@ -16586,14 +16919,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
(define-public r-multidataset
(package
(name "r-multidataset")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiDataSet" version))
(sha256
(base32
- "1qyvwhmdv27xsyljyzyh52pn6x0wqx8rslvr2j7vqcjyywv270x6"))))
+ "1n17bpzj95hkljvgqpyv92jm4bk1d3j3mdg7106pb3dffvwv52sk"))))
(properties `((upstream-name . "MultiDataSet")))
(build-system r-build-system)
(propagated-inputs
@@ -16623,14 +16956,14 @@ packages.")
(define-public r-ropls
(package
(name "r-ropls")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ropls" version))
(sha256
(base32
- "1cq5ixaxag5r6nvl73c8bznxkdjhxw1r7qx90ml7qm4jr7wyi173"))))
+ "1k3j1cbapzqk0qr3v4gijskp487xyz2n4lv4kia9y5pmplddxp7v"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -16665,14 +16998,14 @@ coefficients).")
(define-public r-biosigner
(package
(name "r-biosigner")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biosigner" version))
(sha256
(base32
- "19sl75168zv6qqmgsfnhcyw1z0lp0phmky40lsl6bbmy4k2hfw38"))))
+ "1j3wkqvha6pzd6d3wm2q4lihn8p9ycw0wmddjqpnqvglb1x7c0f8"))))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
@@ -16700,14 +17033,14 @@ datasets.")
(define-public r-annotatr
(package
(name "r-annotatr")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotatr" version))
(sha256
(base32
- "1vjbk1vpqjxy9wv2a6sc32yyk0bhkbvdx9hl3vs5yjifwdswh2pw"))))
+ "16nkxnbsmr0y6km794x2iwbkyrkf0svg6ln3qkqnw0a47a3cbm65"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -16741,14 +17074,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.14.2")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc"))))
+ "0bhq8q3dch09r3digf3snfvhyj6w7j1qqw8gl28b29in8azg6v4d"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs (list zlib))
@@ -16767,13 +17100,13 @@ and to both short and long sequence reads.")
(define-public r-flowai
(package
(name "r-flowai")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "flowAI" version))
(sha256
(base32
- "0ydy98qsiqpw0b6fvmlv09kza94qjcl40ma9pknzgbq21ac4z25g"))))
+ "1bi13f8q7267lai71sl640w9zgd5a1iln5r4ri2dcskkwb2qxzkz"))))
(properties `((upstream-name . "flowAI")))
(build-system r-build-system)
(propagated-inputs
@@ -16833,14 +17166,14 @@ the quality control enables the detection and removal of anomalies.")
(define-public r-consensusclusterplus
(package
(name "r-consensusclusterplus")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ConsensusClusterPlus" version))
(sha256
(base32
- "0ig6xfhd70my5j4xrdy8srg1wi8nb3kcxlrld9py47psrq9vdadm"))))
+ "11xcz9b4mg3inz8c8f2vckgai67s740qjyynjim4ahf9zd0j7rxs"))))
(properties
`((upstream-name . "ConsensusClusterPlus")))
(build-system r-build-system)
@@ -16899,14 +17232,14 @@ of the analyses while minimizing technical noise.")
(define-public r-cytolib
(package
(name "r-cytolib")
- (version "2.12.1")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cytolib" version))
(sha256
(base32
- "0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz"))))
+ "1r2slhzrp3gf45k5gknqgj3vjz7p0rx2yjzrbp020inj82fp4mgi"))))
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
(native-inputs
@@ -16923,14 +17256,14 @@ interact with gated cytometry data.")
(define-public r-flowcore
(package
(name "r-flowcore")
- (version "2.12.2")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowCore" version))
(sha256
(base32
- "1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h"))))
+ "11aic1nzlw0gdpcpmky5jzljxgxcrimi29f0zl3yjvgb48qa88bd"))))
(properties `((upstream-name . "flowCore")))
(build-system r-build-system)
(propagated-inputs
@@ -16955,14 +17288,14 @@ with flow cytometry data.")
(define-public r-flowmeans
(package
(name "r-flowmeans")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowMeans" version))
(sha256
(base32
- "18lp1pickpd68fl7a4nidyvyh4yf53gbgn2f2yxaxfp2mk3mj88w"))))
+ "06n35c5fdkd3l8d5q8a23yslanirwhbf07b4f0zmf9a43zi642bv"))))
(properties `((upstream-name . "flowMeans")))
(build-system r-build-system)
(propagated-inputs
@@ -16978,14 +17311,14 @@ change point detection.")
(define-public r-ncdfflow
(package
(name "r-ncdfflow")
- (version "2.46.0")
+ (version "2.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ncdfFlow" version))
(sha256
(base32
- "0nrj4g02kx763wb70fzvhidmzp82gr1g3fp1aa1bv34cj4lnp47q"))))
+ "0z9vgd8v69iq8gv23iiaxrk77j2aq8y2n5k8x9jmxphbm0cm19a0"))))
(properties `((upstream-name . "ncdfFlow")))
(build-system r-build-system)
(propagated-inputs
@@ -17008,14 +17341,14 @@ manipulation of flow cytometry data.")
(define-public r-ggcyto
(package
(name "r-ggcyto")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggcyto" version))
(sha256
(base32
- "1hgw8g0b62k2lyswp3m81qczzwsyid7zdrnyjvl9388k29w2105s"))))
+ "13zc5952drl187fl07v1nh6gv0g6ba11vxpxl4ghvavnknvi5phd"))))
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
@@ -17045,14 +17378,14 @@ statistics to the plot.")
(define-public r-flowviz
(package
(name "r-flowviz")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowViz" version))
(sha256
(base32
- "0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67"))))
+ "1hn021p2220a47qzlya8qabc9xgmxk9gcs505m7wx6gx6ysdn418"))))
(properties `((upstream-name . "flowViz")))
(build-system r-build-system)
(propagated-inputs
@@ -17076,14 +17409,14 @@ statistics to the plot.")
(define-public r-flowclust
(package
(name "r-flowclust")
- (version "3.38.0")
+ (version "3.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowClust" version))
(sha256
(base32
- "1gmkmx6gzx4w39ijcad3lx2xnr2b833mhs8gcmc6k21k57aznzs2"))))
+ "1xg0hdxh0c1c1wc6d8gcynq8168hi61c3gjdf1223qvqwc39nsby"))))
(properties `((upstream-name . "flowClust")))
(build-system r-build-system)
(arguments
@@ -17110,14 +17443,14 @@ model with Box-Cox transformation.")
(define-public r-rprotobuflib
(package
(name "r-rprotobuflib")
- (version "2.12.1")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RProtoBufLib" version))
(sha256
(base32
- "097nxjijblqyz6nbpal7292qfijmk7x8dbx7plryr132xbaw5hdm"))))
+ "1i1a4ikfdyrrn0r53y1aipfm9dzzn6yzp5w651hvd6zav77cdh6q"))))
(properties `((upstream-name . "RProtoBufLib")))
(build-system r-build-system)
(arguments
@@ -17139,14 +17472,14 @@ for other R packages to compile and link against.")
(define-public r-flowworkspace
(package
(name "r-flowworkspace")
- (version "4.12.2")
+ (version "4.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowWorkspace" version))
(sha256
(base32
- "1g1hym2anysgy7v46fnnxyzac3wzi1713vlih2gqzi23k8r2xx26"))))
+ "09cpbf33b3x9b06yf41qy2fy8zviwrznrpkb9fq3an8vg8gf51lp"))))
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
(propagated-inputs
@@ -17186,19 +17519,20 @@ matches the flowJo analysis.")
(define-public r-flowstats
(package
(name "r-flowstats")
- (version "4.12.0")
+ (version "4.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowStats" version))
(sha256
(base32
- "13mdpdndalm0d6azjancw0xcbdc674ivkj8kp6ccfpdd7gydhr4j"))))
+ "1f7qawn9wb8221npnmmygmvi4w1rq5lb74j3vmfzcak5kyga5xck"))))
(properties `((upstream-name . "flowStats")))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
r-biocgenerics
+ r-clue
r-cluster
r-corpcor
r-fda
@@ -17224,14 +17558,14 @@ package.")
(define-public r-opencyto
(package
(name "r-opencyto")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "openCyto" version))
(sha256
(base32
- "0z0p09mkap1jqlq1x33i2ik87pbhwq85xgqyfsx4r360nhv06pna"))))
+ "12b4a65zgswzddkfdyl4j06qp7w9lkxv4h05m4z8hfff8c9x5bls"))))
(properties `((upstream-name . "openCyto")))
(build-system r-build-system)
(propagated-inputs
@@ -17260,14 +17594,14 @@ sequential way to mimic the manual gating strategy.")
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf"))))
+ "0wq9ganas6l2jw8bnajr7vwli35kykpgv2lca4qh79nfgxlicff9"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
@@ -17305,14 +17639,14 @@ standard to exchange gated cytometry data with other software platforms.")
(define-public r-flowsom
(package
(name "r-flowsom")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "FlowSOM" version))
(sha256
(base32
- "13y0ny61skj14mfhjwpa5zmflzdqxy2vf6gd4m9358g4wxfbhkv0"))))
+ "170xz3b4kfsxpqirfz9vk4j8dkdmz4qd0a1nm3yaya1rddpg9m3l"))))
(properties `((upstream-name . "FlowSOM")))
(build-system r-build-system)
(propagated-inputs
@@ -17341,14 +17675,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.24.0")
+ (version "6.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "0dqndpmi56g772sra49vdrkjs4m9h2gzimwv3bwmw2l0krh2ax8s"))))
+ "0ifi89s611kblncnpvsrbl6sq2zi36binz63njrhya9wkyaxj6pc"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@@ -17356,8 +17690,8 @@ self-organizing map clustering and minimal spanning trees.")
r-corpcor
r-dplyr
r-ellipse
- r-ggrepel
r-ggplot2
+ r-ggrepel
r-gridextra
r-igraph
r-lattice
@@ -17387,18 +17721,19 @@ delete entire rows with missing data.")
(define-public r-depecher
(package ;Source/Weave error
(name "r-depecher")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p"))))
+ "1b3c1wg5xnhh4bdcjls26j6nsp0vx1g5y3grqv7x4ds01vmh3q2w"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
(list r-beanplot
+ r-collapse
r-dosnow
r-dplyr
r-fnn
@@ -17475,14 +17810,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-chicago
(package
(name "r-chicago")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Chicago" version))
(sha256
(base32
- "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s"))))
+ "1mcpx785ag0jcsh08df34hx3wp55zd1vggnl3fflkinb78178n38"))))
(properties `((upstream-name . "Chicago")))
(build-system r-build-system)
(propagated-inputs
@@ -17521,14 +17856,14 @@ expression space.")
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "12zdygnwqjla99wzvvxzcmiwmh4v0rmnx4yix02gbj8xl4bxmm51"))))
+ "19vn31w74r45pq5m9pn5db1sz1qg757mghzzs933cdssnqf4m6y5"))))
(build-system r-build-system)
(propagated-inputs
(list r-assertthat
@@ -17588,14 +17923,14 @@ accessibility data.")
(define-public r-circrnaprofiler
(package
(name "r-circrnaprofiler")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "circRNAprofiler" version))
(sha256
(base32
- "0gagfm7v5bnnfj1zy6zf4cg91bj8nvv4vm38f3a1s4q2xc8pcvfj"))))
+ "098fbrszph5cnh4n9zjhj92sg1bi6h6k57wm2vlaqkq0nab63r63"))))
(properties
`((upstream-name . "circRNAprofiler")))
(build-system r-build-system)
@@ -17723,14 +18058,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
(define-public r-genie3
(package
(name "r-genie3")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GENIE3" version))
(sha256
(base32
- "1q4wi3k95c8vsyfx6359p2p29ascjg1cxmpp9bf99ixbjs71rd33"))))
+ "0bsid8qhcqgalqghr2b2592pzm4viyi7wq8h5dmhrrl7gky8l60k"))))
(properties `((upstream-name . "GENIE3")))
(build-system r-build-system)
(propagated-inputs
@@ -17747,14 +18082,14 @@ regulatory networks from expression data.")
(define-public r-roc
(package
(name "r-roc")
- (version "1.76.0")
+ (version "1.78.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROC" version))
(sha256
(base32
- "0fq59bwc5i8zdw0v0jr5j5lm4hk6p7b88i2xndsgj4fq65yr50g1"))))
+ "12msc6skvcx4ajk20l71k32rj8lsiafjxwcsrd51kyy5x2yj2v4m"))))
(properties `((upstream-name . "ROC")))
(build-system r-build-system)
(native-inputs
@@ -17769,14 +18104,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
(define-public r-watermelon
(package
(name "r-watermelon")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wateRmelon" version))
(sha256
(base32
- "0qslh2xhhyaf0nsgcqav6qgh05n8kp0s6p1zggc02iid30i1ibrj"))))
+ "1ra21qzni9cny52ag9zxi46vb9grabyqjyk01dqqp3r9i0b4999l"))))
(properties `((upstream-name . "wateRmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -17807,14 +18142,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
(define-public r-gdsfmt
(package
(name "r-gdsfmt")
- (version "1.36.1")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gdsfmt" version))
(sha256
(base32
- "11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7"))
+ "03qgiww523kijrkciln3fw3djn20rnvwz2j0i3p518h6fbl7vlpm"))
(modules '((guix build utils)))
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
;; them and link with system libraries instead.
@@ -17865,14 +18200,14 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-bigmelon
(package
(name "r-bigmelon")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigmelon" version))
(sha256
(base32
- "1l1ym89qqbq6qx07bm2p8gcl5zd9xh0nbw10fb7s0pfbrkj8xy64"))))
+ "1j80f7k39p23s6fym3nia73g8d1v44hdiv73igcq6fnsllxg40hr"))))
(properties `((upstream-name . "bigmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -17895,18 +18230,18 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-seqbias
(package
(name "r-seqbias")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqbias" version))
(sha256
(base32
- "1sspl03m2hf6s5rw6nfqrycb236nvcgygql6apdlg3cjnikf090j"))))
+ "18pdpi855y1hhka96xc5886nqffjn1jhz9jr9p305iikdrsvmjp1"))))
(properties `((upstream-name . "seqbias")))
(build-system r-build-system)
(propagated-inputs
- (list r-biostrings r-genomicranges r-rhtslib))
+ (list r-biostrings r-genomicranges r-rhtslib r-zlibbioc))
(home-page "https://bioconductor.org/packages/seqbias/")
(synopsis "Estimation of per-position bias in high-throughput sequencing data")
(description
@@ -17919,14 +18254,14 @@ genome sequence.")
(define-public r-reqon
(package
(name "r-reqon")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReQON" version))
(sha256
(base32
- "1knzla5d8n22121a9licrjh2rxrmh05304a9d4bs2f1r7aiwhgnh"))))
+ "0w28b3ma8r8rshijdm5jj1z64v91my7hcvw18r9pdwjprh05bw0g"))))
(properties `((upstream-name . "ReQON")))
(build-system r-build-system)
(propagated-inputs
@@ -17942,14 +18277,14 @@ format.")
(define-public r-wavcluster
(package
(name "r-wavcluster")
- (version "2.34.0")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wavClusteR" version))
(sha256
(base32
- "0491x3m0015g83m6a7pkc4783768clgykhlcmd2xr6cgrhih10g2"))))
+ "1y2bk1kla0l72xgdam2l9c0k7584ckdqscqnc184cxvqm6fb335j"))))
(properties `((upstream-name . "wavClusteR")))
(build-system r-build-system)
(propagated-inputs
@@ -17989,13 +18324,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
(define-public r-tilingarray
(package
(name "r-tilingarray")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tilingArray" version))
(sha256
(base32
- "0wj3wb4x9s0v189p20rlwghsx82x314yyhhsnfmrl266qb1ambrn"))))
+ "01j4wj0mdfrlyhp2alf1xfy78f17x43w9i0wb41ljw6pm313np58"))))
(properties `((upstream-name . "tilingArray")))
(build-system r-build-system)
(propagated-inputs
@@ -18071,14 +18406,14 @@ provides methods for retrieving enriched pathways.")
(define-public r-variantfiltering
(package
(name "r-variantfiltering")
- (version "1.36.1")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantFiltering" version))
(sha256
(base32
- "0v0shsv0s9fzakdb4p84jfc4z57ryan27r1dkbvb3v25kjrhd8fi"))))
+ "01czx88dzqm8qv44kyy1n7b999wgfklxzgvmjh10chf677phnzsr"))))
(properties
`((upstream-name . "VariantFiltering")))
(build-system r-build-system)
@@ -18115,76 +18450,17 @@ model, amino acid change consequence, minor allele frequencies across human
populations, splice site strength, conservation, etc.")
(license license:artistic2.0)))
-(define-public r-genomegraphs
- (package
- (name "r-genomegraphs")
- (version "1.46.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomeGraphs" version))
- (sha256
- (base32
- "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
- (properties `((upstream-name . "GenomeGraphs")))
- (build-system r-build-system)
- (propagated-inputs
- (list r-biomart))
- (home-page "https://bioconductor.org/packages/GenomeGraphs/")
- (synopsis "Plotting genomic information from Ensembl")
- (description
- "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data. GenomeGraphs uses the biomaRt package
-to perform live annotation queries to Ensembl and translates this to e.g.
-gene/transcript structures in viewports of the grid graphics package. This
-results in genomic information plotted together with your data. Another
-strength of GenomeGraphs is to plot different data types such as array CGH,
-gene expression, sequencing and other data, together in one plot using the
-same genome coordinate system.")
- (license license:artistic2.0)))
-
-(define-public r-wavetiling
- (package
- (name "r-wavetiling")
- (version "1.28.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "waveTiling" version))
- (sha256
- (base32
- "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
- (properties `((upstream-name . "waveTiling")))
- (build-system r-build-system)
- (propagated-inputs
- (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
- "This package is designed to conduct transcriptome analysis for tiling
-arrays based on fast wavelet-based functional models.")
- (license license:gpl2+)))
-
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.30.2")
+ (version "1.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "17jssd327l0miw52iadag2dbk8w4mhv2vwjpzdw89p8gww47bmbv"))))
+ "1pr321hv5q2sl8lc998hkwdl2mfyzcgf2l70ny2m3hfmlclq5lnn"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
@@ -18192,8 +18468,8 @@ arrays based on fast wavelet-based functional models.")
(list r-aod
r-biobase
r-biocparallel
- r-doparallel
- r-foreach
+ r-corpcor
+ r-fancova
r-ggplot2
r-gplots
r-iterators
@@ -18203,7 +18479,6 @@ arrays based on fast wavelet-based functional models.")
r-mass
r-matrix
r-pbkrtest
- r-progress
r-rdpack
r-remacor
r-reshape2
@@ -18226,14 +18501,14 @@ measures.")
(define-public r-htqpcr
(package
(name "r-htqpcr")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HTqPCR" version))
(sha256
(base32
- "12p0jb9bpz4x612vwj77d6l5h8rihfkzmhp8qy1gvv2zmn2a54jf"))))
+ "14cff36ikbqhd5xizihpxzsv9jimcpbgnd381jd154pgi60bil0m"))))
(properties `((upstream-name . "HTqPCR")))
(build-system r-build-system)
(propagated-inputs
@@ -18256,13 +18531,13 @@ features (e.g. genes, microRNAs).")
(define-public r-ucell
(package
(name "r-ucell")
- (version "2.4.0")
+ (version "2.6.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "UCell" version))
(sha256
(base32
- "01qcwmiqri4xvwr3j4k1g062rfj6bbc0bvh0ifq1jq2xrm1azw9y"))))
+ "1ds11f1q6v89sfcj1sinrkv7aw3s0prf5nxf7pz4hdsvqn4zp467"))))
(properties `((upstream-name . "UCell")))
(build-system r-build-system)
(propagated-inputs (list r-biocneighbors
@@ -18287,14 +18562,14 @@ directly interact with SingleCellExperiment and Seurat objects.")
(define-public r-unifiedwmwqpcr
(package
(name "r-unifiedwmwqpcr")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "unifiedWMWqPCR" version))
(sha256
(base32
- "1gza678sd5m2rbki0l5hniki6gmds2cljkmywmk5v5m9swh9azq7"))))
+ "0v3jpnm3nq66xvckmc8447xl7wngfhhiwq6vjx54wgc6f586vmgd"))))
(properties
`((upstream-name . "unifiedWMWqPCR")))
(build-system r-build-system)
@@ -18311,14 +18586,14 @@ data.")
(define-public r-universalmotif
(package
(name "r-universalmotif")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "universalmotif" version))
(sha256
(base32
- "0v1085dl16a3494f1fxc9rk1ffz3si89mdwbmnnczyhj5p13pfx8"))))
+ "0wy7zplypjiqv4wjq0l30xb5xj63fxb7z2wmmfrmzfkbgbm0xyha"))))
(properties
`((upstream-name . "universalmotif")))
(build-system r-build-system)
@@ -18360,13 +18635,13 @@ motifs, and others.")
(define-public r-ace
(package
(name "r-ace")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ACE" version))
(sha256
(base32
- "158v25ivbmsh54ywb5spfsd1nrmvfq83s8fkp14i7q5ckr2kvjhm"))))
+ "0ll0lksz6nzfj5ivmyrp5w24bhfl083amjpr0m8qlzpdw6k3wi98"))))
(properties `((upstream-name . "ACE")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
@@ -18389,13 +18664,13 @@ of @dfn{tumor cells} (cells with divergent segments).")
(define-public r-acgh
(package
(name "r-acgh")
- (version "1.78.0")
+ (version "1.80.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "aCGH" version))
(sha256
(base32
- "0k8fbwhh1w0b0zy5qgixmcnwxi3v78f1bjmjg1yx6paniwk58bzn"))))
+ "1qckqdil1cq8lbrj9di96w9934r1fp48xpmfdwp4f2vw9pjadi1q"))))
(properties `((upstream-name . "aCGH")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
@@ -18413,13 +18688,13 @@ printing and plotting @code{aCGH} objects.")
(define-public r-acme
(package
(name "r-acme")
- (version "2.56.0")
+ (version "2.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ACME" version))
(sha256
(base32
- "1z6j4wy355pljn9wf12zzq4zqrhaik0i2phy7jg89jsys7n2mlxy"))))
+ "0cy1f4ki4j7yxc9cws5s17ljd4ac0yxhijms0pm31im81qz2djax"))))
(properties `((upstream-name . "ACME")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-biocgenerics))
@@ -18440,13 +18715,13 @@ on whole-genome tiling array experiments quite easily with enough memory.")
(define-public r-acde
(package
(name "r-acde")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "acde" version))
(sha256
(base32
- "088dq6mc9m1bx0dprcz8cdpfp447lnxq7420r139mhcik0z21vky"))))
+ "1rqyjj4lgqxs372qx8p3qx2napww0djh4jz8hzgv86x9r202kk9p"))))
(properties `((upstream-name . "acde")))
(build-system r-build-system)
(propagated-inputs (list r-boot))
@@ -18566,14 +18841,14 @@ gene expression.")
(define-public r-bgx
(package
(name "r-bgx")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bgx" version))
(sha256
(base32
- "1g6k3ryj8dz17asa4imnrk77z4dk9an5ssrqr17r0g797d5f4qjm"))))
+ "0v85i0lwmxq5yq9ygfzljgy8fsflqq1p53rq8aasnndd6gsm8ld2"))))
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
(arguments
@@ -18602,14 +18877,14 @@ Affymetrix GeneChips.")
(define-public r-bhc
(package
(name "r-bhc")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BHC" version))
(sha256
(base32
- "0w60h1jr9kwvgg5d6bcrq4gl1aa1v6xrn43ymsc2312019psrrjy"))))
+ "1m289q9bs7i7d15g5mzdmzw7yppnqspr8illkya8kxlv1i2sify1"))))
(properties `((upstream-name . "BHC")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BHC/")
@@ -18628,14 +18903,14 @@ algorithm which is more efficient for larger data sets.")
(define-public r-bicare
(package
(name "r-bicare")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BicARE" version))
(sha256
(base32
- "1q7dsvj6nvczs76jcxyy77298vgk4zk083bldmbbgnwparrgjii9"))))
+ "10inwxl1cmkdp8037wcwkj5wzxsrrcysxfbqhnkh7pzhzvwnzz9h"))))
(properties `((upstream-name . "BicARE")))
(build-system r-build-system)
(propagated-inputs
@@ -18650,14 +18925,14 @@ results.")
(define-public r-bifet
(package
(name "r-bifet")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiFET" version))
(sha256
(base32
- "05lwz2pw2vnhmlhp5vv9j45jrc5ssdw4lx6mkxnsvds8zl3y9294"))))
+ "056zqlql39q44snvx5nzc5snrihpr1kj3jdbpbb401hxi9r64f4r"))))
(properties `((upstream-name . "BiFET")))
(build-system r-build-system)
(propagated-inputs
@@ -18679,14 +18954,14 @@ the read count and GC content bias.")
(define-public r-rsbml
(package
(name "r-rsbml")
- (version "2.58.0")
+ (version "2.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rsbml" version))
(sha256
(base32
- "0mgg1qfvxgyjk6fw4x0cv486vrsgf1kbqr6nqhgxj6lk8w6909fm"))))
+ "0pvj0qgc6hd02g9ppfc610gvfn412rw69rxh43y4dr3n894kdm2i"))))
(properties `((upstream-name . "rsbml")))
(build-system r-build-system)
(inputs
@@ -18705,13 +18980,13 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
(define-public r-hybridmtest
(package
(name "r-hybridmtest")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HybridMTest" version))
(sha256
- (base32 "19pycad35hc7ylnsz75bv029y1r6j9xvrbhzk4i64i7jn8gi7ngh"))))
+ (base32 "1jkihcad453d7jqb78fl03yfqz169jz75c40y53569ndp2j4rg71"))))
(properties `((upstream-name . "HybridMTest")))
(build-system r-build-system)
(propagated-inputs
@@ -18736,14 +19011,14 @@ then the law of total EBPs.")
(define-public r-hypergraph
(package
(name "r-hypergraph")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hypergraph" version))
(sha256
(base32
- "13f3m8m6i99hzm94hriry645jcn0a1ki8z8wmn3mkasdi6bzx20h"))))
+ "16bjjfzcndjfqsywzw2cn551fgqlnll2gi975w0qqxhkh3jssgmi"))))
(properties `((upstream-name . "hypergraph")))
(build-system r-build-system)
(propagated-inputs
@@ -18758,14 +19033,14 @@ manipulating hypergraphs.")
(define-public r-hyperdraw
(package
(name "r-hyperdraw")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hyperdraw" version))
(sha256
(base32
- "0vhfvmv6b3kab6a8hy2y9zwxgzwb5vliaaxhlrgz8i4pvvq5nhqb"))))
+ "1lgfpw9f7095lgk46gdpxq3z52c24xw4ajl7yid3pcgw19bfcgk5"))))
(properties `((upstream-name . "hyperdraw")))
(build-system r-build-system)
(inputs (list graphviz))
@@ -18780,14 +19055,14 @@ manipulating hypergraphs.")
(define-public r-biggr
(package
(name "r-biggr")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiGGR" version))
(sha256
(base32
- "03pd4a3l912zdfk35flagikqimp01wp76nslid32l43d7yg9p57w"))))
+ "1pdsxkh9fkgn80f7p21902pb6xp2qafq10p29ifb55qwz8gma2ff"))))
(properties `((upstream-name . "BiGGR")))
(build-system r-build-system)
(propagated-inputs
@@ -18887,13 +19162,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
(define-public r-chemmineob
(package
(name "r-chemmineob")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChemmineOB" version))
(sha256
- (base32 "0l44d6l078k1w5nf7i4sarah1zn30zqjmcj9qpy4hhg97dfy45ci"))))
+ (base32 "0mfajzwzldmra6g5kni5yw7m2n719456p1vd3hxx2r7l1phdjixi"))))
(properties `((upstream-name . "ChemmineOB")))
(build-system r-build-system)
(arguments
@@ -18928,14 +19203,14 @@ add-on package rather than used directly.")
(define-public r-chemminer
(package
(name "r-chemminer")
- (version "3.52.0")
+ (version "3.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChemmineR" version))
(sha256
(base32
- "1m4vgq3z0kya7kbncawr9csvbwnh74mh012w7g2ialwd3nwdf91x"))))
+ "1328mwmghflrvir1i3crlq8q36wq60x2an11saabg63hnx4paa81"))))
(properties `((upstream-name . "ChemmineR")))
(build-system r-build-system)
(propagated-inputs
@@ -18971,13 +19246,13 @@ structures.")
(define-public r-fmcsr
(package
(name "r-fmcsr")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fmcsR" version))
(sha256
- (base32 "0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp"))))
+ (base32 "17il9mi1iagl474ia1lz0ajx1wq67jw5famkr1fmjlis8ymw8hnd"))))
(properties `((upstream-name . "fmcsR")))
(build-system r-build-system)
(propagated-inputs
@@ -19000,14 +19275,14 @@ searching and clustering.")
(define-public r-bioassayr
(package
(name "r-bioassayr")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioassayR" version))
(sha256
(base32
- "0ilwniyrp3m8mi1vmggd17f9g6wdw7a78l2db190w29alzpbfmp6"))))
+ "1mm1nzdz9cl8mf33yiyaspqkx4sbqhhs6m9jfgl42fhscrhaxfsi"))))
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
@@ -19035,14 +19310,14 @@ available bioactivity data.")
(define-public r-biobroom
(package
(name "r-biobroom")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biobroom" version))
(sha256
(base32
- "0kb6ylq94vywfky0mcrva109darcv361sqvwb19qn92p8vh5199l"))))
+ "1ivclipy2igf8ax7f0pqrcqflcm7h0a8ny6nfa0200vp99an8ymf"))))
(properties `((upstream-name . "biobroom")))
(build-system r-build-system)
(propagated-inputs
@@ -19064,14 +19339,14 @@ visualize bioinformatics analyses.")
(define-public r-graphite
(package
(name "r-graphite")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "graphite" version))
(sha256
(base32
- "1fhjkgl6567qchi5sfdqnznalm1l7c7pabz8jc9d7ib9x4g922q5"))))
+ "1h8j10jx02zsxs6rzids3gy4xchdhgzkifa5grrfbn8faf9ycy2n"))))
(properties `((upstream-name . "graphite")))
(build-system r-build-system)
(propagated-inputs
@@ -19088,14 +19363,14 @@ symbols).")
(define-public r-reactomepa
(package
(name "r-reactomepa")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReactomePA" version))
(sha256
(base32
- "1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn"))))
+ "0kflwlmyckyivr8xh7fsmpl7jfkq5kavwpkswmvdfqckbd0n9xsc"))))
(properties `((upstream-name . "ReactomePA")))
(build-system r-build-system)
(propagated-inputs
@@ -19121,14 +19396,14 @@ enrichment analysis and several functions for visualization.")
(define-public r-ebarrays
(package
(name "r-ebarrays")
- (version "2.64.0")
+ (version "2.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBarrays" version))
(sha256
(base32
- "1k50br4hpkrwv1lnn0wp1c7kj32vk0gg19aivmw5d6brjdd39c1f"))))
+ "1m8dy1lmx9m8p5jjk0i7yllb4pvq77kynszk1nz8cc1niz6xs47q"))))
(properties `((upstream-name . "EBarrays")))
(build-system r-build-system)
(propagated-inputs
@@ -19143,13 +19418,13 @@ microarray data.")
(define-public r-biocbaseutils
(package
(name "r-biocbaseutils")
- (version "1.2.0")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocBaseUtils" version))
(sha256
(base32
- "143fmjbi8spaj3njvc1xvsjszfxs7bv3vxik8pisw5y8lqzx7hqm"))))
+ "189jz8krhv0vdnk47m3cmy95zfg3l328w6dbhg6djvlkca17i275"))))
(properties `((upstream-name . "BiocBaseUtils")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -19187,20 +19462,22 @@ monograph.")
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.36.1")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "0a0fnmqln13iglnw8smbbr4k7hdvacipxa04zhqylygpsq1246bc"))))
+ "11d67dfwxc34n7yzpz58ficjk7sxnbxrajhnqlcxvsifgmybkb4d"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(propagated-inputs
- (list r-biocfilecache
+ (list r-biocbaseutils
+ r-biocfilecache
r-biocmanager
r-biocviews
+ r-callr
r-codetools
r-graph
r-httr
@@ -19217,14 +19494,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-biocgraph
(package
(name "r-biocgraph")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biocGraph" version))
(sha256
(base32
- "0fnncmi82qb9lkg1zfyps7n3nrw1s3wcqbixh420w53hmdyryryl"))))
+ "1yy0bwvfa5b531jvmbiwrd4xg8cdvrgwr8l6bxasrh6yrbv8drml"))))
(properties `((upstream-name . "biocGraph")))
(build-system r-build-system)
(propagated-inputs
@@ -19239,13 +19516,13 @@ different graph related packages produced by Bioconductor.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.28.1")
+ (version "2.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "11v3gzy88fai0rhdymvj9k74g7hjc6n9fihfrrnw0qfr447z1d61"))))
+ "17pkdi3vn62pw1nzmgz0i45czynqjchq078ij8v1xvflg6lf7flw"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
@@ -19263,13 +19540,13 @@ functionality.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.68.2")
+ (version "1.70.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1icnaj1ifndym7nl1yafzd0y0fxyhzjyb4qzqpcnsqhh4yi3pnm5"))))
+ "0fpka47shrxcbc1k057f5zv79406daic0y34v8p5lsvxbgzh0m8b"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -19292,14 +19569,14 @@ also known as views, in a controlled vocabulary.")
(define-public r-experimenthub
(package
(name "r-experimenthub")
- (version "2.8.1")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ExperimentHub" version))
(sha256
(base32
- "1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4"))))
+ "1prl24sg5l142155z3iaxrvig2wv2xqajq02nj30jjjih4p4936w"))))
(properties `((upstream-name . "ExperimentHub")))
(build-system r-build-system)
(propagated-inputs
@@ -19325,14 +19602,14 @@ access.")
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "1zg30cb4s97zdv6c0f53ix6a97aan5w3lx698sa4cqvi4hbz8f35"))))
+ "15ibdbpj7vqypxfnp2w06w9lync11z3azzss6s97xhadkgsbw4vq"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
@@ -19352,14 +19629,14 @@ access.")
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
- "00xgca1q9ai5x730bvx73f25lpwkr3dn2sia3msa49fpl4nrzr20"))))
+ "0dmhqymh800mljcpdf817nbyg20czp8y9bg13p3r4bfj6axxckch"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)
@@ -19389,14 +19666,14 @@ rownames.")
(define-public r-bioconcotk
(package
(name "r-bioconcotk")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocOncoTK" version))
(sha256
(base32
- "11135a4l0vn84qmpyclz052zy45s0m38av94604jqxgb51q9lwyf"))))
+ "1xymgfiv9abyaq5s7m683ml8a1ls9mqvbh9qjiz3jqbbpvmsm502"))))
(properties `((upstream-name . "BiocOncoTK")))
(build-system r-build-system)
(propagated-inputs
@@ -19435,14 +19712,14 @@ tools for genome-scale analysis of cancer studies.")
(define-public r-biocor
(package
(name "r-biocor")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioCor" version))
(sha256
(base32
- "1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p"))))
+ "0710dl05hs590fimp3dhg5hzvk6s79i0kwk6w6sj59pcawx2l6il"))))
(properties `((upstream-name . "BioCor")))
(build-system r-build-system)
(propagated-inputs
@@ -19462,14 +19739,14 @@ gene selection, testing relationships, and so on.")
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "16d0sjkzagc0jxha28qxplg6iihwg2q05sig0s1291lm7kh5k9j8"))
+ "0swi6xiads31xcndc2cfzh0ivdl0wc88s83s1p1gxh51rgmgkb14"))
(snippet
'(for-each delete-file
'("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js"
@@ -19576,14 +19853,14 @@ analytics on packages.")
(define-public r-biocset
(package
(name "r-biocset")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSet" version))
(sha256
(base32
- "1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5"))))
+ "0sk4kmvl86xm85dqaf8gvii0qavyycyn2qp0v6dmfcjqai528v2x"))))
(properties `((upstream-name . "BiocSet")))
(build-system r-build-system)
(propagated-inputs
@@ -19614,14 +19891,14 @@ accessing web references for elements/sets are also available in BiocSet.")
(define-public r-biocworkflowtools
(package
(name "r-biocworkflowtools")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocWorkflowTools" version))
(sha256
(base32
- "1zvjj0hpqwdv7yifqwyb14166ppxw91d964gz4xclism5z5lvyln"))))
+ "0mh7lsiprshq56ns3b8pbv1j1mjcbdzqydvli0ynmvf5smn2j4m5"))))
(properties
`((upstream-name . "BiocWorkflowTools")))
(build-system r-build-system)
@@ -19647,14 +19924,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
(define-public r-biodist
(package
(name "r-biodist")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioDist" version))
(sha256
(base32
- "1mx4abv7p76qsa0yzj0b4d03xklx09im01bx02lwa1w527gdmfc3"))))
+ "0ngpysb89wag4wvcq83ddjxhy1zhl32b2fy2fg5laa4g8xfrqaxz"))))
(properties `((upstream-name . "bioDist")))
(build-system r-build-system)
(propagated-inputs
@@ -19669,14 +19946,14 @@ distance measures.")
(define-public r-pcatools
(package
(name "r-pcatools")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "PCAtools" version))
(sha256
(base32
- "07kl7s2zd7nkhg4hib2mr3w5lhqy780aw53yqsd7bfsjh53k8g95"))))
+ "18rzv4kldjmm2zvz9pzrpspig2hy6mcvb45hgmw49ba4jdcxh31s"))))
(properties `((upstream-name . "PCAtools")))
(build-system r-build-system)
(propagated-inputs
@@ -19715,14 +19992,14 @@ dimensional mass cytometry data.")
(define-public r-rgreat
(package
(name "r-rgreat")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGREAT" version))
(sha256
(base32
- "0qq3fqzd973jlf6ibfww5yicnyz2qvs2b2mn35p77k2mp4d7qp52"))))
+ "09fvmfiavawfwbxaj1585l2n00fibx9z3r17dv06hc6b40a1sa12"))))
(properties `((upstream-name . "rGREAT")))
(build-system r-build-system)
(propagated-inputs
@@ -19742,8 +20019,8 @@ dimensional mass cytometry data.")
r-org-hs-eg-db
r-progress
r-rcolorbrewer
- r-rcurl
r-rcpp
+ r-rcurl
r-rjson
r-s4vectors
r-shiny
@@ -19761,14 +20038,14 @@ user's input and automatically retrieving results from GREAT web server.")
(define-public r-m3c
(package
(name "r-m3c")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "M3C" version))
(sha256
(base32
- "158brq3w5h735s9yq93xx0y4p79yhgz72rpy0cyk4fjia5yaij5c"))))
+ "0q6npc5pglmhzm9270pi11kbp5wg3ncvflp4rhv3w778qza2zlk1"))))
(properties `((upstream-name . "M3C")))
(build-system r-build-system)
(propagated-inputs
@@ -19794,14 +20071,14 @@ hypothesis @code{K=1}.")
(define-public r-icens
(package
(name "r-icens")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Icens" version))
(sha256
(base32
- "1aq4iwk1cp96jzldhx7d4q7i77zbdg8nzkzh12g29yhwzj39nl3q"))))
+ "0fz66bchf41jzgabs1s8drpi3f7g27lid5g50lxwh6ph3i02cpaw"))))
(properties `((upstream-name . "Icens")))
(build-system r-build-system)
(propagated-inputs
@@ -19917,14 +20194,14 @@ generated.")
(define-public r-preprocesscore
(package
(name "r-preprocesscore")
- (version "1.62.1")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "preprocessCore" version))
(sha256
(base32
- "0z37ag22j1wh80vwq1kyr99rvadj9ppkddapfqyql3vj5x44cf4d"))))
+ "15fy3vwnjx6rwrkhbwxyvdykkfdis8c0m18x6y7irvyij9lm6x1y"))))
(properties
`((upstream-name . "preprocessCore")))
(build-system r-build-system)
@@ -19938,13 +20215,13 @@ routines.")
(define-public r-s4arrays
(package
(name "r-s4arrays")
- (version "1.0.6")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Arrays" version))
(sha256
(base32
- "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb"))))
+ "0x420l98f6b10r3qrdjq5ijs2p0msdcg6d6aghr3yvj1f9g06h8y"))))
(properties `((upstream-name . "S4Arrays")))
(build-system r-build-system)
(propagated-inputs
@@ -19975,13 +20252,13 @@ array-like semantic. It also provides:
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.38.2")
+ (version "0.40.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0n1w451647pxii6qrrxbvdi9z6rqdwibczkbs7k7a9j33bv3nqv8"))))
+ "0pja00ssl1pd16v3bls3aybml2cwanylx8igf596zha5srcf5l5h"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -20043,14 +20320,14 @@ data manipulation and visualization.")
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
- (version "2.44.0")
+ (version "2.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
- "1dv1vk73achjz5b5zzw2d517nbjfrlj7gppd48pfhk1w0mvz3q61"))))
+ "03l6yr76inv4fivy10g0h2qafgywrcjnnhs694lwqz1y6r0gm1sy"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
(arguments
@@ -20081,13 +20358,13 @@ objects from the @code{graph} package.")
(define-public r-fishpond
(package
(name "r-fishpond")
- (version "2.6.2")
+ (version "2.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "fishpond" version))
(sha256
(base32
- "0zsw4j6gk25303xpdwnkda2sq3mb4zb4p1mzwiyf7hdyf87zis05"))))
+ "04vl4cp0izghm7h4xk7x48lqkq0dpl47dkd068lva33jygwwpvcz"))))
(properties `((upstream-name . "fishpond")))
(build-system r-build-system)
(propagated-inputs
@@ -20117,13 +20394,13 @@ working with Salmon and Alevin quantification files.")
(define-public r-fithic
(package
(name "r-fithic")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FitHiC" version))
(sha256
(base32
- "0mqrzh1rcwyqlhq9wxcy4gp47hsb70qrsissm9nj0cb9j6ihi407"))))
+ "0ygcq3xi55swsmysn539cr3m504rfb6zm30w747pa46r63dfjda7"))))
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
@@ -20141,13 +20418,13 @@ assays such as Hi-C.")
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.44.0")
+ (version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "00csfr3yhbllwc8797xg49qb0djpvbpfi6mbnps284nlqy5vpdwh"))))
+ "16svq29fm9xl3rl9v6lyxf564manvp8ryxj1mbxc4pb360wmi780"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
@@ -20170,14 +20447,14 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "1riwxxnbi4z0lf42psh3m3ivxlgmmlnqhgsih6911c754r6s39qg"))))
+ "0p52n96mydqszpq1ysmbh5xs4n4icqsd0gbxl5wpkcwvvhxliw8b"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@@ -20202,14 +20479,14 @@ block processing.")
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.22.1")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9"))
+ "10n2grfdnri686sx52shz7y0csmcz4cky23k07803dz6qm1ljvmf"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -20247,8 +20524,6 @@ block processing.")
(substitute* "Makevars"
(("@BUILD_HDF5@") "")
(("@COPY_SZIP@") "")
- (("@ZLIB_LIB@") "-lz")
- (("@ZLIB_INCLUDE@") "")
(("HDF5_CXX_LIB=.*")
(string-append "HDF5_CXX_LIB="
(assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
@@ -20265,6 +20540,9 @@ block processing.")
(("HDF5_HL_CXX_LIB=.*")
(string-append "HDF5_HL_CXX_LIB="
(assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+ (("@ZLIB_LIB_PATH@") "-lz")
+ (("@ZLIB_INCLUDE_PATH@") "")
+
;; szip is non-free software
(("cp \"\\$\\{SZIP_LIB\\}.*") "")
(("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
@@ -20282,17 +20560,17 @@ packages.")
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "0ga9y9npl885jdx7gw5h6lh7fr0z5p7cvcwpz3hvwm4dy235j6gj"))))
+ "1yixv6vs1q2k4vx17bq4nar3g4v2076i5dq77gh63mlka46qr3g2"))))
(build-system r-build-system)
(propagated-inputs
- (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
+ (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray))
(native-inputs
(list r-knitr))
(home-page "https://bioconductor.org/packages/beachmat")
@@ -20305,13 +20583,13 @@ matrices.")
(define-public r-beadarray
(package
(name "r-beadarray")
- (version "2.50.0")
+ (version "2.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "beadarray" version))
(sha256
(base32
- "0rd41193rq6v4a97ibp0l2bz140nsv91plhn7iim8d8n9hgxqhjp"))))
+ "0qwka7549mlv2x80bjrzdsy4a6h35yxrhj2cxss9aigwsbjb7sjr"))))
(properties `((upstream-name . "beadarray")))
(build-system r-build-system)
(propagated-inputs (list r-annotationdbi
@@ -20338,13 +20616,13 @@ quality assessment and low-level analysis are provided.")
(define-public r-beadarraysnp
(package
(name "r-beadarraysnp")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beadarraySNP" version))
(sha256
- (base32 "1pymsm4j3wiyjvgsjb3vhjwdvhfmh91pxdhg4ihrj71pqpif3w9m"))))
+ (base32 "1vrizh7fpzv1w2gki0qxhphrfj1jj6m6bjsjsbw0b4n4invybzps"))))
(properties `((upstream-name . "beadarraySNP")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-quantsmooth))
@@ -20358,13 +20636,13 @@ performs copy number calculations and reports.")
(define-public r-beaddatapackr
(package
(name "r-beaddatapackr")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BeadDataPackR" version))
(sha256
(base32
- "0hm4brxg2rxazdcnhjiz6f4di2q8wssrrp35m79vm93sac9w42y3"))))
+ "0sfpdpw6qqffzb9skzx9w1ggcixc3wry9c6f2kwpsykbdsnk90xz"))))
(properties `((upstream-name . "BeadDataPackR")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -20381,13 +20659,13 @@ decompression of raw bead-level data from the Illumina BeadArray platform.")
(define-public r-cner
(package
(name "r-cner")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CNEr" version))
(sha256
- (base32 "04arfcr2ay71hyy0xsh6jzappmcnnzfr1nyj1l7dqhhhk81ksjfd"))))
+ (base32 "0kpz15l3yz26s2kskxk4093313c7vwi131y24wbpcdahicpqys2m"))))
(properties `((upstream-name . "CNEr")))
(build-system r-build-system)
(inputs (list zlib))
@@ -20429,14 +20707,14 @@ advanced visualization of sets of conserved noncoding elements.")
(define-public r-tfbstools
(package
(name "r-tfbstools")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TFBSTools" version))
(sha256
(base32
- "136s96cmd1aq878xy9mqd4k46awywqpmm55lpvash8mv4gg02vg8"))))
+ "18msr889nygk1c3wsjxc9bv989zakkl9f1h2a6cnfy8rxhbxpvwq"))))
(properties `((upstream-name . "TFBSTools")))
(build-system r-build-system)
(propagated-inputs
@@ -20475,13 +20753,13 @@ provides a wrapper of de novo motif discovery software.")
(define-public r-maftools
(package
(name "r-maftools")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "maftools" version))
(sha256
- (base32 "1jvmqn33hxzscr8j7y9zw5sngglcy0zkl0386053lx5dl5s5iqyq"))))
+ (base32 "025wlqnx13ldzyrf72mrfj492d62i4xyjbhpmgavgld0jwfmr3ga"))))
(properties `((upstream-name . "maftools")))
(build-system r-build-system)
(propagated-inputs
@@ -20504,14 +20782,14 @@ customizable visualzations with minimal effort.")
(define-public r-motifmatchr
(package
(name "r-motifmatchr")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifmatchr" version))
(sha256
(base32
- "0vqsxfbrxs25xr27vsr5syqjn6fwvn5dw0g76w4rdqk5d08p56ci"))))
+ "13kkg9xpyvgqpsaz5f96pd43i8a45jrbnzqmax793zkv4ai8p16j"))))
(properties `((upstream-name . "motifmatchr")))
(build-system r-build-system)
(propagated-inputs
@@ -20538,13 +20816,13 @@ This package wraps C++ code from the MOODS motif calling library.")
(define-public r-chromvar
(package
(name "r-chromvar")
- (version "1.22.1")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromVAR" version))
(sha256
- (base32 "001133rfcwmf4p3dbif933y9i1mkr3krw38g646wj4ikycszwih4"))))
+ (base32 "1vy650625b9b2dgnkgh5h0kw5bkdvfin133091asf1nw4jgnn1vx"))))
(properties `((upstream-name . "chromVAR")))
(build-system r-build-system)
(propagated-inputs
@@ -20585,14 +20863,14 @@ sequence (@code{DNAse-seq}) experiments.")
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "1v2px6gvr0wzj2cyml57hxj5ghynlvizkchbywd3kx05j1h2mckd"))))
+ "0q44n97mly1ldh52r0sb1jwhz8bn4n7sfw99qs5h4s44w9s0fry4"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
@@ -20613,13 +20891,13 @@ libraries.")
(define-public r-singler
(package
(name "r-singler")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleR" version))
(sha256
- (base32 "0dwlg86wkivsag5ffjk81nlq34lwl3kk065k9l6lak24ziq6c4ij"))))
+ (base32 "0s7m3qdbgrqaq93k6rvyj34h36kdjvppn9ilflrcaa5w498fzfhf"))))
(properties `((upstream-name . "SingleR")))
(build-system r-build-system)
(propagated-inputs
@@ -20645,14 +20923,14 @@ cell types to infer the cell of origin of each single cell independently.")
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.10.2")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb"))))
+ "090arfacfs09x7g60qxz4bj2gqb97y3kmhafywkgnrj7pz1z0qzq"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
@@ -20680,13 +20958,13 @@ of other packages.")
(define-public r-scater
(package
(name "r-scater")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0v6qaflv7b504yxxv6bmnlikg36bhfahgqxigpq6qcfrhqapmqck"))))
+ "0a8wfrcp09z0aflalqhhwvz675aa32wgprqphk1axvdppknsg7vf"))))
(build-system r-build-system)
(propagated-inputs
(list r-beachmat
@@ -20695,13 +20973,12 @@ of other packages.")
r-biocparallel
r-biocsingular
r-delayedarray
- r-delayedmatrixstats
- r-densvis
r-ggbeeswarm
r-ggplot2
- r-ggrepel
r-ggrastr
+ r-ggrepel
r-matrix
+ r-matrixgenerics
r-pheatmap
r-rcolorbrewer
r-rcppml
@@ -20725,14 +21002,14 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.28.2")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "1la55s14frvsjp8ly02fbrkzvv7lzvcd7jc1axmwh494b9zy5jmd"))))
+ "0vq3216jk389mjnz5kx0i6fwmkypp21rshvv9ldcy327h6vk1ylj"))))
(build-system r-build-system)
(propagated-inputs
(list r-beachmat
@@ -20765,17 +21042,54 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly
variable and significantly correlated genes.")
(license license:gpl3)))
+(define-public r-sparsearray
+ (package
+ (name "r-sparsearray")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SparseArray" version))
+ (sha256
+ (base32 "0a1xg8vkjybgdr09bk2z4i82m06qnw2nhbzviyijadxiwvz6pgsz"))))
+ (properties `((upstream-name . "SparseArray")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biocgenerics
+ r-iranges
+ r-matrix
+ r-matrixgenerics
+ r-matrixstats
+ r-s4arrays
+ r-s4vectors
+ r-xvector))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/SparseArray")
+ (synopsis
+ "Efficient in-memory representation of multidimensional sparse arrays")
+ (description
+ "The @code{SparseArray} package is an infrastructure package that
+provides an array-like container for efficient in-memory representation of
+multidimensional sparse data in R. The package defines the @code{SparseArray}
+virtual class and two concrete subclasses: @code{COO_SparseArray} and
+@code{SVT_SparseArray}. Each subclass uses its own internal representation of
+the nonzero multidimensional data, the \"COO layout\" and the \"SVT layout\",
+respectively. @code{SVT_SparseArray} objects mimic as much as possible the
+behavior of ordinary matrix and array objects in base R. In particular, they
+suppport most of the \"standard matrix and array API\" defined in base R and
+in the @code{matrixStats} package from CRAN.")
+ (license license:artistic2.0)))
+
(define-public r-sparsematrixstats
(package
(name "r-sparsematrixstats")
- (version "1.12.2")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sparseMatrixStats" version))
(sha256
(base32
- "00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1"))))
+ "0r2jxwha2xjp8iy7al85s5vib4xvl47gmlbbvvjj4wnz2gfzic9r"))))
(properties
`((upstream-name . "sparseMatrixStats")))
(build-system r-build-system)
@@ -20793,18 +21107,17 @@ data in the column sparse format.")
(define-public r-spatialexperiment
(package
(name "r-spatialexperiment")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SpatialExperiment" version))
(sha256
(base32
- "18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70"))))
+ "1s42jzq95f662h39zmbf06qmrrglbch8sgygpnwqblrjbrqgm7n4"))))
(properties `((upstream-name . "SpatialExperiment")))
(build-system r-build-system)
(propagated-inputs (list r-biocfilecache
r-biocgenerics
- r-dropletutils
r-magick
r-rjson
r-s4vectors
@@ -20825,14 +21138,14 @@ Visium platform.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.22.6")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8"))))
+ "18r5rfx46lac0kaakha4gqs4pj8vb39z0908gpclmp3ajca4hzb1"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
@@ -20841,7 +21154,6 @@ Visium platform.")
r-iranges
r-matrix
r-matrixgenerics
- r-matrixstats
r-s4vectors
r-sparsematrixstats))
(native-inputs
@@ -20861,14 +21173,14 @@ memory usage and processing time is minimized.")
(define-public r-mscoreutils
(package
(name "r-mscoreutils")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MsCoreUtils" version))
(sha256
(base32
- "055xzlq37d75ghfk87bxbsv4yifidnwxc3w2gp8mcqxwkxxhd70a"))))
+ "0faj4fxfsv7ir935sn9zainhk55vdfi6abgr0s321kwmvs6prc0p"))))
(properties `((upstream-name . "MsCoreUtils")))
(build-system r-build-system)
(propagated-inputs
@@ -20890,13 +21202,13 @@ within the R for Mass Spectrometry packages.")
(define-public r-msfeatures
(package
(name "r-msfeatures")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MsFeatures" version))
(sha256
- (base32 "0cb4b0mf5yh8amqwa3r0mbk2f3rgq40gdlkhifk50fxnqdy4fjsh"))))
+ (base32 "0vpsc7i6j2skn6wba178iy406yvd4p8xf3lq2qmm2inimxl983cs"))))
(properties `((upstream-name . "MsFeatures")))
(build-system r-build-system)
(propagated-inputs
@@ -20920,14 +21232,14 @@ the respective packages (such as e.g. @code{xcms}).")
(define-public r-biocio
(package
(name "r-biocio")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocIO" version))
(sha256
(base32
- "03hslg7k6khchf54gmlbkvwbkfn5ppz0wp7lh75gsnr0licsjkwx"))))
+ "0bn2jknvj2ag1yv67kjqr7gsq771rmqv3my9njjkwcc9nzrxzhbp"))))
(properties `((upstream-name . "BiocIO")))
(build-system r-build-system)
(propagated-inputs
@@ -20953,14 +21265,14 @@ as well as local access. Developers can register a file extension, e.g.,
(define-public r-msmseda
(package
(name "r-msmseda")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsEDA" version))
(sha256
(base32
- "108azzd6ibcgb1gqgcrz4shk3rdr3vfpzy0z6zknlsxwz7sbcnfi"))))
+ "0xxjkr3x654n61q2yda09cghvssyx4ml9g22gfzfhbzjp8j7pm2c"))))
(properties `((upstream-name . "msmsEDA")))
(build-system r-build-system)
(propagated-inputs
@@ -20976,14 +21288,14 @@ experiments, and visualize de influence of the involved factors.")
(define-public r-msmstests
(package
(name "r-msmstests")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsTests" version))
(sha256
(base32
- "1y3nklhlib2l9smcl6slv1653vyg9ip29if286l59rjrdwh50cwa"))))
+ "0dif4yvm9hfrnamjph5xa9cbf41f2v8lbgyr88f11alwwbf0dg69"))))
(properties `((upstream-name . "msmsTests")))
(build-system r-build-system)
(propagated-inputs
@@ -21005,14 +21317,14 @@ relevant, and the minimum expression of the most abundant condition.")
(define-public r-catalyst
(package
(name "r-catalyst")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CATALYST" version))
(sha256
(base32
- "0f6h0qngv7my83k402rydvi1pla695r5kxq02k1s5caxcsi1caza"))))
+ "0dfg9ib0imk8bmhycqrspnn8yvfdlchwvx39wgqxi5fb9zrppfz4"))))
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs
@@ -21029,7 +21341,6 @@ relevant, and the minimum expression of the most abundant condition.")
r-ggrepel
r-ggridges
r-gridextra
- r-magrittr
r-matrix
r-matrixstats
r-nnls
@@ -21068,14 +21379,14 @@ preprocessing of cytometry data, including:
(define-public r-erma
(package
(name "r-erma")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "14rgj8g9x248p2cc86aqn289qamsd91d6fnydi5d34q605ph73yj"))))
+ "0vapjfzhwlzxd049fsr00jd7lp48h9qwd95m2sqhqryqz1vsi7hz"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -21108,14 +21419,14 @@ by Ernst and Kellis.")
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "0n7nghrrs7fp0b7jk2pfbkzl0lbv55xxk2xqnq2i77ps22ms0h9y"))))
+ "1chs58ifpwz4crcl5ymnb8ah3wf2jrn9lla3ljsywqiqn0r3i1am"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -21276,14 +21587,14 @@ family of feature/genome hypotheses.")
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.44.2")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0laismy8kklzkg81r5vf1194fbhp2hw952g6jc3zvn2z5y2d4524"))))
+ "0b707xxi0ch4kfxid5id16gkh9pnqwrgqpsvgbm0rc89kg73g4jz"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@@ -21325,14 +21636,14 @@ with your data.")
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.32.0")
+ (version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "1i64bk0ac2v0w5yjxdhnbjh05l6n9fi7gxap0zp73wxj7kl75wkd"))))
+ "028n8v1pgkr1q5s9wslql8ayk1cbx6a9a2rjka9pdwz6rq1iyagy"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
@@ -21359,13 +21670,13 @@ EMBL-EBI GWAS catalog.")
(define-public r-gwastools
(package
(name "r-gwastools")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GWASTools" version))
(sha256
(base32
- "1g86xg2d9wi6xijhc89zxhbw190aviw9nkwvbwgz85jf71wf34hv"))))
+ "1rjgdcw65zmmg5dy9mdaz720nvqk03bfsfvkdsa1wwhvlnxmscp8"))))
(properties `((upstream-name . "GWASTools")))
(build-system r-build-system)
(propagated-inputs (list r-biobase
@@ -21380,6 +21691,7 @@ EMBL-EBI GWAS catalog.")
r-rsqlite
r-sandwich
r-survival))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/smgogarten/GWASTools")
(synopsis "Tools for Genome Wide Association Studies")
(description
@@ -21390,13 +21702,13 @@ annotation, and functions for GWAS data cleaning and analysis.")
(define-public r-kegggraph
(package
(name "r-kegggraph")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGgraph" version))
(sha256
- (base32 "0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl"))))
+ (base32 "0i9iqr87mqih0rkbjx3wa383x4yfyzpcb0b0xzairbqgygvcq4kl"))))
(properties `((upstream-name . "KEGGgraph")))
(build-system r-build-system)
(propagated-inputs
@@ -21414,14 +21726,14 @@ functionalities including parsing, graph operation, visualization and etc.")
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "18gqmwwi1i4gndqljy809n5zzx38agawxxwhlknpas6k2iskd1xq"))))
+ "1caxzc99kga2c90m2ydmnvcd8lfp0igmmickpl0ikrhwjlbfnc0p"))))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
@@ -21470,14 +21782,14 @@ on the plot.")
(define-public r-abn
(package
(name "r-abn")
- (version "3.0.1")
+ (version "3.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
- "03g02450l3mckjzwd0w717dbmxhrngkwlfhm5c9q5zv4g10df7nj"))))
+ "06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh"))))
(build-system r-build-system)
(inputs
(list gsl))
@@ -21536,13 +21848,13 @@ other functional sequencing data.")
(define-public r-parody
(package
(name "r-parody")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "parody" version))
(sha256
- (base32 "0n2pmpnpwh16hb58v821xn42jm4a7wjsdf6sqxapjjw9w432mjac"))))
+ (base32 "05mhbkhyh92bwmx37fpviprr9i4z0i6g24l71zk17gq0f8hwb4jj"))))
(properties `((upstream-name . "parody")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -21557,13 +21869,13 @@ methods based on resistant statistics.")
(define-public r-pathview
(package
(name "r-pathview")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pathview" version))
(sha256
- (base32 "0mld7vys6s5k8snk1gniph9wkw3726vsx430nhyyr76fp4ps2mks"))))
+ (base32 "17kl7yvpjhsb52kz1pw3jnk6s480lnpvvh9rragndixsl8bkmqmc"))))
(properties `((upstream-name . "pathview")))
(build-system r-build-system)
(propagated-inputs
@@ -21591,13 +21903,13 @@ large-scale and fully automated analysis.")
(define-public r-snapcgh
(package
(name "r-snapcgh")
- (version "1.70.0")
+ (version "1.72.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "snapCGH" version))
(sha256
(base32
- "0yz5q7w3lqv8ac6a764xlbm4hq3ncnngqng879qbpmzhgb4r155g"))))
+ "0knjspxzc3z5dhx0a6kx9rkic85w65l84vy552x5bv8jzxkcwrsj"))))
(properties `((upstream-name . "snapCGH")))
(build-system r-build-system)
(propagated-inputs
@@ -21619,13 +21931,13 @@ segmented data for individual and multiple arrays.")
(define-public r-snprelate
(package
(name "r-snprelate")
- (version "1.34.1")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SNPRelate" version))
(sha256
(base32
- "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh"))))
+ "0jw9ziz0a472mnnvmqwas5w646xfgx8dn1bdpwz8c99m663d8ayp"))))
(properties `((upstream-name . "SNPRelate")))
(build-system r-build-system)
(propagated-inputs (list r-gdsfmt))
@@ -21654,14 +21966,14 @@ whole-genome and whole-exome variant data.")
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "1v2j2943apphs8i68ap9c8sxd4j5a04qda5scq4dqqkzqd0c5b6i"))))
+ "0a4kyv93ljv7n62ghx66l81q6sw24llr0998nsalidyws1wldbyr"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs (list zlib))
@@ -21678,14 +21990,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(define-public r-chromstar
(package
(name "r-chromstar")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromstaR" version))
(sha256
(base32
- "1qrcmydk080m1rzwbzx2km4vpbahnq5y73mrnpgjjjrxbndz9xz9"))))
+ "1yykcqxp8y7by4jgh6dfl25m0pnghj36qy21990n2sdfv1kpg2x6"))))
(properties `((upstream-name . "chromstaR")))
(build-system r-build-system)
(propagated-inputs
@@ -21716,14 +22028,14 @@ analyses.")
(define-public r-guitar
(package
(name "r-guitar")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Guitar" version))
(sha256
(base32
- "1v1yw90waq0ccj6pxdipipy5bnk0k762m5kadl4h3jgpcrkf2fvc"))))
+ "09i6j8dcmzvd9gh9629523hw0hbng18jdqw5gf1r31ck8m8wwmnc"))))
(properties `((upstream-name . "Guitar")))
(build-system r-build-system)
(propagated-inputs
@@ -21769,14 +22081,14 @@ visualizations for publication-quality multi-panel figures.")
(define-public r-ballgown
(package
(name "r-ballgown")
- (version "2.32.0")
+ (version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ballgown" version))
(sha256
(base32
- "05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx"))))
+ "1r3qz6y97zhp7swcv2ls1h6cz0l66y5ap00wx9wlqxv14sljd135"))))
(properties `((upstream-name . "ballgown")))
(build-system r-build-system)
(propagated-inputs
@@ -21803,14 +22115,14 @@ to annotation.")
(define-public r-megadepth
(package
(name "r-megadepth")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "megadepth" version))
(sha256
(base32
- "1zzhgfnrr3r5ismbbj9jcqss8mr8ll6p4d3z026ya2khb0i7clc7"))))
+ "0g9d4q6vh2ys1la15fqgbc4ckfbjbzzaqa49x9liqrhpnrp59vc3"))))
(properties `((upstream-name . "megadepth")))
(build-system r-build-system)
(inputs (list megadepth))
@@ -21836,14 +22148,14 @@ regions or annotations of your choice from BigWig files.")
(define-public r-beclear
(package
(name "r-beclear")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BEclear" version))
(sha256
(base32
- "1sdw69dhrzkcpc7flvp1gkixvpsbrckyg756rlm17hjjwfxlz5lb"))))
+ "1a8jmlx17qcx9qzcaxbnlk6qji6hqxcnzmr8zvar9jrfhx0cv9x1"))))
(properties `((upstream-name . "BEclear")))
(build-system r-build-system)
(propagated-inputs
@@ -21870,14 +22182,14 @@ real numbers.")
(define-public r-bgeecall
(package
(name "r-bgeecall")
- (version "1.16.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BgeeCall" version))
(sha256
(base32
- "0j83scxpq51bhxwfps7chcawzsqrd7pk7x2jg29zj4zbp1jbrnl0"))))
+ "1ipypkyfqx6mahiwl0gzdsi7z9j9cm5rgfw4ybgh6blfq8kg9qyk"))))
(properties `((upstream-name . "BgeeCall")))
(build-system r-build-system)
(propagated-inputs
@@ -21906,14 +22218,14 @@ all RNA-Seq libraries of each species integrated in Bgee.")
(define-public r-bgeedb
(package
(name "r-bgeedb")
- (version "2.26.0")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BgeeDB" version))
(sha256
(base32
- "1s6v17bavidlfy6habi4bv6lmwkrx8c5was1zcq0kb05qdvpn4ph"))))
+ "1ahip21wihwg9yhq0ya1cyzd2cq423hz9pd6iql6y3yhld4j5rnn"))))
(properties `((upstream-name . "BgeeDB")))
(build-system r-build-system)
(propagated-inputs
@@ -21940,14 +22252,14 @@ anatomical terms, mapped to genes by expression patterns.")
(define-public r-biobtreer
(package
(name "r-biobtreer")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biobtreeR" version))
(sha256
(base32
- "0cbhlxh0w736695niyjd59fcvplna2f2x2av9k0sd1r3dy6lrcd4"))))
+ "18p5r67ppkw8wxxkrj76q68ljlhdbhar5hc89ffdsgr3zzdyk875"))))
(properties `((upstream-name . "biobtreeR")))
(build-system r-build-system)
(propagated-inputs
@@ -21964,14 +22276,14 @@ mappings functionalities.")
(define-public r-minet
(package
(name "r-minet")
- (version "3.58.0")
+ (version "3.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "minet" version))
(sha256
(base32
- "04ll8nqhmyj2v12n2xskia8dh5px8mzj8fbyw1pzahk9vp085gkr"))))
+ "17v2x7cyw74h0zfsz33pyl1kqk976pdzw7mrgprz9l7w5120niw5"))))
(properties `((upstream-name . "minet")))
(build-system r-build-system)
(propagated-inputs
@@ -21986,14 +22298,14 @@ information networks from data.")
(define-public r-genetclassifier
(package
(name "r-genetclassifier")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geNetClassifier" version))
(sha256
(base32
- "1bn7h8jwmmgqzp0s3xdbsicm8pxmrgvnxmjnjs10d1rvp8znzjnn"))))
+ "1k61aka780xmf1vhqm6zvzjr2626hv71f8gp1s81az939crxlrqd"))))
(properties
`((upstream-name . "geNetClassifier")))
(build-system r-build-system)
@@ -22011,14 +22323,14 @@ interface to query the classifier.")
(define-public r-dir-expiry
(package
(name "r-dir-expiry")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dir.expiry" version))
(sha256
(base32
- "1vccq28734s7zk7pc7i9zq4rzbi373xqqvgkzamjpii36phkdmlw"))))
+ "191b8qhldxvsw09l2c0ffc1ldmx0mqxgsx6m074f28l01d3c1d9q"))))
(properties `((upstream-name . "dir.expiry")))
(build-system r-build-system)
(propagated-inputs (list r-filelock))
@@ -22035,14 +22347,14 @@ eliminating obsolete caches generated by old versions of packages.")
(define-public r-basilisk-utils
(package
(name "r-basilisk-utils")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "basilisk.utils" version))
(sha256
(base32
- "0g5apvna9wzjlm7g9hdafy44nrg5rp3qh4anwpgwwp2vr0vxn37k"))))
+ "08wsn2znw56svyv5vpxxzcynz93h5hzw1n2r6hb9h3rvc7afyvxl"))))
(properties
`((upstream-name . "basilisk.utils")))
(build-system r-build-system)
@@ -22059,14 +22371,14 @@ package, primarily for creation of the underlying Conda instance.")
(define-public r-basilisk
(package
(name "r-basilisk")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "basilisk" version))
(sha256
(base32
- "0bg6jfl12jsmhgby7x7g2vfmi61rx0jdksi97hb0zajgh1nvhirh"))))
+ "1z482gw04psvkgspclmxlkd9qi7srgbnr56ajngcng28sc6zqdhs"))))
(properties `((upstream-name . "basilisk")))
(build-system r-build-system)
(propagated-inputs
@@ -22085,14 +22397,14 @@ Python environments in a single R session.")
(define-public r-biocthis
(package
(name "r-biocthis")
- (version "1.10.3")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biocthis" version))
(sha256
(base32
- "1v0qrypdzl1bg85k8i7qamb6709cgk4ypmisjh6bn5r36nqd5qx4"))))
+ "0lxcsw70ib8wvkp3ii1l8vd4g2ddhj6g0x22dwcmwacr2myk3bg8"))))
(properties `((upstream-name . "biocthis")))
(build-system r-build-system)
(arguments
@@ -22149,14 +22461,14 @@ the Bioconductor project.")
(define-public r-biodb
(package
(name "r-biodb")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biodb" version))
(sha256
(base32
- "18j70ma85qb42qqpzz8fw3g4x6cav4j0pc2ab5ym22791dr8izck"))))
+ "18w062s0wwdisl6a9a79in6h4052x3janinc5isip0x6p9g9d9bk"))))
(properties `((upstream-name . "biodb")))
(build-system r-build-system)
(propagated-inputs
@@ -22195,14 +22507,14 @@ separate published packages.")
(define-public r-biomformat
(package
(name "r-biomformat")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biomformat" version))
(sha256
(base32
- "04kl2432wq6ybdhispvp98ylgyk3kkhmjx1nxdvcal7bfpy2vskk"))))
+ "1ccnrz8rkg533kil3sc8wnjqsmiyrpqqmk7av7ls01avglcjdjq1"))))
(properties `((upstream-name . "biomformat")))
(build-system r-build-system)
(propagated-inputs
@@ -22224,14 +22536,14 @@ as extensions of common core functions/methods.")
(define-public r-mvcclass
(package
(name "r-mvcclass")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MVCClass" version))
(sha256
(base32
- "1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6"))))
+ "16finp6q89n6x5q2v1khpfp5ys7d4dvlh3kacv5qbdh1bsb3fpax"))))
(properties `((upstream-name . "MVCClass")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/MVCClass")
@@ -22244,14 +22556,14 @@ design.")
(define-public r-biomvcclass
(package
(name "r-biomvcclass")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioMVCClass" version))
(sha256
(base32
- "07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r"))))
+ "04ckv1y5iqawd0dvnn0bbpnmyys0ivcmf0my6dld3hib3idjzwfx"))))
(properties `((upstream-name . "BioMVCClass")))
(build-system r-build-system)
(propagated-inputs
@@ -22300,14 +22612,14 @@ using aCGH or sequencing.")
(define-public r-bionero
(package
(name "r-bionero")
- (version "1.8.7")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNERO" version))
(sha256
(base32
- "0yvd05yikvblnhimnmn4srcsimab4qml5k582n0c9h4rppffmvy4"))))
+ "0pq5fiacb2x8l5jk3p6bnha9bcwg91grpklgx2nirrlwwr80gf2h"))))
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs
@@ -22356,14 +22668,14 @@ networks.")
(define-public r-bionet
(package
(name "r-bionet")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNet" version))
(sha256
(base32
- "19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1"))))
+ "122rj6rg4j9q9brhxyrbkc91fml3davk044s2yxwyjnwn2yjw0bq"))))
(properties `((upstream-name . "BioNet")))
(build-system r-build-system)
(propagated-inputs
@@ -22385,14 +22697,14 @@ scoring subnetwork.")
(define-public r-bionetstat
(package
(name "r-bionetstat")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNetStat" version))
(sha256
(base32
- "0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4"))
+ "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8"))
(snippet
'(delete-file "inst/datatables/js/jquery.dataTables.min.js"))))
(properties `((upstream-name . "BioNetStat")))
@@ -22440,14 +22752,14 @@ network and metabolic pathways view.")
(define-public r-bioqc
(package
(name "r-bioqc")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioQC" version))
(sha256
(base32
- "0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw"))))
+ "15kmg102259h2yl3b6ncq2p545kdac4hk4kwm1s5492y5rg7qkla"))))
(properties `((upstream-name . "BioQC")))
(build-system r-build-system)
(propagated-inputs
@@ -22466,14 +22778,14 @@ optimised for high performance.")
(define-public r-biotip
(package
(name "r-biotip")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioTIP" version))
(sha256
(base32
- "0lqnxaycrva2092h4swmk6na2pq2kp951dmicyw399djd1i7yj50"))))
+ "1bbjfv3bi20xlk8h7r5ipav6mfs27lmj0zjb5mk1gmp071dmnk0y"))))
(properties `((upstream-name . "BioTIP")))
(build-system r-build-system)
(propagated-inputs
@@ -22496,14 +22808,14 @@ help unravel disease regulatory trajectory.")
(define-public r-biotmle
(package
(name "r-biotmle")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biotmle" version))
(sha256
(base32
- "1hjkhwbld8m52lsy2ba6cnp02n0xykaxm9650r5zmzry38dw9nb5"))))
+ "0h796sxv7fvwx9m8ikamf3bvaac7rimp33lv1j3ngsjifigdkvfy"))))
(properties `((upstream-name . "biotmle")))
(build-system r-build-system)
(propagated-inputs
@@ -22538,14 +22850,14 @@ ensemble machine learning for the estimation of nuisance functions.")
(define-public r-bsseq
(package
(name "r-bsseq")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bsseq" version))
(sha256
(base32
- "1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3"))))
+ "0afpzr52mf2ab7gr9swdf6609787ymw8s8wksis0d4ap0y0wdgg0"))))
(properties `((upstream-name . "bsseq")))
(build-system r-build-system)
(propagated-inputs
@@ -22584,13 +22896,13 @@ visualizing bisulfite sequencing data.")
(define-public r-dada2
(package
(name "r-dada2")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "dada2" version))
(sha256
(base32
- "1vxy2106rzygy0dr38wmw84zrqp9gsvaphliikdmhx0n2gv6xhd1"))))
+ "0rvnwbknvwksm50f4rw9965gnhy13rjgdfvv428xsqixgkkkyrf6"))))
(properties `((upstream-name . "dada2")))
(build-system r-build-system)
(propagated-inputs
@@ -22621,14 +22933,14 @@ fragments by exact matching.")
(define-public r-dmrseq
(package
(name "r-dmrseq")
- (version "1.20.1")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dmrseq" version))
(sha256
(base32
- "1lxrirgy42xnpdj7b2nrabbki33an8ri6j1mgxp3jn4h0a88c280"))))
+ "0z53vh5qirkyn7yw3g2m2kj6dzii96l81vc8j59n2dl7p602l9a2"))))
(properties `((upstream-name . "dmrseq")))
(build-system r-build-system)
(propagated-inputs
@@ -22667,13 +22979,13 @@ interest on transformed methylation proportions.")
(define-public r-omicade4
(package
(name "r-omicade4")
- (version "1.40.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "omicade4" version))
(sha256
(base32
- "086nh0m82gjlxyg6i230wpkin4zc3a7cfla0qzvj28h0n8irkm5r"))))
+ "0i4ln95ayl1irr8sr3639x35ilysdi663kksw7g93q1ry91yav8r"))))
(properties `((upstream-name . "omicade4")))
(build-system r-build-system)
(propagated-inputs (list r-ade4 r-biobase r-made4))
@@ -22686,13 +22998,13 @@ interest on transformed methylation proportions.")
(define-public r-omnipathr
(package
(name "r-omnipathr")
- (version "3.8.2")
+ (version "3.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OmnipathR" version))
(sha256
- (base32 "13ac98jj03vkzrc1ghrs98qrfvr74wz099w26lgc7jw2yxj575as"))))
+ (base32 "1wbzb4kh7bzsvixr3vxzih9rfkpjx00f33i0yl0dqj0yixnrghwr"))))
(properties `((upstream-name . "OmnipathR")))
(build-system r-build-system)
(arguments
@@ -22711,6 +23023,7 @@ interest on transformed methylation proportions.")
r-jsonlite
r-later
r-logger
+ r-lubridate
r-magrittr
r-progress
r-purrr
@@ -22720,6 +23033,7 @@ interest on transformed methylation proportions.")
r-rlang
r-rmarkdown
r-rvest
+ r-stringi
r-stringr
r-tibble
r-tidyr
@@ -22741,14 +23055,14 @@ for ligand activity prediction from transcriptomics data.")
(define-public r-biscuiteer
(package
(name "r-biscuiteer")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biscuiteer" version))
(sha256
(base32
- "07nak6mfw9m8ldl336sqgkl3638ibv1hxwd89hwxdrn914wz3hw3"))))
+ "1q90p14qj5plz6cbvwxq875y29in6jg7adyni5wd33pf9i4gsxzi"))))
(properties `((upstream-name . "biscuiteer")))
(build-system r-build-system)
(propagated-inputs
@@ -22793,13 +23107,13 @@ estimates, etc.")
(define-public r-tcgabiolinks
(package
(name "r-tcgabiolinks")
- (version "2.28.3")
+ (version "2.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TCGAbiolinks" version))
(sha256
- (base32 "1hh09ya4jg062k1ibp1cpvdrgv6gwr95ch57iycgd3cjc5g0xhii"))))
+ (base32 "1k8xiv4bmil420176ckfda2r6y0s46dk1cm8dbywav86q28bmzzx"))))
(properties `((upstream-name . "TCGAbiolinks")))
(build-system r-build-system)
(propagated-inputs
@@ -22848,13 +23162,13 @@ starburst plots) in order to easily develop complete analysis pipelines.")
(define-public r-tricycle
(package
(name "r-tricycle")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tricycle" version))
(sha256
(base32
- "1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6"))))
+ "1dawkp681pz9hf7fp2nag9pcfxx5rq0z4j9czlalf0sylsjbirkd"))))
(properties `((upstream-name . "tricycle")))
(build-system r-build-system)
(propagated-inputs
@@ -22887,14 +23201,14 @@ embeddings and functions to build new reference.")
(define-public r-tximeta
(package
(name "r-tximeta")
- (version "1.18.3")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "tximeta" version))
(sha256
(base32
- "01s8x8a3rb0a5i599pxc5miz84ssvh10b4vha79nmbhkqccffvml"))))
+ "0wn7r1dzckiq3zacvcv2w780fj9bvz1vbyzcazv2qvsicbwc4vd8"))))
(properties `((upstream-name . "tximeta")))
(build-system r-build-system)
(propagated-inputs
@@ -22928,13 +23242,13 @@ reproducibility.")
(define-public r-phyloseq
(package
(name "r-phyloseq")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "phyloseq" version))
(sha256
- (base32 "0rmv8f1m8ck97v991wdly3fma2rjczhi974lh7ikwx6rcx6fp9ah"))))
+ (base32 "06gnpjcniqm8i52xh9xl3nn0wm9nn9rkqd3w3fjv7ii142xypjln"))))
(properties `((upstream-name . "phyloseq")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 508f5ea09a..3572f3d551 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1063,11 +1063,11 @@ plotnames, filenames and paths.")
(license license:gpl3))))
(define-public r-readwriter
- (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058")
+ (let ((commit "12d32cb6533ef4b9eab4d707d1502525c2034aee")
(revision "1"))
(package
(name "r-readwriter")
- (version (git-version "0.2.9" revision commit))
+ (version (git-version "0.3.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1076,7 +1076,7 @@ plotnames, filenames and paths.")
(file-name (git-file-name name version))
(sha256
(base32
- "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7"))))
+ "1hy47g8d7zppr2i9zlkwl2yb0ii8x710hqk07h089ldx9171qxab"))))
(properties `((upstream-name . "ReadWriter")))
(build-system r-build-system)
(propagated-inputs
@@ -5164,13 +5164,25 @@ software to answer ad hoc questions.")
python-pysam
python-pyyaml
python-scipy
+ r-biocmanager
+ r-dplyr
+ r-genomicranges
+ r-here
+ r-openxlsx
+ r-optparse
+ r-readr
+ r-rsamtools
+ r-stringr
+ r-tidyr
+ r-upsetr
+ r-yaml
snakemake-7))
(native-inputs (list python-cython python-pyfakefs python-pytest))
(home-page "https://github.com/dieterich-lab/Baltica")
(synopsis "Integrated splice junction usage analysis")
(description
"This framework facilitates the execution of @dfn{differential junction
-usage} (DJU) methods. Additionally, it enables the integration of results from
+usage} (DJU) methods. Additionally, it enables the integration of results from
multiple DJU methods.")
(license license:expat)))
@@ -10653,6 +10665,40 @@ of transcriptional heterogeneity among single cells.")
;; See https://github.com/hms-dbmi/scde/issues/38
(license license:gpl2)))
+(define-public r-miamiplot
+ (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0")
+ (revision "1"))
+ (package
+ (name "r-miamiplot")
+ (version (git-version "1.1.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/juliedwhite/miamiplot")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9"))))
+ (properties `((upstream-name . "miamiplot")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-checkmate
+ r-dplyr
+ r-ggplot2
+ r-ggrepel
+ r-gridextra
+ r-magrittr
+ r-rlang))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/juliedwhite/miamiplot")
+ (synopsis "Create a ggplot2 miami plot")
+ (description
+ "This package generates a Miami plot with centered chromosome labels.
+The output is a ggplot2 object. Users can specify which data they want
+plotted on top vs. bottom, whether to display significance line(s), what
+colors to give chromosomes, and what points to label.")
+ (license license:gpl2))))
+
(define-public r-millefy
(package
(name "r-millefy")
@@ -18796,6 +18842,73 @@ transcriptional derivatives and visualization of the resulting velocity
patterns.")
(license license:gpl3))))
+(define-public r-voltron
+ (let ((commit "5057b703479239a9aaba761f07e65d849f6111f8")
+ (revision "1"))
+ (package
+ (name "r-voltron")
+ (version (git-version "1.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BIMSBbioinfo/VoltRon")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1nximl4708a7fdwn8ysxpni3mp6dx33cphavlay7hh1pa55pnzgn"))
+ (modules '((guix build utils)))
+ ;; The tripack package is not available under a free license,
+ ;; but interp provides free implementations of "tri.mesh" and
+ ;; "neighbours".
+ (snippet
+ '(substitute* '("DESCRIPTION" "NAMESPACE" "R/spatial.R")
+ (("tripack") "interp")))))
+ (properties `((upstream-name . "VoltRon")))
+ (build-system r-build-system)
+ (inputs (list opencv tbb zlib))
+ (propagated-inputs (list r-anndata
+ r-data-table
+ r-dplyr
+ r-ebimage
+ r-fastdummies
+ r-fnn
+ r-ggforce
+ r-ggplot2
+ r-ggpubr
+ r-ggrepel
+ r-hdf5r
+ r-htmltools
+ r-igraph
+ r-interp
+ r-irlba
+ r-magick
+ r-matrix
+ r-morpho
+ r-raster
+ r-rcpp
+ r-reshape2
+ r-rjson
+ r-rlang
+ r-s4vectors
+ r-scales
+ r-shiny
+ r-shinyjs
+ r-stringr
+ r-terra
+ r-umap
+ r-xml))
+ (native-inputs (list pkg-config))
+ (home-page "https://github.com/BIMSBbioinfo/VoltRon")
+ (synopsis "VoltRon for Spatial Data Integration and Analysis")
+ (description
+ "@code{VoltRon} is a toolbox for spatial data analysis, multi-omics
+integration using spatial image registration. @code{VoltRon} is capable of
+analyzing multiple types and modalities of spatially-aware datasets.
+@code{VoltRon} visualizes and analyzes regions of interests (ROIs), spots,
+cells and even molecules.")
+ (license license:expat))))
+
(define-public methyldackel
(package
(name "methyldackel")
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index b357d96fbc..abf8a609e9 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -83,7 +83,7 @@
(define-public transmission
(package
(name "transmission")
- (version "4.0.3")
+ (version "4.0.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/transmission/transmission"
@@ -91,7 +91,7 @@
version ".tar.xz"))
(sha256
(base32
- "0njlmpcdsxwx8vwdk9dvsby51l6f6awks9d0mgvi9fs2ivaizc5n"))))
+ "19nm7f4x3zq610da5fl63vpycj4kv07np6ldm8czpgyziwqv9xqm"))))
(build-system cmake-build-system)
(outputs '("out" ; library and command-line interface
"gui")) ; graphical user interface
@@ -112,8 +112,9 @@
(replace 'check
(lambda* (#:key tests? parallel-tests? #:allow-other-keys)
(if tests?
- ;; XXX this test fails...
- (invoke "ctest" "-E" "usesBootstrapFile"
+ (invoke "ctest"
+ ;; XXX this test fails...
+ "-E" "usesBootstrapFile"
"-j" (if parallel-tests?
(number->string (parallel-job-count))
"1"))
@@ -155,7 +156,7 @@
(native-inputs
(list intltool pkg-config))
(home-page "https://transmissionbt.com/")
- (synopsis "Fast and easy BitTorrent client")
+ (synopsis "BitTorrent client")
(description
"Transmission is a BitTorrent client that comes with graphical,
textual, and Web user interfaces. Transmission also has a daemon for
diff --git a/gnu/packages/browser-extensions.scm b/gnu/packages/browser-extensions.scm
index 252c95729d..8ae6fbf497 100644
--- a/gnu/packages/browser-extensions.scm
+++ b/gnu/packages/browser-extensions.scm
@@ -28,6 +28,7 @@
#:use-module (gnu build chromium-extension)
#:use-module (gnu build icecat-extension)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages password-utils)
#:use-module (gnu packages python))
(define play-to-kodi
@@ -150,3 +151,73 @@ ungoogled-chromium.")
(define-public ublock-origin/icecat
(make-icecat-extension ublock-origin "firefox"))
+
+(define-public passff-host
+ (package
+ (name "passff-host")
+ (version "1.2.3")
+ (home-page "https://github.com/passff/passff-host")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1p18l1jh20x4v8dj64z9qjlp96fxsl5h069iynxfpbkzj6hd74yl"))))
+ (build-system copy-build-system)
+ (arguments
+ (let ((native-manifests "lib/icecat/native-messaging-hosts"))
+ (list
+ #:install-plan
+ `'(("src" ,native-manifests #:include ("passff.json" "passff.py")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'substitute
+ (lambda _
+ (substitute* "src/passff.json"
+ (("PLACEHOLDER")
+ (format #f "~a/~a/passff.py" #$output #$native-manifests)))
+ (substitute* "src/passff.py"
+ (("_VERSIONHOLDER_") #$version)
+ (("^COMMAND = .*")
+ (format #f "COMMAND = \"~a/bin/pass\"~%"
+ #$(this-package-input "password-store"))))
+ (patch-shebang "src/passff.py")))))))
+ (inputs (list password-store python))
+ (synopsis "Host app for the WebExtension PassFF")
+ (description "This piece of software wraps around the zx2c4 pass shell
+command. It has to be installed for the PassFF browser extension to work
+properly.")
+ (license license:gpl2+)))
+
+(define passff
+ (package
+ (name "passff")
+ (version "1.15")
+ (home-page "https://github.com/passff/passff")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gymqyqppr8k9fqv5js7f6pk6hcc47qpf51x5cy6aahsk2v1qssj"))))
+ (propagated-inputs (list passff-host))
+ (build-system copy-build-system)
+ (properties '((addon-id . "passff@invicem.pro")))
+ (arguments
+ `(#:install-plan '(("src" ,(assq-ref properties 'addon-id)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'substitute-placeholder
+ (lambda _
+ (substitute* "src/manifest.json"
+ (("_VERSIONHOLDER_") ,version)))))))
+ (synopsis "zx2c4 pass management extension for Mozilla Firefox")
+ (description "This extension will allow you to access your zx2c4 pass
+repository directly from your web browser. You can choose to automatically
+fill and submit login forms if a matching password entry is found.")
+ (license license:gpl2+)))
+
+(define-public passff/icecat
+ (make-icecat-extension passff))
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index e0bf59b616..1fa5818b6d 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -59,11 +59,11 @@
#:use-module ((guix search-paths) #:select ($SSL_CERT_DIR)))
(define-public cuirass
- (let ((commit "db6b63371159a735de74eee97c313740c998439a")
- (revision "20"))
+ (let ((commit "eb3f539dc95de705c89b07258efe4663e76f7dab")
+ (revision "0"))
(package
(name "cuirass")
- (version (git-version "1.1.0" revision commit))
+ (version "1.2.0")
(source
(origin
(method git-fetch)
@@ -73,7 +73,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "16d9ylzk8mwsgppfdxyl0k2mkwll7fq17d6v09406rqkgddxg3m2"))))
+ "0rvzcsm0zwwv8rb5z0jdgc7adzzx0cin9n2hhclp5d0kqn582hny"))))
(build-system gnu-build-system)
(arguments
(list #:modules `((guix build utils)
diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm
index bc14286070..1592703f8d 100644
--- a/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@ -263,6 +263,7 @@ and workspaces that can be used in the compiler environment of your choice.")
(package
(inherit cmake-bootstrap)
(name "cmake-minimal")
+ (properties (alist-delete 'hidden? (package-properties cmake-bootstrap)))
(source (origin
(inherit (package-source cmake-bootstrap))
;; Purge CMakes bundled dependencies as they are no longer needed.
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index d89fcaeb1e..0ce60c49de 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1112,6 +1112,10 @@ portable applications targeting all major HPC platforms. For that purpose it
provides abstractions for both parallel execution of code and data management.
Kokkos is designed to target complex node architectures with N-level memory
hierarchies and multiple types of execution resources.")
+
+ ;; Code exhibits integer size mismatches when compiled on 32-bit systems.
+ (supported-systems %64bit-supported-systems)
+
(license license:asl2.0))) ; With LLVM exception
(define-public tweeny
@@ -1250,12 +1254,25 @@ Google's C++ code base.")
(number->string version))
#$flags))))))))
+(define (make-static-abseil-cpp version)
+ (let ((base abseil-cpp))
+ (hidden-package
+ (package/inherit base
+ (arguments
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:configure-flags flags)
+ #~(cons* "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
+ (delete "-DBUILD_SHARED_LIBS=ON" #$flags)))))))))
+
(define-public abseil-cpp-cxxstd17
(abseil-cpp-for-c++-standard 17)) ;XXX: the default with GCC 11?
(define-public abseil-cpp-cxxstd11
(abseil-cpp-for-c++-standard 11))
+(define-public static-abseil-cpp
+ (make-static-abseil-cpp abseil-cpp))
+
(define-public pegtl
(package
(name "pegtl")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de31f44dbd..1a5189cbca 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -305,6 +305,30 @@ are included as well.")
;; Any version of the GPL.
(license license:gpl3+)))
+(define-public r-celestial
+ (package
+ (name "r-celestial")
+ (version "1.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "celestial" version))
+ (sha256
+ (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z"))))
+ (properties `((upstream-name . "celestial")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-nistunits r-pracma r-rann))
+ (home-page "https://cran.r-project.org/package=celestial")
+ (synopsis
+ "Collection of common astronomical conversion routines and functions")
+ (description
+ "This package contains a number of common astronomy conversion routines,
+particularly the HMS and degrees schemes, which can be fiddly to convert between
+on mass due to the textural nature of the former. It allows users to coordinate
+match datasets quickly. It also contains functions for various cosmological
+calculations.")
+ (license license:gpl3)))
+
;; The package sources include multiple non-minified JavaScript files and the
;; v5.1.0 variant of d3.js. The d3.js file is not minified.
(define-public r-chromomap
@@ -341,6 +365,61 @@ Shiny applications.")
(license (list license:gpl3
license:isc)))) ;for bundled d3js
+(define-public r-consort
+ (package
+ (name "r-consort")
+ (version "1.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "consort" version))
+ (sha256
+ (base32
+ "03xkypy4r84mdif6m331c27haxnyi1s87vvj2f83xxw0m0s5im5j"))))
+ (properties `((upstream-name . "consort")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/adayim/consort/")
+ (synopsis "Create Consort Diagrams")
+ (description
+ "To make it easy to create CONSORT diagrams for the transparent reporting of
+participant allocation in randomized, controlled clinical trials. This is done
+by creating a standardized disposition data, and using this data as the source
+for the creation a standard CONSORT diagram. Human effort by supplying text
+labels on the node can also be achieved.")
+ (license license:expat)))
+
+(define-public r-collapse
+ (package
+ (name "r-collapse")
+ (version "2.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "collapse" version))
+ (sha256
+ (base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v"))))
+ (properties `((upstream-name . "collapse")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rcpp))
+ (native-inputs (list r-knitr))
+ (home-page "https://sebkrantz.github.io/collapse/")
+ (synopsis "Advanced and fast data transformation")
+ (description
+ "This is a C/C++ based package for advanced data transformation and
+statistical computing in R that is extremely fast, class-agnostic, robust and
+programmer friendly. Core functionality includes a rich set of S3 generic
+grouped and weighted statistical functions for vectors, matrices and data
+frames, which provide efficient low-level vectorizations, @code{OpenMP}
+multithreading, and skip missing values by default. These are integrated with
+fast grouping and ordering algorithms (also callable from C), and efficient
+data manipulation functions. The package also provides a flexible and
+rigorous approach to time series and panel data in R. It further includes
+fast functions for common statistical procedures, detailed (grouped, weighted)
+summary statistics, powerful tools to work with nested data, fast data object
+conversions, functions for memory efficient R programming, and helpers to
+effectively deal with variable labels, attributes, and missing data.")
+ (license (list license:gpl2+))))
+
(define-public r-collections
(package
(name "r-collections")
@@ -777,6 +856,64 @@ dumbbell charts, the ability to encircle points and coordinate-system-based
text annotations.")
(license license:agpl3)))
+(define-public r-ggbreak
+ (package
+ (name "r-ggbreak")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggbreak" version))
+ (sha256
+ (base32 "14rx16v66xd0fjlywi89dq9dbw41zn7hpq14wgvf0178cxdp2fw4"))))
+ (properties `((upstream-name . "ggbreak")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-aplot r-ggfun r-ggplot2 r-ggplotify r-rlang))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/YuLab-SMU/ggbreak")
+ (synopsis "Set axis break for ggplot2")
+ (description
+ "This package provides an implementation of scale functions for setting
+axis breaks of a ggplot.")
+ (license license:artistic2.0)))
+
+(define-public r-ggdist
+ (package
+ (name "r-ggdist")
+ (version "3.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggdist" version))
+ (sha256
+ (base32 "0b15b972wrllsvqqn0nc2c81fd9jl618fvqsfi50hjxwwpdach8l"))))
+ (properties `((upstream-name . "ggdist")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cli
+ r-distributional
+ r-dplyr
+ r-ggplot2
+ r-glue
+ r-numderiv
+ r-quadprog
+ r-rlang
+ r-scales
+ r-tibble
+ r-tidyselect
+ r-vctrs
+ r-withr))
+ (native-inputs (list r-knitr))
+ (home-page "https://mjskay.github.io/ggdist/")
+ (synopsis "Visualizations of distributions and uncertainty")
+ (description
+ "This package provides primitives for visualizing distributions using
+ggplot2 that are particularly tuned for visualizing uncertainty in either a
+frequentist or Bayesian mode. Both analytical distributions (such as
+frequentist confidence distributions or Bayesian priors) and distributions
+represented as samples (such as bootstrap distributions or Bayesian posterior
+samples) are easily visualized.")
+ (license license:gpl3+)))
+
(define-public r-ggfittext
(package
(name "r-ggfittext")
@@ -1242,6 +1379,37 @@ engines that convert R Markdown into HTML pages. Various themes and syntax
highlight styles are supported.")
(license license:asl2.0)))
+(define-public r-profmem
+ (package
+ (name "r-profmem")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "profmem" version))
+ (sha256
+ (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l"))))
+ (properties `((upstream-name . "profmem")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-before 'install 'set-HOME
+ (lambda _
+ ;; Needed for building vignettes
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list r-r-rsp r-markdown)) ;for vignettes
+ (home-page "https://github.com/HenrikBengtsson/profmem")
+ (synopsis "Simple memory profiling for R")
+ (description
+ "This package provides a simple and light-weight API for memory profiling
+of R expressions. The profiling is built on top of R's built-in memory
+profiler @code{utils::Rprofmem()}, which records every memory allocation done
+by R (also native code).")
+ (license license:lgpl2.1+)))
+
(define-public r-proj4
(package
(name "r-proj4")
@@ -1425,6 +1593,26 @@ Singularity containers. You can execute a command inside a container, mount a
volume or copy a file.")
(license license:expat)))
+(define-public r-bench
+ (package
+ (name "r-bench")
+ (version "1.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bench" version))
+ (sha256
+ (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz"))))
+ (properties `((upstream-name . "bench")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble))
+ (home-page "https://bench.r-lib.org/")
+ (synopsis "High precision timing of R expressions")
+ (description
+ "This package provides tools to accurately benchmark and analyze execution
+times for R expressions.")
+ (license license:expat)))
+
(define-public r-benchmarkmedata
(package
(name "r-benchmarkmedata")
@@ -1561,13 +1749,13 @@ larger than memory.")
(define-public r-bwstest
(package
(name "r-bwstest")
- (version "0.2.2")
+ (version "0.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "BWStest" version))
(sha256
- (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
+ (base32 "1chlszmshda84000jj4q5j2swflj512vfj3h97361aphzhkwri2b"))))
(properties `((upstream-name . "BWStest")))
(build-system r-build-system)
(propagated-inputs (list r-memoise r-rcpp))
@@ -1584,14 +1772,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser
(define-public r-v8
(package
(name "r-v8")
- (version "4.3.3")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "V8" version))
(sha256
(base32
- "04x2dph917dwq6ja69yiizw808zwmm17v78j17mlksdnl6wcmm0c"))))
+ "0ilg9ihx1mp9zj8023rh3lj875vqy253v9gbn1bw61h2p47w4nv3"))))
(properties
`((upstream-name . "V8")
(updater-extra-inputs . ("libnode"))))
@@ -2844,13 +3032,13 @@ excellent candidate for labeling of a polygon.")
(define-public r-poorman
(package
(name "r-poorman")
- (version "0.2.6")
+ (version "0.2.7")
(source (origin
(method url-fetch)
(uri (cran-uri "poorman" version))
(sha256
(base32
- "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij"))))
+ "1amlcbgfnm6yh7lmlzhs7aalv4mdm2ir3s2kpx33ppnz7hlii508"))))
(properties `((upstream-name . "poorman")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -2990,6 +3178,27 @@ functions, including @code{sort}, @code{order}, and @code{match}. The
functions are simplified but can be faster or have other advantages.")
(license license:gpl3)))
+(define-public r-matrixtests
+ (package
+ (name "r-matrixtests")
+ (version "0.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "matrixTests" version))
+ (sha256
+ (base32 "0d7i00cxzszfdnjm8q5b72ildic8nig6fbw7rba6acdnllpp7sza"))))
+ (properties `((upstream-name . "matrixTests")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-matrixstats))
+ (home-page "https://github.com/karoliskoncevicius/matrixTests")
+ (synopsis "Statistical hypothesis tests on rows and columns of matrices")
+ (description
+ "This package offers quick statistical hypothesis testing for matrix
+rows/columns. The main goals are speed through vectorization, detailed and
+user-friendly output, and compatibility with tests implemented in R.")
+ (license license:gpl2)))
+
(define-public r-matrix-utils
(package
(name "r-matrix-utils")
@@ -3432,6 +3641,27 @@ convenience functions useful for using CSS selectors on XML nodes. This
package is a port of the Python package @code{cssselect}.")
(license license:bsd-3)))
+(define-public r-relations
+ (package
+ (name "r-relations")
+ (version "0.6-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "relations" version))
+ (sha256
+ (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq"))))
+ (properties `((upstream-name . "relations")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cluster r-sets r-slam))
+ (home-page "https://cran.r-project.org/package=relations")
+ (synopsis "Data structures and algorithms for relations")
+ (description
+ "This package provides data structures and algorithms for k-ary relations
+with arbitrary domains, featuring relational algebra, predicate functions, and
+fitters for consensus relations.")
+ (license license:gpl2)))
+
(define-public r-repmis
(package
(name "r-repmis")
@@ -3546,6 +3776,27 @@ without affecting the current R process at all. This package does exactly
that.")
(license license:expat)))
+(define-public r-deming
+ (package
+ (name "r-deming")
+ (version "1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "deming" version))
+ (sha256
+ (base32 "1yx3qrbik6jpqgsi0gqgc7y2cra13qlisg2gq8rvnv57nvcvb421"))))
+ (properties `((upstream-name . "deming")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-boot))
+ (home-page "https://cran.r-project.org/package=deming")
+ (synopsis
+ "Deming, Theil-Sen, Passing-Bablock and Total Least Squares regression")
+ (description
+ "This package implements generalized Deming regression, Theil-Sen
+regression and Passing-Bablock regression functions.")
+ (license license:lgpl2.0+)))
+
(define-public r-depmixs4
(package
(name "r-depmixs4")
@@ -3775,40 +4026,24 @@ Zucchini.")
(define-public r-httpuv
(package
(name "r-httpuv")
- (version "1.6.11")
+ (version "1.6.12")
(source (origin
(method url-fetch)
(uri (cran-uri "httpuv" version))
(sha256
(base32
- "1xgf7q8ah9sbgbbjm9nwvry154g8i0gwfrn55npls9sihc59x9wb"))
+ "0x2y5yjj1ha99dv5c8j6pxm8fqhdcx010jl4rcw2qw20qaqp5ndi"))
(modules '((guix build utils)))
;; Cannot unbundle http-parser, because it contains local
;; modifications.
(snippet
'(delete-file-recursively "src/libuv"))))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'unbundle-libuv
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* "src/Makevars"
- (("PKG_LIBS = ./libuv/.libs/libuv.a")
- "PKG_LIBS = -luv")
- (("\\$\\(SHLIB\\): libuv/.libs/libuv.a")
- "$(SHLIB): "))
- (substitute* (find-files "src" "\\.cpp$|\\.h$")
- (("\"libuv/include/uv\\.h\"")
- "<uv.h>"))
- ;; Fix https://github.com/rstudio/httpuv/issues/282
- (substitute* "src/http.cpp"
- (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
- "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
(inputs
(list libuv-for-r-httpuv zlib))
(propagated-inputs
(list r-later r-promises r-r6 r-rcpp))
+ (native-inputs (list pkg-config))
(home-page "https://github.com/rstudio/httpuv")
(synopsis "HTTP and WebSocket server library for R")
(description
@@ -4015,15 +4250,31 @@ applications.")
(define-public r-htmltable
(package
(name "r-htmltable")
- (version "2.4.1")
+ (version "2.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "htmlTable" version))
(sha256
- (base32 "14qg65nw0bpikqs1hb1x7apzdzrnnl3ykjnks67kkp46v1skwzrs"))))
+ (base32 "039nnxnvw5l284n7w8q0hnplm0b58nwhsrpjfi5asg61f9hxv0va"))))
(properties `((upstream-name . "htmlTable")))
(build-system r-build-system)
+ (arguments
+ (list
+ #:modules
+ '((guix build r-build-system)
+ (guix build minify-build-system)
+ (guix build utils))
+ #:imported-modules
+ `(,@%r-build-system-modules
+ (guix build minify-build-system))
+ #:phases
+ #~(modify-phases (@ (guix build r-build-system) %standard-phases)
+ (add-after 'unpack 'replace-bundled-minified-JavaScript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (minify (assoc-ref inputs "js-jquery")
+ #:target
+ "inst/htmlwidgets/lib/jquery/jquery.min.js"))))))
(propagated-inputs
(list r-checkmate
r-htmltools
@@ -4033,7 +4284,15 @@ applications.")
r-rstudioapi
r-stringr))
(native-inputs
- (list r-knitr))
+ `(("esbuild" ,esbuild)
+ ("js-jquery"
+ ,(origin
+ (method url-fetch)
+ (uri "https://code.jquery.com/jquery-3.7.1.js")
+ (sha256
+ (base32
+ "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q"))))
+ ("r-knitr" ,r-knitr)))
(home-page "http://gforge.se/packages/")
(synopsis "Advanced tables for Markdown/HTML")
(description
@@ -4296,13 +4555,13 @@ jQuery.")
(define-public r-jqr
(package
(name "r-jqr")
- (version "1.3.0")
+ (version "1.3.1")
(source (origin
(method url-fetch)
(uri (cran-uri "jqr" version))
(sha256
(base32
- "0gys1b2fiafmm49mkj9iazziwql87s52rjx093ahn8g3v79amirh"))))
+ "0dlz9wwkgz06mnnmwaq4pr68x7zywp2iczfw0bjpzrgpbzkn2972"))))
(properties `((upstream-name . "jqr")))
(build-system r-build-system)
(inputs (list jq))
@@ -4985,13 +5244,13 @@ in a ggplot2 plot.")
(define-public r-mbess
(package
(name "r-mbess")
- (version "4.9.2")
+ (version "4.9.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "MBESS" version))
(sha256
- (base32 "0cq4z7nx361rcw42jflrrdjbqs2q5973dlvhcr7i2wbkj3gzkwla"))))
+ (base32 "05ph8dwigwn0c4qg8smqhsjijvsvfawbzvm74mqpasi8qifz8nd3"))))
(properties `((upstream-name . "MBESS")))
(build-system r-build-system)
(propagated-inputs
@@ -5974,14 +6233,14 @@ functions and compiled functions callable by other packages.")
(define-public r-rcppthread
(package
(name "r-rcppthread")
- (version "2.1.5")
+ (version "2.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppThread" version))
(sha256
(base32
- "0rra7qqbq2y4bj54x76559p5ghpj3r03c4vlpg96phwafwnc2y8m"))))
+ "1997ka0dd36d79fb4crqq0ar3bgzdv4mw5hd6v2pmq7555g0qiz9"))))
(properties `((upstream-name . "RcppThread")))
(build-system r-build-system)
(native-inputs (list r-r-rsp))
@@ -6713,13 +6972,13 @@ most popular ones.")
(define-public r-sp
(package
(name "r-sp")
- (version "2.1-0")
+ (version "2.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sp" version))
(sha256
- (base32 "03041jp74z7l5vs1yzp145w331940kj9gf52jaxdninknikhc0vk"))))
+ (base32 "0ns0n4929db2g8wjmg8nscq286df4hxrv7gr4mj8giymm3icsd1d"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice))
@@ -6738,13 +6997,13 @@ print, summary, etc.")
(define-public r-lambertw
(package
(name "r-lambertw")
- (version "0.6.8")
+ (version "0.6.9")
(source (origin
(method url-fetch)
(uri (cran-uri "LambertW" version))
(sha256
(base32
- "10lqsz44ndm8pl8z75j35fzd1s313q09rs9bs3lkym8d43k50pha"))))
+ "0260sa4w5i4vwxg13g3q0dmairsrbyaijr2gxlppy09nxriccwbr"))))
(properties `((upstream-name . "LambertW")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2
@@ -7589,13 +7848,13 @@ variable models.")
(define-public r-drat
(package
(name "r-drat")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "drat" version))
(sha256
- (base32 "191yxlj9jccakmz27g7n9izfcy19kj3fgnw4w6zl9iq66787qpm6"))))
+ (base32 "13v7dj2688ix6j9nzhvf8q9ynfihwzkppfdjkis6q1r5m4nikya3"))))
(properties `((upstream-name . "drat")))
(build-system r-build-system)
(native-inputs (list r-simplermarkdown))
@@ -7753,6 +8012,33 @@ a variety of functions for the manipulation and analysis of arbitrarily
dimensioned arrays.")
(license license:gpl2)))
+(define-public r-magicaxis
+ (package
+ (name "r-magicaxis")
+ (version "2.2.14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "magicaxis" version))
+ (sha256
+ (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v"))))
+ (properties `((upstream-name . "magicaxis")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-celestial
+ r-mapproj
+ r-mass
+ r-plotrix
+ r-rann
+ r-sm))
+ (home-page "https://cran.r-project.org/package=magicaxis")
+ (synopsis "Scientific plotting with minor-tick and log minor-tick support")
+ (description
+ "This package provides functions to make useful (and pretty) plots for
+scientific plotting. Additional plotting features are added for base plotting,
+with particular emphasis on making attractive log axis plots.")
+ (license license:gpl3)))
+
(define-public r-rmysql
(package
(name "r-rmysql")
@@ -7830,25 +8116,25 @@ to access PostgreSQL database systems.")
(define-public r-rpostgres
(package
(name "r-rpostgres")
- (version "1.4.5")
+ (version "1.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "RPostgres" version))
(sha256
(base32
- "15y732ylnq1h1hw16nh1ichnygh3l76h23m2893avpaipa689zvh"))))
+ "1ld03r9rzfxx6gzy3yn8jhzp9sp2qd9wydpxz955ggjxwdklpvnr"))))
(properties `((upstream-name . "RPostgres")))
(build-system r-build-system)
(inputs (list postgresql))
(propagated-inputs
(list r-bit64
r-blob
+ r-cpp11
r-dbi
r-hms
r-lubridate
r-plogr
- r-rcpp
r-withr))
(native-inputs
(list pkg-config r-knitr))
@@ -8181,14 +8467,14 @@ for certain use cases.")
(define-public r-ggrepel
(package
(name "r-ggrepel")
- (version "0.9.3")
+ (version "0.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggrepel" version))
(sha256
(base32
- "0p00kb1x3q0krk5g8mmwqknnjlsznqs4i7mlfq1dp17fxpia1sxr"))))
+ "0gngsx87rcqijdr684bgpnazdlz3vj4brzw0fic0jdsrf1rb9aw1"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-rcpp r-rlang r-scales r-withr))
@@ -8463,13 +8749,13 @@ distances.")
(define-public r-useful
(package
(name "r-useful")
- (version "1.2.6")
+ (version "1.2.6.1")
(source (origin
(method url-fetch)
(uri (cran-uri "useful" version))
(sha256
(base32
- "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
+ "1gb9hqvbm6pr56dfqlsgz26lan7xargfsm8jpdja18mpgli2gyvc"))))
(properties `((upstream-name . "useful")))
(build-system r-build-system)
(propagated-inputs
@@ -9229,13 +9515,13 @@ script.")
(define-public r-aricode
(package
(name "r-aricode")
- (version "1.0.2")
+ (version "1.0.3")
(source (origin
(method url-fetch)
(uri (cran-uri "aricode" version))
(sha256
(base32
- "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz"))))
+ "02nrw66jfpzf6dy0zy21sbdjxjc8c11iv9fkjqj5akzb7wskk9qh"))))
(properties `((upstream-name . "aricode")))
(build-system r-build-system)
(propagated-inputs (list r-matrix r-rcpp))
@@ -9520,14 +9806,14 @@ packages maintained by Yihui Xie.")
(define-public r-utf8
(package
(name "r-utf8")
- (version "1.2.3")
+ (version "1.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "utf8" version))
(sha256
(base32
- "0iv3ppy7sddzl4sm3qlghpc64k6zx5j0jzcia8xx8jhzb638da60"))))
+ "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1"))))
(build-system r-build-system)
(native-inputs
(list r-knitr r-rmarkdown)) ; for vignettes
@@ -9585,14 +9871,14 @@ estimated from a given sample.")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.6.3")
+ (version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "1hm5rw85ln0mk1mfmhgygnhjgs2lyc74cq12ddc41d78rl6j5p4k"))))
+ "1j01s27ybzn60p17y7k5n5dzsmjqhgjy634sv0dx4977aqiik04a"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-rlang))
@@ -9713,14 +9999,14 @@ their own grammars and easily expose them in R packages.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.47")
+ (version "0.48")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "1py5i4h2vpicl79ypxw061p9byxvj703z1rh8l2shfpq7wqwhxbr"))))
+ "15bnb4fxdzapgj9ws3rfbcxwdzwbq8h5yy4d1db0m9c1lygrh2qx"))))
(build-system r-build-system)
(propagated-inputs
(list r-xfun))
@@ -9795,6 +10081,43 @@ implementation of an approximate nearest neighbor search using hierarchical
@acronym{NSW, Navigable Small World} graphs.")
(license license:asl2.0)))
+(define-public r-nestedcv
+ (package
+ (name "r-nestedcv")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "nestedcv" version))
+ (sha256
+ (base32 "0jpg4il1niyizfq8kkk391x7anhp2s38mrfypa86skr08ca46zss"))))
+ (properties `((upstream-name . "nestedcv")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-caret
+ r-data-table
+ r-doparallel
+ r-foreach
+ r-ggplot2
+ r-glmnet
+ r-matrixstats
+ r-matrixtests
+ r-proc
+ r-rfast
+ r-rlang))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/myles-lewis/nestedcv")
+ (synopsis "Nested cross-validation with glmnet and caret")
+ (description
+ "This package implements nested cross-validation applied to the
+@code{glmnet} and @code{caret} packages. With glmnet this includes
+cross-validation of elastic net alpha parameter. A number of feature
+selection filter functions (t-test, Wilcoxon test, ANOVA, Pearson/Spearman
+correlation, random forest, ReliefF) for feature selection are provided and
+can be embedded within the outer loop of the nested CV. Nested CV can be also
+be performed with the @code{caret} package giving access to the large number
+of prediction methods available in @code{caret}.")
+ (license license:expat)))
+
(define-public r-network
(package
(name "r-network")
@@ -9817,6 +10140,27 @@ implementation of an approximate nearest neighbor search using hierarchical
supports arbitrary vertex/edge/graph attributes.")
(license license:gpl2+)))
+(define-public r-nistunits
+ (package
+ (name "r-nistunits")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NISTunits" version))
+ (sha256
+ (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a"))))
+ (properties `((upstream-name . "NISTunits")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/package=NISTunits")
+ (synopsis "Fundamental physical constants and unit conversions")
+ (description
+ "This package provides fundamental physical constants (quantity, value,
+uncertainty, unit) for @acronym{SI, International System of Units} and non-SI
+units, plus unit conversions based on the data from @acronym{NIST, National
+Institute of Standards and Technology}, USA.")
+ (license license:gpl3+)))
+
(define-public r-stabs
(package
(name "r-stabs")
@@ -9983,15 +10327,16 @@ rules with R.")
(define-public r-leaflet-providers
(package
(name "r-leaflet-providers")
- (version "1.13.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "leaflet.providers" version))
(sha256
- (base32 "1jrfhqmr735maa0mr3ia7441vzd3q95msgicclzdpglmk4aqhhhh"))))
+ (base32 "0rl69bfx2l10x80rl8cppqch3fnd05sk9w29h8589jc8h3ffmkn5"))))
(properties `((upstream-name . "leaflet.providers")))
(build-system r-build-system)
+ (propagated-inputs (list r-htmltools))
(home-page "https://github.com/rstudio/leaflet.providers")
(synopsis "Leaflet map tile providers")
(description
@@ -10532,14 +10877,14 @@ interface.")
(define-public r-trend
(package
(name "r-trend")
- (version "1.1.5")
+ (version "1.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "trend" version))
(sha256
(base32
- "12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66"))))
+ "0991fp6kjk704rfg0l1m7kwbck9fj1rg27zy4llm5ikczd55w05h"))))
(build-system r-build-system)
(propagated-inputs
(list r-extradistr))
@@ -11048,14 +11393,14 @@ local smoothers and many more.")
(define-public r-radiant-data
(package
(name "r-radiant-data")
- (version "1.6.1")
+ (version "1.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "radiant.data" version))
(sha256
(base32
- "00bjq3zpxhd6yjq3jwizgiyzp2qf557ms6mhlz74d0wcm0l3vd72"))
+ "0227ry366v9kmksa4vyjmhix0jbl894gdc6gckg209wna35fn20p"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -12475,14 +12820,14 @@ always locate the files relative to your project root.")
(define-public r-reticulate
(package
(name "r-reticulate")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "reticulate" version))
(sha256
(base32
- "0r9rycwin4yv5k2n1lzybwblb8529yhw5xnl46if6yvxm3bcra9s"))))
+ "01j2dr93r5a18irwbm6hlh2v0s2rc5bl6dcmds1m64c1rli8j3cd"))))
(build-system r-build-system)
(arguments
(list
@@ -12790,14 +13135,14 @@ clustering.")
(define-public r-factominer
(package
(name "r-factominer")
- (version "2.8")
+ (version "2.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
- "0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460"))))
+ "0c2j3xid85qffsdjwndqiwihclzw6k1nkbpzcc7whhd6k79rh9l8"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@@ -12863,6 +13208,30 @@ packages. It contains also functions for simplifying some clustering analysis
steps and provides ggplot2-based elegant data visualization.")
(license license:gpl2)))
+(define-public r-fancova
+ (package
+ (name "r-fancova")
+ (version "0.6-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fANCOVA" version))
+ (sha256
+ (base32 "04mw0blgpwdk6wdg8llrig43psgc0vb42cbimvzbnym8v503dsn3"))))
+ (properties `((upstream-name . "fANCOVA")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/package=fANCOVA")
+ (synopsis "Nonparametric analysis of covariance")
+ (description
+ "This package provides a collection of R functions to perform
+nonparametric analysis of covariance for regression curves or surfaces.
+Testing the equality or parallelism of nonparametric curves or surfaces is
+equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA)
+for one-sample functional data. Three different testing methods are available
+in the package, including one based on L-2 distance, one based on an ANOVA
+statistic, and one based on variance estimators.")
+ (license license:gpl3)))
+
(define-public r-fansi
(package
(name "r-fansi")
@@ -13086,14 +13455,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
(define-public r-rbibutils
(package
(name "r-rbibutils")
- (version "2.2.15")
+ (version "2.2.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "rbibutils" version))
(sha256
(base32
- "1kjk953xqakbxb2z8rcfcni8b9vi1m27n0ksdddil6x7q03flxb5"))))
+ "1brab8vzzf44d9rpp9k3r2ajvrs09cbwf4ak014iffzn8yx0yz4w"))))
(properties `((upstream-name . "rbibutils")))
(build-system r-build-system)
(home-page "https://geobosh.github.io/rbibutils/")
@@ -13134,14 +13503,14 @@ references and Rd files.")
(define-public r-officer
(package
(name "r-officer")
- (version "0.6.2")
+ (version "0.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
- "0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09"))))
+ "0z3phawwxj4h1pwzw8lsl6pnypr77b329mg6r2qnzmj0j81585z5"))))
(build-system r-build-system)
(propagated-inputs
(list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip))
@@ -13371,14 +13740,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.19.5")
+ (version "0.19.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "0794p9dbclj1d7fcka6sqm8jzqsc58hxmmsksd3hmzv0qz49yhkg"))))
+ "1gnxhszwccmvjarq47p7s09jrkhvd8zkz632ysxz6dgxfpqn9zqh"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -13530,14 +13899,14 @@ functions.")
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.9.3")
+ (version "0.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "1jdikfiswxi63vj9xr9a24p8fv50h91pvhv3xllgwwfbs1wqyq4x"))))
+ "1dlsag1y3s7d5lp1dh2kxf1qax4r9xvxycpmxl64gkr50dk13bam"))))
(build-system r-build-system)
(propagated-inputs
(list r-data-table
@@ -13608,16 +13977,16 @@ contains or can be specified by the user.")
(define-public r-wrs2
(package
(name "r-wrs2")
- (version "1.1-4")
+ (version "1.1-5")
(source (origin
(method url-fetch)
(uri (cran-uri "WRS2" version))
(sha256
(base32
- "1838wy59cqd65s0bw6c24xcvx7zflypqcbgs35l9s2fj87vw2hdc"))))
+ "028xs424m879siaf3rrhzl1dacp9j7wcl5fpikyx2n0cc7anq4vq"))))
(properties `((upstream-name . "WRS2")))
(build-system r-build-system)
- (propagated-inputs (list r-mass r-mc2d r-plyr r-reshape))
+ (propagated-inputs (list r-mass r-plyr r-reshape))
(native-inputs (list r-knitr))
(home-page "https://r-forge.r-project.org/projects/psychor/")
(synopsis "Collection of robust statistical methods")
@@ -14161,14 +14530,14 @@ from the @code{stats} package (plus some extra parameters).")
(define-public r-cmplot
(package
(name "r-cmplot")
- (version "4.4.1")
+ (version "4.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "CMplot" version))
(sha256
(base32
- "1y6fs3b7jps4ah0lpniq0ip3x426acql1aibx95pvfykgc2b2hvm"))))
+ "0mkjpmwpd0izczp8jgfcfxw9i4qv82aj1xyhzsxgdxnjdd7ark66"))))
(properties `((upstream-name . "CMplot")))
(build-system r-build-system)
(home-page "https://github.com/YinLiLin/CMplot")
@@ -14186,14 +14555,14 @@ visualization and candidate genes around SNPs.")
(define-public r-precrec
(package
(name "r-precrec")
- (version "0.14.2")
+ (version "0.14.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "precrec" version))
(sha256
(base32
- "159vxdnp7vi6na3cji1rbsr1311ciqn1aldg0nwnd6sb3hgb14w2"))))
+ "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8"))))
(properties `((upstream-name . "precrec")))
(build-system r-build-system)
(propagated-inputs
@@ -14737,14 +15106,14 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
- (version "3.6-23")
+ (version "3.6-26")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "0ng18sfw9kmhi48j8b5bzgh2ylvf5wi2zidn66k4vqaxl5s6hidz"))))
+ "14jmpm6rlhya192ckyjlwhais6fgc16gb600wycsdba6b8i7fmy6"))))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp r-sp r-terra))
@@ -15373,14 +15742,14 @@ samples is large and the number of mixture components is not too large.")
(define-public r-magick
(package
(name "r-magick")
- (version "2.8.0")
+ (version "2.8.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
- "1al1apw9vgdl6ccm4nnpqpnya0pi2cfp62xii7dwnv7pd47m8fp8"))))
+ "13j55dwvcqbyqgx0c6vj9knqrz25pc2xz19f22b2gm0p307d3z6q"))))
(properties
'((updater-extra-inputs . ("imagemagick"))))
(build-system r-build-system)
@@ -15521,13 +15890,13 @@ were influenced by the drake R package by Will Landau (2018)
(define-public r-targets
(package
(name "r-targets")
- (version "1.3.0")
+ (version "1.3.2")
(source (origin
(method url-fetch)
(uri (cran-uri "targets" version))
(sha256
(base32
- "146ylh76sc5vzfgh2xp5mfpgdxvm3j9b2hzh0wqgih6d9d11n8pk"))))
+ "0zlbq658zxflz2fk9pksbjx3r5dmay4411byl33gkp3rnynvchgh"))))
(properties `((upstream-name . "targets")))
(build-system r-build-system)
(propagated-inputs (list r-base64url
@@ -15697,13 +16066,13 @@ estimation problem.")
(define-public r-quickjsr
(package
(name "r-quickjsr")
- (version "1.0.6")
+ (version "1.0.7")
(source (origin
(method url-fetch)
(uri (cran-uri "QuickJSR" version))
(sha256
(base32
- "1n09jivw1qvsniyap0ki5ablvkwgggh981hcs7k5wx3lp3qxxlnk"))))
+ "14wq7qymzrdbg3mhm4gk3vx1dr4yx8di8i2b10as4knnzr1w4q9i"))))
(properties `((upstream-name . "QuickJSR")))
(build-system r-build-system)
(propagated-inputs (list r-jsonlite r-r6 r-rcpp))
@@ -15964,14 +16333,14 @@ the differences were not significantly different.")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.8.8")
+ (version "1.8.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "1v5svzcvkssf3ch10cbi0pdw2xkgdhn8i1d1cqjawwgzmq61c62j"))))
+ "1ipzs88inyif52rbifqwrfv8vwxw8fwq2hb489vgws8xznhz034a"))))
(build-system r-build-system)
(propagated-inputs
(list r-estimability r-mvtnorm r-numderiv))
@@ -16233,14 +16602,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.10.5")
+ (version "0.10.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "1bwcdz2iah6ya1p9ykbj5ybvzwlq9spv6mq3fn68cckymg0hs76r"))))
+ "0zvj0bzbqcy35jcg1s6b1wqbz7rbajzvjm74aks4j6iq4grh4d2j"))))
(build-system r-build-system)
(propagated-inputs
(list r-bayestestr r-datawizard r-insight))
@@ -16259,14 +16628,14 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "1.3.1")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "0cw9j08qqck1gbfqsfyl3nb4rgi5cwsydxazqw8ppfnjqzw3nwmp"))))
+ "1wp9q2zqygxg2ibmrwdh614sdxqhj80rx0ixbz8kxld99b37ixl7"))))
(build-system r-build-system)
(propagated-inputs
(list r-insight))
@@ -18876,13 +19245,13 @@ handling.")
(define-public r-gridpattern
(package
(name "r-gridpattern")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "gridpattern" version))
(sha256
- (base32 "19g8mnc5y68w9pybckmcvr56qkwbs5z9z6zhj0bxmlprwanq4f8x"))))
+ (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i"))))
(properties `((upstream-name . "gridpattern")))
(build-system r-build-system)
(propagated-inputs
@@ -18954,14 +19323,14 @@ PostScript pictures in R plots.")
(define-public r-grimport2
(package
(name "r-grimport2")
- (version "0.3-0")
+ (version "0.3-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "grImport2" version))
(sha256
(base32
- "04k71x2wm1wsgv5fnk8xip2q5brl9cnjp3fv2rs0kdq9jkhs6yhz"))))
+ "1lj58z6yc2p6ns27fkgh11ac90bcihi65hf62gxpsylcn5dilsi1"))))
(properties `((upstream-name . "grImport2")))
(build-system r-build-system)
(propagated-inputs
@@ -19780,14 +20149,14 @@ to throw errors if they aren't in the right form.")
(define-public r-dotcall64
(package
(name "r-dotcall64")
- (version "1.0-2")
+ (version "1.1-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "dotCall64" version))
(sha256
(base32
- "1b546z9r26q4xpr17gy2wzfych52q17sxvzydpqfp9dyxf575iz0"))))
+ "1ibh2f2vcv30k1c919diw6qdmhxmvkl83k3396vy3xigbcny711l"))))
(properties `((upstream-name . "dotCall64")))
(build-system r-build-system)
(native-inputs (list gfortran))
@@ -19804,18 +20173,18 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
(define-public r-spam
(package
(name "r-spam")
- (version "2.9-1")
+ (version "2.10-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spam" version))
(sha256
- (base32 "1nvx965vxzs697k9m2l40a15bykflksn9bwa4py1p2wqg6922bn3"))))
+ (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i"))))
(build-system r-build-system)
(propagated-inputs
- (list r-dotcall64))
+ (list r-dotcall64 r-rcpp))
(native-inputs
- (list gfortran r-knitr))
+ (list gfortran r-knitr r-r-rsp))
(home-page "https://www.math.uzh.ch/pages/spam/")
(synopsis "Sparse matrix algebra")
(description
@@ -22234,14 +22603,14 @@ tessellation.")
(define-public r-wk
(package
(name "r-wk")
- (version "0.8.0")
+ (version "0.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "wk" version))
(sha256
(base32
- "1300x3rfb4fk11mrxzs0vy6aj4nbsvd7zisvdxxhrdibmz38l1xa"))))
+ "1nmrgdp3swl34kr51hypm3azf8yhcalg5nngp70l56afsbaskyqh"))))
(properties `((upstream-name . "wk")))
(build-system r-build-system)
(home-page "https://paleolimbot.github.io/wk/")
@@ -22543,13 +22912,13 @@ either PDF/EPS files.")
(define-public r-polspline
(package
(name "r-polspline")
- (version "1.1.23")
+ (version "1.1.24")
(source
(origin
(method url-fetch)
(uri (cran-uri "polspline" version))
(sha256
- (base32 "1qa9j7s09yzi65fav27zxc1w1wxwsmgjz8a8ghy7hhi5f3gvsqw3"))))
+ (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6"))))
(build-system r-build-system)
(native-inputs (list gfortran))
(home-page "https://cran.r-project.org/web/packages/polspline/")
@@ -22810,13 +23179,13 @@ SELECT or UPDATE queries to an end-point.")
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.35")
+ (version "0.36")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "1fzzppwp2ri4jhl1j2122rhiniay34cccvxr559bypv5b38yjywd"))
+ "0c4pj5sg4cnz2b2kpxgr0wk1n1pf7wkn1npm76aghy4yxj29cj4y"))
;; TODO: there is one more file to replace:
;; inst/resources/gitbook/js/app.min.js
(snippet
@@ -22932,13 +23301,13 @@ that accept short and long options.")
(define-public r-osqp
(package
(name "r-osqp")
- (version "0.6.3.1")
+ (version "0.6.3.2")
(source (origin
(method url-fetch)
(uri (cran-uri "osqp" version))
(sha256
(base32
- "178vvv0yajjy02ww4brrjb4197dp7c0n8zmk1zwh44h9msnnacj3"))))
+ "0i1jh3fr8d45b7inq9s6iyqszhh18hps8jpzkm0hzgj2k8r3nm0q"))))
(properties `((upstream-name . "osqp")))
(build-system r-build-system)
(propagated-inputs (list r-matrix r-r6 r-rcpp))
@@ -23023,14 +23392,14 @@ handle missing genotypes at some SNPs.")
(define-public r-sampling
(package
(name "r-sampling")
- (version "2.9")
+ (version "2.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "sampling" version))
(sha256
(base32
- "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
+ "0x976wblv663aidqmcif1rjv72nbxf4nzms901lmryxbq1p9gv7x"))))
(build-system r-build-system)
(propagated-inputs
(list r-lpsolve r-mass))
@@ -23080,29 +23449,24 @@ the corresponding outputs (tables and graphs).")
(properties `((upstream-name . "rJava")))
(build-system r-build-system)
(arguments
- `(#:modules ((guix build utils)
- (guix build r-build-system)
- (ice-9 match))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'set-JAVA_HOME
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((jdk (assoc-ref inputs "jdk")))
- (setenv "JAVA_HOME" jdk)
- (setenv "JAVA" (which "java"))
- (setenv "JAR" (which "jar"))
- (setenv "JAVAC" (which "javac"))
- (setenv "JAVAH" (which "javah"))
- (setenv "JAVA_CPPFLAGS"
- (string-append "-I" jdk "/include "
- "-I" jdk "/include/linux"))
- (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
- ((lib) (setenv "JAVA_LIBS" lib))
- (_ (error "Could not find libjvm.so"))))
- #t)))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-JAVA_HOME
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((jdk (assoc-ref inputs "jdk")))
+ (setenv "JAVA_HOME" jdk)
+ (setenv "JAVA" (which "java"))
+ (setenv "JAR" (which "jar"))
+ (setenv "JAVAC" (which "javac"))
+ (setenv "JAVAH" (which "javah"))
+ (setenv "JAVA_CPPFLAGS"
+ (string-append "-I" jdk "/include "
+ "-I" jdk "/include/linux"))
+ (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so"))))))))
(inputs
`(("icu4c" ,icu4c)
- ("jdk" ,icedtea-8 "jdk")
+ ("jdk" ,openjdk11 "jdk")
("zlib" ,zlib)))
(home-page "https://www.rforge.net/rJava/")
(synopsis "Low-Level R to Java interface")
@@ -24811,14 +25175,14 @@ from SuiteSparse.")
(define-public r-sctransform
(package
(name "r-sctransform")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sctransform" version))
(sha256
(base32
- "1cxlqscjn33rszigk7bxjj2hdsr8rxalq94fg86qwmx9jv0i1vws"))))
+ "0wgimf7qqgnnmyspn2rpb4a8hl570fv0fwh0r0r4qgjlpvwffssz"))))
(build-system r-build-system)
(propagated-inputs
(list r-dplyr
@@ -25984,14 +26348,15 @@ function and interfaces to external frameworks.")
(define-public r-covr
(package
(name "r-covr")
- (version "3.6.2")
+ (version "3.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "covr" version))
(sha256
- (base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc"))
+ (base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0"))
(modules '((guix build utils)))
+ ;; TODO: still need to replace highlight.js/highlight.pack.js
(snippet
'(with-directory-excursion "inst/www/shared"
(for-each delete-file
@@ -26081,14 +26446,14 @@ both R code and compiled C/C++/FORTRAN code.")
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "1.0.4")
+ (version "1.0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
+ "08sqw5izpwhawcjkcyscvslz914skwfi0s68rdwrqwwkh8fzn3w4"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(propagated-inputs
@@ -26136,14 +26501,14 @@ emphasize hidden group structures in networks or focus on specific nodes.")
(define-public r-terra
(package
(name "r-terra")
- (version "1.7-46")
+ (version "1.7-55")
(source
(origin
(method url-fetch)
(uri (cran-uri "terra" version))
(sha256
(base32
- "0jpni25g9rhsqh71pgr2d3221r9xacsw3kz5qqnifj0jz5g3wyh1"))))
+ "1v1if9ypmra02ngg4r8qg1hldmxan8lyyhgq3j969glihpyvs03h"))))
(properties `((upstream-name . "terra")))
(build-system r-build-system)
(inputs
@@ -26455,13 +26820,13 @@ to ODEs by numerical differencing.")
(define-public r-pmcmrplus
(package
(name "r-pmcmrplus")
- (version "1.9.7")
+ (version "1.9.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "PMCMRplus" version))
(sha256
- (base32 "06i5vsf8hpzv0c8v156072xbqpxk1wf2iami7mnsjfp9xjjjzbhx"))))
+ (base32 "1wqx5nikhpjsqnn7lgb2zy949sxmq7n3phlaix70as0zky534scg"))))
(properties `((upstream-name . "PMCMRplus")))
(build-system r-build-system)
(inputs (list gmp))
@@ -26872,14 +27237,14 @@ cell free DNA} (cfDNA).")
(define-public r-rintrojs
(package
(name "r-rintrojs")
- (version "0.3.2")
+ (version "0.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rintrojs" version))
(sha256
(base32
- "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh"))
+ "1fy5lz9d9njs4yrnwrrn0n1fn0chccgi1gzn4qz4g6adr3v35rgw"))
(snippet
'(delete-file "inst/javascript/introjs/intro.min.js"))))
(properties `((upstream-name . "rintrojs")))
@@ -27994,14 +28359,14 @@ transcription, ...")
(define-public r-seewave
(package
(name "r-seewave")
- (version "2.2.2")
+ (version "2.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "seewave" version))
(sha256
(base32
- "12r09cirqzpg0lki304kfrdvxhdjpvsficba8inmnr4qzpfw7s5a"))))
+ "13c48sn453yp4j0ap8slnnr2gfhlxasz926p2pazkrg817w7m28z"))))
(properties `((upstream-name . "seewave")))
(build-system r-build-system)
(inputs
@@ -28897,14 +29262,14 @@ API; see the package vignette for details.")
(define-public r-actuar
(package
(name "r-actuar")
- (version "3.3-2")
+ (version "3.3-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "0ys7kqqbx9g2mhsn243z9vj7qkdd69d3jy1vin9v8bknwimgdxvb"))))
+ "0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs (list r-expint))
@@ -29125,14 +29490,14 @@ done.")
(define-public r-adagio
(package
(name "r-adagio")
- (version "0.8.5")
+ (version "0.9.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "adagio" version))
(sha256
(base32
- "0icwr3cark67jyg9zzqwyv9q4fs0j0xgb5i7nkwv9s7y5dlldl0b"))))
+ "100mqwlzqml154d0hk7spi4sbwx9y3gh06vkls49kca2q1kf99qz"))))
(properties `((upstream-name . "adagio")))
(build-system r-build-system)
(propagated-inputs
@@ -30306,14 +30671,14 @@ programming} (OOP) using R Reference Class.")
(define-public r-proxyc
(package
(name "r-proxyc")
- (version "0.3.3")
+ (version "0.3.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "proxyC" version))
(sha256
(base32
- "00p3604ny6qax5rr1865c27hfp90v2vga0xcrp3bb81xcfadl99y"))))
+ "1skq5cxd0kh2pccfg4h9bis4wbqb6zm04q4iwfa6dqml6hyiv7gk"))))
(properties `((upstream-name . "proxyC")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@@ -31518,14 +31883,14 @@ techniques to average Bayesian predictive distributions.")
(define-public r-rstan
(package
(name "r-rstan")
- (version "2.26.23")
+ (version "2.32.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstan" version))
(sha256
(base32
- "08hdwrpxbxp2wdnfk2jj2xsdgl7q9nbalz5wgwmy0m878swxxzci"))))
+ "17alp92kj9mnlkzplk7zd83sv2zi2h7yc44fx5f7nz3dpwd9x7d2"))))
(properties `((upstream-name . "rstan")))
(build-system r-build-system)
(arguments
@@ -32474,18 +32839,18 @@ estimation.")
(define-public r-optimx
(package
(name "r-optimx")
- (version "2023-8.13")
+ (version "2023-10.21")
(source
(origin
(method url-fetch)
(uri (cran-uri "optimx" version))
(sha256
(base32
- "00w8h450gs8vf0raghjg2818xzj4gz5jr3hwk9m9zc5k3rwmcf8n"))))
+ "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd"))))
(properties `((upstream-name . "optimx")))
(build-system r-build-system)
(propagated-inputs (list r-nloptr r-numderiv r-pracma))
- (native-inputs (list r-knitr))
+ (native-inputs (list r-r-rsp))
(home-page "https://cran.r-project.org/web/packages/optimx/")
(synopsis "Expanded replacement and extension of the optim function")
(description
@@ -32579,14 +32944,14 @@ including means, variances, intervals, and highest density regions.")
(define-public r-posterior
(package
(name "r-posterior")
- (version "1.4.1")
+ (version "1.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "posterior" version))
(sha256
(base32
- "1lsqpczf8ll8m1a99kwmxdjm8wpavlqw88qha82s3438ipx5729b"))))
+ "1pp233ddrs116w1rmp3khhmibjf6l021b1x79k6z48g3r9zk042a"))))
(properties `((upstream-name . "posterior")))
(build-system r-build-system)
(propagated-inputs
@@ -33356,13 +33721,13 @@ diagonals. This package allows you to compute the tensor product of arrays.")
(define-public r-spatstat-explore
(package
(name "r-spatstat-explore")
- (version "3.2-3")
+ (version "3.2-5")
(source (origin
(method url-fetch)
(uri (cran-uri "spatstat.explore" version))
(sha256
(base32
- "18zhpspq07rcnpmnkc82hzjvjp39fsb06g73gin4x5bwzbi22kgr"))))
+ "053wl87whmkkqp058lwzlwv0wydddizsni9m94f6kxgl5ahia1sc"))))
(properties `((upstream-name . "spatstat.explore")))
(build-system r-build-system)
(propagated-inputs
@@ -33396,13 +33761,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.")
(define-public r-spatstat-model
(package
(name "r-spatstat-model")
- (version "3.2-6")
+ (version "3.2-8")
(source (origin
(method url-fetch)
(uri (cran-uri "spatstat.model" version))
(sha256
(base32
- "1lvs6ns4hna7w6b0nvzsx2rw699ampdm8jmxdzlfpk4hla2lf7wq"))))
+ "1x03fy921rq8dyr6jkpwnx7pf7fc5593mvnl8r1gz3sypnmp6p4d"))))
(properties `((upstream-name . "spatstat.model")))
(build-system r-build-system)
(propagated-inputs
@@ -33440,14 +33805,14 @@ Kolmogorov-Smirnov, ANOVA) are also supported.")
(define-public r-spatstat-utils
(package
(name "r-spatstat-utils")
- (version "3.0-3")
+ (version "3.0-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.utils" version))
(sha256
(base32
- "0j6w9b479qqah2vzbq31v1xa6rjql8a85hdlahqhwqd9j1scd03s"))))
+ "1i1w1ys29s22jfjvliqnbw3zi6zar8bxxz3r8za182p2w0wqwhax"))))
(properties
`((upstream-name . "spatstat.utils")))
(build-system r-build-system)
@@ -33461,14 +33826,14 @@ which may also be useful for other purposes.")
(define-public r-spatstat-sparse
(package
(name "r-spatstat-sparse")
- (version "3.0-2")
+ (version "3.0-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.sparse" version))
(sha256
(base32
- "1gnlgz11dv66b41kdyyzm8nhkhhi4yajlcr2g52h2lfxlryb5g2h"))))
+ "0scdk3ns4nl1v1avbggnsinfpvl4i8391qy3x1iwxvkimr14xg3b"))))
(properties
`((upstream-name . "spatstat.sparse")))
(build-system r-build-system)
@@ -33485,14 +33850,14 @@ matrix calculations that are common in statistics, such as quadratic forms.")
(define-public r-spatstat-data
(package
(name "r-spatstat-data")
- (version "3.0-1")
+ (version "3.0-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.data" version))
(sha256
(base32
- "002kvli3n9cppaar7q062dm4fapdgkyf1daq5zscxsanwcflpswf"))))
+ "0fxd266rza07s73fj1n4rd4i7x1bv1ll36iikxzjhnlh3vjc0hkn"))))
(properties `((upstream-name . "spatstat.data")))
(build-system r-build-system)
(propagated-inputs
@@ -33507,14 +33872,14 @@ package.")
(define-public r-spatstat-geom
(package
(name "r-spatstat-geom")
- (version "3.2-5")
+ (version "3.2-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.geom" version))
(sha256
(base32
- "13xlp88yfp61kl0c3vaqs7lrckkc4ixpp0mpf89h5ggmjyf57nxx"))))
+ "13k85918zd2n64mxjwlgzd986zvs3is8vg06k9i195yymfrik65y"))))
(properties `((upstream-name . "spatstat.geom")))
(build-system r-build-system)
(propagated-inputs
@@ -33563,14 +33928,14 @@ user-level code from spatstat, except for the code for linear networks.")
(define-public r-spatstat-linnet
(package
(name "r-spatstat-linnet")
- (version "3.1-1")
+ (version "3.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.linnet" version))
(sha256
(base32
- "0adha3bi1a250p8wm7agqdmwzznd6blsfg0km11n25ad8y2r5q0c"))))
+ "1ybjl5ccp9r5ilbihwzk93zcm46pbpldn3nfbfpdw458xh894r3q"))))
(properties
`((upstream-name . "spatstat.linnet")))
(build-system r-build-system)
@@ -33593,13 +33958,13 @@ for spatial data on a linear network.")
(define-public r-spatstat-random
(package
(name "r-spatstat-random")
- (version "3.1-6")
+ (version "3.2-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.random" version))
(sha256
- (base32 "0vrx0mxzcd6yr6rzn9jk2wj5d2l7yn0ij1n58yb3hw2g7nasad06"))))
+ (base32 "1p1imyqrpvdhsc24pq3mvdg9n29h6q8zlawdyahqiymynyp22m4j"))))
(properties `((upstream-name . "spatstat.random")))
(build-system r-build-system)
(propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
@@ -33621,14 +33986,14 @@ sampler).")
(define-public r-spatstat
(package
(name "r-spatstat")
- (version "3.0-6")
+ (version "3.0-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat" version))
(sha256
(base32
- "0vlpa5a1b5s27lgxkq65iixrsbbj0x4zahg0sfsak0ackj8ks577"))))
+ "1h6fnri3ma5kgzkwv4lr2i2jvsx8sg4am3rgzb29h7l89x59yxrk"))))
(properties `((upstream-name . "spatstat")))
(build-system r-build-system)
(propagated-inputs
@@ -33750,18 +34115,18 @@ aggregation for comparing different implementations in order to provide a
(define-public r-rfast
(package
(name "r-rfast")
- (version "2.0.8")
+ (version "2.0.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rfast" version))
(sha256
(base32
- "1c64j8hg6id4ri3m32aa1r0qyn09kl3dvl865dzf43qdb3qcichv"))))
+ "12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz"))))
(properties `((upstream-name . "Rfast")))
(build-system r-build-system)
(propagated-inputs
- (list r-rcpp r-rcpparmadillo r-rcppziggurat))
+ (list r-rcpp r-rcpparmadillo r-rcppparallel r-rcppziggurat))
(home-page "https://github.com/RfastOfficial/Rfast")
(synopsis "Collection of efficient and fast R functions")
(description
@@ -34690,14 +35055,14 @@ different palettes and includes both diverging and sequential types.")
(define-public r-slider
(package
(name "r-slider")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "slider" version))
(sha256
(base32
- "18gw0bxpbb00qcafmyv2avyj83s710hrj10x998ch9qbbyx1fsmw"))))
+ "1c19lk0ddh5qh0jzx7178l314zyygmlpmbvn7670bcmdbxwjc2i0"))))
(properties `((upstream-name . "slider")))
(build-system r-build-system)
(propagated-inputs
@@ -34938,14 +35303,14 @@ results.")
(define-public r-tidyposterior
(package
(name "r-tidyposterior")
- (version "1.0.0")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyposterior" version))
(sha256
(base32
- "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86"))))
+ "1yi0pihglp683dmfg0bn9lnb0qsl2xprj3al65v642rcfzrr7h4h"))))
(properties `((upstream-name . "tidyposterior")))
(build-system r-build-system)
(propagated-inputs
@@ -35636,25 +36001,28 @@ data to rasters. It speeds up plotting of data with millions of points.")
(define-public r-seuratobject
(package
(name "r-seuratobject")
- (version "4.1.4")
+ (version "5.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "SeuratObject" version))
(sha256
(base32
- "1vqhad76hnr0l47klg56fniah4cvpzbkkl0j1cn9cp3rv6d69rvl"))))
+ "0wlr53cswq7a7zzzzkif82iy4xrrd2afz093b265kjlq4qxmzn9d"))))
(properties `((upstream-name . "SeuratObject")))
(build-system r-build-system)
(propagated-inputs
(list r-future
r-future-apply
+ r-generics
+ r-lifecycle
r-matrix
r-progressr
r-rcpp
r-rcppeigen
r-rlang
- r-sp))
+ r-sp
+ r-spam))
(home-page "https://satijalab.org/seurat")
(synopsis "Data structures for single cell data")
(description
@@ -36795,14 +37163,14 @@ clusterings as resolution increases.")
(define-public r-textshaping
(package
(name "r-textshaping")
- (version "0.3.6")
+ (version "0.3.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "textshaping" version))
(sha256
(base32
- "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
+ "0hpcjz66ykji89g2lzpp6hfkz10388py8vn2ss08n4xl3yz4v4ps"))))
(properties `((upstream-name . "textshaping")))
(build-system r-build-system)
(inputs
@@ -36823,14 +37191,14 @@ the font tool-set provided by the @code{systemfonts} package.")
(define-public r-ragg
(package
(name "r-ragg")
- (version "1.2.5")
+ (version "1.2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "ragg" version))
(sha256
(base32
- "1yd89p4f2b7r2n1kl6lybbgd04kqvlf14zgmp7pxw770w1slsvwk"))))
+ "1izpw02b8kq6pm37kvxp9pbd9srvfp5bzfjg27j9hbmm794xq50h"))))
(properties `((upstream-name . "ragg")))
(build-system r-build-system)
(inputs
@@ -37013,14 +37381,14 @@ visualized at any level of the experiment's design.")
(define-public r-qdapregex
(package
(name "r-qdapregex")
- (version "0.7.5")
+ (version "0.7.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "qdapRegex" version))
(sha256
(base32
- "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
+ "1pf1cz03i6sn83d1aaj4cv4jfavs6k81nn5sy7b0aw4i1hpkyiwz"))))
(properties `((upstream-name . "qdapRegex")))
(build-system r-build-system)
(propagated-inputs (list r-stringi))
@@ -37292,13 +37660,13 @@ user streams, and to parse the output into data frames.")
(define-public r-strex
(package
(name "r-strex")
- (version "1.6.0")
+ (version "1.6.1")
(source (origin
(method url-fetch)
(uri (cran-uri "strex" version))
(sha256
(base32
- "1fxg07n8cjvvgpbzqhyx5ma5bv6vax1yw0rbfdqfzr79v6k5x3n7"))))
+ "1vz5zrvf052bg2y48yvkci4hciknvyw5gpbvnklgyny5lzlqvyiq"))))
(properties `((upstream-name . "strex")))
(build-system r-build-system)
(propagated-inputs
@@ -37626,18 +37994,18 @@ supply the workflow to create thematic maps. This package also facilitates
(define-public r-rworldmap
(package
(name "r-rworldmap")
- (version "1.3-6")
+ (version "1.3-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "rworldmap" version))
(sha256
(base32
- "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
+ "007avjl7jhllybp82illrn8v38a85j6xbzk5pvykfx8ayx4wc3m6"))))
(properties `((upstream-name . "rworldmap")))
(build-system r-build-system)
(propagated-inputs
- (list r-fields r-maptools r-sp))
+ (list r-fields r-raster r-sp r-terra))
(home-page
"https://github.com/AndySouth/rworldmap/")
(synopsis "Mapping Global Data")
@@ -37648,14 +38016,14 @@ supply the workflow to create thematic maps. This package also facilitates
(define-public r-rtweet
(package
(name "r-rtweet")
- (version "1.1.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rtweet" version))
(sha256
(base32
- "0dq6ckf2mp6wm6y8xzjby21s356760fmck1m8nsnv5gz8lhy6dhg"))))
+ "18ynravc5vz7ywm1n7ww48gx06dndcishl6lq8nqajxsjwiphq3r"))))
(properties `((upstream-name . "rtweet")))
(build-system r-build-system)
(propagated-inputs
@@ -38149,17 +38517,18 @@ utility operations.")
(define-public r-rsq
(package
(name "r-rsq")
- (version "2.5")
+ (version "2.6")
(source (origin
(method url-fetch)
(uri (cran-uri "rsq" version))
(sha256
(base32
- "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f"))))
+ "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp"))))
(properties `((upstream-name . "rsq")))
(build-system r-build-system)
(propagated-inputs
- (list r-deriv
+ (list r-deming
+ r-deriv
r-lme4
r-mass
r-matrix
@@ -38836,14 +39205,14 @@ fully reproducible.")
(define-public r-paws-common
(package
(name "r-paws-common")
- (version "0.6.1")
+ (version "0.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "paws.common" version))
(sha256
(base32
- "0haw72885xmzl6rmb8vlkqwnxh7iq5cr89d852j2vk56sxjxv1y5"))))
+ "1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d"))))
(properties `((upstream-name . "paws.common")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/crates-gtk.scm b/gnu/packages/crates-gtk.scm
index 3c6f833145..266a513dc2 100644
--- a/gnu/packages/crates-gtk.scm
+++ b/gnu/packages/crates-gtk.scm
@@ -3,6 +3,7 @@
;;; Copyright © 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
;;; Copyright © 2022 Aleksandr Vityazev <avityazev@posteo.org>
+;;; Copyright © 2023 Steve George <steve@futurile.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -29,6 +30,7 @@
#:use-module (gnu packages crates-graphics)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
+ #:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages webkit))
@@ -1709,6 +1711,255 @@
(("rust-shell-words" ,rust-shell-words-0.1)
("rust-tempfile" ,rust-tempfile-3))))))
+(define-public rust-gstreamer-0.18
+ (package
+ (name "rust-gstreamer")
+ (version "0.18.8")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0mjlnw9917j3wwij8225bjp54k7408lxqjjnh6r6wksyryx66qyn"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:tests? #f ; https://github.com/gtk-rs/gtk3-rs/issues/768
+ #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+ ("rust-cfg-if" ,rust-cfg-if-1)
+ ("rust-futures-channel" ,rust-futures-channel-0.3)
+ ("rust-futures-core" ,rust-futures-core-0.3)
+ ("rust-futures-util" ,rust-futures-util-0.3)
+ ("rust-glib" ,rust-glib-0.15)
+ ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-muldiv" ,rust-muldiv-1)
+ ("rust-num-integer" ,rust-num-integer-0.1)
+ ("rust-num-rational" ,rust-num-rational-0.4)
+ ("rust-once-cell" ,rust-once-cell-1)
+ ("rust-option-operations" ,rust-option-operations-0.4)
+ ("rust-paste" ,rust-paste-1)
+ ("rust-pretty-hex" ,rust-pretty-hex-0.3)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-bytes" ,rust-serde-bytes-0.11)
+ ("rust-thiserror" ,rust-thiserror-1))
+ #:cargo-development-inputs
+ `(("rust-futures-executor" ,rust-futures-executor-0.3)
+ ("rust-gir-format-check" ,rust-gir-format-check-0.1)
+ ("rust-ron" ,rust-ron-0.7)
+ ("rust-serde-json" ,rust-serde-json-1))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "Rust bindings for GStreamer")
+ (description "Rust bindings for GStreamer.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-app-0.18
+ (package
+ (name "rust-gstreamer-app")
+ (version "0.18.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-app" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "115nykpdvfccyzvfi73qkhn061f6rdyhcaj9ajnw2ik5pimdyjk6"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; https://github.com/gtk-rs/gtk3-rs/issues/768
+ #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-futures-core" ,rust-futures-core-0.3)
+ ("rust-futures-sink" ,rust-futures-sink-0.3)
+ ("rust-glib" ,rust-glib-0.15)
+ ("rust-gstreamer" ,rust-gstreamer-0.18)
+ ("rust-gstreamer-app-sys" ,rust-gstreamer-app-sys-0.18)
+ ("rust-gstreamer-base" ,rust-gstreamer-base-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-once-cell" ,rust-once-cell-1))
+ #:cargo-development-inputs (("rust-futures-executor" ,rust-futures-executor-0.3)
+ ("rust-futures-util" ,rust-futures-util-0.3)
+ ("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer gst-plugins-base))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "Rust bindings for GStreamer App library")
+ (description "Rust bindings for the GStreamer App library.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-app-sys-0.18
+ (package
+ (name "rust-gstreamer-app-sys")
+ (version "0.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-app-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1fsgdb3b23s45xc7s06xw96x7avza0jpyj02x1fkw6vk3pr03d63"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+ ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+ ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-system-deps" ,rust-system-deps-6))
+ #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer gst-plugins-base))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "FFI bindings to libgstapp-1.0")
+ (description "FFI bindings to libgstapp-1.0, part of Gstreamer.")
+ (license license:expat)))
+
+(define-public rust-gstreamer-audio-0.18
+ (package
+ (name "rust-gstreamer-audio")
+ (version "0.18.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-audio" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0zl0bj03rz19qlrm50w7i5sagh0i0p5d8gr7ig1k6k5yd7k47sww"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; https://github.com/gtk-rs/gtk3-rs/issues/768
+ #:cargo-inputs (("rust-array-init" ,rust-array-init-2)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-cfg-if" ,rust-cfg-if-1)
+ ("rust-glib" ,rust-glib-0.15)
+ ("rust-gstreamer" ,rust-gstreamer-0.18)
+ ("rust-gstreamer-audio-sys" ,rust-gstreamer-audio-sys-0.18)
+ ("rust-gstreamer-base" ,rust-gstreamer-base-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-once-cell" ,rust-once-cell-1))
+ #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)
+ ("rust-itertools" ,rust-itertools-0.10))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer gst-plugins-base))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "Rust bindings for the GStreamer Audio library")
+ (description "Rust bindings for the GStreamer Audio library.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-audio-sys-0.18
+ (package
+ (name "rust-gstreamer-audio-sys")
+ (version "0.18.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-audio-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0z3xryblh75xp08xyw3m6jfz9azarcvl06dd3psc0n65agxmhhm3"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-test-flags
+ (list "--release" "--"
+ "--skip=cross_validate_constants_with_c")
+ #:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+ ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+ ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+ ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-system-deps" ,rust-system-deps-6))
+ #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer gst-plugins-base))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "FFI bindings to libgstaudio-1.0")
+ (description "FFI bindings to libgstaudio, part of Gstreamer.")
+ (license license:expat)))
+
+(define-public rust-gstreamer-base-0.18
+ (package
+ (name "rust-gstreamer-base")
+ (version "0.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-base" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0gw6sr75h01y3j6lpxhc7p1frvkba9a4imyyb2ppqh42cprkakr2"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; https://github.com/gtk-rs/gtk3-rs/issues/768
+ #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-cfg-if" ,rust-cfg-if-1)
+ ("rust-glib" ,rust-glib-0.15)
+ ("rust-gstreamer" ,rust-gstreamer-0.18)
+ ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+ ("rust-libc" ,rust-libc-0.2))
+ #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "Rust bindings for GStreamer Base library")
+ (description "Rust bindings for GStreamer Base library.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-base-sys-0.18
+ (package
+ (name "rust-gstreamer-base-sys")
+ (version "0.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-base-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "13h79fcn3b9bkg7h8j0vxc1zryp92shbvvk6gkx723il7hy4k0x0"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+ ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+ ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-system-deps" ,rust-system-deps-6))
+ #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "FFI bindings to libgstbase-1.0")
+ (description "FFI bindings to libgstbase-1.0, part of GStreamer.")
+ (license license:expat)))
+
+(define-public rust-gstreamer-sys-0.18
+ (package
+ (name "rust-gstreamer-sys")
+ (version "0.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "gstreamer-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1qikgp5m3xj41fbfyfl6ckb5i8dxadfvlvj5bf8girn2sdjpllg3"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-inputs `(("rust-glib-sys" ,rust-glib-sys-0.15)
+ ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-system-deps" ,rust-system-deps-6))
+ #:cargo-development-inputs `(("rust-shell-words" ,rust-shell-words-1)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (native-inputs (list pkg-config))
+ (inputs (list glib gstreamer))
+ (home-page "https://gstreamer.freedesktop.org")
+ (synopsis "FFI bindings to libgstreamer-1.0")
+ (description
+ "Foreign Function Interface (FFI) bindings to libgstreamer-1.0.")
+ (license license:expat)))
+
(define-public rust-gtk-0.14
(package
(name "rust-gtk")
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 1fba8641a8..fc26147157 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -59,6 +59,7 @@
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages admin)
+ #:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
#:use-module (gnu packages avahi)
#:use-module (gnu packages bash)
@@ -81,6 +82,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages mail)
+ #:use-module (gnu packages mp3)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages nettle)
#:use-module (gnu packages pcre)
@@ -2788,6 +2790,28 @@ using AES-NI for high performance.")
("rust-rand" ,rust-rand-0.3)
("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))))
+(define-public rust-al-sys-0.6
+ (package
+ (name "rust-al-sys")
+ (version "0.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "al-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08whlcfrhn4gqi4nbglkdqv5ysdpnvnlsqg51q34q9hh9l7rp3gz"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-inputs
+ `(("rust-cmake" ,rust-cmake-0.1)
+ ("rust-libloading" ,rust-libloading-0.5)
+ ("rust-rental" ,rust-rental-0.5))))
+ (home-page "https://github.com/jpernst/alto")
+ (synopsis "Raw bindings for OpenAL 1.1")
+ (description "Rust bindings for OpenAL, this crate contains FFI elements.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-alacritty-config-0.1
(package
(name "rust-alacritty-config")
@@ -3070,6 +3094,125 @@ be used with the stdlib.")
(description "Mirror of Rust's allocator API.")
(license (list license:expat license:asl2.0))))
+(define-public rust-alsa-0.7
+ (package
+ (name "rust-alsa")
+ (version "0.7.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "alsa" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0iwbdgb6lr81iji9sr4f91mys24pia5avnkgbkv8kxzhvkc2lmp2"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-test-flags `(list "--release"
+ ;; Not the doc tests.
+ "--lib" "--bins" "--tests"
+ "--"
+ ;; These try to use the audio interface
+ "--skip=pcm::drop"
+ "--skip=pcm::info_from_default"
+ "--skip=pcm::playback_to_default"
+ "--skip=pcm::record_from_default"
+ "--skip=seq::print_seqs"
+ "--skip=seq::seq_loopback"
+ "--skip=seq::seq_portsubscribeiter"
+ "--skip=seq::seq_subscribe")
+ #:cargo-inputs `(("rust-alsa-sys" ,rust-alsa-sys-0.3)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-nix" ,rust-nix-0.24))))
+ (native-inputs (list pkg-config alsa-lib))
+ (home-page "https://github.com/diwic/alsa-rs")
+ (synopsis "Thin and safe wrapper around ALSA")
+ (description
+ "A thin and safe wrapper around ALSA. Provides APIs for
+many parts of ALSA including audio playback, audio recording, HCtl API, raw
+MIDI and MIDI sequencer.")
+ (license license:expat)))
+
+(define-public rust-alsa-0.6
+ (package
+ (inherit rust-alsa-0.7)
+ (name "rust-alsa")
+ (version "0.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "alsa" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0szx8finhqbffh08fp3bgh4ywz0b572vcdyh4hwyhrfgw8pza5ar"))))
+ (arguments
+ (list #:cargo-test-flags `(list "--release"
+ ;; Not the doc tests.
+ "--lib" "--bins" "--tests"
+ "--"
+ ;; These try to use the audio interface
+ "--skip=pcm::drop"
+ "--skip=pcm::info_from_default"
+ "--skip=pcm::playback_to_default"
+ "--skip=pcm::record_from_default"
+ "--skip=seq::print_seqs"
+ "--skip=seq::seq_loopback"
+ "--skip=seq::seq_portsubscribeiter"
+ "--skip=seq::seq_subscribe")
+ #:cargo-inputs `(("rust-alsa-sys" ,rust-alsa-sys-0.3)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-nix" ,rust-nix-0.23))))))
+
+(define-public rust-alsa-sys-0.3
+ (package
+ (name "rust-alsa-sys")
+ (version "0.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "alsa-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "09qmmnpmlcj23zcgx2xsi4phcgm5i02g9xaf801y7i067mkfx3yv"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:tests? #f ; doc tests fail
+ #:cargo-inputs `(("rust-libc" ,rust-libc-0.2)
+ ("rust-pkg-config" ,rust-pkg-config-0.3))))
+ (native-inputs (list pkg-config alsa-lib))
+ (home-page "https://github.com/diwic/alsa-sys")
+ (synopsis "FFI bindings for the ALSA sound API")
+ (description
+ "FFI bindings for the ALSA sound API. This package contains
+the code to interact with the underlying operating system ALSA interface.")
+ (license license:expat)))
+
+(define-public rust-alto-3
+ (package
+ (name "rust-alto")
+ (version "3.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "alto" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1rgsdmh346s3rwhzqacjc6nz7jap4dd72c1gfmkaq9sgzh9fhnyp"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:tests? #f ; Not all files included.
+ #:cargo-inputs
+ `(("rust-al-sys" ,rust-al-sys-0.6)
+ ("rust-lazy-static" ,rust-lazy-static-0.2)
+ ("rust-parking-lot" ,rust-parking-lot-0.4))))
+ (home-page "https://github.com/jpernst/alto")
+ (synopsis
+ "Idiomatic Rust bindings for OpenAL 1.1 and extensions (including EFX)")
+ (description
+ "Rust bindings for OpenAL 1.1 and extensions (including EFX).")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-always-assert-0.1
(package
(name "rust-always-assert")
@@ -3946,6 +4089,26 @@ initializing large arrays (greater than 32 elements), or arrays of types which
do not implement the copy or default traits.")
(license (list license:expat license:asl2.0))))
+(define-public rust-array-init-2
+ (package
+ (name "rust-array-init")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "array-init" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1z0bh6grrkxlbknq3xyipp42rasngi806y92fiddyb2n99lvfqix"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/Manishearth/array-init/")
+ (synopsis "Safe wrapper for initializing fixed-size arrays")
+ (description
+ "A crate that removes the need to fill an array before running
+initialisers. Provides an init closure that's called for each element of the
+array.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-array-macro-1
(package
(name "rust-array-macro")
@@ -4316,6 +4479,33 @@ the abi_stable and structural crates.")
("rust-serde-derive" ,rust-serde-derive-1)
("rust-syn" ,rust-syn-1))))))
+(define-public rust-asio-sys-0.2
+ (package
+ (name "rust-asio-sys")
+ (version "0.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "asio-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "16lbavksj2aasadyxbdnbrll6a1m8cwl4skbxgbvr1ma2wpwv82c"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:skip-build? #t
+ #:cargo-inputs `(("rust-bindgen" ,rust-bindgen-0.56)
+ ("rust-cc" ,rust-cc-1)
+ ("rust-num-derive" ,rust-num-derive-0.3)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-once-cell" ,rust-once-cell-1)
+ ("rust-walkdir" ,rust-walkdir-2))))
+ (home-page "https://github.com/RustAudio/cpal/")
+ (synopsis
+ "Low-level interface and binding generation for the Steinberg ASIO SDK")
+ (description
+ "Low-level interface and binding generation for the Steinberg ASIO SDK.")
+ (license license:asl2.0)))
+
(define-public rust-askama-escape-0.10
(package
(name "rust-askama-escape")
@@ -7328,6 +7518,41 @@ bindings to C and C++ libraries.")
(inputs
(list clang))))
+(define-public rust-bindgen-0.56
+ (package
+ (inherit rust-bindgen-0.57)
+ (name "rust-bindgen")
+ (version "0.56.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "bindgen" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0fajmgk2064ca1z9iq1jjkji63qwwz38z3d67kv6xdy0xgdpk8rd"))))
+ (arguments
+ (list #:cargo-test-flags ``("--release" "--"
+ "--skip=test::commandline_multiple_headers")
+ #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+ ("rust-cexpr" ,rust-cexpr-0.4)
+ ("rust-clang-sys" ,rust-clang-sys-1)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-env-logger" ,rust-env-logger-0.8)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-lazycell" ,rust-lazycell-1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-rustc-hash" ,rust-rustc-hash-1)
+ ("rust-shlex" ,rust-shlex-0.1)
+ ("rust-which" ,rust-which-3))
+ #:cargo-development-inputs `(("rust-clap" ,rust-clap-2)
+ ("rust-diff" ,rust-diff-0.1)
+ ("rust-shlex" ,rust-shlex-0.1))))
+ (inputs (list clang))))
+
(define-public rust-bindgen-0.55
(package
(inherit rust-bindgen-0.57)
@@ -12418,6 +12643,25 @@ usage.")
(description "This package provides Rust bindings for libclang.")
(license license:asl2.0)))
+(define-public rust-claxon-0.4
+ (package
+ (name "rust-claxon")
+ (version "0.4.3")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "claxon" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1206mxvw833ysg10029apcsjjwly8zmsvksgza5cm7ma4ikzbysb"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:skip-build? #t)) ; Cut the dependency graph.
+ (home-page "https://github.com/ruuda/claxon#readme")
+ (synopsis "FLAC decoding library")
+ (description "This package provides a FLAC decoding library.")
+ (license license:asl2.0)))
+
(define-public rust-cipher-0.4
(package
(name "rust-cipher")
@@ -15362,6 +15606,50 @@ contents of the OS-level clipboard.")
numbers using the CORDIC method.")
(license license:bsd-3)))
+(define-public rust-coreaudio-rs-0.10
+ (package
+ (name "rust-coreaudio-rs")
+ (version "0.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "coreaudio-rs" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "125d4zr3n363ybga4629p41ym7iqjfb2alnwrc1zj7zyxch4p28i"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t ; Only builds for macos or ios.
+ #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-coreaudio-sys" ,rust-coreaudio-sys-0.2))))
+ (home-page "https://github.com/RustAudio/coreaudio-rs")
+ (synopsis "Rust interface for Apple's CoreAudio API")
+ (description
+ "This package provides a rust interface for Apple's CoreAudio API.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-coreaudio-sys-0.2
+ (package
+ (name "rust-coreaudio-sys")
+ (version "0.2.12")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "coreaudio-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "091b4sq3kl8n4dy86l4mxq9vjzsn8w8b51xzfcpxwjkciqjv4d7h"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t ; Only builds for macos or ios.
+ #:cargo-inputs (("rust-bindgen" ,rust-bindgen-0.64))))
+ (home-page "https://github.com/RustAudio/coreaudio-sys")
+ (synopsis
+ "Bindings for Apple's CoreAudio frameworks generated via rust-bindgen")
+ (description
+ "Bindings for Apple's CoreAudio frameworks generated via rust-bindgen.")
+ (license license:expat)))
+
(define-public rust-core-extensions-1
(package
(name "rust-core-extensions")
@@ -15864,6 +16152,63 @@ intrinsics.")
"This package provides a counts the number of live instances of types.")
(license (list license:expat license:asl2.0))))
+(define-public rust-cpal-0.13
+ (package
+ (name "rust-cpal")
+ (version "0.13.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cpal" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "05j11vz8rw19gqqvpd48i7wvm6j77v8fwx5lwhlkckqjllv7h4bl"))
+ (snippet
+ #~(begin (use-modules (guix build utils))
+ ;; Force cpal-0.13.5 to accept any version of jack, so
+ ;; that other packages like librespot-playback can use
+ ;; the one they want.
+ (substitute* "Cargo.toml.orig"
+ (("(jack = \\{ version = \").*(\", optional.*)" _ jack optional)
+ (string-append jack "*" optional))
+ ;; Remove path for asio-sys, use packaged crate.
+ ((", path =.*,") ","))
+ (copy-file "Cargo.toml.orig" "Cargo.toml")))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-alsa" ,rust-alsa-0.6)
+ ("rust-asio-sys" ,rust-asio-sys-0.2)
+ ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8)
+ ("rust-coreaudio-rs" ,rust-coreaudio-rs-0.10)
+ ("rust-jack" ,rust-jack-0.8)
+ ("rust-jni" ,rust-jni-0.19)
+ ("rust-js-sys" ,rust-js-sys-0.3)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-mach" ,rust-mach-0.3)
+ ("rust-ndk" ,rust-ndk-0.6)
+ ("rust-ndk-glue" ,rust-ndk-glue-0.6)
+ ("rust-nix" ,rust-nix-0.23)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-oboe" ,rust-oboe-0.4)
+ ("rust-parking-lot" ,rust-parking-lot-0.11)
+ ("rust-stdweb" ,rust-stdweb-0.1)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
+ ("rust-web-sys" ,rust-web-sys-0.3)
+ ("rust-winapi" ,rust-winapi-0.3))
+ #:cargo-development-inputs (("rust-anyhow" ,rust-anyhow-1)
+ ("rust-clap" ,rust-clap-3)
+ ("rust-hound" ,rust-hound-3)
+ ("rust-ringbuf" ,rust-ringbuf-0.2))))
+ (native-inputs (list pkg-config))
+ (inputs (list alsa-lib))
+ (home-page "https://github.com/rustaudio/cpal")
+ (synopsis "Low-level cross-platform audio I/O library in pure Rust")
+ (description "Low-level cross-platform audio I/O library in pure Rust.
+Supports Linux through either JACK or ALSA.")
+ (license license:asl2.0)))
+
(define-public rust-cpp-demangle-0.4
(package
(name "rust-cpp-demangle")
@@ -17245,6 +17590,34 @@ abstractions around common WinAPI calls.")
number ``crunching``.")
(license license:expat)))
+(define-public rust-rodio-0.15
+ (package
+ (name "rust-rodio")
+ (version "0.15.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "rodio" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "07kkrx0hxfcqgkpg0lrh9355bj1rl0k65nwsk3qwdri6yvlkj2gc"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-claxon" ,rust-claxon-0.4)
+ ("rust-cpal" ,rust-cpal-0.13)
+ ("rust-hound" ,rust-hound-3)
+ ("rust-lewton" ,rust-lewton-0.10)
+ ("rust-minimp3" ,rust-minimp3-0.5)
+ ("rust-symphonia" ,rust-symphonia-0.4))
+ #:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.9))))
+ (native-inputs (list pkg-config))
+ (inputs (list alsa-lib))
+ (home-page "https://github.com/RustAudio/rodio")
+ (synopsis "Pure Rust audio playback library")
+ (description "Audio playback library written in pure Rust that supports
+many formats including AAC, FLAC, MP3, MP4 and WAV.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-roxmltree-0.14
(package
(name "rust-roxmltree")
@@ -25249,6 +25622,31 @@ Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed")
"This package provides a simple, efficient logging system for Rust.")
(license license:expat)))
+(define-public rust-fetch-unroll-0.3
+ (package
+ (name "rust-fetch-unroll")
+ (version "0.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "fetch_unroll" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1l3cf8fhcrw354hdmjf03f5v4bxgn2wkjna8n0fn8bgplh8b3666"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:tests? #f ; Tries to connect to github.com
+ #:cargo-inputs `(("rust-libflate" ,rust-libflate-1)
+ ("rust-tar" ,rust-tar-0.4)
+ ("rust-ureq" ,rust-ureq-2))))
+ ; perl required for building rust-ring
+ (inputs (list perl))
+ (home-page "https://github.com/katyo/fetch_unroll")
+ (synopsis "Simple utilities for fetching and unrolling .tar.gz archives")
+ (description
+ "Simple utilities for fetching and unrolling .tar.gz archives.")
+ (license license:asl2.0)))
+
(define-public rust-fever-api-0.2
(package
(name "rust-fever-api")
@@ -31539,6 +31937,25 @@ Hash-based Message Authentication Code algorithm} for SHA1.")
(("rust-libc" ,rust-libc-0.2)
("rust-winutil" ,rust-winutil-0.1))))))
+(define-public rust-hound-3
+ (package
+ (name "rust-hound")
+ (version "3.5.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "hound" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0kw5yybfc7hdwxwm6d3m3h4ms52fkw0n0zch35drb52ci2xsmbb2"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:skip-build? #t)) ; Cut the dependency graph.
+ (home-page "https://github.com/ruuda/hound")
+ (synopsis "Wav encoding and decoding library")
+ (description "This package provides a wav encoding and decoding library.")
+ (license license:asl2.0)))
+
(define-public rust-html5ever-0.26
(package
(name "rust-html5ever")
@@ -34854,6 +35271,101 @@ format.")
(description "This package provides a simple ivf muxer.")
(license license:bsd-2)))
+(define-public rust-jack-0.10
+ (package
+ (name "rust-jack")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "jack" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0djs3j0icxbzbivhj73vgjrvjw6ncpfak2vyxjcbn4wvl9ajcwnf"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:tests? #f
+ #:cargo-inputs
+ `(("rust-bitflags" ,rust-bitflags-1)
+ ("rust-jack-sys" ,rust-jack-sys-0.4)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-log" ,rust-log-0.4))
+ #:cargo-development-inputs
+ `(("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5))))
+ (native-inputs (list pkg-config))
+ (inputs (list jack-2))
+ (home-page "https://github.com/RustAudio/rust-jack")
+ (synopsis "Real time audio and midi with JACK")
+ (description "Real time audio and midi with JACK.")
+ (license license:expat)))
+
+(define-public rust-jack-0.8
+ (package
+ (inherit rust-jack-0.10)
+ (name "rust-jack")
+ (version "0.8.4")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "jack" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0lz10s0n2gy128m65pf96is9ip00vfgvnkfja0y9ydmv24pw2ajx"))))
+ (arguments
+ (list #:tests? #f
+ #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+ ("rust-jack-sys" ,rust-jack-sys-0.2)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5))))))
+
+(define-public rust-jack-sys-0.4
+ (package
+ (name "rust-jack-sys")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "jack-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "17vaq4i8q5nx39rjqx9sixqn1xraf1vxs3bmrf618v8nzxchbmz9"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; cannot find value `library` in this scope
+ #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-libloading" ,rust-libloading-0.7)
+ ("rust-pkg-config" ,rust-pkg-config-0.3))))
+ (native-inputs (list pkg-config))
+ (inputs (list jack-2))
+ (home-page "https://github.com/RustAudio/rust-jack/tree/main/jack-sys")
+ (synopsis "Low-level binding to the JACK audio API")
+ (description "Low-level binding to the JACK audio API.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-jack-sys-0.2
+ (package
+ (inherit rust-jack-sys-0.4)
+ (name "rust-jack-sys")
+ (version "0.2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "jack-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1h9c9za19nyr1prx77gkia18ia93f73lpyjdiyrvmhhbs79g54bv"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-inputs `(("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-libloading" ,rust-libloading-0.6)
+ ("rust-pkg-config" ,rust-pkg-config-0.3))))))
+
(define-public rust-javascriptcore-rs-sys-0.2
(package
(name "rust-javascriptcore-rs-sys")
@@ -36078,6 +36590,34 @@ requires non-const function calls to be computed.")
sending emails from Rust applications.")
(license license:expat)))
+(define-public rust-lewton-0.10
+ (package
+ (name "rust-lewton")
+ (version "0.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "lewton" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0c60fn004awg5c3cvx82d6na2pirf0qdz9w3b93mbcdakbglhyvp"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-inputs
+ `(("rust-byteorder" ,rust-byteorder-1)
+ ("rust-futures" ,rust-futures-0.1)
+ ("rust-ogg" ,rust-ogg-0.8)
+ ("rust-tinyvec" ,rust-tinyvec-1)
+ ("rust-tokio-io" ,rust-tokio-io-0.1))
+ #:cargo-development-inputs
+ `(("rust-alto" ,rust-alto-3)
+ ("rust-ogg" ,rust-ogg-0.8))))
+ (home-page "https://github.com/RustAudio/lewton")
+ (synopsis "Pure Rust Vorbis decoder")
+ (description "A pure Rust Vorbis decoder. Vorbis is a free and open
+source audio format.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-lexical-core-0.8
(package
(name "rust-lexical-core")
@@ -37082,21 +37622,17 @@ file.
@end itemize")
(license license:gpl2+)))
-;; https://github.com/jnqnfe/pulse-binding-rust/blob/c788a8069f455f864d2ba5f0aa5f62e6648dfd26/pulse-sys/build.rs
-;; fix location of pulseaudio
(define-public rust-libpulse-binding-2
(package
(name "rust-libpulse-binding")
- (version "2.23.1")
+ (version "2.28.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "libpulse-binding" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "1qx85j489mmad9cvw5k71271l3qy4s8a5qq8a9wac6cfi4viz5fv"))))
+ (base32 "1zza12f22wf1qs6h71lq1i73aj3kmv3036hqc7qci063vyi5fdgd"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -37109,7 +37645,7 @@ file.
#:phases
(modify-phases %standard-phases
(add-before 'check 'set-HOME
- (lambda _ (setenv "HOME" "/tmp") #t)))))
+ (lambda _ (setenv "HOME" "/tmp"))))))
(native-inputs
(list pkg-config))
(inputs
@@ -37121,19 +37657,67 @@ file.
library.")
(license (list license:expat license:asl2.0))))
+(define-public rust-libpulse-simple-binding-2
+ (package
+ (name "rust-libpulse-simple-binding")
+ (version "2.28.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "libpulse-simple-binding" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "139hiksmxrmj8zcdqvswgjnwl1rivh915vg6cl92asizydl6pz85"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-libpulse-binding" ,rust-libpulse-binding-2)
+ ("rust-libpulse-simple-sys" ,rust-libpulse-simple-sys-1)
+ ("rust-libpulse-sys" ,rust-libpulse-sys-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (native-inputs (list pkg-config))
+ (inputs (list pulseaudio))
+ (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+ (synopsis "Rust language bindings for PulseAudio's libpulse-simple library")
+ (description
+ "A Rust language binding for the PulseAudio libpulse-simple library.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-libpulse-simple-sys-1
+ (package
+ (name "rust-libpulse-simple-sys")
+ (version "1.21.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "libpulse-simple-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0lj13ibdwf69ghy1zlldxq5vsyxi1h13wqpvvh79z2wx36s16rpa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs (("rust-libpulse-sys" ,rust-libpulse-sys-1)
+ ("rust-pkg-config" ,rust-pkg-config-0.3))))
+ (native-inputs (list pkg-config))
+ (inputs (list pulseaudio))
+ (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+ (synopsis "FFI indings for PulseAudio's libpulse-simple system library")
+ (description
+ "FFI bindings for the PulseAudio libpulse-simple system library.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-libpulse-sys-1
(package
(name "rust-libpulse-sys")
- (version "1.18.0")
+ (version "1.21.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "libpulse-sys" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "10msfr8f951v86ag0fl2bsm4a3siq2r7hz9bqhhg7i234s1yj5yg"))))
+ (base32 "16vs0qk6xadckb5qxlrhg0f4jn2zakfd7xih1lk1fb7lzc8f26dw"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -37368,6 +37952,54 @@ Spotify. This package contains the discovery logic.")
Spotify. This package contains the metadata logic.")
(license license:expat)))
+(define-public rust-librespot-playback-0.4
+ (package
+ (name "rust-librespot-playback")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "librespot-playback" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1dygnzldvkv1qpagr9nl62hmqh0xfcf4lsva37j0xxy7pjws142i"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-alsa" ,rust-alsa-0.6)
+ ("rust-byteorder" ,rust-byteorder-1)
+ ("rust-cpal" ,rust-cpal-0.13)
+ ("rust-futures-executor" ,rust-futures-executor-0.3)
+ ("rust-futures-util" ,rust-futures-util-0.3)
+ ("rust-glib" ,rust-glib-0.15)
+ ("rust-gstreamer" ,rust-gstreamer-0.18)
+ ("rust-gstreamer-app" ,rust-gstreamer-app-0.18)
+ ("rust-gstreamer-audio" ,rust-gstreamer-audio-0.18)
+ ("rust-jack" ,rust-jack-0.10)
+ ("rust-lewton" ,rust-lewton-0.10)
+ ("rust-libpulse-binding" ,rust-libpulse-binding-2)
+ ("rust-libpulse-simple-binding" ,rust-libpulse-simple-binding-2)
+ ("rust-librespot-audio" ,rust-librespot-audio-0.4)
+ ("rust-librespot-core" ,rust-librespot-core-0.4)
+ ("rust-librespot-metadata" ,rust-librespot-metadata-0.4)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-ogg" ,rust-ogg-0.8)
+ ("rust-parking-lot" ,rust-parking-lot-0.12)
+ ("rust-portaudio-rs" ,rust-portaudio-rs-0.3)
+ ("rust-rand" ,rust-rand-0.8)
+ ("rust-rand-distr" ,rust-rand-distr-0.4)
+ ("rust-rodio" ,rust-rodio-0.15)
+ ("rust-sdl2" ,rust-sdl2-0.35)
+ ("rust-shell-words" ,rust-shell-words-1)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-tokio" ,rust-tokio-1)
+ ("rust-zerocopy" ,rust-zerocopy-0.6))))
+ (home-page "https://github.com/librespot-org/librespot")
+ (synopsis "Audio playback for Librespot")
+ (description "Audio playback for Librespot, an open source client
+library for Spotify.")
+ (license license:expat)))
+
(define-public rust-librespot-protocol-0.4
(package
(name "rust-librespot-protocol")
@@ -40867,6 +41499,53 @@ efficient round-trip float parsing. Minimal-lexical implements a correct, fast
float parser.")
(license (list license:expat license:asl2.0))))
+(define-public rust-minimp3-0.5
+ (package
+ (name "rust-minimp3")
+ (version "0.5.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "minimp3" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0wj3nzj1swnvwsk3a4a3hkfj1d21jsi7babi40wlrxzbbzvkhm4q"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; no method named `next_frame_future` found for struct `Decoder`
+ #:cargo-inputs (("rust-minimp3-sys" ,rust-minimp3-sys-0.3)
+ ("rust-slice-deque" ,rust-slice-deque-0.3)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-tokio" ,rust-tokio-1))
+ #:cargo-development-inputs (("rust-futures" ,rust-futures-0.3)
+ ("rust-tokio" ,rust-tokio-1))))
+ (home-page "https://github.com/germangb/minimp3-rs")
+ (synopsis "Rust bindings for the minimp3 library")
+ (description "Rust bindings for the minimp3 library.")
+ (license license:expat)))
+
+(define-public rust-minimp3-sys-0.3
+ (package
+ (name "rust-minimp3-sys")
+ (version "0.3.2")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "minimp3-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "144vmf3s89kad0smjprzigcp2c9r5dm95n4ydilrbp399irp6772"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; Not all files included.
+ #:cargo-inputs (("rust-cc" ,rust-cc-1))))
+ (native-inputs (list pkg-config))
+ (inputs (list minimp3))
+ (home-page "https://github.com/germangb/minimp3-rs")
+ (synopsis "Rust bindings for the minimp3 library")
+ (description "Rust bindings for the minimp3 library.")
+ (license license:expat)))
+
(define-public rust-miniz-oxide-0.7
(package
(name "rust-miniz-oxide")
@@ -41453,6 +42132,27 @@ select the mock struct at compile time. Used with the Mockall crate.")
(description "mp4 is a Rust library to read and write ISO-MP4 files.")
(license license:expat)))
+(define-public rust-muldiv-1
+ (package
+ (name "rust-muldiv")
+ (version "1.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "muldiv" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1c6ljsp41n8ijsx7zicwfm135drgyhcms12668ivvsbm1r98frwm"))))
+ (build-system cargo-build-system)
+ (arguments
+ (list #:cargo-inputs `(("rust-quickcheck" ,rust-quickcheck-1))))
+ (home-page "https://github.com/sdroege/rust-muldiv")
+ (synopsis "Trait for numeric types to combine multiplication and division")
+ (description
+ "This package provides a trait for numeric types to perform combined
+multiplication and division with overflow protection.")
+ (license license:expat)))
+
(define-public rust-multimap-0.8
(package
(name "rust-multimap")
@@ -42631,6 +43331,28 @@ general elements and for numerics.")
"This package provides safe Rust bindings to the Android NDK.")
(license (list license:expat license:asl2.0))))
+(define-public rust-ndk-0.6
+ (package
+ (inherit rust-ndk-0.7)
+ (name "rust-ndk")
+ (version "0.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "ndk" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1m1dfjw35qpys1hr4qib6mm3zacd01k439l7cx5f7phd0dzcfci0"))))
+ (arguments
+ `(#:skip-build? #t ; Android only
+ #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-jni" ,rust-jni-0.18)
+ ("rust-jni-glue" ,rust-jni-glue-0.0)
+ ("rust-jni-sys" ,rust-jni-sys-0.3)
+ ("rust-ndk-sys" ,rust-ndk-sys-0.3)
+ ("rust-num-enum" ,rust-num-enum-0.5)
+ ("rust-thiserror" ,rust-thiserror-1))))))
+
(define-public rust-ndk-0.5
(package
(inherit rust-ndk-0.7)
@@ -42696,35 +43418,56 @@ general elements and for numerics.")
"This package provides handles for accessing Android APIs.")
(license (list license:expat license:asl2.0))))
-(define-public rust-ndk-glue-0.5
+(define-public rust-ndk-glue-0.6
(package
(name "rust-ndk-glue")
- (version "0.5.2")
- (source
- (origin
- (method url-fetch)
- (uri (crate-uri "ndk-glue" version))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32 "1m44jh4f9sirs757ikc8sracg6dzw77h9l4bw9vm8s1dly7fw6y7"))))