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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages perl-maths)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system perl)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-check))

(define-public perl-math-cephes
  (package
    (name "perl-math-cephes")
    (version "0.5305")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://cpan/authors/id/S/SH/SHLOMIF/Math-Cephes-"
                    version ".tar.gz"))
              (sha256
               (base32
                "18c3xg53d1vv7hlj43601jj7ks119fm6ndpwpv94irr2905806jn"))
              ;; For reproducibility
              (modules '((guix build utils)))
              (snippet
               '(substitute* "libmd/Makefile.PL"
                  (("readdir DIR") "sort readdir DIR")))))
    (build-system perl-build-system)
    (home-page "https://metacpan.org/release/Math-Cephes")
    (synopsis "Perl interface to the Cephes math library")
    (description "The Math::Cephes module provides a Perl interface to over
150 functions of the Cephes math library.")
    (license license:perl-license)))

(define-public perl-math-matrixreal
  (package
    (name "perl-math-matrixreal")
    (version "2.13")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://cpan/authors/id/L/LE/LETO/Math-MatrixReal-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1cml5wqd99hm398gl8f147ccsck9v179l7a6vqjj4kfkdnja37sg"))))
    (build-system perl-build-system)
    (native-inputs
     (list perl-module-build perl-test-most))
    (home-page "https://metacpan.org/release/Math-MatrixReal")
    (synopsis "Manipulate NxN matrices of real numbers")
    (description "This package provides the @code{Math::MatrixReal} module.
It implements the data type \"matrix of real numbers\" (and consequently also
\"vector of real numbers\").")
    (license license:perl-license)))
67196a8fb8cbebd9c329a79dd&id2=e7f0835b07d868fd447aa64c873174fa385e1699'>gnu/packages/admin.scm42
-rw-r--r--gnu/packages/algebra.scm4
-rw-r--r--gnu/packages/animation.scm78
-rw-r--r--gnu/packages/aspell.scm4
-rw-r--r--gnu/packages/astronomy.scm4
-rw-r--r--gnu/packages/audio.scm32
-rw-r--r--gnu/packages/axoloti.scm5
-rw-r--r--gnu/packages/benchmark.scm19
-rw-r--r--gnu/packages/bioconductor.scm3531
-rw-r--r--gnu/packages/bioinformatics.scm2178
-rw-r--r--gnu/packages/check.scm9
-rw-r--r--gnu/packages/chromium.scm31
-rw-r--r--gnu/packages/ci.scm8
-rw-r--r--gnu/packages/cluster.scm45
-rw-r--r--gnu/packages/compression.scm14
-rw-r--r--gnu/packages/cran.scm904
-rw-r--r--gnu/packages/crates-graphics.scm119
-rw-r--r--gnu/packages/crates-io.scm1664
-rw-r--r--gnu/packages/crypto.scm12
-rw-r--r--gnu/packages/cryptsetup.scm26
-rw-r--r--gnu/packages/curl.scm15
-rw-r--r--gnu/packages/databases.scm20
-rw-r--r--gnu/packages/dictionaries.scm5
-rw-r--r--gnu/packages/diffoscope.scm4
-rw-r--r--gnu/packages/disk.scm50
-rw-r--r--gnu/packages/django.scm17
-rw-r--r--gnu/packages/dns.scm3
-rw-r--r--gnu/packages/education.scm38
-rw-r--r--gnu/packages/emacs-xyz.scm1660
-rw-r--r--gnu/packages/emacs.scm12
-rw-r--r--gnu/packages/emulators.scm404
-rw-r--r--gnu/packages/engineering.scm4
-rw-r--r--gnu/packages/entr.scm5
-rw-r--r--gnu/packages/file-systems.scm37
-rw-r--r--gnu/packages/fltk.scm6
-rw-r--r--gnu/packages/fonts.scm28
-rw-r--r--gnu/packages/fpga.scm7
-rw-r--r--gnu/packages/freeipmi.scm6
-rw-r--r--gnu/packages/ftp.scm4
-rw-r--r--gnu/packages/game-development.scm4
-rw-r--r--gnu/packages/games.scm72
-rw-r--r--gnu/packages/gcc.scm4
-rw-r--r--gnu/packages/gnome.scm20
-rw-r--r--gnu/packages/gnucash.scm12
-rw-r--r--gnu/packages/gnuzilla.scm63
-rw-r--r--gnu/packages/guile-xyz.scm39
-rw-r--r--gnu/packages/guile.scm4
-rw-r--r--gnu/packages/hardware.scm4
-rw-r--r--gnu/packages/i2p.scm74
-rw-r--r--gnu/packages/icu4c.scm16
-rw-r--r--gnu/packages/image-processing.scm5
-rw-r--r--gnu/packages/image.scm4
-rw-r--r--gnu/packages/installers.scm3
-rw-r--r--gnu/packages/jami.scm13
-rw-r--r--gnu/packages/julia-jll.scm2667
-rw-r--r--gnu/packages/julia-xyz.scm1334
-rw-r--r--gnu/packages/kde.scm4
-rw-r--r--gnu/packages/libreoffice.scm4
-rw-r--r--gnu/packages/linux.scm77
-rw-r--r--gnu/packages/lisp-xyz.scm458
-rw-r--r--gnu/packages/lisp.scm18
-rw-r--r--gnu/packages/llvm.scm10
-rw-r--r--gnu/packages/lxqt.scm211
-rw-r--r--gnu/packages/mail.scm19
-rw-r--r--gnu/packages/markup.scm6
-rw-r--r--gnu/packages/maths.scm179
-rw-r--r--gnu/packages/mc.scm32
-rw-r--r--gnu/packages/mes.scm5
-rw-r--r--gnu/packages/messaging.scm41
-rw-r--r--gnu/packages/monitoring.scm30
-rw-r--r--gnu/packages/mpd.scm4
-rw-r--r--gnu/packages/mtools.scm4
-rw-r--r--gnu/packages/music.scm93
-rw-r--r--gnu/packages/networking.scm190
-rw-r--r--gnu/packages/ocaml.scm789
-rw-r--r--gnu/packages/package-management.scm46
-rw-r--r--gnu/packages/parallel.scm36
-rw-r--r--gnu/packages/patches/amule-crypto-6.patch45
-rw-r--r--gnu/packages/patches/emacs-geiser-autoload-activate-implementation.patch26
-rw-r--r--gnu/packages/patches/emacs-geiser-guile-auto-activate.patch34
-rw-r--r--gnu/packages/patches/freebayes-devendor-deps.patch152
-rw-r--r--gnu/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch32
-rw-r--r--gnu/packages/patches/minimap2-aarch64-support.patch52
-rw-r--r--gnu/packages/patches/mosaicatcher-unbundle-htslib.patch49
-rw-r--r--gnu/packages/patches/nsis-source-date-epoch.patch23
-rw-r--r--gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch148
-rw-r--r--gnu/packages/patches/wgetpaste-update-bpaste.patch27
-rw-r--r--gnu/packages/pep.scm143
-rw-r--r--gnu/packages/perl.scm156
-rw-r--r--gnu/packages/php.scm4
-rw-r--r--gnu/packages/protobuf.scm10
-rw-r--r--gnu/packages/python-check.scm39
-rw-r--r--gnu/packages/python-science.scm86
-rw-r--r--gnu/packages/python-web.scm40
-rw-r--r--gnu/packages/python-xyz.scm391
-rw-r--r--gnu/packages/python.scm4
-rw-r--r--gnu/packages/racket.scm6
-rw-r--r--gnu/packages/radio.scm434
-rw-r--r--gnu/packages/readline.scm28
-rw-r--r--gnu/packages/rsync.scm41
-rw-r--r--gnu/packages/rust-apps.scm67
-rw-r--r--gnu/packages/security-token.scm46
-rw-r--r--gnu/packages/sequoia.scm74
-rw-r--r--gnu/packages/serialization.scm4
-rw-r--r--gnu/packages/shells.scm4
-rw-r--r--gnu/packages/smalltalk.scm15
-rw-r--r--gnu/packages/sphinx.scm56
-rw-r--r--gnu/packages/statistics.scm163
-rw-r--r--gnu/packages/suckless.scm8
-rw-r--r--gnu/packages/telephony.scm6
-rw-r--r--gnu/packages/text-editors.scm11
-rw-r--r--gnu/packages/tls.scm23
-rw-r--r--gnu/packages/tryton.scm239
-rw-r--r--gnu/packages/version-control.scm14
-rw-r--r--gnu/packages/video.scm125
-rw-r--r--gnu/packages/vim.scm2
-rw-r--r--gnu/packages/virtualization.scm30
-rw-r--r--gnu/packages/vnc.scm4
-rw-r--r--gnu/packages/web-browsers.scm22
-rw-r--r--gnu/packages/web.scm28
-rw-r--r--gnu/packages/wget.scm20
-rw-r--r--gnu/packages/xdisorg.scm79
-rw-r--r--gnu/packages/xiph.scm39
-rw-r--r--gnu/packages/xml.scm21
-rw-r--r--gnu/packages/xorg.scm31
-rw-r--r--gnu/services/cuirass.scm12
-rw-r--r--gnu/services/dns.scm10
-rw-r--r--gnu/services/networking.scm3
-rw-r--r--gnu/services/vpn.scm4
-rw-r--r--gnu/tests/linux-modules.scm13
-rw-r--r--gnu/tests/web.scm14
-rw-r--r--guix/build-system/r.scm2
-rw-r--r--guix/ci.scm25
-rw-r--r--guix/download.scm1
-rw-r--r--guix/git-download.scm79
-rw-r--r--guix/gnu-maintenance.scm32
-rw-r--r--guix/hg-download.scm24
-rw-r--r--guix/import/cran.scm4
-rw-r--r--guix/import/egg.scm352
-rw-r--r--guix/import/hackage.scm27
-rw-r--r--guix/import/opam.scm4
-rw-r--r--guix/licenses.scm8
-rw-r--r--guix/lint.scm171
-rw-r--r--guix/profiles.scm5
-rw-r--r--guix/progress.scm16
-rw-r--r--guix/scripts/archive.scm3
-rw-r--r--guix/scripts/build.scm3
-rw-r--r--guix/scripts/copy.scm9
-rw-r--r--guix/scripts/deploy.scm12
-rw-r--r--guix/scripts/edit.scm4
-rw-r--r--guix/scripts/environment.scm3
-rw-r--r--guix/scripts/graph.scm5
-rw-r--r--guix/scripts/import.scm4
-rw-r--r--guix/scripts/import/egg.scm107
-rw-r--r--guix/scripts/package.scm8
-rw-r--r--guix/scripts/publish.scm160
-rwxr-xr-xguix/scripts/substitute.scm11
-rw-r--r--guix/store.scm16
-rw-r--r--guix/swh.scm20
-rw-r--r--guix/ui.scm60
-rw-r--r--po/guix/POTFILES.in3
-rw-r--r--tests/egg.scm132
-rw-r--r--tests/gnu-maintenance.scm3
-rw-r--r--tests/hackage.scm7
-rw-r--r--tests/lint.scm55
-rw-r--r--tests/opam.scm4
176 files changed, 16004 insertions, 6402 deletions
diff --git a/Makefile.am b/Makefile.am
index a10e06e5a7..f06b294f28 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -247,6 +247,7 @@ MODULES = \
guix/import/cpan.scm \
guix/import/cran.scm \
guix/import/crate.scm \
+ guix/import/egg.scm \
guix/import/elpa.scm \
guix/import/gem.scm \
guix/import/github.scm \
@@ -292,6 +293,7 @@ MODULES = \
guix/scripts/challenge.scm \
guix/scripts/import/crate.scm \
guix/scripts/import/cran.scm \
+ guix/scripts/import/egg.scm \
guix/scripts/import/elpa.scm \
guix/scripts/import/gem.scm \
guix/scripts/import/gnu.scm \
@@ -450,6 +452,7 @@ SCM_TESTS = \
tests/debug-link.scm \
tests/derivations.scm \
tests/discovery.scm \
+ tests/egg.scm \
tests/elpa.scm \
tests/file-systems.scm \
tests/gem.scm \
diff --git a/configure.ac b/configure.ac
index 583b902361..84592f6041 100644
--- a/configure.ac
+++ b/configure.ac
@@ -96,16 +96,12 @@ m4_pattern_forbid([^GUIX_])
dnl Search for 'guile' and 'guild'. This macro defines
dnl 'GUILE_EFFECTIVE_VERSION'.
-GUILE_PKG([3.0 2.2])
+GUILE_PKG([3.0])
GUILE_PROGS
if test "x$GUILD" = "x"; then
AC_MSG_ERROR(['guild' binary not found; please check your Guile installation.])
fi
-if test "x$GUILE_EFFECTIVE_VERSION" = "x2.2"; then
- PKG_CHECK_MODULES([GUILE], [guile-2.2 >= 2.2.6])
-fi
-
dnl Get CFLAGS and LDFLAGS for libguile.
GUILE_FLAGS
diff --git a/doc/contributing.texi b/doc/contributing.texi
index c3419912a1..fa8c0cf3ba 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -1018,20 +1018,21 @@ Make sure the package builds on your platform, using @code{guix build
We recommend you also try building the package on other supported
platforms. As you may not have access to actual hardware platforms, we
recommend using the @code{qemu-binfmt-service-type} to emulate them. In
-order to enable it, add the following service to the list of services in
-your @code{operating-system} configuration:
+order to enable it, add the @code{virtualization} service module and the
+following service to the list of services in your @code{operating-system}
+configuration:
@lisp
(service qemu-binfmt-service-type
(qemu-binfmt-configuration
- (platforms (lookup-qemu-platforms "arm" "aarch64"))
+ (platforms (lookup-qemu-platforms "arm" "aarch64"))))
@end lisp
Then reconfigure your system.
You can then build packages for different platforms by specifying the
@code{--system} option. For example, to build the "hello" package for
-the armhf, aarch64, or mips64 architectures, you would run the following
+the armhf or aarch64 architectures, you would run the following
commands, respectively:
@example
guix build --system=armhf-linux --rounds=2 hello
@@ -1062,7 +1063,7 @@ and which optional dependencies should be used. In particular, avoid adding
the @code{texlive-tiny} package or @code{texlive-union} procedure instead.
@item
-For important changes, check that dependent package (if applicable) are
+For important changes, check that dependent packages (if applicable) are
not affected by the change; @code{guix refresh --list-dependent
@var{package}} will help you do that (@pxref{Invoking guix refresh}).
@@ -1180,6 +1181,11 @@ MIME attachments. You are advised to pay attention if your email client
changes anything like line breaks or indentation which could potentially
break the patches.
+Expect some delay when you submit your very first patch to
+@email{guix-patches@@gnu.org}. You have to wait until you get an
+acknowledgement with the assigned tracking number. Future acknowledgements
+should not be delayed.
+
When a bug is resolved, please close the thread by sending an email to
@email{@var{NNN}-done@@debbugs.gnu.org}.
@@ -1517,20 +1523,20 @@ doubt, please contact us, we will be happy to help!
@table @asis
@item guix
Guix is written in the Guile programming language, and some strings contain
-special formating that is interpreted by Guile. These special formating
+special formatting that is interpreted by Guile. These special formatting
should be highlighted by Weblate. They start with @code{~} followed by one
or more characters.
-When printing the string, Guile replaces the special formating symbols with
+When printing the string, Guile replaces the special formatting symbols with
actual values. For instance, the string @samp{ambiguous package specification
`~a'} would be substituted to contain said package specification instead of
-@code{~a}. To properly translate this string, you must keep the formating
+@code{~a}. To properly translate this string, you must keep the formatting
code in your translation, although you can place it where it makes sense in
your language. For instance, the French translation says @samp{spécification
du paquet « ~a » ambiguë} because the adjective needs to be placed in the
end of the sentence.
-If there are multiple formating symbols, make sure to respect the order.
+If there are multiple formatting symbols, make sure to respect the order.
Guile does not know in which order you intended the string to be read, so it
will substitute the symbols in the same order as the English sentence.
@@ -1538,9 +1544,9 @@ As an example, you cannot translate @samp{package '~a' has been superseded by
'~a'} by @samp{'~a' superseeds package '~a'}, because the meaning would be
reversed. If @var{foo} is superseded by @var{bar}, the translation would read
@samp{'foo' superseeds package 'bar'}. To work around this problem, it
-is possible to use more advanced formating to select a given piece of data,
+is possible to use more advanced formatting to select a given piece of data,
instead of following the default English order. @xref{Formatted Output,,,
-guile, GNU Guile Reference Manual}, for more information on formating in Guile.
+guile, GNU Guile Reference Manual}, for more information on formatting in Guile.
@item packages
@@ -1551,7 +1557,7 @@ and Descriptions}). Texinfo markup looks like @samp{@@code@{rm -rf@}},
The characters after ``@@'' form the name of the markup, and the text between
``@{'' and ``@}'' is its content. In general, you should not translate the
content of markup like @code{@@code}, as it contains literal code that do not
-change with language. You can translate the content of formating markup such
+change with language. You can translate the content of formatting markup such
as @code{@@emph}, @code{@@i}, @code{@@itemize}, @code{@@item}. However, do
not translate the name of the markup, or it will not be recognized. Do
not translate the word after @code{@@end}, it is the name of the markup that
@@ -1581,10 +1587,10 @@ The manual and the cookbook both use Texinfo. As for @code{packages}, please
keep Texinfo markup as is. There are more possible markup types in the manual
than in the package descriptions. In general, do not translate the content
of @code{@@code}, @code{@@file}, @code{@@var}, @code{@@value}, etc. You
-should translate the content of formating markup such as @code{@@emph},
+should translate the content of formatting markup such as @code{@@emph},
@code{@@i}, etc.
-The manual contains sections that can be refered to by name by @code{@@ref},
+The manual contains sections that can be referred to by name by @code{@@ref},
@code{@@xref} and @code{@@pxref}. We have a mechanism in place so you do
not have to translate their content. If you keep the English title, we will
automatically replace it with your translation of that title. This ensures
@@ -1664,7 +1670,7 @@ synchronize it with our guix and artworks repositories after checking no issue
was introduced in the translation.
Developers can download the latest PO files from weblate in the Guix
-repository by runnig the @command{make download-po} target. It will
+repository by running the @command{make download-po} command. It will
automatically download the latest files from weblate, reformat them to a
canonical form, and check they do not contain issues. The manual needs to be
built again to check for additional issues that might crash Texinfo.
diff --git a/doc/guix.texi b/doc/guix.texi
index 3557c977e1..750483706b 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -76,7 +76,7 @@ Copyright @copyright{} 2020 Damien Cassou@*
Copyright @copyright{} 2020 Jakub Kądziołka@*
Copyright @copyright{} 2020 Jack Hill@*
Copyright @copyright{} 2020 Naga Malleswari@*
-Copyright @copyright{} 2020 Brice Waegeneire@*
+Copyright @copyright{} 2020, 2021 Brice Waegeneire@*
Copyright @copyright{} 2020 R Veera Kumar@*
Copyright @copyright{} 2020 Pierre Langlois@*
Copyright @copyright{} 2020 pinoaffe@*
@@ -787,6 +787,13 @@ To use substitutes from @code{@value{SUBSTITUTE-SERVER}} or one of its mirrors
~root/.config/guix/current/share/guix/@value{SUBSTITUTE-SERVER}.pub
@end example
+@quotation Note
+If you do not enable substitutes, Guix will end up building
+@emph{everything} from source on your machine, making each installation
+and upgrade very expensive. @xref{On Trusting Binaries}, for a
+discussion of reasons why one might want do disable substitutes.
+@end quotation
+
@item
Each user may need to perform a few additional steps to make their Guix
environment ready for use, @pxref{Application Setup}.
@@ -833,8 +840,7 @@ GNU Guix is available for download from its website at
GNU Guix depends on the following packages:
@itemize
-@item @url{https://gnu.org/software/guile/, GNU Guile}, version 3.0.x or
-2.2.x;
+@item @url{https://gnu.org/software/guile/, GNU Guile}, version 3.0.x;
@item @url{https://notabug.org/cwebber/guile-gcrypt, Guile-Gcrypt}, version
0.1.0 or later;
@item
@@ -11624,6 +11630,28 @@ using this mode, the symbol of the package is made by appending the
version to its name, so that multiple versions of the same package can
coexist.
@end table
+
+@item egg
+@cindex egg
+Import metadata for @uref{https://wiki.call-cc.org/eggs, CHICKEN eggs}.
+The information is taken from @file{PACKAGE.egg} files found in the
+@uref{git://code.call-cc.org/eggs-5-latest, eggs-5-latest} Git
+repository. However, it does not provide all the information that we
+need, there is no ``description'' field, and the licenses used are not
+always precise (BSD is often used instead of BSD-N).
+
+@example
+guix import egg sourcehut
+@end example
+
+Additional options include:
+@table @code
+@item --recursive
+@itemx -r
+Traverse the dependency graph of the given upstream package recursively
+and generate package expressions for all those packages that are not yet
+in Guix.
+@end table
@end table
The structure of the @command{guix import} code is modular. It would be
@@ -11778,6 +11806,8 @@ the updater for KDE packages;
the updater for X.org packages;
@item kernel.org
the updater for packages hosted on kernel.org;
+@item egg
+the updater for @uref{https://wiki.call-cc.org/eggs/, Egg} packages;
@item elpa
the updater for @uref{https://elpa.gnu.org/, ELPA} packages;
@item cran
@@ -16450,6 +16480,7 @@ configuration rejecting all incoming connections except those to the ssh port
:INPUT ACCEPT
:FORWARD ACCEPT
:OUTPUT ACCEPT
+-A INPUT -m conntrack --ctstate ESTABLISHED,RELATED -j ACCEPT
-A INPUT -p tcp --dport 22 -j ACCEPT
-A INPUT -j REJECT --reject-with icmp-port-unreachable
COMMIT
@@ -16458,6 +16489,7 @@ COMMIT
:INPUT ACCEPT
:FORWARD ACCEPT
:OUTPUT ACCEPT
+-A INPUT -m conntrack --ctstate ESTABLISHED,RELATED -j ACCEPT
-A INPUT -p tcp --dport 22 -j ACCEPT
-A INPUT -j REJECT --reject-with icmp6-port-unreachable
COMMIT
@@ -19236,7 +19268,7 @@ The MATE package to use.
@end deftp
@deffn {Scheme Variable} lxqt-desktop-service-type
-This is the type of the service that runs the @uref{https://lxqt.github.io,
+This is the type of the service that runs the @uref{https://lxqt-project.org,
LXQt desktop environment}. Its value is a @code{lxqt-desktop-configuration}
object (see below).
@@ -33868,6 +33900,13 @@ every time you modify your @command{config.scm} file and the
@command{-o StrictHostKeyChecking=no} prevents you from having to allow a
connection to an unknown host every time you connect.
+@quotation Note
+If you find the above @samp{hostfwd} example not to be working (e.g.,
+your SSH client hangs attempting to connect to the mapped port of your
+VM), make sure that your Guix System VM has networking support, such as
+by using the @code{dhcp-client-service-type} service type.
+@end quotation
+
@subsection Using @command{virt-viewer} with Spice
As an alternative to the default @command{qemu} graphical client you can
@@ -34395,13 +34434,10 @@ This service type is intended to be extended by other service types,
such as below:
@lisp
-(define module-installing-service-type
- (service-type
- (name 'module-installing-service)
- (extensions (list (service-extension linux-loadable-module-service-type
- (const (list module-to-install-1
- module-to-install-2)))))
- (default-value #f)))
+(simple-service 'installing-module
+ linux-loadable-module-service-type
+ (list module-to-install-1
+ module-to-install-2))
@end lisp
This does not actually load modules at bootup, only adds it to the
diff --git a/etc/guix-daemon.cil.in b/etc/guix-daemon.cil.in
index 4f52157354..c9f4e3186d 100644
--- a/etc/guix-daemon.cil.in
+++ b/etc/guix-daemon.cil.in
@@ -301,7 +301,7 @@
open read write)))
(allow guix_daemon_t
guix_daemon_conf_t
- (lnk_file (create getattr rename unlink)))
+ (lnk_file (create getattr rename unlink read)))
(allow guix_daemon_t net_conf_t
(file (getattr open read)))
(allow guix_daemon_t net_conf_t
@@ -328,6 +328,9 @@
(allow guix_daemon_t
cache_home_t
(dir (search)))
+ (allow guix_daemon_t
+ cache_home_t
+ (lnk_file (getattr read)))
;; self upgrades
(allow guix_daemon_t
@@ -340,7 +343,7 @@
;; Socket operations
(allow guix_daemon_t
guix_daemon_socket_t
- (sock_file (unlink)))
+ (sock_file (unlink write)))
(allow guix_daemon_t
init_t
(fd (use)))
diff --git a/etc/news.scm b/etc/news.scm
index 65d83061df..25bc0d40a2 100644
--- a/etc/news.scm
+++ b/etc/news.scm
@@ -14,6 +14,7 @@
;; Copyright © 2021 Zhu Zihao <all_but_last@163.com>
;; Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
+;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
;;
;; Copying and distribution of this file, with or without modification, are
;; permitted in any medium without royalty provided the copyright notice and
@@ -22,6 +23,40 @@
(channel-news
(version 0)
+ (entry (commit "bdc298ecee15283451d3aa20a849dd7bb22c8538")
+ (title
+ (en "New @command{guix import egg} command")
+ (de "Neuer Befehl @command{guix import egg}")
+ (zh "新的 @command{guix import egg} 命令"))
+ (body
+ (en "The new @command{guix import egg} command allows packagers to
+generate a package definition or a template thereof given the name of a
+CHICKEN egg package, like so:
+
+@example
+guix import egg sourcehut
+@end example
+
+Run @command{info \"(guix) Invoking guix import\"} for more info.")
+ (de "Mit dem neuen Befehl @command{guix import egg} können
+Paketautoren eine Paketdefinition oder eine Vorlage dafür anhand des Namens
+eines „Egg“-Pakets für CHICKEN erzeugen, etwa so:
+
+@example
+guix import egg sourcehut
+@end example
+
+Führen Sie @command{info \"(guix.de) Aufruf von guix import\"} aus, um mehr
+Informationen zu bekommen.")
+ (zh "新的 @command{guix import egg} 命令能让贡献者从一个CHICKEN egg生
+成一个包装或包装样板。
+x
+@example
+guix import egg sourcehut
+@end example
+
+想了解更多可以运行 @command{info \"(guix) Invoking guix import\"}。")))
+
(entry (commit "2161820ebbbab62a5ce76c9101ebaec54dc61586")
(title
(en "Risk of local privilege escalation during user account creation")
diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm
index 122c7c9861..6cad33b741 100644
--- a/gnu/bootloader/u-boot.scm
+++ b/gnu/bootloader/u-boot.scm
@@ -73,9 +73,12 @@
(define install-allwinner64-u-boot
#~(lambda (bootloader root-index image)
- (let ((spl (string-append bootloader "/libexec/u-boot-sunxi-with-spl.fit.itb")))
+ (let ((spl (string-append bootloader "/libexec/u-boot-sunxi-with-spl.bin"))
+ (u-boot (string-append bootloader "/libexec/u-boot-sunxi-with-spl.fit.itb")))
(write-file-on-device spl (stat:size (stat spl))
- image (* 8 1024)))))
+ image (* 8 1024))
+ (write-file-on-device u-boot (stat:size (stat u-boot))
+ image (* 40 1024)))))
(define install-imx-u-boot
#~(lambda (bootloader root-index image)
diff --git a/gnu/build/linux-boot.scm b/gnu/build/linux-boot.scm
index f20eeaac9f..7d1b3ee835 100644
--- a/gnu/build/linux-boot.scm
+++ b/gnu/build/linux-boot.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2019–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
;;;
@@ -411,11 +411,13 @@ the last argument of `mknod'."
(filter-map string->number (scandir "/proc")))))
(define* (mount-root-file-system root type
- #:key volatile-root? (flags 0) options)
+ #:key volatile-root? (flags 0) options
+ check?)
"Mount the root file system of type TYPE at device ROOT. If VOLATILE-ROOT? is
true, mount ROOT read-only and make it an overlay with a writable tmpfs using
the kernel built-in overlayfs. FLAGS and OPTIONS indicates the options to use
-to mount ROOT, and behave the same as for the `mount' procedure."
+to mount ROOT, and behave the same as for the `mount' procedure.
+If CHECK? is true, first run ROOT's fsck tool (if any) non-interactively."
(if volatile-root?
(begin
@@ -436,7 +438,8 @@ to mount ROOT, and behave the same as for the `mount' procedure."
(mount "none" "/root" "overlay" 0
"lowerdir=/real-root,upperdir=/rw-root/upper,workdir=/rw-root/work"))
(begin
- (check-file-system root type)
+ (when check?
+ (check-file-system root type))
(mount root "/root" type flags options)))
;; Make sure /root/etc/mtab is a symlink to /proc/self/mounts.
@@ -600,7 +603,10 @@ upon error."
root-fs-type
#:volatile-root? volatile-root?
#:flags root-fs-flags
- #:options root-options)
+ #:options root-options
+ #:check? (if root-fs
+ (file-system-check? root-fs)
+ #t))
(mount "none" "/root" "tmpfs"))
;; Mount the specified file systems.
diff --git a/gnu/local.mk b/gnu/local.mk
index fdd1227873..890227c160 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -42,6 +42,7 @@
# Copyright © 2021 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
# Copyright © 2021 Greg Hogan <code@greghogan.com>
# Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
+# Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
#
# This file is part of GNU Guix.
#
@@ -308,6 +309,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/jrnl.scm \
%D%/packages/jose.scm \
%D%/packages/julia.scm \
+ %D%/packages/julia-jll.scm \
%D%/packages/julia-xyz.scm \
%D%/packages/jupyter.scm \
%D%/packages/kawa.scm \
@@ -601,6 +603,7 @@ GNU_SYSTEM_MODULES = \
%D%/services/base.scm \
%D%/services/certbot.scm \
%D%/services/cgit.scm \
+ %D%/services/ci.scm \
%D%/services/configuration.scm \
%D%/services/cuirass.scm \
%D%/services/cups.scm \
@@ -692,6 +695,7 @@ GNU_SYSTEM_MODULES = \
%D%/tests.scm \
%D%/tests/audio.scm \
%D%/tests/base.scm \
+ %D%/tests/ci.scm \
%D%/tests/cups.scm \
%D%/tests/databases.scm \
%D%/tests/desktop.scm \
@@ -807,7 +811,6 @@ dist_patch_DATA = \
%D%/packages/patches/akonadi-not-relocatable.patch \
%D%/packages/patches/akonadi-timestamps.patch \
%D%/packages/patches/allegro-mesa-18.2.5-and-later.patch \
- %D%/packages/patches/amule-crypto-6.patch \
%D%/packages/patches/anki-mpv-args.patch \
%D%/packages/patches/antiword-CVE-2014-8123.patch \
%D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \
@@ -974,8 +977,6 @@ dist_patch_DATA = \
%D%/packages/patches/emacs-exec-path.patch \
%D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch \
%D%/packages/patches/emacs-fix-scheme-indent-function.patch \
- %D%/packages/patches/emacs-geiser-guile-auto-activate.patch \
- %D%/packages/patches/emacs-geiser-autoload-activate-implementation.patch \
%D%/packages/patches/emacs-ignore-empty-xim-styles.patch \
%D%/packages/patches/emacs-json-reformat-fix-tests.patch \
%D%/packages/patches/emacs-highlight-stages-add-gexp.patch \
@@ -1018,7 +1019,6 @@ dist_patch_DATA = \
%D%/packages/patches/fpc-reproducibility.patch \
%D%/packages/patches/fplll-std-fenv.patch \
%D%/packages/patches/freedink-engine-fix-sdl-hints.patch \
- %D%/packages/patches/freebayes-devendor-deps.patch \
%D%/packages/patches/freeglut-gcc-compat.patch \
%D%/packages/patches/freeimage-unbundle.patch \
%D%/packages/patches/fuse-overlapping-headers.patch \
@@ -1254,7 +1254,6 @@ dist_patch_DATA = \
%D%/packages/patches/libffi-float128-powerpc64le.patch \
%D%/packages/patches/libvirt-add-install-prefix.patch \
%D%/packages/patches/libziparchive-add-includes.patch \
- %D%/packages/patches/lksctp-tools-1.0.18-fix-header-file-name.patch \
%D%/packages/patches/localed-xorg-keyboard.patch \
%D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \
%D%/packages/patches/kiki-level-selection-crash.patch \
@@ -1398,7 +1397,6 @@ dist_patch_DATA = \
%D%/packages/patches/mingw-w64-6.0.0-gcc.patch \
%D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \
%D%/packages/patches/mingw-w64-reproducible-gendef.patch \
- %D%/packages/patches/minimap2-aarch64-support.patch \
%D%/packages/patches/minisat-friend-declaration.patch \
%D%/packages/patches/minisat-install.patch \
%D%/packages/patches/mit-krb5-hurd.patch \
@@ -1407,6 +1405,7 @@ dist_patch_DATA = \
%D%/packages/patches/module-init-tools-moduledir.patch \
%D%/packages/patches/monero-use-system-miniupnpc.patch \
%D%/packages/patches/mono-mdoc-timestamping.patch \
+ %D%/packages/patches/mosaicatcher-unbundle-htslib.patch \
%D%/packages/patches/mozjs17-aarch64-support.patch \
%D%/packages/patches/mozjs24-aarch64-support.patch \
%D%/packages/patches/mozjs38-pkg-config-version.patch \
@@ -1439,6 +1438,7 @@ dist_patch_DATA = \
%D%/packages/patches/network-manager-plugin-path.patch \
%D%/packages/patches/nginx-socket-cloexec.patch \
%D%/packages/patches/nsis-env-passthru.patch \
+ %D%/packages/patches/nsis-source-date-epoch.patch \
%D%/packages/patches/nss-getcwd-nonnull.patch \
%D%/packages/patches/nss-increase-test-timeout.patch \
%D%/packages/patches/nss-3.56-pkgconfig.patch \
@@ -1766,7 +1766,6 @@ dist_patch_DATA = \
%D%/packages/patches/webkitgtk-share-store.patch \
%D%/packages/patches/webkitgtk-bind-all-fonts.patch \
%D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch \
- %D%/packages/patches/wgetpaste-update-bpaste.patch \
%D%/packages/patches/wicd-bitrate-none-fix.patch \
%D%/packages/patches/wicd-get-selected-profile-fix.patch \
%D%/packages/patches/wicd-urwid-1.3.patch \
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index fa942169c4..ecd02e336c 100644
--- a/gnu/machine/ssh.scm
+++ b/gnu/machine/ssh.scm
@@ -38,6 +38,9 @@
#:use-module (guix store)
#:use-module (guix utils)
#:use-module ((guix self) #:select (make-config.scm))
+ #:use-module ((guix inferior)
+ #:select (inferior-exception?
+ inferior-exception-arguments))
#:use-module (gcrypt pk-crypto)
#:use-module (ice-9 format)
#:use-module (ice-9 match)
@@ -443,17 +446,47 @@ have you run 'guix archive --generate-key?'")
(mlet %store-monad ((_ (check-deployment-sanity machine))
(boot-parameters (machine-boot-parameters machine)))
(let* ((os (machine-operating-system machine))
+ (host (machine-ssh-configuration-host-name
+ (machine-configuration machine)))
(eval (cut machine-remote-eval machine <>))
(menu-entries (map boot-parameters->menu-entry boot-parameters))
(bootloader-configuration (operating-system-bootloader os))
(bootcfg (operating-system-bootcfg os menu-entries)))
+ (define-syntax-rule (eval/error-handling condition handler ...)
+ ;; Return a wrapper around EVAL such that HANDLER is evaluated if an
+ ;; exception is raised.
+ (lambda (exp)
+ (lambda (store)
+ (guard (condition ((inferior-exception? condition)
+ (values (begin handler ...) store)))
+ (values (run-with-store store (eval exp))
+ store)))))
+
(mbegin %store-monad
(with-roll-back #f
- (switch-to-system eval os))
+ (switch-to-system (eval/error-handling c
+ (raise (formatted-message
+ (G_ "\
+failed to switch systems while deploying '~a':~%~{~s ~}")
+ host
+ (inferior-exception-arguments c))))
+ os))
(with-roll-back #t
(mbegin %store-monad
- (upgrade-shepherd-services eval os)
- (install-bootloader eval bootloader-configuration bootcfg)))))))
+ (upgrade-shepherd-services (eval/error-handling c
+ (warning (G_ "\
+an error occurred while upgrading services on '~a':~%~{~s ~}~%")
+ host
+ (inferior-exception-arguments
+ c)))
+ os)
+ (install-bootloader (eval/error-handling c
+ (raise (formatted-message
+ (G_ "\
+failed to install bootloader on '~a':~%~{~s ~}~%")
+ host
+ (inferior-exception-arguments c))))
+ bootloader-configuration bootcfg)))))))
;;;
@@ -540,4 +573,6 @@ for environment of type '~a'")
;; Local Variables:
;; eval: (put 'remote-let 'scheme-indent-function 1)
+;; eval: (put 'with-roll-back 'scheme-indent-function 1)
+;; eval: (put 'eval/error-handling 'scheme-indent-function 1)
;; End:
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 531686fdbb..48b9c8b893 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1162,14 +1162,14 @@ connection alive.")
bind-release-version)))
(package
(name "isc-dhcp")
- (version "4.4.2")
+ (version "4.4.2-P1")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.isc.org/isc/dhcp/"
version "/dhcp-" version ".tar.gz"))
(sha256
(base32
- "08a5003zdxgl41b29zjkxa92h2i40zyjgxg0npvnhpkfl5jcsz0s"))))
+ "06jsr0cg5rsmyibshrpcb9za0qgwvqccashdma7mlm1rflrh8pmh"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f
@@ -1292,7 +1292,7 @@ connection alive.")
("coreutils*" ,coreutils)
("sed*" ,sed)))
- (home-page "https://www.isc.org/products/DHCP/")
+ (home-page "https://www.isc.org/dhcp/")
(synopsis "Dynamic Host Configuration Protocol (DHCP) tools")
(description
"ISC's Dynamic Host Configuration Protocol (DHCP) distribution provides a
@@ -3608,14 +3608,14 @@ information tool.")
(define-public nnn
(package
(name "nnn")
- (version "4.0")
+ (version "4.1.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/jarun/nnn/releases/download/v"
version "/nnn-v" version ".tar.gz"))
(sha256
- (base32 "0m07nh1cdfikn4bkpni29j61hr9jdwbl0n5fmlm53l1xmn7yq6d2"))))
+ (base32 "1fnf35s3b2nfp18s712n5vhg6idx4rfgwdfv74nc2933v9l2dq7h"))))
(build-system gnu-build-system)
(inputs
`(("ncurses" ,ncurses)
@@ -3626,30 +3626,26 @@ information tool.")
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
- (delete 'configure) ; no configure script
- (add-after 'unpack 'patch-pkg-config
- (lambda _
- (substitute* "Makefile"
- (("pkg-config")
- ,(pkg-config-for-target))))))
+ (delete 'configure)) ; no configure script
#:make-flags
(list
(string-append "PREFIX="
(assoc-ref %outputs "out"))
- (string-append "CC=" ,(cc-for-target)))))
+ (string-append "CC=" ,(cc-for-target))
+ (string-append "PKG_CONFIG=" ,(pkg-config-for-target)))))
(home-page "https://github.com/jarun/nnn")
(synopsis "Terminal file browser")
- (description "@command{nnn} is a fork of @command{noice}, a blazing-fast
-lightweight terminal file browser with easy keyboard shortcuts for
-navigation, opening files and running tasks. There is no config file and
-mime associations are hard-coded. The incredible user-friendliness and speed
-make it a perfect utility on modern distros.")
+ (description
+ "@command{nnn} is a fork of @command{noice}, a fast and minimal text
+terminal file browser with keyboard shortcuts for navigation, opening files and
+running tasks. There is no configuration file and MIME associations are
+hard-coded.")
(license license:bsd-2)))
(define-public thermald
(package
(name "thermald")
- (version "2.4.4")
+ (version "2.4.5")
(source
(origin
(method git-fetch)
@@ -3658,7 +3654,7 @@ make it a perfect utility on modern distros.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1k0r2c13fihjndwfh0byw0i8ni4lzsjgwz874pvpj1l1nvjj0ajx"))))
+ (base32 "1y8s0cpjm01bz4isp3ksvnrbhpp3phivdhsb0w2kxhv09sfxkc5g"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -3672,13 +3668,7 @@ make it a perfect utility on modern distros.")
(modify-phases %standard-phases
(add-before 'bootstrap 'no-early-./configure
(lambda _
- (setenv "NO_CONFIGURE" "yet")
- ;; XXX thd_trip_point.h redefines "__STDC_LIMIT_MACROS" after
- ;; <xz>/include/lzma.h. ./configure forcibly appends -Werror
- ;; to CXXFLAGS, overriding any -Wno-error we'd add.
- (substitute* "configure.ac"
- (("-Werror") ""))
- #t)))))
+ (setenv "NO_CONFIGURE" "yet"))))))
(native-inputs
`(("autoconf" ,autoconf)
("autoconf-archive" ,autoconf-archive)
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index a4d3f5ac68..d0312426d0 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -341,7 +341,7 @@ precision.")
(define-public giac
(package
(name "giac")
- (version "1.7.0-9")
+ (version "1.7.0-11")
(source
(origin
(method url-fetch)
@@ -353,7 +353,7 @@ precision.")
"~parisse/debian/dists/stable/main/source/"
"giac_" version ".tar.gz"))
(sha256
- (base32 "0yl5h13rnis8gqg48g9z719d5xfgxjcxz7bwbdqlwsvdy42crrim"))))
+ (base32 "12njy2akcc3sj1fmq52v19m4qd1ysrdcpc9a3zslkxsnidjix81m"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index 3a915c7fda..71fc8f20b0 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Pkill -9 <pkill9@runbox.com>
-;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -25,10 +25,12 @@
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages assembly)
#:use-module (gnu packages autotools)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
@@ -45,6 +47,8 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages jemalloc)
+ #:use-module (gnu packages networking)
+ #:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pulseaudio)
@@ -320,6 +324,78 @@ audio or video backends, ensuring good performance.")
(home-page "https://www.gnu.org/software/gnash/")
(license license:gpl3+))))
+;; This package provides a standalone (no browser plugin) version of
+;; Lightspark.
+(define-public lightspark
+ (package
+ (name "lightspark")
+ (version "0.8.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lightspark/lightspark")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "17l5gzb7p8nivx1a2frca2jklcjdsk2qj4jniv3z8bh307ksz254"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #f ;requires Adobe Flex SDK, see README.tests
+ ;; Disable browser plugins because neither NPAPI nor PPAPI is
+ ;; supported in the browsers we have.
+ #:configure-flags
+ '("-DCOMPILE_NPAPI_PLUGIN=FALSE"
+ "-DCOMPILE_PPAPI_PLUGIN=FALSE")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'prepare-build-environment
+ (lambda _
+ ;; Use relative etc path.
+ (substitute* "CMakeLists.txt" (("\\/etc") "etc"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "./tests")))))))
+ (native-inputs
+ `(("gettext" ,gettext-minimal)
+ ("glib:bin" ,glib "bin")
+ ("nasm" ,nasm)
+ ("perl" ,perl)
+ ("pkg-config" ,pkg-config)
+ ("python" ,python-wrapper)))
+ (inputs
+ `(("cairo" ,cairo)
+ ("curl" ,curl)
+ ("ffmpeg" ,ffmpeg)
+ ("freeglut" ,freeglut)
+ ("glew" ,glew)
+ ("glibmm" ,glibmm)
+ ("gnash" ,gnash)
+ ("gnutls" ,gnutls)
+ ("libjpeg" ,libjpeg-turbo)
+ ("openssl" ,openssl)
+ ("pango" ,pango)
+ ("pcre2" ,pcre2)
+ ("rtmpdump" ,rtmpdump)
+ ("sdl2" ,sdl2)
+ ("sdl2-mixer" ,sdl2-mixer)
+ ("zlib" ,zlib)))
+ (home-page "https://lightspark.github.io/")
+ (synopsis "Flash player implementation")
+ (description
+ "Lightspark is a Flash player implementation for playing files in the SWF
+format. It supports SWF files written on all versions of the ActionScript
+language.")
+ ;; NOTE: The bundled pugixml is a fork specific to Lightspark and
+ ;; incompatible with the one we have.
+ ;; FIXME: we also have jxrlib, but the build fails to find JXRMeta.h so we
+ ;; use the bundled one for now.
+ (license (list license:lgpl3+ ;lightspark
+ license:mpl2.0 ;avmplus
+ license:bsd-2 ;jxrlib
+ license:expat)))) ;pugixml, PerlinNoise
+
(define-public papagayo
(let ((commit "e143684b30e59fe4a554f965cb655d23cbe93ee7")
(revision "1"))
diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm
index e19c369517..a86984b28c 100644
--- a/gnu/packages/aspell.scm
+++ b/gnu/packages/aspell.scm
@@ -489,14 +489,14 @@ under permissive licensing terms. See the 'Copyright' file."))))
(define-public ispell
(package
(name "ispell")
- (version "3.4.02")
+ (version "3.4.04")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.cs.hmc.edu/~geoff/tars/ispell-"
version ".tar.gz"))
(sha256
- (base32 "0b6rqzqjdhwf323sf1dv8qzx5pxa5asz618922r59zjp65660yb6"))))
+ (base32 "0gp1rwn8grkvz28wgisc2j9w9svldnaiahl3lyis118xabqddg47"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6d1c4ddfe6..c4a686957d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -228,7 +228,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.")
(define-public gnuastro
(package
(name "gnuastro")
- (version "0.14")
+ (version "0.15")
(source
(origin
(method url-fetch)
@@ -236,7 +236,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.")
version ".tar.lz"))
(sha256
(base32
- "1xp6n42qxv0x6yigi2w2l5k8006smv27lhrcssysgsvzbydghzg5"))))
+ "1jjr3ixxbpsr5m4s7ahh12ymcnlvjzwcp02ya16b1lvzrz1wmhy4"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--disable-static")))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 930c111d5e..b250bc3af0 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -302,7 +302,7 @@ Linux kernel.")
(define-public libopenmpt
(package
(name "libopenmpt")
- (version "0.5.8")
+ (version "0.5.9")
(source
(origin
(method url-fetch)
@@ -310,7 +310,7 @@ Linux kernel.")
(string-append "https://download.openmpt.org/archive/libopenmpt/src/"
"libopenmpt-" version "+release.autotools.tar.gz"))
(sha256
- (base32 "1kca5nc870mfv7i4ww2g1q9jn61gsq46irsypbr6fgxpfh8w5qi9"))))
+ (base32 "0h86p8mnpm98vc4v6jbvrmm02fch7dnn332i26fg3a2s1738m04d"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -1022,7 +1022,7 @@ generators of mostly elementary and occasionally exotic nature.")
(define-public infamous-plugins
(package
(name "infamous-plugins")
- (version "0.2.04")
+ (version "0.3.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1031,7 +1031,7 @@ generators of mostly elementary and occasionally exotic nature.")
(file-name (git-file-name name version))
(sha256
(base32
- "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
+ "1r72agk5nxf5k0mghcc2j90z43j5d9i7rqjmf49jfyqnd443isip"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -1041,6 +1041,12 @@ generators of mostly elementary and occasionally exotic nature.")
(lambda _
(substitute* (find-files "." "CMakeLists.txt")
(("-msse2 -mfpmath=sse") ""))
+ #t))
+ (add-after 'unpack 'fix-build-with-newer-lv2
+ (lambda _
+ ;; https://github.com/ssj71/infamousPlugins/commit/4c7275b1fa8ea3296446421cbd29ec2df66588c0
+ (substitute* (find-files "src" ".*\\.cxx")
+ (("_LV2UI_Descriptor") "LV2UI_Descriptor"))
#t)))))
(inputs
`(("cairo" ,cairo)
@@ -4313,7 +4319,7 @@ representations.")
(define-public cava
(package
(name "cava")
- (version "0.7.3")
+ (version "0.7.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4322,7 +4328,7 @@ representations.")
(file-name (git-file-name name version))
(sha256
(base32
- "04j5hb29hivcbk542sfsx9m57dbnj2s6qpvy9fs488zvgjbgxrai"))))
+ "1mziklmqifhnb4kg9ia2r56r8wjn6xp40bkpf484hsgqvnrccl86"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
@@ -4465,7 +4471,7 @@ library.")
(define-public faudio
(package
(name "faudio")
- (version "21.05")
+ (version "21.06")
(source
(origin
(method git-fetch)
@@ -4474,7 +4480,7 @@ library.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0lzvfx5gg5m6jbdzqwkjl4wq4fdg5n98fxn5x8n65vgvrj95sx6z"))))
+ (base32 "1nnx4l1r5hwdaw824d4fmd558qsqa22qzpvnkhs8nkjr40cnidkr"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DGSTREAMER=ON")))
@@ -5165,14 +5171,18 @@ while still staying in time.")
(define-public butt
(package
(name "butt")
- (version "0.1.29")
+ (version "0.1.30")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/butt/butt/butt-"
version "/butt-" version ".tar.gz"))
(sha256
(base32
- "0nbz0z4d7krvhmnwn10594gwc61gn2dlb5fazmynjfisrfdswqlg"))))
+ "1dfspdh3f18lpp7asxpj63b9zfpvazi7shgrdacg17gd42ycayq5"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "src/butt.cpp"
+ ((".*zica.*") "")))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -5209,7 +5219,7 @@ while still staying in time.")
version "_manual.pdf"))
(sha256
(base32
- "1hhgdhdg5s86hjcbwh856gcd3kcch0i5xgi3i3v02zz3xmzl7gg3"))))))
+ "1w3krh7f2v5vdz18hqycnpn0qv1x6xl6pa1najgp4jbfisjc1mn8"))))))
(home-page "https://danielnoethen.de/butt/")
(synopsis "Audio streaming tool")
(description "Butt is a tool to stream audio to a ShoutCast or
diff --git a/gnu/packages/axoloti.scm b/gnu/packages/axoloti.scm
index 0b12e4fe29..c6dd748773 100644
--- a/gnu/packages/axoloti.scm
+++ b/gnu/packages/axoloti.scm
@@ -125,6 +125,11 @@
(("arm-none-eabi-(gcc|g\\+\\+|objcopy|objdump)" tool)
(which tool)))
+ ;; XXX: for some reason the whitespace substitution does not
+ ;; work, so we disable it.
+ (substitute* "firmware/Makefile.patch"
+ (("^BDIR=.*") "BDIR=${axoloti_home}/build\n"))
+
;; Hardcode full path to compiler tools
(substitute* '("firmware/Makefile"
"firmware/flasher/Makefile"
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index a537cd46f3..6a6ac1d8d5 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -5,7 +5,7 @@
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2021 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 malte Frank Gerdes <malte.f.gerdes@gmail.com>
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -52,14 +52,14 @@
(define-public fio
(package
(name "fio")
- (version "3.26")
+ (version "3.27")
(source (origin
(method url-fetch)
(uri (string-append "https://brick.kernel.dk/snaps/"
"fio-" version ".tar.bz2"))
(sha256
(base32
- "1114h60vw63bim872an33xpvjfib6sc9dwj9xvk0yw41xjzfpp06"))))
+ "0akaixip86ycbxr13bjff2121rgfbz35fa9l39677wpwzckp4f4d"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@@ -126,13 +126,9 @@ is to write a job file matching the I/O load one wants to simulate.")
(license (list license:gpl2 license:gpl2+ license:bsd-2
license:public-domain))))
-;; Parameterized in anticipation of m(va)pich support
-(define (intel-mpi-benchmarks mpi)
+(define-public intel-mpi-benchmarks/openmpi
(package
- (name (string-append "intel-mpi-benchmarks"
- (if (string=? (package-name mpi) "openmpi")
- ""
- (string-append "-" (package-name mpi)))))
+ (name "intel-mpi-benchmarks")
(version "2019.6")
(source (origin
(method git-fetch)
@@ -154,7 +150,7 @@ is to write a job file matching the I/O load one wants to simulate.")
#t))))
(build-system gnu-build-system)
(inputs
- `(("mpi" ,mpi)))
+ `(("openmpi" ,openmpi)))
(arguments
`(#:phases
(modify-phases %standard-phases
@@ -194,9 +190,6 @@ Efficiency of the MPI implementation.
@end itemize")
(license license:cpl1.0)))
-(define-public intel-mpi-benchmarks/openmpi
- (intel-mpi-benchmarks openmpi))
-
(define-public imb-openmpi
(deprecated-package "imb-openmpi" intel-mpi-benchmarks/openmpi))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 45e31a5760..d84481bdb8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,15 +1,16 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
+;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -35,8 +36,10 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages boost)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
@@ -103,6 +106,29 @@ analysis.")
database, assembled using data from REACTOME.")
(license license:cc-by4.0)))
+(define-public r-bsgenome-btaurus-ucsc-bostau8
+ (package
+ (name "r-bsgenome-btaurus-ucsc-bostau8")
+ (version "1.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
+ version 'annotation))
+ (sha256
+ (base32
+ "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
+ (properties
+ `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
+ (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
+ (description "This package provides the full genome sequences for Bos
+taurus (UCSC version bosTau8).")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
@@ -412,6 +438,28 @@ in Biostrings objects.")
ID and species. It is used by functions in the GenomeInfoDb package.")
(license license:artistic2.0)))
+(define-public r-go-db
+ (package
+ (name "r-go-db")
+ (version "3.7.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GO.db" version 'annotation))
+ (sha256
+ (base32
+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
+ (properties
+ `((upstream-name . "GO.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/GO.db")
+ (synopsis "Annotation maps describing the entire Gene Ontology")
+ (description
+ "The purpose of this GO.db annotation package is to provide detailed
+information about the latest version of the Gene Ontologies.")
+ (license license:artistic2.0)))
+
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
@@ -934,6 +982,64 @@ datasets which are derived from the Allen Brain Atlas:
All datasets are restricted to protein coding genes.")
(license license:gpl2+)))
+(define-public r-aneufinderdata
+ (package
+ (name "r-aneufinderdata")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AneuFinderData" version 'experiment))
+ (sha256
+ (base32
+ "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks"))))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/AneuFinderData/")
+ (synopsis "Data package for @code{AneuFinder}")
+ (description "This package contains data used by @code{AneuFinder}.")
+ (license license:artistic2.0)))
+
+(define-public r-aneufinder
+ (package
+ (name "r-aneufinder")
+ (version "1.20.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AneuFinder" version))
+ (sha256
+ (base32
+ "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-aneufinderdata" ,r-aneufinderdata)
+ ("r-ecp" ,r-ecp)
+ ("r-foreach" ,r-foreach)
+ ("r-doparallel" ,r-doparallel)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-bamsignals" ,r-bamsignals)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-reordercluster" ,r-reordercluster)
+ ("r-mclust" ,r-mclust)
+ ("r-cowplot" ,r-cowplot)))
+ (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
+calling, plotting, export and analysis from whole-genome single cell
+sequencing data.")
+ (license license:artistic2.0)))
+
(define-public r-arrmdata
(package
(name "r-arrmdata")
@@ -974,6 +1080,30 @@ from Illumina 450k methylation arrays.")
chromstaR package.")
(license license:gpl3)))
+(define-public r-copyhelper
+ (package
+ (name "r-copyhelper")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
+ (sha256
+ (base32
+ "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+ (properties `((upstream-name . "CopyhelpeR")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/CopyhelpeR/")
+ (synopsis "Helper files for CopywriteR")
+ (description
+ "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10. In addition, it contains a blacklist filter to remove regions that
+display copy number variation. Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+ (license license:gpl2)))
+
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
@@ -998,6 +1128,32 @@ chromstaR package.")
genomes and gene ID formats, largely based on the UCSC table browser.")
(license license:lgpl2.0+)))
+(define-public r-genomationdata
+ (package
+ (name "r-genomationdata")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomationData" version 'experiment))
+ (sha256
+ (base32
+ "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+ (properties
+ `((upstream-name . "genomationData")))
+ (build-system r-build-system)
+ ;; As this package provides little more than large data files, it doesn't
+ ;; make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Experimental data for use with the genomation package")
+ (description
+ "This package contains experimental genetic data for use with the
+genomation package. Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+ (license license:gpl3+)))
+
(define-public r-pasilla
(package
(name "r-pasilla")
@@ -1165,14 +1321,14 @@ across the entire multi-'omics experiment.")
(define-public r-biocversion
(package
(name "r-biocversion")
- (version "3.12.0")
+ (version "3.13.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocVersion" version))
(sha256
(base32
- "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
+ "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi"))))
(properties `((upstream-name . "BiocVersion")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1185,13 +1341,13 @@ of Bioconductor.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.36.1")
+ (version "0.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5"))))
+ "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@@ -1205,13 +1361,13 @@ packages.")
(define-public r-coverageview
(package
(name "r-coverageview")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
- "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
+ "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
@@ -1232,13 +1388,13 @@ how the coverage distributed across the genome.")
(define-public r-cummerbund
(package
(name "r-cummerbund")
- (version "2.32.0")
+ (version "2.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
- "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
+ "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -1259,16 +1415,76 @@ data. In addition, provides numerous plotting functions for commonly
used visualizations.")
(license license:artistic2.0)))
+(define-public r-decipher
+ (package
+ (name "r-decipher")
+ (version "2.20.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DECIPHER" version))
+ (sha256
+ (base32
+ "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-iranges" ,r-iranges)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://www.bioconductor.org/packages/DECIPHER/")
+ (synopsis "Tools for deciphering and managing biological sequences")
+ (description "This package provides a toolset for deciphering and managing
+biological sequences.")
+ (license license:gpl3)))
+
+(define-public r-deepsnv
+ (package
+ (name "r-deepsnv")
+ (version "1.38.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "deepSNV" version))
+ (sha256
+ (base32
+ "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs"))))
+ (properties `((upstream-name . "deepSNV")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)
+ ("r-vgam" ,r-vgam)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/gerstung-lab/deepSNV/")
+ (synopsis "Detection of subclonal SNVs in deep sequencing data")
+ (description
+ "This package provides quantitative variant callers for detecting
+subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
+The deepSNV algorithm is used for a comparative setup with a control experiment
+of the same loci and uses a beta-binomial model and a likelihood ratio test to
+discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
+computes a Bayes classifier based on a beta-binomial model for variant calling
+with multiple samples for precisely estimating model parameters - such as local
+error rates and dispersion - and prior knowledge, e.g. from variation data
+bases such as COSMIC.")
+ (license license:gpl3)))
+
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.16.3")
+ (version "0.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
+ "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
@@ -1295,18 +1511,19 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-bluster
(package
(name "r-bluster")
- (version "1.0.0")
+ (version "1.2.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "bluster" version))
(sha256
(base32
- "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
+ "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg"))))
(properties `((upstream-name . "bluster")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocneighbors" ,r-biocneighbors)
("r-biocparallel" ,r-biocparallel)
+ ("r-cluster" ,r-cluster)
("r-igraph" ,r-igraph)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
@@ -1324,13 +1541,13 @@ and evaluate clustering results.")
(define-public r-ideoviz
(package
(name "r-ideoviz")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
- "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
+ "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -1348,13 +1565,13 @@ arbitrary genomic intervals along chromosomal ideogram.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.24.1")
+ (version "2.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
+ "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -1406,18 +1623,20 @@ absolute GSEA.")
(define-public r-bisquerna
(package
(name "r-bisquerna")
- (version "1.0.4")
+ (version "1.0.5")
(source (origin
(method url-fetch)
(uri (cran-uri "BisqueRNA" version))
(sha256
(base32
- "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+ "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
(properties `((upstream-name . "BisqueRNA")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-limsolve" ,r-limsolve)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://www.biorxiv.org/content/10.1101/669911v1")
(synopsis "Decomposition of bulk expression with single-cell sequencing")
(description "This package provides tools to accurately estimate cell type
@@ -1501,17 +1720,45 @@ optimized in C++, and the main interface function provides an easy way of
performing parallel computations on multicore machines.")
(license license:gpl2+)))
+(define-public r-affy
+ (package
+ (name "r-affy")
+ (version "1.70.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affy" version))
+ (sha256
+ (base32
+ "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://bioconductor.org/packages/affy")
+ (synopsis "Methods for affymetrix oligonucleotide arrays")
+ (description
+ "This package contains functions for exploratory oligonucleotide array
+analysis.")
+ (license license:lgpl2.0+)))
+
(define-public r-affycomp
(package
(name "r-affycomp")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycomp" version))
(sha256
(base32
- "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
+ "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2"))))
(properties `((upstream-name . "affycomp")))
(build-system r-build-system)
(propagated-inputs `(("r-biobase" ,r-biobase)))
@@ -1525,14 +1772,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
(define-public r-affycompatible
(package
(name "r-affycompatible")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AffyCompatible" version))
(sha256
(base32
- "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
+ "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj"))))
(properties
`((upstream-name . "AffyCompatible")))
(build-system r-build-system)
@@ -1553,14 +1800,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
(define-public r-affycontam
(package
(name "r-affycontam")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyContam" version))
(sha256
(base32
- "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
+ "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj"))))
(properties `((upstream-name . "affyContam")))
(build-system r-build-system)
(propagated-inputs
@@ -1578,14 +1825,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
(define-public r-affycoretools
(package
(name "r-affycoretools")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycoretools" version))
(sha256
(base32
- "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
+ "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh"))))
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
@@ -1617,17 +1864,41 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
to streamline the more common analyses that a Biostatistician might see.")
(license license:artistic2.0)))
+(define-public r-affyio
+ (package
+ (name "r-affyio")
+ (version "1.62.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affyio" version))
+ (sha256
+ (base32
+ "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/bmbolstad/affyio")
+ (synopsis "Tools for parsing Affymetrix data files")
+ (description
+ "This package provides routines for parsing Affymetrix data files based
+upon file format information. The primary focus is on accessing the CEL and
+CDF file formats.")
+ (license license:lgpl2.0+)))
+
(define-public r-affxparser
(package
(name "r-affxparser")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affxparser" version))
(sha256
(base32
- "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
+ "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l"))))
(properties `((upstream-name . "affxparser")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1648,14 +1919,14 @@ structure.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
+ "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -1675,13 +1946,13 @@ microarrays.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
+ "117zh7iqa6phsrxrkv45kxraamm3vbfz5i1a8vkhyalhdbs5ssph"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -1689,6 +1960,7 @@ microarrays.")
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-dbi" ,r-dbi)
+ ("r-keggrest" ,r-keggrest)
("r-iranges" ,r-iranges)
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)))
@@ -1701,17 +1973,43 @@ microarrays.")
annotation data packages using SQLite data storage.")
(license license:artistic2.0)))
+(define-public r-annotationfilter
+ (package
+ (name "r-annotationfilter")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationFilter" version))
+ (sha256
+ (base32
+ "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"))))
+ (properties
+ `((upstream-name . "AnnotationFilter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-lazyeval" ,r-lazyeval)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/Bioconductor/AnnotationFilter")
+ (synopsis "Facilities for filtering Bioconductor annotation resources")
+ (description
+ "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources. The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+ (license license:artistic2.0)))
+
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
+ "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@@ -1733,16 +2031,114 @@ annotation data packages using SQLite data storage.")
databases. Packages produced are intended to be used with AnnotationDbi.")
(license license:artistic2.0)))
+(define-public r-annotationhub
+ (package
+ (name "r-annotationhub")
+ (version "3.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationHub" version))
+ (sha256
+ (base32
+ "1p9773fv7j7q4x1sjqqaw32qy9lqn2gf6gkynh1d8n1kd7v7sclp"))))
+ (properties `((upstream-name . "AnnotationHub")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocfilecache" ,r-biocfilecache)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biocversion" ,r-biocversion)
+ ("r-curl" ,r-curl)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+ ("r-rappdirs" ,r-rappdirs)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/AnnotationHub")
+ (synopsis "Client to access AnnotationHub resources")
+ (description
+ "This package provides a client for the Bioconductor AnnotationHub web
+resource. The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification. The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+ (license license:artistic2.0)))
+
+(define-public r-aroma-light
+ (package
+ (name "r-aroma-light")
+ (version "3.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "aroma.light" version))
+ (sha256
+ (base32
+ "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5"))))
+ (properties `((upstream-name . "aroma.light")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrixstats" ,r-matrixstats)
+ ("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/aroma.light")
+ (synopsis "Methods for normalization and visualization of microarray data")
+ (description
+ "This package provides methods for microarray analysis that take basic
+data types such as matrices and lists of vectors. These methods can be used
+standalone, be utilized in other packages, or be wrapped up in higher-level
+classes.")
+ (license license:gpl2+)))
+
+(define-public r-bamsignals
+ (package
+ (name "r-bamsignals")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bamsignals" version))
+ (sha256
+ (base32
+ "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/bamsignals")
+ (synopsis "Extract read count signals from bam files")
+ (description
+ "This package efficiently obtains count vectors from indexed bam
+files. It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles. It also handles
+paired-end data.")
+ (license license:gpl2+)))
+
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.50.0")
+ (version "2.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
+ "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
@@ -1758,26 +2154,25 @@ on Bioconductor or which replace R functions.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.46.3")
+ (version "2.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+ "1h8lzd63qvy1y75nlnhazpkyhl6g1hz80baqg20gpxbv38wkyf55"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biocfilecache" ,r-biocfilecache)
+ ("r-digest" ,r-digest)
("r-httr" ,r-httr)
- ("r-openssl" ,r-openssl)
("r-progress" ,r-progress)
("r-rappdirs" ,r-rappdirs)
("r-stringr" ,r-stringr)
- ("r-xml" ,r-xml)
- ("r-xml2" ,r-xml2)))
+ ("r-xml" ,r-xml)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/biomaRt")
@@ -1796,13 +2191,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.24.1")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
+ "17w4gdajxxmsfgiwycp1d7rbxdqhc5jnngcb58ky0fv5xbv9f4j0"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -1851,19 +2246,20 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.58.0")
+ (version "2.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
+ "0xidh6wp0l47g1j9x8d4fs91ky6pi5nzf85ry801gqd2gqajh2zy"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-crayon" ,r-crayon)
+ ("r-genomeinfodb" ,r-genomeinfodb)
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
@@ -1875,17 +2271,90 @@ matching algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.")
(license license:artistic2.0)))
+(define-public r-biovizbase
+ (package
+ (name "r-biovizbase")
+ (version "1.40.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biovizBase" version))
+ (sha256
+ (base32
+ "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23"))))
+ (properties `((upstream-name . "biovizBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dichromat" ,r-dichromat)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rlang" ,r-rlang)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/biovizBase")
+ (synopsis "Basic graphic utilities for visualization of genomic data")
+ (description
+ "The biovizBase package is designed to provide a set of utilities, color
+schemes and conventions for genomic data. It serves as the base for various
+high-level packages for biological data visualization. This saves development
+effort and encourages consistency.")
+ (license license:artistic2.0)))
+
+(define-public r-bsgenome
+ (package
+ (name "r-bsgenome")
+ (version "1.60.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BSgenome" version))
+ (sha256
+ (base32
+ "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn"))))
+ (properties
+ `((upstream-name . "BSgenome")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/BSgenome")
+ (synopsis "Infrastructure for Biostrings-based genome data packages")
+ (description
+ "This package provides infrastructure shared by all Biostrings-based
+genome data packages and support for efficient SNP representation.")
+ (license license:artistic2.0)))
+
(define-public r-category
(package
(name "r-category")
- (version "2.56.0")
+ (version "2.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
+ "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
@@ -1906,17 +2375,201 @@ biological sequences or sets of sequences.")
analysis.")
(license license:artistic2.0)))
+(define-public r-chipseeker
+ (package
+ (name "r-chipseeker")
+ (version "1.28.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ChIPseeker" version))
+ (sha256
+ (base32
+ "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-boot" ,r-boot)
+ ("r-enrichplot" ,r-enrichplot)
+ ("r-iranges" ,r-iranges)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-gtools" ,r-gtools)
+ ("r-dplyr" ,r-dplyr)
+ ("r-plotrix" ,r-plotrix)
+ ("r-dplyr" ,r-dplyr)
+ ("r-magrittr" ,r-magrittr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-txdb-hsapiens-ucsc-hg19-knowngene"
+ ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+ (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
+ (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
+ (description "This package implements functions to retrieve the nearest
+genes around the peak, annotate genomic region of the peak, statstical methods
+for estimate the significance of overlap among ChIP peak data sets, and
+incorporate GEO database for user to compare the own dataset with those
+deposited in database. The comparison can be used to infer cooperative
+regulation and thus can be used to generate hypotheses. Several visualization
+functions are implemented to summarize the coverage of the peak experiment,
+average profile and heatmap of peaks binding to TSS regions, genomic
+annotation, distance to TSS, and overlap of peaks or genes.")
+ (license license:artistic2.0)))
+
+(define-public r-chipseq
+ (package
+ (name "r-chipseq")
+ (version "1.42.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chipseq" version))
+ (sha256
+ (base32
+ "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://bioconductor.org/packages/chipseq")
+ (synopsis "Package for analyzing ChIPseq data")
+ (description
+ "This package provides tools for processing short read data from ChIPseq
+experiments.")
+ (license license:artistic2.0)))
+
+(define-public r-complexheatmap
+ (package
+ (name "r-complexheatmap")
+ (version "2.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ComplexHeatmap" version))
+ (sha256
+ (base32
+ "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f"))))
+ (properties
+ `((upstream-name . "ComplexHeatmap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cairo" ,r-cairo)
+ ("r-circlize" ,r-circlize)
+ ("r-clue" ,r-clue)
+ ("r-colorspace" ,r-colorspace)
+ ("r-digest" ,r-digest)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-globaloptions" ,r-globaloptions)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-png" ,r-png)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://github.com/jokergoo/ComplexHeatmap")
+ (synopsis "Making Complex Heatmaps")
+ (description
+ "Complex heatmaps are efficient to visualize associations between
+different sources of data sets and reveal potential structures. This package
+provides a highly flexible way to arrange multiple heatmaps and supports
+self-defined annotation graphics.")
+ (license license:gpl2+)))
+
+(define-public r-copywriter
+ (package
+ (name "r-copywriter")
+ (version "2.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopywriteR" version))
+ (sha256
+ (base32
+ "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"))))
+ (properties `((upstream-name . "CopywriteR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-chipseq" ,r-chipseq)
+ ("r-copyhelper" ,r-copyhelper)
+ ("r-data-table" ,r-data-table)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-futile-logger" ,r-futile-logger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/PeeperLab/CopywriteR")
+ (synopsis "Copy number information from targeted sequencing")
+ (description
+ "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads. It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels. Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+ (license license:gpl2)))
+
+(define-public r-deseq
+ (package
+ (name "r-deseq")
+ (version "1.39.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq" version))
+ (sha256
+ (base32
+ "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
+ (properties `((upstream-name . "DESeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-lattice" ,r-lattice)
+ ("r-locfit" ,r-locfit)
+ ("r-mass" ,r-mass)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "https://www-huber.embl.de/users/anders/DESeq/")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides tools for estimating variance-mean dependence in
+count data from high-throughput genetic sequencing assays and for testing for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:gpl3+)))
+
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.30.1")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
+ "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
@@ -1947,14 +2600,14 @@ distribution.")
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+ "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -1989,16 +2642,85 @@ testing. The package also provides functions for the visualization and
exploration of the results.")
(license license:gpl3+)))
+(define-public r-dirichletmultinomial
+ (package
+ (name "r-dirichletmultinomial")
+ (version "1.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DirichletMultinomial" version))
+ (sha256
+ (base32
+ "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl"))))
+ (properties
+ `((upstream-name . "DirichletMultinomial")))
+ (build-system r-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/DirichletMultinomial")
+ (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
+ (description
+ "Dirichlet-multinomial mixture models can be used to describe variability
+in microbial metagenomic data. This package is an interface to code
+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
+1-15.")
+ (license license:lgpl3)))
+
+(define-public r-edaseq
+ (package
+ (name "r-edaseq")
+ (version "2.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EDASeq" version))
+ (sha256
+ (base32
+ "1mqpi2iz4azr31b3ajsqb4n9izjh85dx642844n059c8s2pfmivh"))))
+ (properties `((upstream-name . "EDASeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-aroma-light" ,r-aroma-light)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/drisso/EDASeq")
+ (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+ (description
+ "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data. Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization. Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+ (license license:artistic2.0)))
+
(define-public r-edger
(package
(name "r-edger")
- (version "3.32.1")
+ (version "3.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
+ "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -2017,17 +2739,123 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
CAGE.")
(license license:gpl2+)))
+(define-public r-ensembldb
+ (package
+ (name "r-ensembldb")
+ (version "2.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ensembldb" version))
+ (sha256
+ (base32
+ "100m2mzxl4pmldqixzfdznnd4nqbykk2l7n4xazqjpnlpcldy2dj"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-curl" ,r-curl)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/jotsetung/ensembldb")
+ (synopsis "Utilities to create and use Ensembl-based annotation databases")
+ (description
+ "The package provides functions to create and use transcript-centric
+annotation databases/packages. The annotation for the databases are directly
+fetched from Ensembl using their Perl API. The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+ ;; No version specified
+ (license license:lgpl3+)))
+
+(define-public r-fastseg
+ (package
+ (name "r-fastseg")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fastseg" version))
+ (sha256
+ (base32
+ "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
+ (synopsis "Fast segmentation algorithm for genetic sequencing data")
+ (description
+ "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments. Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts. Most
+generally, it can segment data given as a matrix or as a vector. Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+ (license license:lgpl2.0+)))
+
+(define-public r-gage
+ (package
+ (name "r-gage")
+ (version "2.42.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gage" version))
+ (sha256
+ (base32
+ "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-keggrest" ,r-keggrest)))
+ (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+ "articles/10.1186/1471-2105-10-161"))
+ (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+ (description
+ "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis. GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity. The gage package provides functions for
+basic GAGE analysis, result processing and presentation. In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms. These functions and data are also useful for gene set
+analysis using other methods.")
+ (license license:gpl2+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.72.1")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
+ "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)
@@ -2045,16 +2873,83 @@ CAGE.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-geneoverlap
+ (package
+ (name "r-geneoverlap")
+ (version "1.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GeneOverlap" version))
+ (sha256
+ (base32
+ "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-gplots" ,r-gplots)))
+ (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
+ (synopsis "Test and visualize gene overlaps")
+ (description "This package can be used to test two sets of gene lists
+and visualize the results.")
+ (license license:gpl3)))
+
+(define-public r-genomation
+ (package
+ (name "r-genomation")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomation" version))
+ (sha256
+ (base32
+ "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plotrix" ,r-plotrix)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqpattern" ,r-seqpattern)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Summary, annotation and visualization of genomic data")
+ (description
+ "This package provides a package for summary and annotation of genomic
+intervals. Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc. The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc. The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals. In addition, it can use BAM or BigWig files as input.")
+ (license license:artistic2.0)))
+
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.26.7")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516"))))
+ "0wjd7sh7kr9lfcdbzm5jdynl84nfsl7nqvly92qqrdcxd2sjfr63"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -2075,16 +2970,127 @@ translation between different chromosome sequence naming conventions (e.g.,
names in their natural, rather than lexicographic, order.")
(license license:artistic2.0)))
+(define-public r-genomicalignments
+ (package
+ (name "r-genomicalignments")
+ (version "1.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicAlignments" version))
+ (sha256
+ (base32
+ "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2"))))
+ (properties
+ `((upstream-name . "GenomicAlignments")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/GenomicAlignments")
+ (synopsis "Representation and manipulation of short genomic alignments")
+ (description
+ "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome). This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+ (license license:artistic2.0)))
+
+(define-public r-genomicfeatures
+ (package
+ (name "r-genomicfeatures")
+ (version "1.44.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFeatures" version))
+ (sha256
+ (base32
+ "0y7lnvfcfrs72xbkn67xcqyz9csl5696mr2zl425fkhmnmimm4fg"))))
+ (properties
+ `((upstream-name . "GenomicFeatures")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocio" ,r-biocio)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GenomicFeatures")
+ (synopsis "Tools for working with transcript centric annotations")
+ (description
+ "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations. With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future). This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes. Flexible methods are provided for
+extracting the desired features in a convenient format.")
+ (license license:artistic2.0)))
+
+(define-public r-genomicfiles
+ (package
+ (name "r-genomicfiles")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFiles" version))
+ (sha256
+ (base32
+ "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y"))))
+ (properties `((upstream-name . "GenomicFiles")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixgenerics" ,r-matrixgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/GenomicFiles")
+ (synopsis "Distributed computing by file or by range")
+ (description
+ "This package provides infrastructure for parallel computations
+distributed by file or by range. User defined mapper and reducer functions
+provide added flexibility for data combination and manipulation.")
+ (license license:artistic2.0)))
+
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
+ "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
@@ -2109,14 +3115,14 @@ manipulating genomic intervals and variables defined along a genome.")
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.56.0")
+ (version "2.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
+ "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
@@ -2140,14 +3146,14 @@ testing and other simple calculations.")
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.52.1")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
+ "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
@@ -2169,14 +3175,14 @@ Enrichment Analysis} (GSEA).")
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.32.1")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
+ "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -2186,16 +3192,120 @@ Enrichment Analysis} (GSEA).")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-rhtslib
+ (package
+ (name "r-rhtslib")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhtslib" version))
+ (sha256
+ (base32
+ "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf"))))
+ (properties `((upstream-name . "Rhtslib")))
+ (build-system r-build-system)
+ ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+ ;; which makes R abort the build.
+ (arguments '(#:configure-flags '("--no-staged-install")))
+ (propagated-inputs
+ `(("curl" ,curl)
+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/nhayden/Rhtslib")
+ (synopsis "High-throughput sequencing library as an R package")
+ (description
+ "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis. The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+ (license license:lgpl2.0+)))
+
+(define-public r-impute
+ (package
+ (name "r-impute")
+ (version "1.66.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "impute" version))
+ (sha256
+ (base32
+ "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k"))))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/impute")
+ (synopsis "Imputation for microarray data")
+ (description
+ "This package provides a function to impute missing gene expression
+microarray data, using nearest neighbor averaging.")
+ (license license:gpl2+)))
+
+(define-public r-interactivedisplaybase
+ (package
+ (name "r-interactivedisplaybase")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "interactiveDisplayBase" version))
+ (sha256
+ (base32
+ "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv"))))
+ (properties
+ `((upstream-name . "interactiveDisplayBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-dt" ,r-dt)
+ ("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
+ (synopsis "Base package for web displays of Bioconductor objects")
+ (description
+ "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+ (license license:artistic2.0)))
+
+(define-public r-keggrest
+ (package
+ (name "r-keggrest")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "KEGGREST" version))
+ (sha256
+ (base32
+ "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"))))
+ (properties `((upstream-name . "KEGGREST")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-httr" ,r-httr)
+ ("r-png" ,r-png)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/KEGGREST")
+ (synopsis "Client-side REST access to KEGG")
+ (description
+ "This package provides a package that provides a client interface to the
+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
+ (license license:artistic2.0)))
+
(define-public r-limma
(package
(name "r-limma")
- (version "3.46.0")
+ (version "3.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
+ "1mkpl2b1ksylc6dih4a6kgjjia8advikzmqmv762j4r7gya950pf"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -2205,17 +3315,408 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3"))))
+ (properties `((upstream-name . "methylKit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-emdbook" ,r-emdbook)
+ ("r-fastseg" ,r-fastseg)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-mclust" ,r-mclust)
+ ("r-mgcv" ,r-mgcv)
+ ("r-qvalue" ,r-qvalue)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://github.com/al2na/methylKit")
+ (synopsis
+ "DNA methylation analysis from high-throughput bisulfite sequencing results")
+ (description
+ "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing. The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing. It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+ (license license:artistic2.0)))
+
+(define-public r-motifrg
+ (package
+ (name "r-motifrg")
+ (version "1.31.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifRG" version))
+ (sha256
+ (base32
+ "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
+ (properties `((upstream-name . "motifRG")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-iranges" ,r-iranges)
+ ("r-seqlogo" ,r-seqlogo)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/motifRG")
+ (synopsis "Discover motifs in high throughput sequencing data")
+ (description
+ "This package provides tools for discriminative motif discovery in high
+throughput genetic sequencing data sets using regression methods.")
+ (license license:artistic2.0)))
+
+(define-public r-mutationalpatterns
+ (package
+ (name "r-mutationalpatterns")
+ (version "3.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MutationalPatterns" version))
+ (sha256
+ (base32
+ "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ;; These two packages are suggested packages
+ ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggalluvial" ,r-ggalluvial)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-magrittr" ,r-magrittr)
+ ("r-nmf" ,r-nmf)
+ ("r-pracma" ,r-pracma)
+ ("r-purrr" ,r-purrr)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/MutationalPatterns/")
+ (synopsis "Extract and visualize mutational patterns in genomic data")
+ (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in SNV base substitution data.")
+ (license license:expat)))
+
+(define-public r-msnbase
+ (package
+ (name "r-msnbase")
+ (version "2.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MSnbase" version))
+ (sha256
+ (base32
+ "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr"))))
+ (properties `((upstream-name . "MSnbase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-digest" ,r-digest)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-maldiquant" ,r-maldiquant)
+ ("r-mass" ,r-mass)
+ ("r-mscoreutils" ,r-mscoreutils)
+ ("r-mzid" ,r-mzid)
+ ("r-mzr" ,r-mzr)
+ ("r-pcamethods" ,r-pcamethods)
+ ("r-plyr" ,r-plyr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-vsn" ,r-vsn)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/lgatto/MSnbase")
+ (synopsis "Base functions and classes for MS-based proteomics")
+ (description
+ "This package provides basic plotting, data manipulation and processing
+of mass spectrometry based proteomics data.")
+ (license license:artistic2.0)))
+
+(define-public r-msnid
+ (package
+ (name "r-msnid")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MSnID" version))
+ (sha256
+ (base32
+ "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2"))))
+ (properties `((upstream-name . "MSnID")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-biostrings" ,r-biostrings)
+ ("r-data-table" ,r-data-table)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iterators" ,r-iterators)
+ ("r-msnbase" ,r-msnbase)
+ ("r-msmstests" ,r-msmstests)
+ ("r-mzid" ,r-mzid)
+ ("r-mzr" ,r-mzr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-purrr" ,r-purrr)
+ ("r-r-cache" ,r-r-cache)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
+ ("r-runit" ,r-runit)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://bioconductor.org/packages/MSnID")
+ (synopsis "Utilities for LC-MSn proteomics identifications")
+ (description
+ "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
+from mzIdentML (leveraging the mzID package) or text files. After collating
+the search results from multiple datasets it assesses their identification
+quality and optimize filtering criteria to achieve the maximum number of
+identifications while not exceeding a specified false discovery rate. It also
+contains a number of utilities to explore the MS/MS results and assess missed
+and irregular enzymatic cleavages, mass measurement accuracy, etc.")
+ (license license:artistic2.0)))
+
+(define-public r-mzid
+ (package
+ (name "r-mzid")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mzID" version))
+ (sha256
+ (base32
+ "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys"))))
+ (properties `((upstream-name . "mzID")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-iterators" ,r-iterators)
+ ("r-plyr" ,r-plyr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/mzID")
+ (synopsis "Parser for mzIdentML files")
+ (description
+ "This package provides a parser for mzIdentML files implemented using the
+XML package. The parser tries to be general and able to handle all types of
+mzIdentML files with the drawback of having less pretty output than a vendor
+specific parser.")
+ (license license:gpl2+)))
+
+(define-public r-mzr
+ (package
+ (name "r-mzr")
+ (version "2.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mzR" version))
+ (sha256
+ (base32
+ "1m5xvnv0rxyrfri4jwyyryr13d55nyhqvfc5xxg5mpskw2v029kp"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/boost")
+ #t))))
+ (properties `((upstream-name . "mzR")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-boost
+ (lambda _
+ (substitute* "src/Makevars"
+ (("\\./boost/libs.*") "")
+ (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+ (("\\ARCH_OBJS=" line)
+ (string-append line
+ "\nBOOST_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+ #t)))))
+ (inputs
+ `(;; Our default boost package won't work here, unfortunately, even with
+ ;; mzR version 2.26.0.
+ ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-ncdf4" ,r-ncdf4)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhdf5lib" ,r-rhdf5lib)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/sneumann/mzR/")
+ (synopsis "Parser for mass spectrometry data files")
+ (description
+ "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data. It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML. The netCDF reading code has
+previously been used in XCMS.")
+ (license license:artistic2.0)))
+
+(define-public r-organismdbi
+ (package
+ (name "r-organismdbi")
+ (version "1.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "OrganismDbi" version))
+ (sha256
+ (base32
+ "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi"))))
+ (properties `((upstream-name . "OrganismDbi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-dbi" ,r-dbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-graph" ,r-graph)
+ ("r-iranges" ,r-iranges)
+ ("r-rbgl" ,r-rbgl)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/OrganismDbi")
+ (synopsis "Software to enable the smooth interfacing of database packages")
+ (description "The package enables a simple unified interface to several
+annotation packages each of which has its own schema by taking advantage of
+the fact that each of these packages implements a select methods.")
+ (license license:artistic2.0)))
+
+(define-public r-pcamethods
+ (package
+ (name "r-pcamethods")
+ (version "1.84.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pcaMethods" version))
+ (sha256
+ (base32
+ "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5"))))
+ (properties `((upstream-name . "pcaMethods")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/hredestig/pcamethods")
+ (synopsis "Collection of PCA methods")
+ (description
+ "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
+Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
+for missing value estimation is included for comparison. BPCA, PPCA and
+NipalsPCA may be used to perform PCA on incomplete data as well as for
+accurate missing value estimation. A set of methods for printing and plotting
+the results is also provided. All PCA methods make use of the same data
+structure (pcaRes) to provide a common interface to the PCA results.")
+ (license license:gpl3+)))
+
+(define-public r-protgenerics
+ (package
+ (name "r-protgenerics")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ProtGenerics" version))
+ (sha256
+ (base32
+ "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq"))))
+ (properties `((upstream-name . "ProtGenerics")))
+ (build-system r-build-system)
+ (home-page "https://github.com/lgatto/ProtGenerics")
+ (synopsis "S4 generic functions for proteomics infrastructure")
+ (description
+ "This package provides S4 generic functions needed by Bioconductor
+proteomics packages.")
+ (license license:artistic2.0)))
+
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
+ "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs
@@ -2228,17 +3729,67 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
the graph algorithms contained in the Boost library.")
(license license:artistic2.0)))
+(define-public r-rcas
+ (package
+ (name "r-rcas")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RCAS" version))
+ (sha256
+ (base32
+ "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p"))))
+ (properties `((upstream-name . "RCAS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-dt" ,r-dt)
+ ("r-genomation" ,r-genomation)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-gprofiler2" ,r-gprofiler2)
+ ("r-iranges" ,r-iranges)
+ ("r-knitr" ,r-knitr)
+ ("r-pbapply" ,r-pbapply)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plotly" ,r-plotly)
+ ("r-plotrix" ,r-plotrix)
+ ("r-proxy" ,r-proxy)
+ ("r-ranger" ,r-ranger)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-s4vectors" ,r-s4vectors)
+ ("pandoc" ,pandoc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (synopsis "RNA-centric annotation system")
+ (description
+ "RCAS aims to be a standalone RNA-centric annotation system that provides
+intuitive reports and publication-ready graphics. This package provides the R
+library implementing most of the pipeline's features.")
+ (home-page "https://github.com/BIMSBbioinfo/RCAS")
+ (license license:artistic2.0)))
+
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
+ "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -2262,14 +3813,14 @@ region sets and other genomic features.")
(define-public r-reportingtools
(package
(name "r-reportingtools")
- (version "2.30.2")
+ (version "2.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReportingTools" version))
(sha256
(base32
- "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
+ "0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj"))))
(properties
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
@@ -2309,16 +3860,70 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rhdf5
+ (package
+ (name "r-rhdf5")
+ (version "2.36.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5" version))
+ (sha256
+ (base32
+ "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rhdf5filters" ,r-rhdf5filters)
+ ("r-rhdf5lib" ,r-rhdf5lib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/rhdf5")
+ (synopsis "HDF5 interface to R")
+ (description
+ "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format. The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software
+package, and for letting R applications work on datasets that are larger than
+the available RAM.")
+ (license license:artistic2.0)))
+
+(define-public r-rhdf5filters
+ (package
+ (name "r-rhdf5filters")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5filters" version))
+ (sha256
+ (base32
+ "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc"))))
+ (properties `((upstream-name . "rhdf5filters")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rhdf5lib" ,r-rhdf5lib)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/grimbough/rhdf5filters")
+ (synopsis "HDF5 compression filters")
+ (description
+ "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+ (license license:bsd-2)))
+
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "2.6.0")
+ (version "2.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+ "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@@ -2330,8 +3935,7 @@ browser.")
(substitute* "DESCRIPTION"
(("zlibbioc, ") ""))
(substitute* "NAMESPACE"
- (("import\\(zlibbioc\\)") ""))
- #t)))))
+ (("import\\(zlibbioc\\)") "")))))))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
@@ -2352,17 +3956,173 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
tab-delimited (tabix) files.")
(license license:expat)))
+;; This is a CRAN package, but it depends on a Bioconductor package:
+;; s4vectors.
+(define-public r-restfulr
+ (package
+ (name "r-restfulr")
+ (version "0.0.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "restfulr" version))
+ (sha256
+ (base32
+ "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv"))))
+ (properties `((upstream-name . "restfulr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcurl" ,r-rcurl)
+ ("r-rjson" ,r-rjson)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://cran.r-project.org/package=restfulr")
+ (synopsis "R interface to RESTful web services")
+ (description
+ "This package models a RESTful service as if it were a nested R list.")
+ (license license:artistic2.0)))
+
+(define-public r-rtracklayer
+ (package
+ (name "r-rtracklayer")
+ (version "1.52.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rtracklayer" version))
+ (sha256
+ (base32
+ "0iic0g0clsjd9ypdmfs6k52hrnmfszhxzg0xx89nszpasf69wghv"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ ((" zlibbioc,") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") "")))))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocio" ,r-biocio)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-restfulr" ,r-restfulr)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/rtracklayer")
+ (synopsis "R interface to genome browsers and their annotation tracks")
+ (description
+ "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in). The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+ (license license:artistic2.0)))
+
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-samr
+ (package
+ (name "r-samr")
+ (version "3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "samr" version))
+ (sha256
+ (base32
+ "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+ (properties `((upstream-name . "samr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gsa" ,r-gsa)
+ ("r-impute" ,r-impute)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-openxlsx" ,r-openxlsx)
+ ("r-shiny" ,r-shiny)
+ ("r-shinyfiles" ,r-shinyfiles)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://statweb.stanford.edu/~tibs/SAM/")
+ (synopsis "Significance analysis of Microarrays")
+ (description
+ "This is a package for significance analysis of Microarrays for
+differential expression analysis, RNAseq data and related problems.")
+ ;; Any version of the LGPL
+ (license license:lgpl3+)))
+
+(define-public r-seqlogo
+ (package
+ (name "r-seqlogo")
+ (version "1.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "seqLogo" version))
+ (sha256
+ (base32
+ "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"))))
+ (properties `((upstream-name . "seqLogo")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/seqLogo")
+ (synopsis "Sequence logos for DNA sequence alignments")
+ (description
+ "seqLogo takes the position weight matrix of a DNA sequence motif and
+plots the corresponding sequence logo as introduced by Schneider and
+Stephens (1990).")
+ (license license:lgpl2.0+)))
+
+(define-public r-seqpattern
+ (package
+ (name "r-seqpattern")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "seqPattern" version))
+ (sha256
+ (base32
+ "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"))))
+ (properties
+ `((upstream-name . "seqPattern")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-plotrix" ,r-plotrix)))
+ (home-page "https://bioconductor.org/packages/seqPattern")
+ (synopsis "Visualising oligonucleotide patterns and motif occurrences")
+ (description
+ "This package provides tools to visualize oligonucleotide patterns and
+sequence motif occurrences across a large set of sequences centred at a common
+reference point and sorted by a user defined feature.")
+ (license license:gpl3+)))
+
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+ "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@@ -2395,16 +4155,111 @@ purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
+(define-public r-trajectoryutils
+ (package
+ (name "r-trajectoryutils")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "TrajectoryUtils" version))
+ (sha256
+ (base32
+ "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b"))))
+ (properties
+ `((upstream-name . "TrajectoryUtils")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/TrajectoryUtils")
+ (synopsis "Single-cell trajectory analysis utilities")
+ (description
+ "This package implements low-level utilities for single-cell trajectory
+analysis, primarily intended for re-use inside higher-level packages. It
+includes a function to create a cluster-level minimum spanning tree and data
+structures to hold pseudotime inference results.")
+ (license license:gpl3)))
+
+(define-public r-slingshot
+ (package
+ (name "r-slingshot")
+ (version "2.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "slingshot" version))
+ (sha256
+ (base32
+ "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-princurve" ,r-princurve)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-trajectoryutils" ,r-trajectoryutils)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/slingshot")
+ (synopsis "Tools for ordering single-cell sequencing")
+ (description "This package provides functions for inferring continuous,
+branching lineage structures in low-dimensional data. Slingshot was designed
+to model developmental trajectories in single-cell RNA sequencing data and
+serve as a component in an analysis pipeline after dimensionality reduction
+and clustering. It is flexible enough to handle arbitrarily many branching
+events and allows for the incorporation of prior knowledge through supervised
+graph construction.")
+ (license license:artistic2.0)))
+
+(define-public r-structuralvariantannotation
+ (package
+ (name "r-structuralvariantannotation")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "StructuralVariantAnnotation" version))
+ (sha256
+ (base32
+ "10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rlang" ,r-rlang)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-stringr" ,r-stringr)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
+ (synopsis "R package designed to simplify structural variant analysis")
+ (description
+ "This package contains useful helper functions for dealing with structural
+variants in VCF format. The packages contains functions for parsing VCFs from
+a number of popular callers as well as functions for dealing with breakpoints
+involving two separate genomic loci encoded as GRanges objects.")
+ (license license:gpl3)))
+
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
+ "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -2429,17 +4284,48 @@ typically represent genomic ranges of interest and the columns represent
samples.")
(license license:artistic2.0)))
+(define-public r-sva
+ (package
+ (name "r-sva")
+ (version "3.40.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sva" version))
+ (sha256
+ (base32
+ "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-edger" ,r-edger)
+ ("r-genefilter" ,r-genefilter)
+ ("r-mgcv" ,r-mgcv)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-limma" ,r-limma)))
+ (home-page "https://bioconductor.org/packages/sva")
+ (synopsis "Surrogate variable analysis")
+ (description
+ "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment. It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets. Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+ (license license:artistic2.0)))
+
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.24.6")
+ (version "1.26.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp"))))
+ "1apqi5ih06s37v7wpp13ybksiinrwj0ii6mx6vvvfkb6ix0wljws"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
@@ -2465,6 +4351,7 @@ samples.")
("r-shortread" ,r-shortread)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-testthat" ,r-testthat)
("r-yaml" ,r-yaml)
("r-variantannotation" ,r-variantannotation)))
(native-inputs
@@ -2483,16 +4370,73 @@ experimental designs is facilitated by a consistently implemented sample
annotation infrastructure.")
(license license:artistic2.0)))
+(define-public r-topgo
+ (package
+ (name "r-topgo")
+ (version "2.44.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "topGO" version))
+ (sha256
+ (base32
+ "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a"))))
+ (properties
+ `((upstream-name . "topGO")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dbi" ,r-dbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-lattice" ,r-lattice)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-sparsem" ,r-sparsem)))
+ (home-page "https://bioconductor.org/packages/topGO")
+ (synopsis "Enrichment analysis for gene ontology")
+ (description
+ "The topGO package provides tools for testing @dfn{gene ontology} (GO)
+terms while accounting for the topology of the GO graph. Different test
+statistics and different methods for eliminating local similarities and
+dependencies between GO terms can be implemented and applied.")
+ ;; Any version of the LGPL applies.
+ (license license:lgpl2.1+)))
+
+(define-public r-tximport
+ (package
+ (name "r-tximport")
+ (version "1.20.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tximport" version))
+ (sha256
+ (base32
+ "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/tximport")
+ (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+ (description
+ "This package provides tools to import transcript-level abundance,
+estimated counts and transcript lengths, and to summarize them into matrices
+for use with downstream gene-level analysis packages. Average transcript
+length, weighted by sample-specific transcript abundance estimates, is
+provided as a matrix which can be used as an offset for different expression
+of gene-level counts.")
+ (license license:gpl2+)))
+
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
+ "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh"))))
(properties
`((upstream-name . "VariantAnnotation")))
(propagated-inputs
@@ -2521,16 +4465,52 @@ annotation infrastructure.")
coding changes and predict coding outcomes.")
(license license:artistic2.0)))
+(define-public r-vsn
+ (package
+ (name "r-vsn")
+ (version "3.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "vsn" version))
+ (sha256
+ (base32
+ "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lattice" ,r-lattice)
+ ("r-limma" ,r-limma)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
+ (synopsis "Variance stabilization and calibration for microarray data")
+ (description
+ "The package implements a method for normalising microarray intensities,
+and works for single- and multiple-color arrays. It can also be used for data
+from other technologies, as long as they have similar format. The method uses
+a robust variant of the maximum-likelihood estimator for an
+additive-multiplicative error model and affine calibration. The model
+incorporates data calibration step (a.k.a. normalization), a model for the
+dependence of the variance on the mean intensity and a variance stabilizing
+data transformation. Differences between transformed intensities are
+analogous to \"normalized log-ratios\". However, in contrast to the latter,
+their variance is independent of the mean, and they are usually more sensitive
+and specific in detecting differential transcription.")
+ (license license:artistic2.0)))
+
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.30.0")
+ (version "0.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
+ "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
@@ -2557,17 +4537,36 @@ coding changes and predict coding outcomes.")
\"externally\" (behind an R external pointer, or on disk).")
(license license:artistic2.0)))
+(define-public r-zlibbioc
+ (package
+ (name "r-zlibbioc")
+ (version "1.38.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "zlibbioc" version))
+ (sha256
+ (base32
+ "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip"))))
+ (properties
+ `((upstream-name . "zlibbioc")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/zlibbioc")
+ (synopsis "Provider for zlib-1.2.5 to R packages")
+ (description "This package uses the source code of zlib-1.2.5 to create
+libraries for systems that do not have these available via other means.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
+ "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -2585,14 +4584,14 @@ coding changes and predict coding outcomes.")
(define-public r-oligoclasses
(package
(name "r-oligoclasses")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligoClasses" version))
(sha256
(base32
- "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
+ "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7"))))
(properties `((upstream-name . "oligoClasses")))
(build-system r-build-system)
(propagated-inputs
@@ -2620,14 +4619,14 @@ packages.")
(define-public r-oligo
(package
(name "r-oligo")
- (version "1.54.1")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligo" version))
(sha256
(base32
- "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
+ "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al"))))
(properties `((upstream-name . "oligo")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -2656,14 +4655,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.22.0")
+ (version "2.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
+ "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -2711,13 +4710,13 @@ integration with @code{Rcpp}.")
(define-public r-apeglm
(package
(name "r-apeglm")
- (version "1.12.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "apeglm" version))
(sha256
(base32
- "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
+ "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh"))))
(properties `((upstream-name . "apeglm")))
(build-system r-build-system)
(propagated-inputs
@@ -2738,13 +4737,13 @@ posterior for individual coefficients.")
(define-public r-greylistchip
(package
(name "r-greylistchip")
- (version "1.22.0")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GreyListChIP" version))
(sha256
(base32
- "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
+ "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3"))))
(properties `((upstream-name . "GreyListChIP")))
(build-system r-build-system)
(propagated-inputs
@@ -2765,14 +4764,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.0.15")
+ (version "3.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
+ "12x80z1a8gihqrlaxmzk80nc5700la72lival58s4wjv4k2lhyf3"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
@@ -2840,17 +4839,49 @@ package comprehensively addressing issues ranging from post-alignments
processing to visualization and annotation.")
(license license:gpl2)))
+(define-public r-mbkmeans
+ (package
+ (name "r-mbkmeans")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mbkmeans" version))
+ (sha256
+ (base32
+ "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-benchmarkme" ,r-benchmarkme)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-clusterr" ,r-clusterr)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rhdf5lib" ,r-rhdf5lib)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/mbkmeans")
+ (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
+ (description "This package implements the mini-batch k-means algorithm for
+large datasets, including support for on-disk data representation.")
+ (license license:expat)))
+
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.46.0")
+ (version "2.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
+ "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
@@ -2881,13 +4912,13 @@ expressed genes in DNA microarray experiments.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.68.0")
+ (version "1.70.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
+ "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -2979,14 +5010,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.24.2")
+ (version "3.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
+ "1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -3003,6 +5034,7 @@ determining dependencies between variables, code improvement suggestions.")
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-graph" ,r-graph)
+ ("r-interactionset" ,r-interactionset)
("r-iranges" ,r-iranges)
("r-keggrest" ,r-keggrest)
("r-matrixstats" ,r-matrixstats)
@@ -3032,13 +5064,13 @@ enrichedGO (addGeneIDs).")
(define-public r-matrixgenerics
(package
(name "r-matrixgenerics")
- (version "1.2.1")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MatrixGenerics" version))
(sha256
(base32
- "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
+ "1xq3a9ls125wfnhn13rdbsxzq3f6klsspx7h0znd6l67f5j5k25s"))))
(properties
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
@@ -3059,12 +5091,12 @@ incompatibilities.")
(define-public r-marray
(package
(name "r-marray")
- (version "1.68.0")
+ (version "1.70.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
+ (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
@@ -3078,12 +5110,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.50.0")
+ (version "1.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
+ (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@@ -3098,12 +5130,12 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.52.0")
+ (version "2.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
+ (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
@@ -3121,12 +5153,12 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
+ (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
@@ -3154,14 +5186,14 @@ respectively.")
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
+ "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
@@ -3180,14 +5212,14 @@ more complex hypotheses) via empirical Bayesian methods.")
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
+ "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
@@ -3214,14 +5246,14 @@ datasets.")
(define-public r-riboprofiling
(package
(name "r-riboprofiling")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
- "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
+ "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl"))))
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
@@ -3255,14 +5287,14 @@ assessment, principal component analysis on codon coverage.")
(define-public r-riboseqr
(package
(name "r-riboseqr")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
- "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
+ "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa"))))
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
@@ -3283,14 +5315,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
(define-public r-interactionset
(package
(name "r-interactionset")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
- "0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4"))))
+ "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
@@ -3317,14 +5349,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
+ "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -3358,14 +5390,14 @@ information and producing various plots and statistics.")
(define-public r-ctc
(package
(name "r-ctc")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
- "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
+ "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh"))))
(build-system r-build-system)
(propagated-inputs `(("r-amap" ,r-amap)))
(home-page "https://bioconductor.org/packages/ctc/")
@@ -3378,14 +5410,14 @@ trees and clusters to other programs.")
(define-public r-goseq
(package
(name "r-goseq")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
- "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
+ "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -3404,14 +5436,14 @@ defined categories which are over/under represented in RNA-seq data.")
(define-public r-glimma
(package
(name "r-glimma")
- (version "2.0.0")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
- "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
+ "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa"))))
(properties `((upstream-name . "Glimma")))
(build-system r-build-system)
(propagated-inputs
@@ -3437,14 +5469,14 @@ information.")
(define-public r-rots
(package
(name "r-rots")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
- "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
+ "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl"))))
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
@@ -3461,14 +5493,14 @@ in omics data.")
(define-public r-plgem
(package
(name "r-plgem")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "plgem" version))
(sha256
(base32
- "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
+ "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -3486,14 +5518,14 @@ genes or proteins in these datasets.")
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
+ "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@@ -3533,14 +5565,14 @@ modeling the rates that determines changes in mature mRNA levels.")
(define-public r-dnabarcodes
(package
(name "r-dnabarcodes")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
- "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
+ "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"))))
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
@@ -3562,14 +5594,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
(define-public r-ruvseq
(package
(name "r-ruvseq")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
- "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
+ "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac"))))
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -3590,14 +5622,14 @@ samples.")
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.8.2")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
+ "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
@@ -3619,17 +5651,142 @@ to search for all neighbors within a given distance. Parallelization is
achieved for all methods using the BiocParallel framework.")
(license license:gpl3)))
+(define-public r-scaledmatrix
+ (package
+ (name "r-scaledmatrix")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ScaledMatrix" version))
+ (sha256
+ (base32
+ "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06"))))
+ (properties `((upstream-name . "ScaledMatrix")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-delayedarray" ,r-delayedarray)
+ ("r-matrix" ,r-matrix)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/LTLA/ScaledMatrix")
+ (synopsis "Create a DelayedMatrix of scaled and centered values")
+ (description
+ "This package provides delayed computation of a matrix of scaled and
+centered values. The result is equivalent to using the @code{scale} function
+but avoids explicit realization of a dense matrix during block processing.
+This permits greater efficiency in common operations, most notably matrix
+multiplication.")
+ (license license:gpl3)))
+
+(define-public r-treeio
+ (package
+ (name "r-treeio")
+ (version "1.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "treeio" version))
+ (sha256
+ (base32
+ "0ypl4h80m08sf7r4zfvqgvpsz46x15wvcl1idq5pd813bp1w2sws"))))
+ (properties `((upstream-name . "treeio")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-dplyr" ,r-dplyr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-magrittr" ,r-magrittr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidytree" ,r-tidytree)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/YuLab-SMU/treeio")
+ (synopsis "Base classes and functions for Phylogenetic tree input and output")
+ (description
+ "This is an R package to make it easier to import and store phylogenetic
+trees with associated data; and to link external data from different sources
+to phylogeny. It also supports exporting phylogenetic trees with
+heterogeneous associated data to a single tree file and can be served as a
+platform for merging tree with associated data and converting file formats.")
+ (license license:artistic2.0)))
+
+(define-public r-ggtree
+ (package
+ (name "r-ggtree")
+ (version "3.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ggtree" version))
+ (sha256
+ (base32
+ "0i665b5jxgsv3ncxmczy7n0h911br44dw9f7m4jwv3pjmr5mm6vk"))))
+ (properties `((upstream-name . "ggtree")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-aplot" ,r-aplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-rvcheck" ,r-rvcheck)
+ ("r-scales" ,r-scales)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tidytree" ,r-tidytree)
+ ("r-treeio" ,r-treeio)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://yulab-smu.top/treedata-book/")
+ (synopsis "R package for visualization of trees and annotation data")
+ (description
+ "This package extends the ggplot2 plotting system which implements a
+grammar of graphics. ggtree is designed for visualization and annotation of
+phylogenetic trees and other tree-like structures with their annotation
+data.")
+ (license license:artistic2.0)))
+
+(define-public r-metapod
+ (package
+ (name "r-metapod")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "metapod" version))
+ (sha256
+ (base32
+ "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv"))))
+ (properties `((upstream-name . "metapod")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/metapod")
+ (synopsis "Meta-analyses on p-values of differential analyses")
+ (description
+ "This package implements a variety of methods for combining p-values in
+differential analyses of genome-scale datasets. Functions can combine
+p-values across different tests in the same analysis (e.g., genomic windows in
+ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
+analyses (e.g., replicated comparisons, effect of different treatment
+conditions). Support is provided for handling log-transformed input p-values,
+missing values and weighting where appropriate.")
+ (license license:gpl3)))
+
(define-public r-biocsingular
(package
(name "r-biocsingular")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
+ "1l0xgc3z5ci5sid198nsgg0k5i40rh877jybzmy0ify7rzv8carp"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
@@ -3641,7 +5798,8 @@ achieved for all methods using the BiocParallel framework.")
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
("r-rsvd" ,r-rsvd)
- ("r-s4vectors" ,r-s4vectors)))
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scaledmatrix" ,r-scaledmatrix)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/LTLA/BiocSingular")
@@ -3700,14 +5858,14 @@ maps.")
(define-public r-savr
(package
(name "r-savr")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "savR" version))
(sha256
(base32
- "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
+ "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq"))))
(properties `((upstream-name . "savR")))
(build-system r-build-system)
(propagated-inputs
@@ -3726,14 +5884,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
(define-public r-chipexoqual
(package
(name "r-chipexoqual")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPexoQual" version))
(sha256
(base32
- "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
+ "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424"))))
(properties `((upstream-name . "ChIPexoQual")))
(build-system r-build-system)
(propagated-inputs
@@ -3766,13 +5924,13 @@ sequencing data.")
(define-public r-copynumber
(package
(name "r-copynumber")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
- "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
+ "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
@@ -3789,14 +5947,14 @@ penalized least squares regression method.")
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
+ "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"))))
(properties `((upstream-name . "DNAcopy")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -3889,14 +6047,14 @@ and regression inferences from RNA-sequencing data.")
(define-public r-ebseq
(package
(name "r-ebseq")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBSeq" version))
(sha256
(base32
- "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
+ "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz"))))
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -3913,13 +6071,13 @@ gene and isoform level using RNA-seq data")
(define-public r-karyoploter
(package
(name "r-karyoploter")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
- "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
+ "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -3951,14 +6109,14 @@ coordinates.")
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lpsymphony" version))
(sha256
(base32
- "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
+ "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -3981,14 +6139,14 @@ to install interface to SYMPHONY.")
(define-public r-ihw
(package
(name "r-ihw")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IHW" version))
(sha256
(base32
- "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
+ "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"))))
(properties `((upstream-name . "IHW")))
(build-system r-build-system)
(propagated-inputs
@@ -4013,14 +6171,14 @@ independent of the p-value under the null hypothesis.")
(define-public r-icobra
(package
(name "r-icobra")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iCOBRA" version))
(sha256
(base32
- "183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50"))))
+ "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn"))))
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
@@ -4049,14 +6207,14 @@ interactive exploration of results.")
(define-public r-mast
(package
(name "r-mast")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MAST" version))
(sha256
(base32
- "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
+ "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d"))))
(properties `((upstream-name . "MAST")))
(build-system r-build-system)
(propagated-inputs
@@ -4084,14 +6242,14 @@ single cell assay data.")
(define-public r-monocle
(package
(name "r-monocle")
- (version "2.18.0")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "monocle" version))
(sha256
(base32
- "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
+ "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -4203,14 +6361,14 @@ qPCR data, but could be used with other types as well.")
(define-public r-noiseq
(package
(name "r-noiseq")
- (version "2.34.0")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "NOISeq" version))
(sha256
(base32
- "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
+ "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz"))))
(properties `((upstream-name . "NOISeq")))
(build-system r-build-system)
(propagated-inputs
@@ -4230,14 +6388,14 @@ assumptions.")
(define-public r-scdd
(package
(name "r-scdd")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scDD" version))
(sha256
(base32
- "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
+ "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji"))))
(properties `((upstream-name . "scDD")))
(build-system r-build-system)
(propagated-inputs
@@ -4268,14 +6426,14 @@ distributions.")
(define-public r-scone
(package
(name "r-scone")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scone" version))
(sha256
(base32
- "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
+ "1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-aroma-light" ,r-aroma-light)
@@ -4290,12 +6448,14 @@ distributions.")
("r-gplots" ,r-gplots)
("r-hexbin" ,r-hexbin)
("r-limma" ,r-limma)
+ ("r-matrixgenerics" ,r-matrixgenerics)
("r-matrixstats" ,r-matrixstats)
("r-mixtools" ,r-mixtools)
("r-rarpack" ,r-rarpack)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rhdf5" ,r-rhdf5)
("r-ruvseq" ,r-ruvseq)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -4310,14 +6470,14 @@ high-throughput analyses.")
(define-public r-geoquery
(package
(name "r-geoquery")
- (version "2.58.0")
+ (version "2.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GEOquery" version))
(sha256
(base32
- "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
+ "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am"))))
(properties `((upstream-name . "GEOquery")))
(build-system r-build-system)
(propagated-inputs
@@ -4343,14 +6503,14 @@ the bridge between GEO and BioConductor.")
(define-public r-illuminaio
(package
(name "r-illuminaio")
- (version "0.32.0")
+ (version "0.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "illuminaio" version))
(sha256
(base32
- "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
+ "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64" ,r-base64)))
@@ -4364,14 +6524,14 @@ files, including IDAT.")
(define-public r-siggenes
(package
(name "r-siggenes")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "siggenes" version))
(sha256
(base32
- "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
+ "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -4390,14 +6550,14 @@ Bayes Analyses of Microarrays} (EBAM).")
(define-public r-bumphunter
(package
(name "r-bumphunter")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bumphunter" version))
(sha256
(base32
- "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
+ "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -4424,14 +6584,14 @@ studies.")
(define-public r-minfi
(package
(name "r-minfi")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "minfi" version))
(sha256
(base32
- "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
+ "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beanplot" ,r-beanplot)
@@ -4475,14 +6635,14 @@ methylation arrays.")
(define-public r-methylumi
(package
(name "r-methylumi")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "methylumi" version))
(sha256
(base32
- "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
+ "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -4521,14 +6681,14 @@ and Infinium HD arrays are also included.")
(define-public r-lumi
(package
(name "r-lumi")
- (version "2.42.0")
+ (version "2.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lumi" version))
(sha256
(base32
- "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
+ "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -4560,14 +6720,14 @@ especially Illumina Infinium methylation microarrays.")
(define-public r-linnorm
(package
(name "r-linnorm")
- (version "2.14.0")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Linnorm" version))
(sha256
(base32
- "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
+ "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7"))))
(properties `((upstream-name . "Linnorm")))
(build-system r-build-system)
(propagated-inputs
@@ -4621,14 +6781,14 @@ evaluation of DEG analysis methods.")
(define-public r-ioniser
(package
(name "r-ioniser")
- (version "2.14.0")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IONiseR" version))
(sha256
(base32
- "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
+ "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3"))))
(properties `((upstream-name . "IONiseR")))
(build-system r-build-system)
(propagated-inputs
@@ -4715,6 +6875,52 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
published results; and a routine for graphical display.")
(license license:gpl2)))
+(define-public r-tradeseq
+ (package
+ (name "r-tradeseq")
+ (version "1.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tradeSeq" version))
+ (sha256
+ (base32
+ "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-edger" ,r-edger)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-mgcv" ,r-mgcv)
+ ("r-monocle" ,r-monocle)
+ ("r-pbapply" ,r-pbapply)
+ ("r-princurve" ,r-princurve)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-slingshot" ,r-slingshot)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tibble" ,r-tibble)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://statomics.github.io/tradeSeq/index.html")
+ (synopsis "Trajectory-based differential expression analysis")
+ (description
+ "This package provides a flexible method for fitting regression models that
+can be used to find genes that are differentially expressed along one or
+multiple lineages in a trajectory. Based on the fitted models, it uses a
+variety of tests suited to answer different questions of interest, e.g. the
+discovery of genes for which expression is associated with pseudotime, or which
+are differentially expressed (in a specific region) along the trajectory. It
+fits a negative binomial generalized additive model (GAM) for each gene, and
+performs inference on the parameters of the GAM.")
+ (license license:expat)))
+
(define-public r-triform
(package
(name "r-triform")
@@ -4742,14 +6948,14 @@ peak definition in combination with known profile characteristics.")
(define-public r-varianttools
(package
(name "r-varianttools")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantTools" version))
(sha256
(base32
- "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
+ "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c"))))
(properties `((upstream-name . "VariantTools")))
(build-system r-build-system)
(propagated-inputs
@@ -4782,14 +6988,14 @@ gmapR.")
(define-public r-heatplus
(package
(name "r-heatplus")
- (version "2.36.0")
+ (version "3.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
- "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
+ "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
@@ -4807,14 +7013,14 @@ information about samples and features can be added to the plot.")
(define-public r-gosemsim
(package
(name "r-gosemsim")
- (version "2.16.1")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOSemSim" version))
(sha256
(base32
- "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
+ "1fzmaxjzyvq6xj5ny1sjijdwi4krzjgyaz52fczpwrxijq5pnyn1"))))
(properties `((upstream-name . "GOSemSim")))
(build-system r-build-system)
(propagated-inputs
@@ -4836,14 +7042,14 @@ sets of GO terms, gene products and gene clusters.")
(define-public r-anota
(package
(name "r-anota")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "anota" version))
(sha256
(base32
- "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
+ "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-multtest" ,r-multtest)
@@ -4867,14 +7073,14 @@ the data set is suitable for such analysis.")
(define-public r-sigpathway
(package
(name "r-sigpathway")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sigPathway" version))
(sha256
(base32
- "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
+ "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8"))))
(properties `((upstream-name . "sigPathway")))
(build-system r-build-system)
(home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -4889,14 +7095,14 @@ phenotype of interest.")
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
+ "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@@ -4921,14 +7127,14 @@ to multiple hypothesis correction.")
(define-public r-dose
(package
(name "r-dose")
- (version "3.16.0")
+ (version "3.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DOSE" version))
(sha256
(base32
- "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
+ "1x9cg6qlvbcdb965jh01w07ibc4lj30ikq1v312rdih3sn6zsdck"))))
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
@@ -4956,20 +7162,21 @@ data.")
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.10.2")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
+ "0nvjwwzpmhsfkxqrn8v1a1wcrvr3xl1wn5dy89vsrdydyv31gdc6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
("r-dose" ,r-dose)
("r-ggplot2" ,r-ggplot2)
("r-ggraph" ,r-ggraph)
+ ("r-ggtree" ,r-ggtree)
("r-gosemsim" ,r-gosemsim)
("r-igraph" ,r-igraph)
("r-magrittr" ,r-magrittr)
@@ -4992,14 +7199,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
- (version "3.18.1")
+ (version "4.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
+ "1lmrb6ddpx1p3kdrwszhxq6nndmbiqipzrclk64mnp63y7g50q56"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
@@ -5026,17 +7233,63 @@ All the visualization methods are developed based on ggplot2 graphics.")
profiles (GO and KEGG) of gene and gene clusters.")
(license license:artistic2.0)))
+(define-public r-clusterexperiment
+ (package
+ (name "r-clusterexperiment")
+ (version "2.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "clusterExperiment" version))
+ (sha256
+ (base32
+ "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-cluster" ,r-cluster)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-edger" ,r-edger)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-howmany" ,r-howmany)
+ ("r-kernlab" ,r-kernlab)
+ ("r-limma" ,r-limma)
+ ("r-locfdr" ,r-locfdr)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-mbkmeans" ,r-mbkmeans)
+ ("r-nmf" ,r-nmf)
+ ("r-phylobase" ,r-phylobase)
+ ("r-pracma" ,r-pracma)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-zinbwave" ,r-zinbwave)))
+ (home-page "https://bioconductor.org/packages/clusterExperiment/")
+ (synopsis "Compare clusterings for single-cell sequencing")
+ (description "This package provides functionality for running and comparing
+many different clusterings of single-cell sequencing data or other large mRNA
+expression data sets.")
+ (license license:artistic2.0)))
+
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
+ "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
@@ -5050,6 +7303,7 @@ profiles (GO and KEGG) of gene and gene clusters.")
("r-genefilter" ,r-genefilter)
("r-ggvis" ,r-ggvis)
("r-hwriter" ,r-hwriter)
+ ("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
("r-mlbench" ,r-mlbench)
("r-pls" ,r-pls)
@@ -5070,14 +7324,14 @@ data in R and Bioconductor containers.")
(define-public r-annaffy
(package
(name "r-annaffy")
- (version "1.62.0")
+ (version "1.63.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annaffy" version))
(sha256
(base32
- "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
+ "071qr68dn8k3mvwgpllbk2a4g6f6yyv2087q5rmpb22lkfvi4hwv"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -5085,11 +7339,11 @@ data in R and Bioconductor containers.")
(add-after 'unpack 'remove-reference-to-non-free-data
(lambda _
(substitute* "DESCRIPTION"
- ((", KEGG.db") ""))
- #t)))))
+ ((", KEGG.db") "")))))))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
("r-dbi" ,r-dbi)
("r-go-db" ,r-go-db)))
(home-page "https://bioconductor.org/packages/annaffy/")
@@ -5106,14 +7360,14 @@ It allows searching of biological metadata using various criteria.")
(define-public r-a4core
(package
(name "r-a4core")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Core" version))
(sha256
(base32
- "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
+ "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10"))))
(properties `((upstream-name . "a4Core")))
(build-system r-build-system)
(propagated-inputs
@@ -5131,14 +7385,14 @@ arrays.")
(define-public r-a4classif
(package
(name "r-a4classif")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Classif" version))
(sha256
(base32
- "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
+ "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw"))))
(properties `((upstream-name . "a4Classif")))
(build-system r-build-system)
(propagated-inputs
@@ -5161,14 +7415,14 @@ Affymetrix arrays.")
(define-public r-a4preproc
(package
(name "r-a4preproc")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Preproc" version))
(sha256
(base32
- "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
+ "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri"))))
(properties `((upstream-name . "a4Preproc")))
(build-system r-build-system)
(propagated-inputs
@@ -5186,14 +7440,14 @@ is used for preprocessing the arrays.")
(define-public r-a4reporting
(package
(name "r-a4reporting")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Reporting" version))
(sha256
(base32
- "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
+ "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86"))))
(properties `((upstream-name . "a4Reporting")))
(build-system r-build-system)
(propagated-inputs
@@ -5210,14 +7464,14 @@ provides reporting features.")
(define-public r-a4base
(package
(name "r-a4base")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Base" version))
(sha256
(base32
- "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
+ "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p"))))
(properties `((upstream-name . "a4Base")))
(build-system r-build-system)
(propagated-inputs
@@ -5241,14 +7495,14 @@ Affymetrix arrays.")
(define-public r-a4
(package
(name "r-a4")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4" version))
(sha256
(base32
- "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
+ "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-a4base" ,r-a4base)
@@ -5266,14 +7520,14 @@ Affymetrix arrays.")
(define-public r-abseqr
(package
(name "r-abseqr")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "abseqR" version))
(sha256
(base32
- "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
+ "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c"))))
(properties `((upstream-name . "abseqR")))
(build-system r-build-system)
(inputs
@@ -5314,14 +7568,14 @@ further downstream analysis on its output.")
(define-public r-bacon
(package
(name "r-bacon")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bacon" version))
(sha256
(base32
- "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
+ "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocparallel" ,r-biocparallel)
@@ -5341,14 +7595,14 @@ fitting a three-component normal mixture on z-scores.")
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.38.0")
+ (version "2.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
+ "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
@@ -5399,12 +7653,12 @@ distributions, modules and filter motifs.")
(define-public r-motifdb
(package
(name "r-motifdb")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MotifDb" version))
(sha256
- (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
+ (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z"))))
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
@@ -5426,12 +7680,12 @@ frequency matrices from nine public sources, for multiple organisms.")
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
- (version "2.4.0")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
- (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
+ (base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
@@ -5477,14 +7731,14 @@ Bioconductor.")
(define-public r-motifstack
(package
(name "r-motifstack")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifStack" version))
(sha256
(base32
- "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
+ "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"))))
(properties `((upstream-name . "motifStack")))
(build-system r-build-system)
(propagated-inputs
@@ -5508,14 +7762,14 @@ type and symbol colors.")
(define-public r-genomicscores
(package
(name "r-genomicscores")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicScores" version))
(sha256
(base32
- "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
+ "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w"))))
(properties `((upstream-name . "GenomicScores")))
(build-system r-build-system)
(propagated-inputs
@@ -5545,14 +7799,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.14.4")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
+ "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -5592,14 +7846,14 @@ footprints.")
(define-public r-gofuncr
(package
(name "r-gofuncr")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOfuncR" version))
(sha256
(base32
- "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
+ "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd"))))
(properties `((upstream-name . "GOfuncR")))
(build-system r-build-system)
(propagated-inputs
@@ -5641,14 +7895,14 @@ annotations and ontologies.")
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
- "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
+ "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
@@ -5698,14 +7952,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
(define-public r-annotationtools
(package
(name "r-annotationtools")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotationTools" version))
(sha256
(base32
- "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
+ "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w"))))
(properties
`((upstream-name . "annotationTools")))
(build-system r-build-system)
@@ -5723,14 +7977,14 @@ text files).")
(define-public r-allelicimbalance
(package
(name "r-allelicimbalance")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AllelicImbalance" version))
(sha256
(base32
- "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
+ "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc"))))
(properties
`((upstream-name . "AllelicImbalance")))
(build-system r-build-system)
@@ -5766,14 +8020,14 @@ investigation using RNA-seq data.")
(define-public r-aucell
(package
(name "r-aucell")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AUCell" version))
(sha256
(base32
- "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
+ "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr"))))
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
@@ -5805,14 +8059,14 @@ needed.")
(define-public r-ebimage
(package
(name "r-ebimage")
- (version "4.32.0")
+ (version "4.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBImage" version))
(sha256
(base32
- "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
+ "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3"))))
(properties `((upstream-name . "EBImage")))
(build-system r-build-system)
(propagated-inputs
@@ -5844,14 +8098,14 @@ visualization with image data.")
(define-public r-yamss
(package
(name "r-yamss")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yamss" version))
(sha256
(base32
- "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
+ "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -5878,14 +8132,14 @@ analysis.")
(define-public r-gtrellis
(package
(name "r-gtrellis")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gtrellis" version))
(sha256
(base32
- "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
+ "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-circlize" ,r-circlize)
@@ -5907,14 +8161,14 @@ genomic categories and to add self-defined graphics in the plot.")
(define-public r-somaticsignatures
(package
(name "r-somaticsignatures")
- (version "2.26.0")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SomaticSignatures" version))
(sha256
(base32
- "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
+ "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9"))))
(properties
`((upstream-name . "SomaticSignatures")))
(build-system r-build-system)
@@ -5946,14 +8200,14 @@ decomposition algorithms.")
(define-public r-yapsa
(package
(name "r-yapsa")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "YAPSA" version))
(sha256
(base32
- "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
+ "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2"))))
(properties `((upstream-name . "YAPSA")))
(build-system r-build-system)
(propagated-inputs
@@ -5995,14 +8249,14 @@ provided.")
(define-public r-gcrma
(package
(name "r-gcrma")
- (version "2.62.0")
+ (version "2.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gcrma" version))
(sha256
(base32
- "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
+ "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -6081,14 +8335,14 @@ chips with the MAQC reference datasets.")
(define-public r-quantro
(package
(name "r-quantro")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "quantro" version))
(sha256
(base32
- "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
+ "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6114,14 +8368,14 @@ groups.")
(define-public r-yarn
(package
(name "r-yarn")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yarn" version))
(sha256
(base32
- "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
+ "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6151,14 +8405,14 @@ large RNA-seq experiments.")
(define-public r-roar
(package
(name "r-roar")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "roar" version))
(sha256
(base32
- "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
+ "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -6219,14 +8473,14 @@ genes.")
(define-public r-massspecwavelet
(package
(name "r-massspecwavelet")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MassSpecWavelet" version))
(sha256
(base32
- "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
+ "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z"))))
(properties
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
@@ -6243,14 +8497,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.12.0")
+ (version "3.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
+ "1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6283,14 +8537,14 @@ data for high-throughput, untargeted analyte profiling.")
(define-public r-wrench
(package
(name "r-wrench")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Wrench" version))
(sha256
(base32
- "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
+ "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0"))))
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
@@ -6309,14 +8563,14 @@ that arising from 16s metagenomic surveys.")
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
+ "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -6343,14 +8597,14 @@ visualization of exonic read coverage.")
(define-public r-widgettools
(package
(name "r-widgettools")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "widgetTools" version))
(sha256
(base32
- "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
+ "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2"))))
(properties `((upstream-name . "widgetTools")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/widgetTools/")
@@ -6364,14 +8618,14 @@ widgets in R.")
(define-public r-webbioc
(package
(name "r-webbioc")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "webbioc" version))
(sha256
(base32
- "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
+ "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx"))))
(build-system r-build-system)
(inputs
`(("netpbm" ,netpbm)
@@ -6394,17 +8648,50 @@ deployed as a centralized bioinformatics resource for use by many users.
Currently only Affymetrix oligonucleotide analysis is supported.")
(license license:gpl2+)))
+(define-public r-zinbwave
+ (package
+ (name "r-zinbwave")
+ (version "1.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "zinbwave" version))
+ (sha256
+ (base32
+ "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-edger" ,r-edger)
+ ("r-genefilter" ,r-genefilter)
+ ("r-matrix" ,r-matrix)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-softimpute" ,r-softimpute)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/zinbwave")
+ (synopsis "Zero-inflated negative binomial model for RNA-seq data")
+ (description "This package implements a general and flexible zero-inflated
+negative binomial model that can be used to provide a low-dimensional
+representations of single-cell RNA-seq data. The model accounts for zero
+inflation (dropouts), over-dispersion, and the count nature of the data.
+The model also accounts for the difference in library sizes and optionally
+for batch effects and/or other covariates, avoiding the need for pre-normalize
+the data.")
+ (license license:artistic2.0)))
+
(define-public r-zfpkm
(package
(name "r-zfpkm")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zFPKM" version))
(sha256
(base32
- "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
+ "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2"))))
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
@@ -6426,14 +8713,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
(define-public r-rbowtie2
(package
(name "r-rbowtie2")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie2" version))
(sha256
(base32
- "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
+ "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih"))))
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
(inputs
@@ -6451,14 +8738,14 @@ rapid adapter trimming, identification, and read merging.")
(define-public r-progeny
(package
(name "r-progeny")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "progeny" version))
(sha256
(base32
- "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
+ "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6481,14 +8768,14 @@ expression\".")
(define-public r-arrmnormalization
(package
(name "r-arrmnormalization")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ARRmNormalization" version))
(sha256
(base32
- "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
+ "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r"))))
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
@@ -6504,14 +8791,14 @@ Infinium HumanMethylation 450k assay.")
(define-public r-biocfilecache
(package
(name "r-biocfilecache")
- (version "1.14.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocFileCache" version))
(sha256
(base32
- "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
+ "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv"))))
(properties `((upstream-name . "BiocFileCache")))
(build-system r-build-system)
(propagated-inputs
@@ -6519,6 +8806,7 @@ Infinium HumanMethylation 450k assay.")
("r-dbi" ,r-dbi)
("r-dbplyr" ,r-dbplyr)
("r-dplyr" ,r-dplyr)
+ ("r-filelock" ,r-filelock)
("r-httr" ,r-httr)
("r-rappdirs" ,r-rappdirs)
("r-rsqlite" ,r-rsqlite)))
@@ -6536,14 +8824,14 @@ and data files used across sessions.")
(define-public r-iclusterplus
(package
(name "r-iclusterplus")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iClusterPlus" version))
(sha256
(base32
- "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
+ "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1"))))
(properties `((upstream-name . "iClusterPlus")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -6566,14 +8854,14 @@ Gaussian distributions.")
(define-public r-rbowtie
(package
(name "r-rbowtie")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie" version))
(sha256
(base32
- "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
+ "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy"))))
(properties `((upstream-name . "Rbowtie")))
(build-system r-build-system)
(inputs
@@ -6591,14 +8879,14 @@ alignment tool.")
(define-public r-sgseq
(package
(name "r-sgseq")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SGSeq" version))
(sha256
(base32
- "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
+ "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6"))))
(properties `((upstream-name . "SGSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6634,14 +8922,14 @@ interpretation.")
(define-public r-rhisat2
(package
(name "r-rhisat2")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhisat2" version))
(sha256
(base32
- "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
+ "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8"))))
(properties `((upstream-name . "Rhisat2")))
(build-system r-build-system)
(arguments
@@ -6674,14 +8962,14 @@ index.")
(define-public r-quasr
(package
(name "r-quasr")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "QuasR" version))
(sha256
(base32
- "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
+ "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1"))))
(properties `((upstream-name . "QuasR")))
(build-system r-build-system)
(propagated-inputs
@@ -6693,13 +8981,11 @@ index.")
("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicfiles" ,r-genomicfiles)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-rbowtie" ,r-rbowtie)
- ("r-rhisat2" ,r-rhisat2)
("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
@@ -6719,14 +9005,14 @@ quantification of genomic regions of interest.")
(define-public r-rqc
(package
(name "r-rqc")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rqc" version))
(sha256
(base32
- "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
+ "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f"))))
(properties `((upstream-name . "Rqc")))
(build-system r-build-system)
(propagated-inputs
@@ -6762,14 +9048,14 @@ graphics.")
(define-public r-birewire
(package
(name "r-birewire")
- (version "3.22.0")
+ (version "3.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiRewire" version))
(sha256
(base32
- "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
+ "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry"))))
(properties `((upstream-name . "BiRewire")))
(build-system r-build-system)
(propagated-inputs
@@ -6820,14 +9106,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
(define-public r-multidataset
(package
(name "r-multidataset")
- (version "1.18.2")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiDataSet" version))
(sha256
(base32
- "1wzhxgprriicw6lx1h91z4r9d5yaxar859scp83bm8pr9aznqk2z"))))
+ "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"))))
(properties `((upstream-name . "MultiDataSet")))
(build-system r-build-system)
(propagated-inputs
@@ -6857,14 +9143,14 @@ packages.")
(define-public r-ropls
(package
(name "r-ropls")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ropls" version))
(sha256
(base32
- "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
+ "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6895,14 +9181,14 @@ coefficients).")
(define-public r-biosigner
(package
(name "r-biosigner")
- (version "1.18.2")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biosigner" version))
(sha256
(base32
- "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
+ "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6928,14 +9214,14 @@ datasets.")
(define-public r-annotatr
(package
(name "r-annotatr")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotatr" version))
(sha256
(base32
- "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
+ "0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -6969,14 +9255,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.4.3")
+ (version "2.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
+ "007pbvxkhh930zdkgjaihannjbpbfnbizp3ffc2vyxygw0r4vz68"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -6995,14 +9281,14 @@ and to both short and long sequence reads.")
(define-public r-flowutils
(package
(name "r-flowutils")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowUtils" version))
(sha256
(base32
- "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
+ "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w"))))
(properties `((upstream-name . "flowUtils")))
(build-system r-build-system)
(propagated-inputs
@@ -7021,14 +9307,14 @@ and to both short and long sequence reads.")
(define-public r-consensusclusterplus
(package
(name "r-consensusclusterplus")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ConsensusClusterPlus" version))
(sha256
(base32
- "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
+ "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"))))
(properties
`((upstream-name . "ConsensusClusterPlus")))
(build-system r-build-system)
@@ -7046,30 +9332,18 @@ cluster count and membership by stability evidence in unsupervised analysis.")
(define-public r-cytolib
(package
(name "r-cytolib")
- (version "2.2.1")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cytolib" version))
(sha256
(base32
- "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
+ "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv"))))
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars.in"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a")))
- #t)))))
(native-inputs
- `(("r-knitr" ,r-knitr)
- ("pkg-config" ,pkg-config)))
+ `(("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-rcpp" ,r-rcpp)
@@ -7087,14 +9361,14 @@ interact with gated cytometry data.")
(define-public r-flowcore
(package
(name "r-flowcore")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowCore" version))
(sha256
(base32
- "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
+ "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc"))))
(properties `((upstream-name . "flowCore")))
(build-system r-build-system)
(propagated-inputs
@@ -7119,14 +9393,14 @@ with flow cytometry data.")
(define-public r-flowmeans
(package
(name "r-flowmeans")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowMeans" version))
(sha256
(base32
- "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
+ "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg"))))
(properties `((upstream-name . "flowMeans")))
(build-system r-build-system)
(propagated-inputs
@@ -7145,27 +9419,16 @@ change point detection.")
(define-public r-ncdfflow
(package
(name "r-ncdfflow")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ncdfFlow" version))
(sha256
(base32
- "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
+ "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0"))))
(properties `((upstream-name . "ncdfFlow")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a")))
- #t)))))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-biobase" ,r-biobase)
@@ -7187,14 +9450,14 @@ manipulation of flow cytometry data.")
(define-public r-ggcyto
(package
(name "r-ggcyto")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggcyto" version))
(sha256
(base32
- "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
+ "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg"))))
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
@@ -7224,14 +9487,14 @@ statistics to the plot.")
(define-public r-flowviz
(package
(name "r-flowviz")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowViz" version))
(sha256
(base32
- "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
+ "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v"))))
(properties `((upstream-name . "flowViz")))
(build-system r-build-system)
(propagated-inputs
@@ -7255,14 +9518,14 @@ statistics to the plot.")
(define-public r-flowclust
(package
(name "r-flowclust")
- (version "3.28.0")
+ (version "3.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowClust" version))
(sha256
(base32
- "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
+ "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b"))))
(properties `((upstream-name . "flowClust")))
(build-system r-build-system)
(arguments
@@ -7295,14 +9558,14 @@ model with Box-Cox transformation.")
(define-public r-rprotobuflib
(package
(name "r-rprotobuflib")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RProtoBufLib" version))
(sha256
(base32
- "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
+ "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb"))))
(properties `((upstream-name . "RProtoBufLib")))
(build-system r-build-system)
(arguments
@@ -7311,8 +9574,7 @@ model with Box-Cox transformation.")
(add-after 'unpack 'unpack-bundled-sources
(lambda _
(with-directory-excursion "src"
- (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
- #t)))))
+ (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/RProtoBufLib/")
@@ -7325,27 +9587,16 @@ for other R packages to compile and link against.")
(define-public r-flowworkspace
(package
(name "r-flowworkspace")
- (version "4.2.0")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowWorkspace" version))
(sha256
(base32
- "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
+ "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9"))))
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\{h5lib\\}" match)
- (string-append match "/libhdf5.a")))
- #t)))))
(propagated-inputs
`(("r-aws-s3" ,r-aws-s3)
("r-aws-signature" ,r-aws-signature)
@@ -7354,6 +9605,7 @@ for other R packages to compile and link against.")
("r-biocgenerics" ,r-biocgenerics)
("r-cytolib" ,r-cytolib)
("r-data-table" ,r-data-table)
+ ("r-delayedarray" ,r-delayedarray)
("r-digest" ,r-digest)
("r-dplyr" ,r-dplyr)
("r-flowcore" ,r-flowcore)
@@ -7370,6 +9622,7 @@ for other R packages to compile and link against.")
("r-rgraphviz" ,r-rgraphviz)
("r-rhdf5lib" ,r-rhdf5lib)
("r-rprotobuflib" ,r-rprotobuflib)
+ ("r-s4vectors" ,r-s4vectors)
("r-scales" ,r-scales)
("r-xml" ,r-xml)))
(native-inputs
@@ -7388,14 +9641,14 @@ matches the flowJo analysis.")
(define-public r-flowstats
(package
(name "r-flowstats")
- (version "4.2.0")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowStats" version))
(sha256
(base32
- "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
+ "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6"))))
(properties `((upstream-name . "flowStats")))
(build-system r-build-system)
(propagated-inputs
@@ -7424,14 +9677,14 @@ package.")
(define-public r-opencyto
(package
(name "r-opencyto")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "openCyto" version))
(sha256
(base32
- "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
+ "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x"))))
(properties `((upstream-name . "openCyto")))
(build-system r-build-system)
(propagated-inputs
@@ -7468,27 +9721,16 @@ sequential way to mimic the manual gating strategy.")
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.2.2")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
+ "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars.in"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\{h5lib\\}" match)
- (string-append match "/libhdf5.a")))
- #t)))))
(inputs
`(("libxml2" ,libxml2)
("zlib" ,zlib)))
@@ -7532,25 +9774,38 @@ standard to exchange gated cytometry data with other software platforms.")
(define-public r-flowsom
(package
(name "r-flowsom")
- (version "1.22.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "FlowSOM" version))
(sha256
(base32
- "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
+ "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82"))))
(properties `((upstream-name . "FlowSOM")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-colorramps" ,r-colorramps)
("r-consensusclusterplus" ,r-consensusclusterplus)
("r-cytoml" ,r-cytoml)
+ ("r-dplyr" ,r-dplyr)
("r-flowcore" ,r-flowcore)
("r-flowworkspace" ,r-flowworkspace)
+ ("r-ggforce" ,r-ggforce)
+ ("r-ggnewscale" ,r-ggnewscale)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggpointdensity" ,r-ggpointdensity)
+ ("r-ggpubr" ,r-ggpubr)
+ ("r-ggrepel" ,r-ggrepel)
("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-pheatmap" ,r-pheatmap)
("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-tsne" ,r-tsne)
+ ("r-rlang" ,r-rlang)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scattermore" ,r-scattermore)
+ ("r-tidyr" ,r-tidyr)
("r-xml" ,r-xml)))
(home-page "https://bioconductor.org/packages/FlowSOM/")
(synopsis "Visualize and interpret cytometry data")
@@ -7562,14 +9817,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.14.1")
+ (version "6.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk"))))
+ "1hri5rrqf8vq3c6pivfamv60yz9mf9rrdpdd5bw2h24lghm2x8rw"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@@ -7608,14 +9863,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package ;Source/Weave error
(name "r-depecher")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
+ "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@@ -7654,24 +9909,29 @@ data, to only emphasize the data that actually matters.")
(define-public r-rcistarget
(package
(name "r-rcistarget")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RcisTarget" version))
(sha256
(base32
- "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
+ "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f"))))
(properties `((upstream-name . "RcisTarget")))
(build-system r-build-system)
(propagated-inputs
- `(("r-aucell" ,r-aucell)
+ `(("r-arrow" ,r-arrow)
+ ("r-aucell" ,r-aucell)
("r-biocgenerics" ,r-biocgenerics)
("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
("r-feather" ,r-feather)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
("r-gseabase" ,r-gseabase)
("r-r-utils" ,r-r-utils)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tibble" ,r-tibble)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://aertslab.org/#scenic")
@@ -7691,14 +9951,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
+ "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -7758,14 +10018,14 @@ accessibility data.")
(define-public r-circrnaprofiler
(package
(name "r-circrnaprofiler")
- (version "1.4.2")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "circRNAprofiler" version))
(sha256
(base32
- "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
+ "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2"))))
(properties
`((upstream-name . "circRNAprofiler")))
(build-system r-build-system)
@@ -7855,17 +10115,19 @@ cisTopics and explore the nature and regulatory proteins driving them.")
(define-public r-genie3
(package
(name "r-genie3")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GENIE3" version))
(sha256
(base32
- "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
+ "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b"))))
(properties `((upstream-name . "GENIE3")))
(build-system r-build-system)
- (propagated-inputs `(("r-reshape2" ,r-reshape2)))
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-reshape2" ,r-reshape2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/GENIE3")
@@ -7878,14 +10140,14 @@ regulatory networks from expression data.")
(define-public r-roc
(package
(name "r-roc")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROC" version))
(sha256
(base32
- "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
+ "0ff5rcpyybgjzsfbhaslim0m02n3bksv1r9v7bq0gg0iyzll0rjc"))))
(properties `((upstream-name . "ROC")))
(build-system r-build-system)
(propagated-inputs
@@ -7926,14 +10188,14 @@ data.")
(define-public r-watermelon
(package
(name "r-watermelon")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wateRmelon" version))
(sha256
(base32
- "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
+ "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw"))))
(properties `((upstream-name . "wateRmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -7963,14 +10225,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
(define-public r-gdsfmt
(package
(name "r-gdsfmt")
- (version "1.26.1")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gdsfmt" version))
(sha256
(base32
- "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
+ "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy"))
(modules '((guix build utils)))
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
;; them and link with system libraries instead.
@@ -8022,14 +10284,14 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-bigmelon
(package
(name "r-bigmelon")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigmelon" version))
(sha256
(base32
- "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
+ "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri"))))
(properties `((upstream-name . "bigmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -8050,14 +10312,14 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-seqbias
(package
(name "r-seqbias")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqbias" version))
(sha256
(base32
- "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
+ "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"))))
(properties `((upstream-name . "seqbias")))
(build-system r-build-system)
(propagated-inputs
@@ -8114,14 +10376,14 @@ injected in that sequence).")
(define-public r-reqon
(package
(name "r-reqon")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReQON" version))
(sha256
(base32
- "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
+ "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza"))))
(properties `((upstream-name . "ReQON")))
(build-system r-build-system)
(propagated-inputs
@@ -8139,14 +10401,14 @@ format.")
(define-public r-wavcluster
(package
(name "r-wavcluster")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wavClusteR" version))
(sha256
(base32
- "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
+ "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych"))))
(properties `((upstream-name . "wavClusteR")))
(build-system r-build-system)
(propagated-inputs
@@ -8186,14 +10448,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
(define-public r-timeseriesexperiment
(package
(name "r-timeseriesexperiment")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TimeSeriesExperiment" version))
(sha256
(base32
- "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
+ "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy"))))
(properties
`((upstream-name . "TimeSeriesExperiment")))
(build-system r-build-system)
@@ -8227,14 +10489,14 @@ provides methods for retrieving enriched pathways.")
(define-public r-variantfiltering
(package
(name "r-variantfiltering")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantFiltering" version))
(sha256
(base32
- "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
+ "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd"))))
(properties
`((upstream-name . "VariantFiltering")))
(build-system r-build-system)
@@ -8333,14 +10595,14 @@ arrays based on fast wavelet-based functional models.")
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
+ "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
@@ -8377,14 +10639,14 @@ measures.")
(define-public r-htqpcr
(package
(name "r-htqpcr")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HTqPCR" version))
(sha256
(base32
- "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
+ "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l"))))
(properties `((upstream-name . "HTqPCR")))
(build-system r-build-system)
(propagated-inputs
@@ -8411,14 +10673,14 @@ features (e.g. genes, microRNAs).")
(define-public r-unifiedwmwqpcr
(package
(name "r-unifiedwmwqpcr")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "unifiedWMWqPCR" version))
(sha256
(base32
- "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
+ "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896"))))
(properties
`((upstream-name . "unifiedWMWqPCR")))
(build-system r-build-system)
@@ -8436,14 +10698,14 @@ data.")
(define-public r-universalmotif
(package
(name "r-universalmotif")
- (version "1.8.5")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "universalmotif" version))
(sha256
(base32
- "07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly"))))
+ "1hwp7802r4pr7yafzir9afqaim9l0vznglm35b0gxaca8k7a3jvy"))))
(properties
`((upstream-name . "universalmotif")))
(build-system r-build-system)
@@ -8458,12 +10720,10 @@ data.")
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-ggplot2" ,r-ggplot2)
- ("r-ggseqlogo" ,r-ggseqlogo)
("r-iranges" ,r-iranges)
("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp)
("r-rcppthread" ,r-rcppthread)
- ("r-rdpack" ,r-rdpack)
("r-rlang" ,r-rlang)
("r-s4vectors" ,r-s4vectors)
("r-yaml" ,r-yaml)))
@@ -8552,14 +10812,14 @@ cellular organization in health and disease.")
(define-public r-bgmix
(package
(name "r-bgmix")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BGmix" version))
(sha256
(base32
- "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
+ "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv"))))
(properties `((upstream-name . "BGmix")))
(build-system r-build-system)
(propagated-inputs
@@ -8574,14 +10834,14 @@ gene expression.")
(define-public r-bgx
(package
(name "r-bgx")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bgx" version))
(sha256
(base32
- "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
+ "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4"))))
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
(propagated-inputs
@@ -8599,14 +10859,14 @@ Affymetrix GeneChips.")
(define-public r-bhc
(package
(name "r-bhc")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BHC" version))
(sha256
(base32
- "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
+ "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9"))))
(properties `((upstream-name . "BHC")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BHC/")
@@ -8625,14 +10885,14 @@ algorithm which is more efficient for larger data sets.")
(define-public r-bicare
(package
(name "r-bicare")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BicARE" version))
(sha256
(base32
- "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
+ "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9"))))
(properties `((upstream-name . "BicARE")))
(build-system r-build-system)
(propagated-inputs
@@ -8649,14 +10909,14 @@ results.")
(define-public r-bifet
(package
(name "r-bifet")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiFET" version))
(sha256
(base32
- "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
+ "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj"))))
(properties `((upstream-name . "BiFET")))
(build-system r-build-system)
(propagated-inputs
@@ -8679,19 +10939,18 @@ the read count and GC content bias.")
(define-public r-rsbml
(package
(name "r-rsbml")
- (version "2.48.0")
+ (version "2.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rsbml" version))
(sha256
(base32
- "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
+ "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh"))))
(properties `((upstream-name . "rsbml")))
(build-system r-build-system)
(inputs
- `(("libsbml" ,libsbml)
- ("zlib" ,zlib)))
+ `(("libsbml" ,libsbml)))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-graph" ,r-graph)))
@@ -8707,14 +10966,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
(define-public r-hypergraph
(package
(name "r-hypergraph")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hypergraph" version))
(sha256
(base32
- "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
+ "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7"))))
(properties `((upstream-name . "hypergraph")))
(build-system r-build-system)
(propagated-inputs
@@ -8729,14 +10988,14 @@ manipulating hypergraphs.")
(define-public r-hyperdraw
(package
(name "r-hyperdraw")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hyperdraw" version))
(sha256
(base32
- "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
+ "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r"))))
(properties `((upstream-name . "hyperdraw")))
(build-system r-build-system)
(inputs `(("graphviz" ,graphviz)))
@@ -8753,14 +11012,14 @@ manipulating hypergraphs.")
(define-public r-biggr
(package
(name "r-biggr")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiGGR" version))
(sha256
(base32
- "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
+ "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf"))))
(properties `((upstream-name . "BiGGR")))
(build-system r-build-system)
(propagated-inputs
@@ -8817,14 +11076,14 @@ a file-backed matrix with factor properties.")
(define-public r-bigpint
(package
(name "r-bigpint")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigPint" version))
(sha256
(base32
- "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
+ "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6"))))
(properties `((upstream-name . "bigPint")))
(build-system r-build-system)
(propagated-inputs
@@ -8860,14 +11119,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
(define-public r-chemminer
(package
(name "r-chemminer")
- (version "3.42.2")
+ (version "3.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChemmineR" version))
(sha256
(base32
- "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
+ "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8"))))
(properties `((upstream-name . "ChemmineR")))
(build-system r-build-system)
(propagated-inputs
@@ -8901,14 +11160,14 @@ structures.")
(define-public r-bioassayr
(package
(name "r-bioassayr")
- (version "1.28.3")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioassayR" version))
(sha256
(base32
- "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y"))))
+ "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1"))))
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
@@ -8936,14 +11195,14 @@ available bioactivity data.")
(define-public r-biobroom
(package
(name "r-biobroom")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biobroom" version))
(sha256
(base32
- "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
+ "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn"))))
(properties `((upstream-name . "biobroom")))
(build-system r-build-system)
(propagated-inputs
@@ -8968,14 +11227,14 @@ visualize bioinformatics analyses.")
(define-public r-graphite
(package
(name "r-graphite")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "graphite" version))
(sha256
(base32
- "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
+ "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf"))))
(properties `((upstream-name . "graphite")))
(build-system r-build-system)
(propagated-inputs
@@ -8984,6 +11243,8 @@ visualize bioinformatics analyses.")
("r-graph" ,r-graph)
("r-httr" ,r-httr)
("r-rappdirs" ,r-rappdirs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/graphite/")
(synopsis "Networks from pathway databases")
(description
@@ -8995,14 +11256,14 @@ symbols).")
(define-public r-reactomepa
(package
(name "r-reactomepa")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReactomePA" version))
(sha256
(base32
- "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
+ "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"))))
(properties `((upstream-name . "ReactomePA")))
(build-system r-build-system)
(propagated-inputs
@@ -9027,14 +11288,14 @@ enrichment analysis and several functions for visualization.")
(define-public r-ebarrays
(package
(name "r-ebarrays")
- (version "2.54.0")
+ (version "2.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBarrays" version))
(sha256
(base32
- "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
+ "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422"))))
(properties `((upstream-name . "EBarrays")))
(build-system r-build-system)
(propagated-inputs
@@ -9073,35 +11334,16 @@ monograph.")
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
+ "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- ;; This package can be used by calling BiocCheck(<package>) from
- ;; within R, or by running R CMD BiocCheck <package>. This phase
- ;; makes sure the latter works. For this to work, the BiocCheck
- ;; script must be somewhere on the PATH (not the R bin directory).
- (add-after 'install 'install-bioccheck-subcommand
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (dest-dir (string-append out "/bin"))
- (script-dir
- (string-append out "/site-library/BiocCheck/script/")))
- (mkdir-p dest-dir)
- (symlink (string-append script-dir "/checkBadDeps.R")
- (string-append dest-dir "/checkBadDeps.R"))
- (symlink (string-append script-dir "/BiocCheck")
- (string-append dest-dir "/BiocCheck")))
- #t)))))
(propagated-inputs
`(("r-codetools" ,r-codetools)
("r-graph" ,r-graph)
@@ -9122,14 +11364,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-biocgraph
(package
(name "r-biocgraph")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biocGraph" version))
(sha256
(base32
- "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
+ "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3"))))
(properties `((upstream-name . "biocGraph")))
(build-system r-build-system)
(propagated-inputs
@@ -9147,13 +11389,13 @@ different graph related packages produced by Bioconductor.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.18.1")
+ (version "2.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
+ "062zhy33a2c70ibqghnjxcys0wbqc998aza8nnygk4zmpd4iyy1z"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
@@ -9175,13 +11417,13 @@ functionality.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.58.1")
+ (version "1.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
+ "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -9203,14 +11445,14 @@ also known as views, in a controlled vocabulary.")
(define-public r-experimenthub
(package
(name "r-experimenthub")
- (version "1.16.1")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ExperimentHub" version))
(sha256
(base32
- "1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g"))))
+ "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4"))))
(properties `((upstream-name . "ExperimentHub")))
(build-system r-build-system)
(propagated-inputs
@@ -9237,14 +11479,14 @@ access.")
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
+ "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
@@ -9264,14 +11506,14 @@ access.")
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
- "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
+ "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)
@@ -9299,14 +11541,14 @@ rownames.")
(define-public r-bioconcotk
(package
(name "r-bioconcotk")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocOncoTK" version))
(sha256
(base32
- "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
+ "0y396lx2mh9izb07lz83j35wydfj808ihc74jlgras03a3g335p2"))))
(properties `((upstream-name . "BiocOncoTK")))
(build-system r-build-system)
(propagated-inputs
@@ -9344,14 +11586,14 @@ tools for genome-scale analysis of cancer studies.")
(define-public r-biocor
(package
(name "r-biocor")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioCor" version))
(sha256
(base32
- "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
+ "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b"))))
(properties `((upstream-name . "BioCor")))
(build-system r-build-system)
(propagated-inputs
@@ -9373,14 +11615,14 @@ gene selection, testing relationships, and so on.")
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.8.2")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw"))))
+ "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc"))))
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
@@ -9397,7 +11639,6 @@ gene selection, testing relationships, and so on.")
("r-igraph" ,r-igraph)
("r-jsonlite" ,r-jsonlite)
("r-magrittr" ,r-magrittr)
- ("r-rappdirs" ,r-rappdirs)
("r-rbgl" ,r-rbgl)
("r-readr" ,r-readr)
("r-rex" ,r-rex)
@@ -9423,14 +11664,14 @@ analytics on packages.")
(define-public r-biocset
(package
(name "r-biocset")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSet" version))
(sha256
(base32
- "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
+ "18zr0r4b4rblfmsiilipqdfxn9fgymx75hlxzx1wk3bm71ryk078"))))
(properties `((upstream-name . "BiocSet")))
(build-system r-build-system)
(propagated-inputs
@@ -9461,14 +11702,14 @@ accessing web references for elements/sets are also available in BiocSet.")
(define-public r-biocworkflowtools
(package
(name "r-biocworkflowtools")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocWorkflowTools" version))
(sha256
(base32
- "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
+ "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av"))))
(properties
`((upstream-name . "BiocWorkflowTools")))
(build-system r-build-system)
@@ -9494,14 +11735,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
(define-public r-biodist
(package
(name "r-biodist")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioDist" version))
(sha256
(base32
- "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
+ "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw"))))
(properties `((upstream-name . "bioDist")))
(build-system r-build-system)
(propagated-inputs
@@ -9517,14 +11758,14 @@ distance measures.")
(define-public r-pcatools
(package
(name "r-pcatools")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "PCAtools" version))
(sha256
(base32
- "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
+ "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31"))))
(properties `((upstream-name . "PCAtools")))
(build-system r-build-system)
(propagated-inputs
@@ -9563,14 +11804,14 @@ dimensional mass cytometry data.")
(define-public r-rgreat
(package
(name "r-rgreat")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGREAT" version))
(sha256
(base32
- "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
+ "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji"))))
(properties `((upstream-name . "rGREAT")))
(build-system r-build-system)
(propagated-inputs
@@ -9591,14 +11832,14 @@ user's input and automatically retrieving results from GREAT web server.")
(define-public r-m3c
(package
(name "r-m3c")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "M3C" version))
(sha256
(base32
- "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
+ "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc"))))
(properties `((upstream-name . "M3C")))
(build-system r-build-system)
(propagated-inputs
@@ -9624,14 +11865,14 @@ hypothesis @code{K=1}.")
(define-public r-icens
(package
(name "r-icens")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Icens" version))
(sha256
(base32
- "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
+ "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz"))))
(properties `((upstream-name . "Icens")))
(build-system r-build-system)
(propagated-inputs
@@ -9754,14 +11995,14 @@ generated.")
(define-public r-preprocesscore
(package
(name "r-preprocesscore")
- (version "1.52.1")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "preprocessCore" version))
(sha256
(base32
- "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
+ "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20"))))
(properties
`((upstream-name . "preprocessCore")))
(build-system r-build-system)
@@ -9775,13 +12016,13 @@ routines.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.28.1")
+ (version "0.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
+ "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -9842,14 +12083,14 @@ data manipulation and visualization.")
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
- (version "2.34.0")
+ (version "2.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
- "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
+ "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
(arguments
@@ -9880,13 +12121,13 @@ objects from the @code{graph} package.")
(define-public r-fithic
(package
(name "r-fithic")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FitHiC" version))
(sha256
(base32
- "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
+ "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx"))))
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
@@ -9906,13 +12147,13 @@ assays such as Hi-C.")
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
+ "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
@@ -9935,27 +12176,16 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
+ "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5LIB_LIBS\\)" match)
- (string-append match "/libhdf5.a")))
- #t)))))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
@@ -9964,6 +12194,7 @@ provided.")
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-rhdf5" ,r-rhdf5)
+ ("r-rhdf5filters" ,r-rhdf5filters)
("r-rhdf5lib" ,r-rhdf5lib)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/HDF5Array")
@@ -9976,22 +12207,21 @@ block processing.")
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
+ "1ypqmd4nz4hxlb2qsay7f5784dqdjhc3b19pckzkhb65bfycdn87"))
(modules '((guix build utils)))
(snippet
'(begin
;; Delete bundled binaries
(delete-file-recursively "src/wininclude/")
- (delete-file-recursively "src/winlib-4.9.3/")
(delete-file-recursively "src/winlib-8.3.0/")
- (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+ (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")
#t))))
(properties `((upstream-name . "Rhdf5lib")))
(build-system r-build-system)
@@ -10003,7 +12233,9 @@ block processing.")
(for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R"
- ((" \"%s/libsz.a\"") ""))
+ ((" \"%s/libsz.a\"") "")
+ (("patharch, .getDynamicLinks")
+ ".getDynamicLinks"))
(with-directory-excursion "src"
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@@ -10042,12 +12274,10 @@ block processing.")
(assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
;; szip is non-free software
(("cp \"\\$\\{SZIP_LIB\\}.*") "")
- (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
- #t)))))
- (inputs
- `(("zlib" ,zlib)))
+ (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
(propagated-inputs
- `(("hdf5" ,hdf5-1.10)))
+ `(("hdf5" ,hdf5-1.10)
+ ("zlib" ,zlib)))
(native-inputs
`(("hdf5-source" ,(package-source hdf5-1.10))
("r-knitr" ,r-knitr)))
@@ -10060,19 +12290,20 @@ packages.")
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "2.6.4")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
+ "16p6shab4y8sy1adn4qr05ysvwmvs9idliccixafvx9icv5sla86"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)))
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/beachmat")
@@ -10088,13 +12319,13 @@ matrices.")
(define-public r-cner
(package
(name "r-cner")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CNEr" version))
(sha256
- (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
+ (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k"))))
(properties `((upstream-name . "CNEr")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -10136,14 +12367,14 @@ advanced visualization of sets of conserved noncoding elements.")
(define-public r-tfbstools
(package
(name "r-tfbstools")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TFBSTools" version))
(sha256
(base32
- "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
+ "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var"))))
(properties `((upstream-name . "TFBSTools")))
(build-system r-build-system)
(propagated-inputs
@@ -10182,14 +12413,14 @@ provides a wrapper of de novo motif discovery software.")
(define-public r-motifmatchr
(package
(name "r-motifmatchr")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifmatchr" version))
(sha256
(base32
- "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
+ "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"))))
(properties `((upstream-name . "motifmatchr")))
(build-system r-build-system)
(propagated-inputs
@@ -10216,13 +12447,13 @@ This package wraps C++ code from the MOODS motif calling library.")
(define-public r-chromvar
(package
(name "r-chromvar")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromVAR" version))
(sha256
- (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
+ (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar"))))
(properties `((upstream-name . "chromVAR")))
(build-system r-build-system)
(propagated-inputs
@@ -10263,19 +12494,21 @@ sequence (@code{DNAse-seq}) experiments.")
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.12.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
+ "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-genomicranges" ,r-genomicranges)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(native-inputs
@@ -10292,14 +12525,14 @@ libraries.")
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.0.4")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
+ "1vxmgm52n5z2m1a7d4c5ajp5d35rdq7j3hln9qn7188zk9ijjsz5"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
@@ -10327,16 +12560,17 @@ of other packages.")
(define-public r-scater
(package
(name "r-scater")
- (version "1.18.6")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
+ "0rppbd0mfyi41wb56i499mk3nj2ljhgnv3bv0k2p31bngvmb03j5"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
+ `(("r-beachmat" ,r-beachmat)
+ ("r-biocgenerics" ,r-biocgenerics)
("r-biocneighbors" ,r-biocneighbors)
("r-biocparallel" ,r-biocparallel)
("r-biocsingular" ,r-biocsingular)
@@ -10346,7 +12580,9 @@ of other packages.")
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-matrix" ,r-matrix)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rlang" ,r-rlang)
+ ("r-rtsne" ,r-rtsne)
("r-s4vectors" ,r-s4vectors)
("r-scuttle" ,r-scuttle)
("r-singlecellexperiment" ,r-singlecellexperiment)
@@ -10364,20 +12600,19 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.18.7")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4"))))
+ "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-bh" ,r-bh)
("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
("r-biocparallel" ,r-biocparallel)
("r-biocsingular" ,r-biocsingular)
("r-bluster" ,r-bluster)
@@ -10388,6 +12623,7 @@ quality control.")
("r-igraph" ,r-igraph)
("r-limma" ,r-limma)
("r-matrix" ,r-matrix)
+ ("r-metapod" ,r-metapod)
("r-rcpp" ,r-rcpp)
("r-s4vectors" ,r-s4vectors)
("r-scuttle" ,r-scuttle)
@@ -10407,14 +12643,14 @@ variable and significantly correlated genes.")
(define-public r-sparsematrixstats
(package
(name "r-sparsematrixstats")
- (version "1.2.1")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sparseMatrixStats" version))
(sha256
(base32
- "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
+ "0ilspddfkqpnf2lng9jjs2ahv6vlc6sap69fzkcw314rha59kncr"))))
(properties
`((upstream-name . "sparseMatrixStats")))
(build-system r-build-system)
@@ -10435,21 +12671,19 @@ data in the column sparse format.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.12.3")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
+ "02r68rzmc54m353fpw5ampyv26i5622bc7iihfqlpy6p3033lpqk"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-delayedarray" ,r-delayedarray)
- ("r-hdf5array" ,r-hdf5array)
+ `(("r-delayedarray" ,r-delayedarray)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-matrixgenerics" ,r-matrixgenerics)
@@ -10473,18 +12707,19 @@ memory usage and processing time is minimized.")
(define-public r-mscoreutils
(package
(name "r-mscoreutils")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MsCoreUtils" version))
(sha256
(base32
- "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
+ "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8"))))
(properties `((upstream-name . "MsCoreUtils")))
(build-system r-build-system)
(propagated-inputs
- `(("r-mass" ,r-mass)
+ `(("r-clue" ,r-clue)
+ ("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
@@ -10504,21 +12739,19 @@ within the R for Mass Spectrometry packages.")
(define-public r-biocio
(package
(name "r-biocio")
- (version "1.0.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocIO" version))
(sha256
(base32
- "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
+ "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph"))))
(properties `((upstream-name . "BiocIO")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rcurl" ,r-rcurl)
- ("r-s4vectors" ,r-s4vectors)))
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/BiocIO")
@@ -10540,14 +12773,14 @@ as well as local access. Developers can register a file extension, e.g.,
(define-public r-msmseda
(package
(name "r-msmseda")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsEDA" version))
(sha256
(base32
- "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
+ "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc"))))
(properties `((upstream-name . "msmsEDA")))
(build-system r-build-system)
(propagated-inputs
@@ -10566,14 +12799,14 @@ experiments, and visualize de influence of the involved factors.")
(define-public r-msmstests
(package
(name "r-msmstests")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsTests" version))
(sha256
(base32
- "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
+ "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh"))))
(properties `((upstream-name . "msmsTests")))
(build-system r-build-system)
(propagated-inputs
@@ -10598,14 +12831,14 @@ relevant, and the minimum expression of the most abundant condition.")
(define-public r-catalyst
(package
(name "r-catalyst")
- (version "1.14.1")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CATALYST" version))
(sha256
(base32
- "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn"))))
+ "1lzi3wylx94k3gmfw5lsqh3cvg485ik3n5xd51jllczgavwvki16"))))
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs
@@ -10656,14 +12889,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(define-public r-erma
(package
(name "r-erma")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
+ "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -10696,14 +12929,14 @@ by Ernst and Kellis.")
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+ "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -10864,14 +13097,14 @@ family of feature/genome hypotheses.")
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.34.1")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
+ "19vjf4sdz5sxbcdilsqx7m57fq5a8xnxjf354zx2l5mgjrkzkk3h"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@@ -10913,17 +13146,18 @@ with your data.")
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.22.0")
+ (version "2.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
+ "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
("r-biocfilecache" ,r-biocfilecache)
("r-biostrings" ,r-biostrings)
("r-genomeinfodb" ,r-genomeinfodb)
@@ -10946,18 +13180,19 @@ EMBL-EBI GWAS catalog.")
(define-public r-kegggraph
(package
(name "r-kegggraph")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGgraph" version))
(sha256
- (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
+ (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs"))))
(properties `((upstream-name . "KEGGgraph")))
(build-system r-build-system)
(propagated-inputs
`(("r-graph" ,r-graph)
("r-rcurl" ,r-rcurl)
+ ("r-rgraphviz" ,r-rgraphviz)
("r-xml" ,r-xml)))
(home-page "https://bioconductor.org/packages/KEGGgraph")
(synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
@@ -10972,14 +13207,14 @@ functionalities including parsing, graph operation, visualization and etc.")
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
+ "075jncvfbn3lydg0jvfhnv5025mnw79saa0k557vpcwdvs9y4p0c"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -11069,16 +13304,42 @@ network models for a given data set, where these models are used to identify
statistical dependencies in messy, complex data.")
(license license:gpl2+)))
+;; This is a CRAN package, but it depends on r-rsamtools, which is a
+;; Bioconductor package.
+(define-public r-spp
+ (package
+ (name "r-spp")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "spp" version))
+ (sha256
+ (base32
+ "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-catools" ,r-catools)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rsamtools" ,r-rsamtools)))
+ (home-page "https://cran.r-project.org/web/packages/spp/")
+ (synopsis "ChIP-Seq processing pipeline")
+ (description "This package provides tools for analysis of ChIP-seq and
+other functional sequencing data.")
+ (license license:gpl2)))
+
(define-public r-pathview
(package
(name "r-pathview")
- (version "1.30.1")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pathview" version))
(sha256
- (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
+ (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1"))))
(properties `((upstream-name . "pathview")))
(build-system r-build-system)
(propagated-inputs
@@ -11106,14 +13367,14 @@ large-scale and fully automated analysis.")
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
+ "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -11133,14 +13394,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(define-public r-chromstar
(package
(name "r-chromstar")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromstaR" version))
(sha256
(base32
- "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
+ "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h"))))
(properties `((upstream-name . "chromstaR")))
(build-system r-build-system)
(propagated-inputs
@@ -11171,14 +13432,14 @@ analyses.")
(define-public r-guitar
(package
(name "r-guitar")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Guitar" version))
(sha256
(base32
- "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz"))))
+ "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6"))))
(properties `((upstream-name . "Guitar")))
(build-system r-build-system)
(propagated-inputs
@@ -11203,13 +13464,13 @@ starting site, start codon, stop codon and transcription ending site.")
(define-public r-sushi
(package
(name "r-sushi")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Sushi" version))
(sha256
(base32
- "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
+ "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4"))))
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc2fc867ac..64fc6173db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -122,6 +122,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
@@ -310,6 +311,37 @@ instance, it implements several methods to assess contig-wise read coverage.")
BAM files.")
(license license:expat)))
+(define-public bamutils
+ (package
+ (name "bamutils")
+ (version "1.0.13")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://genome.sph.umich.edu/w/images/7/70/"
+ "BamUtilLibStatGen." version ".tgz"))
+ (sha256
+ (base32
+ "0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ #:make-flags `("USER_WARNINGS=-std=gnu++98"
+ ,(string-append "INSTALLDIR="
+ (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://genome.sph.umich.edu/wiki/BamUtil")
+ (synopsis "Programs for working on SAM/BAM files")
+ (description "This package provides several programs that perform
+operations on SAM/BAM files. All of these programs are built into a
+single executable called @code{bam}.")
+ (license license:gpl3+)))
+
(define-public bcftools
(package
(name "bcftools")
@@ -830,6 +862,30 @@ input/output delimiter. When the new functionality is not used, bioawk is
intended to behave exactly the same as the original BWK awk.")
(license license:x11)))
+(define-public python-htsget
+ (package
+ (name "python-htsget")
+ (version "0.2.5")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "htsget" version))
+ (sha256
+ (base32
+ "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)))
+ (propagated-inputs
+ `(("python-humanize" ,python-humanize)
+ ("python-requests" ,python-requests)
+ ("python-six" ,python-six)))
+ (home-page "https://pypi.org/project/htsget/")
+ (synopsis "Python API and command line interface for the GA4GH htsget API")
+ (description "This package is a client implementation of the GA4GH htsget
+protocol. It provides a simple and reliable way to retrieve genomic data from
+servers supporting the protocol.")
+ (license license:asl2.0)))
+
(define-public python-pybedtools
(package
(name "python-pybedtools")
@@ -1942,6 +1998,45 @@ multiple sequence alignments.")
(define-public python2-bx-python
(package-with-python2 python-bx-python))
+(define-public python-pyega3
+ (package
+ (name "python-pyega3")
+ (version "3.4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyega3" version))
+ (sha256
+ (base32
+ "1k736in8g27rarx65ym9xk50x53zjg75h37bb8ljynxv04rypx2q"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; The tests require network access.
+ (native-inputs
+ `(("python-psutil" ,python-psutil)
+ ("python-htsget" ,python-htsget)))
+ (propagated-inputs
+ `(("python-requests" ,python-requests)
+ ("python-tqdm" ,python-tqdm)
+ ("python-urllib3" ,python-urllib3)
+ ("python-responses" ,python-responses)))
+ (home-page "https://github.com/EGA-archive/ega-download-client")
+ (synopsis "Python client for EGA")
+ (description "This package is a python-based tool for viewing and
+downloading files from authorized EGA datasets. It uses the EGA data API and
+has several key features:
+@itemize
+@item Files are transferred over secure https connections and received
+ unencrypted, so no need for decryption after download.
+@item Downloads resume from where they left off in the event that the
+ connection is interrupted.
+@item Supports file segmenting and parallelized download of segments,
+ improving overall performance.
+@item After download completes, file integrity is verified using checksums.
+@item Implements the GA4GH-compliant htsget protocol for download of genomic
+ ranges for data files with accompanying index files.
+@end itemize\n")
+ (license license:asl2.0)))
+
(define-public python-pysam
(package
(name "python-pysam")
@@ -6065,6 +6160,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
;; 2. MD5 implementation - RSA Data Security, RFC 1321
(license (list license:gpl2+ license:public-domain)))))
+(define-public mosaicatcher
+ (package
+ (name "mosaicatcher")
+ (version "0.3.1")
+ (source (origin
+ ;; There are no release tarballs nor tags.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/friendsofstrandseq/mosaicatcher")
+ (commit (string-append version "-dev"))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd"))
+ (patches (search-patches "mosaicatcher-unbundle-htslib.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #false ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "src")))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((target (assoc-ref outputs "out"))
+ (bin (string-append target "/bin"))
+ (share (string-append target "/share/mosaicatcher")))
+ (install-file "mosaic" bin)
+ (mkdir-p share)
+ (copy-recursively "../R" share)))))))
+ (inputs
+ `(("boost" ,boost)
+ ("htslib" ,htslib)))
+ (home-page "https://github.com/friendsofstrandseq/mosaicatcher")
+ (synopsis "Count and classify Strand-seq reads")
+ (description
+ "Mosaicatcher counts Strand-seq reads and classifies strand states of
+each chromosome in each cell using a Hidden Markov Model.")
+ (license license:expat)))
+
(define-public ngs-sdk
(package
(name "ngs-sdk")
@@ -7790,409 +7925,54 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomicalignments
- (package
- (name "r-genomicalignments")
- (version "1.26.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicAlignments" version))
- (sha256
- (base32
- "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
- (properties
- `((upstream-name . "GenomicAlignments")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (home-page "https://bioconductor.org/packages/GenomicAlignments")
- (synopsis "Representation and manipulation of short genomic alignments")
- (description
- "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome). This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
- (license license:artistic2.0)))
-
-(define-public r-rtracklayer
- (package
- (name "r-rtracklayer")
- (version "1.50.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rtracklayer" version))
- (sha256
- (base32
- "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-zlib
- (lambda _
- (substitute* "DESCRIPTION"
- ((" zlibbioc,") ""))
- (substitute* "NAMESPACE"
- (("import\\(zlibbioc\\)") ""))
- #t)))))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/rtracklayer")
- (synopsis "R interface to genome browsers and their annotation tracks")
- (description
- "rtracklayer is an extensible framework for interacting with multiple
-genome browsers (currently UCSC built-in) and manipulating annotation tracks
-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
-built-in). The user may export/import tracks to/from the supported browsers,
-as well as query and modify the browser state, such as the current viewport.")
- (license license:artistic2.0)))
-
-(define-public r-genomicfeatures
- (package
- (name "r-genomicfeatures")
- (version "1.42.3")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicFeatures" version))
- (sha256
- (base32
- "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
- (properties
- `((upstream-name . "GenomicFeatures")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/GenomicFeatures")
- (synopsis "Tools for working with transcript centric annotations")
- (description
- "This package provides a set of tools and methods for making and
-manipulating transcript centric annotations. With these tools the user can
-easily download the genomic locations of the transcripts, exons and cds of a
-given organism, from either the UCSC Genome Browser or a BioMart
-database (more sources will be supported in the future). This information is
-then stored in a local database that keeps track of the relationship between
-transcripts, exons, cds and genes. Flexible methods are provided for
-extracting the desired features in a convenient format.")
- (license license:artistic2.0)))
-
-(define-public r-go-db
- (package
- (name "r-go-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/GO.db_"
- version ".tar.gz"))
- (sha256
- (base32
- "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
- (properties
- `((upstream-name . "GO.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://bioconductor.org/packages/GO.db")
- (synopsis "Annotation maps describing the entire Gene Ontology")
- (description
- "The purpose of this GO.db annotation package is to provide detailed
-information about the latest version of the Gene Ontologies.")
- (license license:artistic2.0)))
-
-(define-public r-topgo
- (package
- (name "r-topgo")
- (version "2.42.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "topGO" version))
- (sha256
- (base32
- "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
- (properties
- `((upstream-name . "topGO")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dbi" ,r-dbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-lattice" ,r-lattice)
- ("r-matrixstats" ,r-matrixstats)
- ("r-sparsem" ,r-sparsem)))
- (home-page "https://bioconductor.org/packages/topGO")
- (synopsis "Enrichment analysis for gene ontology")
- (description
- "The topGO package provides tools for testing @dfn{gene ontology} (GO)
-terms while accounting for the topology of the GO graph. Different test
-statistics and different methods for eliminating local similarities and
-dependencies between GO terms can be implemented and applied.")
- ;; Any version of the LGPL applies.
- (license license:lgpl2.1+)))
-
-(define-public r-bsgenome
- (package
- (name "r-bsgenome")
- (version "1.58.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "BSgenome" version))
- (sha256
- (base32
- "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
- (properties
- `((upstream-name . "BSgenome")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/BSgenome")
- (synopsis "Infrastructure for Biostrings-based genome data packages")
- (description
- "This package provides infrastructure shared by all Biostrings-based
-genome data packages and support for efficient SNP representation.")
- (license license:artistic2.0)))
-
-(define-public r-impute
- (package
- (name "r-impute")
- (version "1.64.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "impute" version))
- (sha256
- (base32
- "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
- (native-inputs
- `(("gfortran" ,gfortran)))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/impute")
- (synopsis "Imputation for microarray data")
- (description
- "This package provides a function to impute missing gene expression
-microarray data, using nearest neighbor averaging.")
- (license license:gpl2+)))
-
-(define-public r-seqpattern
- (package
- (name "r-seqpattern")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "seqPattern" version))
- (sha256
- (base32
- "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
- (properties
- `((upstream-name . "seqPattern")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-plotrix" ,r-plotrix)))
- (home-page "https://bioconductor.org/packages/seqPattern")
- (synopsis "Visualising oligonucleotide patterns and motif occurrences")
- (description
- "This package provides tools to visualize oligonucleotide patterns and
-sequence motif occurrences across a large set of sequences centred at a common
-reference point and sorted by a user defined feature.")
- (license license:gpl3+)))
-
-(define-public r-genomation
- (package
- (name "r-genomation")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "genomation" version))
- (sha256
- (base32
- "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-data-table" ,r-data-table)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridbase" ,r-gridbase)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-plotrix" ,r-plotrix)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-runit" ,r-runit)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqpattern" ,r-seqpattern)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Summary, annotation and visualization of genomic data")
- (description
- "This package provides a package for summary and annotation of genomic
-intervals. Users can visualize and quantify genomic intervals over
-pre-defined functional regions, such as promoters, exons, introns, etc. The
-genomic intervals represent regions with a defined chromosome position, which
-may be associated with a score, such as aligned reads from HT-seq experiments,
-TF binding sites, methylation scores, etc. The package can use any tabular
-genomic feature data as long as it has minimal information on the locations of
-genomic intervals. In addition, it can use BAM or BigWig files as input.")
- (license license:artistic2.0)))
-
-(define-public r-genomationdata
- (package
- (name "r-genomationdata")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "genomationData_" version ".tar.gz"))
- (sha256
- (base32
- "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
- (build-system r-build-system)
- ;; As this package provides little more than large data files, it doesn't
- ;; make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Experimental data for use with the genomation package")
- (description
- "This package contains experimental genetic data for use with the
-genomation package. Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
- (license license:gpl3+)))
-
-(define-public r-seqlogo
- (package
- (name "r-seqlogo")
- (version "1.56.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "seqLogo" version))
- (sha256
- (base32
- "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
- (properties `((upstream-name . "seqLogo")))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/seqLogo")
- (synopsis "Sequence logos for DNA sequence alignments")
- (description
- "seqLogo takes the position weight matrix of a DNA sequence motif and
-plots the corresponding sequence logo as introduced by Schneider and
-Stephens (1990).")
- (license license:lgpl2.0+)))
-
-(define-public r-motifrg
- (package
- (name "r-motifrg")
- (version "1.31.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "motifRG" version))
- (sha256
- (base32
- "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
- (properties `((upstream-name . "motifRG")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-iranges" ,r-iranges)
- ("r-seqlogo" ,r-seqlogo)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/motifRG")
- (synopsis "Discover motifs in high throughput sequencing data")
- (description
- "This package provides tools for discriminative motif discovery in high
-throughput genetic sequencing data sets using regression methods.")
- (license license:artistic2.0)))
-
-(define-public r-zlibbioc
- (package
- (name "r-zlibbioc")
- (version "1.36.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "zlibbioc" version))
- (sha256
- (base32
- "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
- (properties
- `((upstream-name . "zlibbioc")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/zlibbioc")
- (synopsis "Provider for zlib-1.2.5 to R packages")
- (description "This package uses the source code of zlib-1.2.5 to create
-libraries for systems that do not have these available via other means.")
- (license license:artistic2.0)))
+(define-public r-phantompeakqualtools
+ (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42")
+ (revision "1"))
+ (package
+ (name "r-phantompeakqualtools")
+ (version (git-version "1.2.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/kundajelab/phantompeakqualtools")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((script (string-append (assoc-ref outputs "out")
+ "/share/scripts")))
+ (install-file "run_spp.R" script)))))))
+ (inputs
+ `(("r" ,r-minimal)))
+ (propagated-inputs
+ `(("r-catools" ,r-catools)
+ ("r-snow" ,r-snow)
+ ("r-snowfall" ,r-snowfall)
+ ("r-bitops" ,r-bitops)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-spp" ,r-spp)
+ ("gawk" ,gawk)
+ ("samtools" ,samtools)
+ ("boost" ,boost)
+ ("gzip" ,gzip)))
+ (home-page "https://github.com/kundajelab/phantompeakqualtools")
+ (synopsis "Informative enrichment for ChIP-seq data")
+ (description "This package computes informative enrichment and quality
+measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be
+used to obtain robust estimates of the predominant fragment length or
+characteristic tag shift values in these assays.")
+ (license license:bsd-3))))
(define-public r-r4rna
(package
@@ -8217,116 +7997,6 @@ libraries for systems that do not have these available via other means.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-rhtslib
- (package
- (name "r-rhtslib")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhtslib" version))
- (sha256
- (base32
- "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
- (properties `((upstream-name . "Rhtslib")))
- (build-system r-build-system)
- ;; Without this a temporary directory ends up in the Rhtslib.so binary,
- ;; which makes R abort the build.
- (arguments '(#:configure-flags '("--no-staged-install")))
- (propagated-inputs
- `(("curl" ,curl)
- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
- (home-page "https://github.com/nhayden/Rhtslib")
- (synopsis "High-throughput sequencing library as an R package")
- (description
- "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis. The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
- (license license:lgpl2.0+)))
-
-(define-public r-bamsignals
- (package
- (name "r-bamsignals")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "bamsignals" version))
- (sha256
- (base32
- "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/bamsignals")
- (synopsis "Extract read count signals from bam files")
- (description
- "This package efficiently obtains count vectors from indexed bam
-files. It counts the number of nucleotide sequence reads in given genomic
-ranges and it computes reads profiles and coverage profiles. It also handles
-paired-end data.")
- (license license:gpl2+)))
-
-(define-public r-rcas
- (package
- (name "r-rcas")
- (version "1.16.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "RCAS" version))
- (sha256
- (base32
- "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
- (properties `((upstream-name . "RCAS")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-cowplot" ,r-cowplot)
- ("r-data-table" ,r-data-table)
- ("r-dt" ,r-dt)
- ("r-genomation" ,r-genomation)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggseqlogo" ,r-ggseqlogo)
- ("r-gprofiler2" ,r-gprofiler2)
- ("r-iranges" ,r-iranges)
- ("r-pbapply" ,r-pbapply)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plotly" ,r-plotly)
- ("r-plotrix" ,r-plotrix)
- ("r-proxy" ,r-proxy)
- ("r-ranger" ,r-ranger)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-s4vectors" ,r-s4vectors)
- ("pandoc" ,pandoc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (synopsis "RNA-centric annotation system")
- (description
- "RCAS aims to be a standalone RNA-centric annotation system that provides
-intuitive reports and publication-ready graphics. This package provides the R
-library implementing most of the pipeline's features.")
- (home-page "https://github.com/BIMSBbioinfo/RCAS")
- (license license:artistic2.0)))
-
(define-public rcas-web
(package
(name "rcas-web")
@@ -8378,64 +8048,19 @@ library implementing most of the pipeline's features.")
@dfn{RNA-centric annotation system} (RCAS).")
(license license:agpl3+)))
-(define-public r-mutationalpatterns
- (package
- (name "r-mutationalpatterns")
- (version "3.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MutationalPatterns" version))
- (sha256
- (base32
- "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ;; These two packages are suggested packages
- ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggalluvial" ,r-ggalluvial)
- ("r-ggdendro" ,r-ggdendro)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-magrittr" ,r-magrittr)
- ("r-nmf" ,r-nmf)
- ("r-pracma" ,r-pracma)
- ("r-purrr" ,r-purrr)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/MutationalPatterns/")
- (synopsis "Extract and visualize mutational patterns in genomic data")
- (description "This package provides an extensive toolset for the
-characterization and visualization of a wide range of mutational patterns
-in SNV base substitution data.")
- (license license:expat)))
-
(define-public r-chipkernels
(let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
(revision "1"))
(package
(name "r-chipkernels")
- (version (string-append "1.1-" revision "." (string-take commit 9)))
+ (version (git-version "1.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ManuSetty/ChIPKernels")
(commit commit)))
- (file-name (string-append name "-" version))
+ (file-name (git-file-name name version))
(sha256
(base32
"14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
@@ -8490,121 +8115,6 @@ bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
(license license:gpl2+)))
-(define-public r-tximport
- (package
- (name "r-tximport")
- (version "1.18.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "tximport" version))
- (sha256
- (base32
- "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/tximport")
- (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
- (description
- "This package provides tools to import transcript-level abundance,
-estimated counts and transcript lengths, and to summarize them into matrices
-for use with downstream gene-level analysis packages. Average transcript
-length, weighted by sample-specific transcript abundance estimates, is
-provided as a matrix which can be used as an offset for different expression
-of gene-level counts.")
- (license license:gpl2+)))
-
-(define-public r-rhdf5filters
- (package
- (name "r-rhdf5filters")
- (version "1.2.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "rhdf5filters" version))
- (sha256
- (base32
- "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
- (properties `((upstream-name . "rhdf5filters")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-rhdf5lib" ,r-rhdf5lib)))
- (inputs
- `(("zlib" ,zlib)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/grimbough/rhdf5filters")
- (synopsis "HDF5 compression filters")
- (description
- "This package provides a collection of compression filters for use with
-HDF5 datasets.")
- (license license:bsd-2)))
-
-(define-public r-rhdf5
- (package
- (name "r-rhdf5")
- (version "2.34.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rhdf5" version))
- (sha256
- (base32
- "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a")))
- #t)))))
- (propagated-inputs
- `(("r-rhdf5filters" ,r-rhdf5filters)
- ("r-rhdf5lib" ,r-rhdf5lib)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/rhdf5")
- (synopsis "HDF5 interface to R")
- (description
- "This R/Bioconductor package provides an interface between HDF5 and R.
-HDF5's main features are the ability to store and access very large and/or
-complex datasets and a wide variety of metadata on mass storage (disk) through
-a completely portable file format. The rhdf5 package is thus suited for the
-exchange of large and/or complex datasets between R and other software
-package, and for letting R applications work on datasets that are larger than
-the available RAM.")
- (license license:artistic2.0)))
-
-(define-public r-annotationfilter
- (package
- (name "r-annotationfilter")
- (version "1.14.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "AnnotationFilter" version))
- (sha256
- (base32
- "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
- (properties
- `((upstream-name . "AnnotationFilter")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-lazyeval" ,r-lazyeval)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/Bioconductor/AnnotationFilter")
- (synopsis "Facilities for filtering Bioconductor annotation resources")
- (description
- "This package provides classes and other infrastructure to implement
-filters for manipulating Bioconductor annotation resources. The filters are
-used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
- (license license:artistic2.0)))
-
(define-public emboss
(package
(name "emboss")
@@ -8675,13 +8185,13 @@ tools for sequence analysis into a seamless whole.")
(name "bits")
;; The version is 2.13.0 even though no release archives have been
;; published as yet.
- (version (string-append "2.13.0-" revision "." (string-take commit 9)))
+ (version (git-version "2.13.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/arq5x/bits")
(commit commit)))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
"17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
@@ -8721,7 +8231,7 @@ intervals (e.g. genes, sequence alignments).")
(commit "0466d364b71117d01e4471b74c514436cc281233"))
(package
(name "piranha")
- (version (string-append "1.2.1-" revision "." (string-take commit 9)))
+ (version (git-version "1.2.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -8810,10 +8320,11 @@ group or two ChIP groups run under different conditions.")
(license license:gpl3+)))
(define-public filevercmp
- (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
+ (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")
+ (revision "1"))
(package
(name "filevercmp")
- (version (string-append "0-1." (string-take commit 7)))
+ (version (git-version "0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -8927,176 +8438,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-chipseq
- (package
- (name "r-chipseq")
- (version "1.40.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "chipseq" version))
- (sha256
- (base32
- "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shortread" ,r-shortread)))
- (home-page "https://bioconductor.org/packages/chipseq")
- (synopsis "Package for analyzing ChIPseq data")
- (description
- "This package provides tools for processing short read data from ChIPseq
-experiments.")
- (license license:artistic2.0)))
-
-(define-public r-copyhelper
- (package
- (name "r-copyhelper")
- (version "1.6.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://bioconductor.org/packages/release/"
- "data/experiment/src/contrib/CopyhelpeR_"
- version ".tar.gz"))
- (sha256
- (base32
- "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
- (properties `((upstream-name . "CopyhelpeR")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/CopyhelpeR/")
- (synopsis "Helper files for CopywriteR")
- (description
- "This package contains the helper files that are required to run the
-Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
-mm10. In addition, it contains a blacklist filter to remove regions that
-display copy number variation. Files are stored as GRanges objects from the
-GenomicRanges Bioconductor package.")
- (license license:gpl2)))
-
-(define-public r-copywriter
- (package
- (name "r-copywriter")
- (version "2.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "CopywriteR" version))
- (sha256
- (base32
- "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
- (properties `((upstream-name . "CopywriteR")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-chipseq" ,r-chipseq)
- ("r-copyhelper" ,r-copyhelper)
- ("r-data-table" ,r-data-table)
- ("r-dnacopy" ,r-dnacopy)
- ("r-futile-logger" ,r-futile-logger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://github.com/PeeperLab/CopywriteR")
- (synopsis "Copy number information from targeted sequencing")
- (description
- "CopywriteR extracts DNA copy number information from targeted sequencing
-by utilizing off-target reads. It allows for extracting uniformly distributed
-copy number information, can be used without reference, and can be applied to
-sequencing data obtained from various techniques including chromatin
-immunoprecipitation and target enrichment on small gene panels. Thereby,
-CopywriteR constitutes a widely applicable alternative to available copy
-number detection tools.")
- (license license:gpl2)))
-
-(define-public r-methylkit
- (package
- (name "r-methylkit")
- (version "1.16.1")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "methylKit" version))
- (sha256
- (base32
- "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
- (properties `((upstream-name . "methylKit")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-emdbook" ,r-emdbook)
- ("r-fastseg" ,r-fastseg)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-limma" ,r-limma)
- ("r-mclust" ,r-mclust)
- ("r-mgcv" ,r-mgcv)
- ("r-qvalue" ,r-qvalue)
- ("r-r-utils" ,r-r-utils)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "https://github.com/al2na/methylKit")
- (synopsis
- "DNA methylation analysis from high-throughput bisulfite sequencing results")
- (description
- "MethylKit is an R package for DNA methylation analysis and annotation
-from high-throughput bisulfite sequencing. The package is designed to deal
-with sequencing data from @dfn{Reduced representation bisulfite
-sequencing} (RRBS) and its variants, but also target-capture methods and whole
-genome bisulfite sequencing. It also has functions to analyze base-pair
-resolution 5hmC data from experimental protocols such as oxBS-Seq and
-TAB-Seq.")
- (license license:artistic2.0)))
-
-(define-public r-sva
- (package
- (name "r-sva")
- (version "3.38.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "sva" version))
- (sha256
- (base32
- "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-edger" ,r-edger)
- ("r-genefilter" ,r-genefilter)
- ("r-mgcv" ,r-mgcv)
- ("r-biocparallel" ,r-biocparallel)
- ("r-matrixstats" ,r-matrixstats)
- ("r-limma" ,r-limma)))
- (home-page "https://bioconductor.org/packages/sva")
- (synopsis "Surrogate variable analysis")
- (description
- "This package contains functions for removing batch effects and other
-unwanted variation in high-throughput experiment. It also contains functions
-for identifying and building surrogate variables for high-dimensional data
-sets. Surrogate variables are covariates constructed directly from
-high-dimensional data like gene expression/RNA sequencing/methylation/brain
-imaging data that can be used in subsequent analyses to adjust for unknown,
-unmodeled, or latent sources of noise.")
- (license license:artistic2.0)))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
@@ -9129,807 +8470,6 @@ for analyzing gene-level association tests in meta-analyses for binary
trait.")
(license license:gpl3)))
-(define-public r-protgenerics
- (package
- (name "r-protgenerics")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ProtGenerics" version))
- (sha256
- (base32
- "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
- (properties `((upstream-name . "ProtGenerics")))
- (build-system r-build-system)
- (home-page "https://github.com/lgatto/ProtGenerics")
- (synopsis "S4 generic functions for proteomics infrastructure")
- (description
- "This package provides S4 generic functions needed by Bioconductor
-proteomics packages.")
- (license license:artistic2.0)))
-
-(define-public r-mzr
- (package
- (name "r-mzr")
- (version "2.24.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "mzR" version))
- (sha256
- (base32
- "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (delete-file-recursively "src/boost")
- #t))))
- (properties `((upstream-name . "mzR")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-boost
- (lambda _
- (substitute* "src/Makevars"
- (("\\./boost/libs.*") "")
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a"))
- (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
- (("\\ARCH_OBJS=" line)
- (string-append line
- "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
- #t)))))
- (inputs
- `(;; Our default boost package won't work here, unfortunately, even with
- ;; mzR version 2.24.1.
- ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
- ("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-ncdf4" ,r-ncdf4)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/sneumann/mzR/")
- (synopsis "Parser for mass spectrometry data files")
- (description
- "The mzR package provides a unified API to the common file formats and
-parsers available for mass spectrometry data. It comes with a wrapper for the
-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
-The package contains the original code written by the ISB, and a subset of the
-proteowizard library for mzML and mzIdentML. The netCDF reading code has
-previously been used in XCMS.")
- (license license:artistic2.0)))
-
-(define-public r-affyio
- (package
- (name "r-affyio")
- (version "1.60.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "affyio" version))
- (sha256
- (base32
- "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
- (home-page "https://github.com/bmbolstad/affyio")
- (synopsis "Tools for parsing Affymetrix data files")
- (description
- "This package provides routines for parsing Affymetrix data files based
-upon file format information. The primary focus is on accessing the CEL and
-CDF file formats.")
- (license license:lgpl2.0+)))
-
-(define-public r-affy
- (package
- (name "r-affy")
- (version "1.68.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "affy" version))
- (sha256
- (base32
- "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
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- (propagated-inputs
- `(("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
- (home-page "https://bioconductor.org/packages/affy")
- (synopsis "Methods for affymetrix oligonucleotide arrays")
- (description
- "This package contains functions for exploratory oligonucleotide array
-analysis.")
- (license license:lgpl2.0+)))
-
-(define-public r-vsn
- (package
- (name "r-vsn")
- (version "3.58.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "vsn" version))
- (sha256
- (base32
- "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-ggplot2" ,r-ggplot2)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
- (synopsis "Variance stabilization and calibration for microarray data")
- (description
- "The package implements a method for normalising microarray intensities,
-and works for single- and multiple-color arrays. It can also be used for data
-from other technologies, as long as they have similar format. The method uses
-a robust variant of the maximum-likelihood estimator for an
-additive-multiplicative error model and affine calibration. The model
-incorporates data calibration step (a.k.a. normalization), a model for the
-dependence of the variance on the mean intensity and a variance stabilizing
-data transformation. Differences between transformed intensities are
-analogous to \"normalized log-ratios\". However, in contrast to the latter,
-their variance is independent of the mean, and they are usually more sensitive
-and specific in detecting differential transcription.")
- (license license:artistic2.0)))
-
-(define-public r-mzid
- (package
- (name "r-mzid")
- (version "1.28.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "mzID" version))
- (sha256
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- (properties `((upstream-name . "mzID")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-iterators" ,r-iterators)
- ("r-plyr" ,r-plyr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/mzID")
- (synopsis "Parser for mzIdentML files")
- (description
- "This package provides a parser for mzIdentML files implemented using the
-XML package. The parser tries to be general and able to handle all types of
-mzIdentML files with the drawback of having less pretty output than a vendor
-specific parser.")
- (license license:gpl2+)))
-
-(define-public r-pcamethods
- (package
- (name "r-pcamethods")
- (version "1.82.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "pcaMethods" version))
- (sha256
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- (properties `((upstream-name . "pcaMethods")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-mass" ,r-mass)
- ("r-rcpp" ,r-rcpp)))
- (home-page "https://github.com/hredestig/pcamethods")
- (synopsis "Collection of PCA methods")
- (description
- "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
-Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
-for missing value estimation is included for comparison. BPCA, PPCA and
-NipalsPCA may be used to perform PCA on incomplete data as well as for
-accurate missing value estimation. A set of methods for printing and plotting
-the results is also provided. All PCA methods make use of the same data
-structure (pcaRes) to provide a common interface to the PCA results.")
- (license license:gpl3+)))
-
-(define-public r-msnbase
- (package
- (name "r-msnbase")
- (version "2.16.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MSnbase" version))
- (sha256
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- (properties `((upstream-name . "MSnbase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-digest" ,r-digest)
- ("r-ggplot2" ,r-ggplot2)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-maldiquant" ,r-maldiquant)
- ("r-mass" ,r-mass)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-pcamethods" ,r-pcamethods)
- ("r-plyr" ,r-plyr)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-vsn" ,r-vsn)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/lgatto/MSnbase")
- (synopsis "Base functions and classes for MS-based proteomics")
- (description
- "This package provides basic plotting, data manipulation and processing
-of mass spectrometry based proteomics data.")
- (license license:artistic2.0)))
-
-(define-public r-msnid
- (package
- (name "r-msnid")
- (version "1.24.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MSnID" version))
- (sha256
- (base32
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- (properties `((upstream-name . "MSnID")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocstyle" ,r-biocstyle)
- ("r-biostrings" ,r-biostrings)
- ("r-data-table" ,r-data-table)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iterators" ,r-iterators)
- ("r-msnbase" ,r-msnbase)
- ("r-msmstests" ,r-msmstests)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-purrr" ,r-purrr)
- ("r-r-cache" ,r-r-cache)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-runit" ,r-runit)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-xtable" ,r-xtable)))
- (home-page "https://bioconductor.org/packages/MSnID")
- (synopsis "Utilities for LC-MSn proteomics identifications")
- (description
- "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
-from mzIdentML (leveraging the mzID package) or text files. After collating
-the search results from multiple datasets it assesses their identification
-quality and optimize filtering criteria to achieve the maximum number of
-identifications while not exceeding a specified false discovery rate. It also
-contains a number of utilities to explore the MS/MS results and assess missed
-and irregular enzymatic cleavages, mass measurement accuracy, etc.")
- (license license:artistic2.0)))
-
-(define-public r-aroma-light
- (package
- (name "r-aroma-light")
- (version "3.20.0")
- (source
- (origin
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- (uri (bioconductor-uri "aroma.light" version))
- (sha256
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- (properties `((upstream-name . "aroma.light")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-matrixstats" ,r-matrixstats)
- ("r-r-methodss3" ,r-r-methodss3)
- ("r-r-oo" ,r-r-oo)
- ("r-r-utils" ,r-r-utils)))
- (home-page "https://github.com/HenrikBengtsson/aroma.light")
- (synopsis "Methods for normalization and visualization of microarray data")
- (description
- "This package provides methods for microarray analysis that take basic
-data types such as matrices and lists of vectors. These methods can be used
-standalone, be utilized in other packages, or be wrapped up in higher-level
-classes.")
- (license license:gpl2+)))
-
-(define-public r-deseq
- (package
- (name "r-deseq")
- (version "1.39.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DESeq" version))
- (sha256
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- (properties `((upstream-name . "DESeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-lattice" ,r-lattice)
- ("r-locfit" ,r-locfit)
- ("r-mass" ,r-mass)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
- (home-page "https://www-huber.embl.de/users/anders/DESeq/")
- (synopsis "Differential gene expression analysis")
- (description
- "This package provides tools for estimating variance-mean dependence in
-count data from high-throughput genetic sequencing assays and for testing for
-differential expression based on a model using the negative binomial
-distribution.")
- (license license:gpl3+)))
-
-(define-public r-edaseq
- (package
- (name "r-edaseq")
- (version "2.24.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "EDASeq" version))
- (sha256
- (base32
- "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
- (properties `((upstream-name . "EDASeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-aroma-light" ,r-aroma-light)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-shortread" ,r-shortread)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/drisso/EDASeq")
- (synopsis "Exploratory data analysis and normalization for RNA-Seq")
- (description
- "This package provides support for numerical and graphical summaries of
-RNA-Seq genomic read data. Provided within-lane normalization procedures to
-adjust for GC-content effect (or other gene-level effects) on read counts:
-loess robust local regression, global-scaling, and full-quantile
-normalization. Between-lane normalization procedures to adjust for
-distributional differences between lanes (e.g., sequencing depth):
-global-scaling and full-quantile normalization.")
- (license license:artistic2.0)))
-
-(define-public r-interactivedisplaybase
- (package
- (name "r-interactivedisplaybase")
- (version "1.28.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "interactiveDisplayBase" version))
- (sha256
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- (properties
- `((upstream-name . "interactiveDisplayBase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-dt" ,r-dt)
- ("r-shiny" ,r-shiny)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
- (synopsis "Base package for web displays of Bioconductor objects")
- (description
- "This package contains the basic methods needed to generate interactive
-Shiny-based display methods for Bioconductor objects.")
- (license license:artistic2.0)))
-
-(define-public r-annotationhub
- (package
- (name "r-annotationhub")
- (version "2.22.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "AnnotationHub" version))
- (sha256
- (base32
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- (properties `((upstream-name . "AnnotationHub")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biocversion" ,r-biocversion)
- ("r-curl" ,r-curl)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-interactivedisplaybase" ,r-interactivedisplaybase)
- ("r-rappdirs" ,r-rappdirs)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/AnnotationHub")
- (synopsis "Client to access AnnotationHub resources")
- (description
- "This package provides a client for the Bioconductor AnnotationHub web
-resource. The AnnotationHub web resource provides a central location where
-genomic files (e.g. VCF, bed, wig) and other resources from standard
-locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
-metadata about each resource, e.g., a textual description, tags, and date of
-modification. The client creates and manages a local cache of files retrieved
-by the user, helping with quick and reproducible access.")
- (license license:artistic2.0)))
-
-(define-public r-fastseg
- (package
- (name "r-fastseg")
- (version "1.36.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "fastseg" version))
- (sha256
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- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
- (synopsis "Fast segmentation algorithm for genetic sequencing data")
- (description
- "Fastseg implements a very fast and efficient segmentation algorithm.
-It can segment data from DNA microarrays and data from next generation
-sequencing for example to detect copy number segments. Further it can segment
-data from RNA microarrays like tiling arrays to identify transcripts. Most
-generally, it can segment data given as a matrix or as a vector. Various data
-formats can be used as input to fastseg like expression set objects for
-microarrays or GRanges for sequencing data.")
- (license license:lgpl2.0+)))
-
-(define-public r-keggrest
- (package
- (name "r-keggrest")
- (version "1.30.1")
- (source
- (origin
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- (uri (bioconductor-uri "KEGGREST" version))
- (sha256
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- (properties `((upstream-name . "KEGGREST")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-httr" ,r-httr)
- ("r-png" ,r-png)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/KEGGREST")
- (synopsis "Client-side REST access to KEGG")
- (description
- "This package provides a package that provides a client interface to the
-@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
- (license license:artistic2.0)))
-
-(define-public r-gage
- (package
- (name "r-gage")
- (version "2.40.2")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gage" version))
- (sha256
- (base32
- "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-keggrest" ,r-keggrest)))
- (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
- "articles/10.1186/1471-2105-10-161"))
- (synopsis "Generally applicable gene-set enrichment for pathway analysis")
- (description
- "GAGE is a published method for gene set (enrichment or GSEA) or pathway
-analysis. GAGE is generally applicable independent of microarray or RNA-Seq
-data attributes including sample sizes, experimental designs, assay platforms,
-and other types of heterogeneity. The gage package provides functions for
-basic GAGE analysis, result processing and presentation. In addition, it
-provides demo microarray data and commonly used gene set data based on KEGG
-pathways and GO terms. These functions and data are also useful for gene set
-analysis using other methods.")
- (license license:gpl2+)))
-
-(define-public r-genomicfiles
- (package
- (name "r-genomicfiles")
- (version "1.26.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicFiles" version))
- (sha256
- (base32
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- (properties `((upstream-name . "GenomicFiles")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/GenomicFiles")
- (synopsis "Distributed computing by file or by range")
- (description
- "This package provides infrastructure for parallel computations
-distributed by file or by range. User defined mapper and reducer functions
-provide added flexibility for data combination and manipulation.")
- (license license:artistic2.0)))
-
-(define-public r-complexheatmap
- (package
- (name "r-complexheatmap")
- (version "2.6.2")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ComplexHeatmap" version))
- (sha256
- (base32
- "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
- (properties
- `((upstream-name . "ComplexHeatmap")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-cairo" ,r-cairo)
- ("r-circlize" ,r-circlize)
- ("r-clue" ,r-clue)
- ("r-colorspace" ,r-colorspace)
- ("r-digest" ,r-digest)
- ("r-getoptlong" ,r-getoptlong)
- ("r-globaloptions" ,r-globaloptions)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-png" ,r-png)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page
- "https://github.com/jokergoo/ComplexHeatmap")
- (synopsis "Making Complex Heatmaps")
- (description
- "Complex heatmaps are efficient to visualize associations between
-different sources of data sets and reveal potential structures. This package
-provides a highly flexible way to arrange multiple heatmaps and supports
-self-defined annotation graphics.")
- (license license:gpl2+)))
-
-(define-public r-dirichletmultinomial
- (package
- (name "r-dirichletmultinomial")
- (version "1.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DirichletMultinomial" version))
- (sha256
- (base32
- "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
- (properties
- `((upstream-name . "DirichletMultinomial")))
- (build-system r-build-system)
- (inputs
- `(("gsl" ,gsl)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://bioconductor.org/packages/DirichletMultinomial")
- (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
- (description
- "Dirichlet-multinomial mixture models can be used to describe variability
-in microbial metagenomic data. This package is an interface to code
-originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
-1-15.")
- (license license:lgpl3)))
-
-(define-public r-ensembldb
- (package
- (name "r-ensembldb")
- (version "2.14.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ensembldb" version))
- (sha256
- (base32
- "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-curl" ,r-curl)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/jotsetung/ensembldb")
- (synopsis "Utilities to create and use Ensembl-based annotation databases")
- (description
- "The package provides functions to create and use transcript-centric
-annotation databases/packages. The annotation for the databases are directly
-fetched from Ensembl using their Perl API. The functionality and data is
-similar to that of the TxDb packages from the @code{GenomicFeatures} package,
-but, in addition to retrieve all gene/transcript models and annotations from
-the database, the @code{ensembldb} package also provides a filter framework
-allowing to retrieve annotations for specific entries like genes encoded on a
-chromosome region or transcript models of lincRNA genes.")
- ;; No version specified
- (license license:lgpl3+)))
-
-(define-public r-organismdbi
- (package
- (name "r-organismdbi")
- (version "1.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "OrganismDbi" version))
- (sha256
- (base32
- "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
- (properties `((upstream-name . "OrganismDbi")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-dbi" ,r-dbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-graph" ,r-graph)
- ("r-iranges" ,r-iranges)
- ("r-rbgl" ,r-rbgl)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://bioconductor.org/packages/OrganismDbi")
- (synopsis "Software to enable the smooth interfacing of database packages")
- (description "The package enables a simple unified interface to several
-annotation packages each of which has its own schema by taking advantage of
-the fact that each of these packages implements a select methods.")
- (license license:artistic2.0)))
-
-(define-public r-biovizbase
- (package
- (name "r-biovizbase")
- (version "1.38.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "biovizBase" version))
- (sha256
- (base32
- "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
- (properties `((upstream-name . "biovizBase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dichromat" ,r-dichromat)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/biovizBase")
- (synopsis "Basic graphic utilities for visualization of genomic data")
- (description
- "The biovizBase package is designed to provide a set of utilities, color
-schemes and conventions for genomic data. It serves as the base for various
-high-level packages for biological data visualization. This saves development
-effort and encourages consistency.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
@@ -10549,13 +9089,13 @@ browser.")
(revision "1"))
(package
(name "f-seq")
- (version (string-append "1.1-" revision "." (string-take commit 7)))
+ (version (git-version "1.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aboyle/F-seq")
(commit commit)))
- (file-name (string-append name "-" version))
+ (file-name (git-file-name name version))
(sha256
(base32
"1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
@@ -10613,7 +9153,7 @@ Browser.")
(uri (git-reference
(url "https://github.com/FelixKrueger/Bismark")
(commit version)))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
"0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9"))))
@@ -11753,7 +10293,7 @@ once. This package provides tools to perform Drop-seq analyses.")
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.10")
+ (version "0.0.13")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -11761,7 +10301,7 @@ once. This package provides tools to perform Drop-seq analyses.")
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "0z3hr120wk2vrlmlpz1vp3n9wy3rq4y2mnzh2vf08qgqn2xfdwcw"))))
+ "0z9zid2c8q16lfzlnjd63nparknhv31qgv4h79algmvhkakm2pgk"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
@@ -11771,19 +10311,17 @@ once. This package provides tools to perform Drop-seq analyses.")
(add-after 'unpack 'disable-resource-intensive-test
(lambda _
(substitute* "Makefile.in"
- (("(^ tests/test_trim_galore/test.sh).*" _ m) m)
(("^ tests/test_multiqc/test.sh") "")
- (("^ test.sh") ""))
- #t)))))
+ (("^ test.sh") "")))))))
(inputs
`(("coreutils" ,coreutils)
("sed" ,sed)
("gzip" ,gzip)
("snakemake" ,snakemake)
- ("fastqc" ,fastqc)
("multiqc" ,multiqc)
("star" ,star-for-pigx)
- ("trim-galore" ,trim-galore)
+ ("hisat2" ,hisat2)
+ ("fastp" ,fastp)
("htseq" ,htseq)
("samtools" ,samtools)
("r-minimal" ,r-minimal)
@@ -12032,6 +10570,54 @@ and interactive quality reports. The pipeline is designed to work with UMI
based methods.")
(license license:gpl3+)))
+(define-public pigx-sars-cov2-ww
+ (package
+ (name "pigx-sars-cov2-ww")
+ (version "0.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
+ "releases/download/v" version
+ "/pigx_sars-cov2-ww-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1h1rfl3dyf7pid74xxgiyr4x1l5yj000wcz5crm1bdbaz8p7b7ic"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("bash-minimal" ,bash-minimal)
+ ("bwa" ,bwa)
+ ("ensembl-vep" ,ensembl-vep)
+ ("fastqc" ,fastqc)
+ ("kraken2" ,kraken2)
+ ("krona-tools" ,krona-tools)
+ ("lofreq" ,lofreq)
+ ("multiqc" ,multiqc)
+ ("prinseq" ,prinseq)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-wrapper" ,python-wrapper)
+ ("r-base64url" ,r-base64url)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dt" ,r-dt)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-minimal" ,r-minimal)
+ ("r-plotly" ,r-plotly)
+ ("r-qpcr" ,r-qpcr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-stringr" ,r-stringr)
+ ("r-tidyr" ,r-tidyr)
+ ("samtools" ,samtools)
+ ("snakemake" ,snakemake)))
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipeline for wastewater sequencing")
+ (description "PiGx SARS-CoV-2 is a pipeline for analysing data from
+sequenced wastewater samples and identifying given variants-of-concern of
+SARS-CoV-2. The pipeline can be used for continuous sampling. The output
+report will provide an intuitive visual overview about the development of
+variant abundance over time and location.")
+ (license license:gpl3+)))
+
(define-public pigx
(package
(name "pigx")
@@ -12190,7 +10776,7 @@ version does count multisplits.")
(define-public minimap2
(package
(name "minimap2")
- (version "2.17")
+ (version "2.18")
(source
(origin
(method url-fetch)
@@ -12199,11 +10785,13 @@ version does count multisplits.")
"minimap2-" version ".tar.bz2"))
(sha256
(base32
- "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))
- (patches (search-patches "minimap2-aarch64-support.patch"))))
+ "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
+ #:modules ((guix build utils)
+ (guix build gnu-build-system)
+ (srfi srfi-26))
#:make-flags
(list (string-append "CC=" ,(cc-for-target))
(let ((system ,(or (%current-target-system)
@@ -12226,10 +10814,30 @@ version does count multisplits.")
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (inc (string-append out "/include"))
(man (string-append out "/share/man/man1")))
(install-file "minimap2" bin)
- (mkdir-p man)
- (install-file "minimap2.1" man))
+ (install-file "libminimap2.a" lib)
+ (install-file "minimap2.1" man)
+ (map (cut install-file <> inc)
+ (find-files "." "\\.h$"))
+ ;; Not this file.
+ (delete-file (string-append inc "/emmintrin.h"))
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/minimap2.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include~@
+ ~@
+ Name: libminimap2~@
+ Version: ~a~@
+ Description: A versatile pairwise aligner for genomic and spliced nucleotide sequence~@
+ Libs: -L${libdir} -lminimap2~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(inputs
`(("zlib" ,zlib)))
@@ -12346,6 +10954,96 @@ contigs alone.")
(license (list license:gpl2+ ; bundled ogdf
license:gpl3+))))
+(define-public libmaus2
+ (package
+ (name "libmaus2")
+ (version "2.0.786")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/german.tischler/libmaus2")
+ (commit (string-append version "-release-20210531143054"))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564"))))
+ (build-system gnu-build-system)
+ ;; The test suite attempts to execute ../test-driver, which does not exist.
+ (arguments '(#:tests? #false))
+ (propagated-inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("gcc" ,gcc-10) ;Code has C++17 requirements
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://gitlab.com/german.tischler/libmaus2")
+ (synopsis "Collection of data structures and algorithms useful for bioinformatics")
+ (description "libmaus2 is a collection of data structures and
+algorithms. It contains:
+
+@itemize
+@item I/O classes (single byte and UTF-8);
+@item @code{bitio} classes (input, output and various forms of bit level
+ manipulation);
+@item text indexing classes (suffix and LCP array, fulltext and minute (FM),
+ etc.);
+@item BAM sequence alignment files input/output (simple and collating);
+and many lower level support classes.
+@end itemize\n")
+ ;; The code is explicitly available under the terms of either GPLv2 or
+ ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+
+ ;; license header.
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public biobambam2
+ (package
+ (name "biobambam2")
+ (version "2.0.182")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/german.tischler/biobambam2")
+ (commit (string-append version "-release-20210412001032"))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5"))))
+ (build-system gnu-build-system)
+ (arguments
+ ;; The test suite attempts to execute ../test-driver, which does not exist.
+ `(#:tests? #false
+ #:configure-flags
+ (list (string-append "--with-libmaus2="
+ (assoc-ref %build-inputs "libmaus2")))))
+ (inputs
+ `(("libmaus2" ,libmaus2)
+ ("xerces-c" ,xerces-c)))
+ (native-inputs
+ `(("gcc" ,gcc-10) ;Code has C++17 requirements
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://gitlab.com/german.tischler/biobambam2")
+ (synopsis "Tools for processing BAM files")
+ (description "This package contains some tools for processing BAM files
+including:
+
+@itemize
+@item bamsormadup: parallel sorting and duplicate marking
+@item bamcollate2: reads BAM and writes BAM reordered such that alignment or
+ collated by query name
+@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments
+ marked using the BAM flags field
+@item bammaskflags: reads BAM and writes BAM while masking (removing) bits
+ from the flags column
+@item bamrecompress: reads BAM and writes BAM with a defined compression
+ setting. This tool is capable of multi-threading.
+@item bamsort: reads BAM and writes BAM resorted by coordinates or query name
+@item bamtofastq: reads BAM and writes FastQ; output can be collated or
+ uncollated by query name.
+@end itemize
+")
+ ;; The COPYING file states that the code is distributed under version 3 of
+ ;; the GPL, but the license headers include the "or later" clause.
+ (license license:gpl3+)))
+
(define-public r-circus
(package
(name "r-circus")
@@ -12501,17 +11199,80 @@ spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
in RNA-seq data.")
(license license:gpl3))))
+(define-public fit-sne
+ (package
+ (name "fit-sne")
+ (version "1.2.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/KlugerLab/FIt-SNE")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1imq4577awc226wvygf94kpz156qdfw8xl0w0f7ss4w10lhmpmf5"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #false ; there are none
+ #:phases
+ ;; There is no build system.
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (invoke "g++" "-std=c++11" "-O3"
+ "src/sptree.cpp"
+ "src/tsne.cpp"
+ "src/nbodyfft.cpp"
+ "-o" "bin/fast_tsne"
+ "-pthread" "-lfftw3" "-lm"
+ "-Wno-address-of-packed-member")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (share (string-append out "/share/fit-sne")))
+ (for-each (lambda (file) (install-file file bin))
+ (find-files "bin"))
+
+ (substitute* "fast_tsne.R"
+ (("^FAST_TSNE_SCRIPT_DIR.*")
+ (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n")))
+ (install-file "fast_tsne.R" share)))))))
+ (inputs
+ `(("fftw" ,fftw)))
+ (home-page "https://github.com/KlugerLab/FIt-SNE")
+ (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE")
+ (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a
+method for dimensionality reduction and visualization of high dimensional
+datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
+approximate the gradient at each iteration of gradient descent. This
+implementation differs in these ways:
+
+@itemize
+@item Instead of approximating the N-body simulation using Barnes-Hut, we
+ interpolate onto an equispaced grid and use FFT to perform the convolution.
+@item Instead of computing nearest neighbors using vantage-point trees, we
+ approximate nearest neighbors using the Annoy library. The neighbor lookups
+ are multithreaded to take advantage of machines with multiple cores.
+@end itemize
+")
+ ;; See LICENSE.txt for details on what license applies to what files.
+ (license (list license:bsd-4 license:expat license:asl2.0))))
+
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.4.6")
+ (version "1.7.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(sha256
(base32
- "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
+ "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -12522,12 +11283,28 @@ in RNA-seq data.")
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
+ (delete-file "scanpy/tests/test_highly_variable_genes.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
+ ;; The following tests need anndata.tests, which aren't included
+ ;; in the final python-anndata package.
+ (delete-file "scanpy/tests/test_combat.py")
+ (delete-file "scanpy/tests/test_embedding_plots.py")
+ (delete-file "scanpy/tests/test_normalization.py")
+ (delete-file "scanpy/tests/test_pca.py")
+ (delete-file "scanpy/tests/external/test_scrublet.py")
+
+ ;; The following tests requires 'scanorama', which isn't
+ ;; packaged yet.
+ (delete-file "scanpy/tests/external/test_scanorama_integrate.py")
+
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":"
+ (getenv "PYTHONPATH")))
(invoke "pytest"))))))
(propagated-inputs
`(("python-anndata" ,python-anndata)
@@ -12548,11 +11325,14 @@ in RNA-seq data.")
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
+ ("python-pytoml" ,python-pytoml)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-setuptools-scm" ,python-setuptools-scm)))
+ `(("python-leidenalg" ,python-leidenalg)
+ ("python-pytest" ,python-pytest)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-sinfo" ,python-sinfo)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
@@ -12874,15 +11654,39 @@ fasta subsequences.")
(define-public python-cooler
(package
(name "python-cooler")
- (version "0.8.7")
+ (version "0.8.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cooler" version))
(sha256
(base32
- "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+ "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ (substitute* "tests/test_create.py"
+ (("def test_roundtrip")
+ (string-append "@pytest.mark.skip(reason=\"requires network "
+ "access to genome.ucsc.edu\")\n"
+ "def test_roundtrip")))
+ (substitute* "tests/test_util.py"
+ (("def test_fetch_chromsizes")
+ (string-append "@pytest.mark.skip(reason=\"requires network "
+ "access to genome.ucsc.edu\")\n"
+ "def test_fetch_chromsizes")))
+ ;; This test depends on ipytree, which contains a lot of minified
+ ;; JavaScript.
+ (substitute* "tests/test_fileops.py"
+ (("def test_print_trees")
+ "def _test_print_trees"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
`(("python-asciitree" ,python-asciitree)
("python-biopython" ,python-biopython)
@@ -12898,11 +11702,17 @@ fasta subsequences.")
("python-pysam" ,python-pysam)
("python-pyyaml" ,python-pyyaml)
("python-scipy" ,python-scipy)
- ("python-simplejson" ,python-simplejson)))
+ ("python-simplejson" ,python-simplejson)
+ ("python-six" ,python-six)
+ ("python-sparse" ,python-sparse)))
(native-inputs
- `(("python-mock" ,python-mock)
- ("python-pytest" ,python-pytest)))
- (home-page "https://github.com/mirnylab/cooler")
+ `(("python-codecov" ,python-codecov)
+ ("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-flake8" ,python-pytest-flake8)))
+ ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
+ (home-page "https://github.com/open2c/cooler")
(synopsis "Sparse binary format for genomic interaction matrices")
(description
"Cooler is a support library for a sparse, compressed, binary persistent
@@ -14701,7 +13511,7 @@ manipulations on VCF files.")
(define-public freebayes
(package
(name "freebayes")
- (version "1.3.3")
+ (version "1.3.5")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -14709,8 +13519,7 @@ manipulations on VCF files.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
- (patches (search-patches "freebayes-devendor-deps.patch"))
+ (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -14722,8 +13531,7 @@ manipulations on VCF files.")
("htslib" ,htslib)
("smithwaterman" ,smithwaterman)
("tabixpp" ,tabixpp)
- ("vcflib" ,vcflib)
- ("zlib" ,zlib)))
+ ("vcflib" ,vcflib)))
(native-inputs
`(("bash-tap" ,bash-tap)
("bc" ,bc)
@@ -14756,13 +13564,13 @@ manipulations on VCF files.")
(string-append bash-tap "/bin/bash-tap-bootstrap"))
(("source.*bash-tap-bootstrap")
(string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
- (substitute* "meson.build"
- ;; Some inputs aren't actually needed.
- ((".*bamtools/src.*") "")
- ((".*multichoose.*") ""))
(substitute* '("src/BedReader.cpp"
"src/BedReader.h")
(("../intervaltree/IntervalTree.h") "IntervalTree.h"))
+ (substitute* "meson.build"
+ ;; Our pkg-config file is vcflib.pc
+ (("libvcflib") "vcflib")
+ (("vcflib_inc,") ""))
#t)))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 4e82da869e..739870dc77 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -431,6 +431,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
(uri (git-reference
(url "git://git.liw.fi/cmdtest/")
(commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
"1yhcwsqcpckkq5kw3h07k0xg6infyiyzq9ni3nqphrzxis7hxjf1"))))
@@ -697,8 +698,8 @@ generation.")
(license license:bsd-3)))
(define-public googletest-1.8
- (package/inherit
- googletest
+ (package
+ (inherit googletest)
(version "1.8.1")
(source (origin
(method git-fetch)
@@ -1144,8 +1145,8 @@ contacting the real http server.")
;; python-bleach 3.1.0 requires this ancient version of pytest-runner.
;; Remove once no longer needed.
(define-public python-pytest-runner-2
- (package/inherit
- python-pytest-runner
+ (package
+ (inherit python-pytest-runner)
(version "2.12.2")
(source (origin
(method url-fetch)
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index f06767f305..6a98867cc8 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -163,6 +163,7 @@
"third_party/google_input_tools/third_party/closure_library/third_party/closure" ;Expat
"third_party/googletest" ;BSD-3
"third_party/harfbuzz-ng" ;Expat
+ "third_party/highway" ;ASL2.0
"third_party/hunspell" ;MPL1.1/GPL2+/LGPL2.1+
"third_party/iccjpeg" ;IJG
"third_party/inspector_protocol" ;BSD-3
@@ -179,6 +180,7 @@
"third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3
"third_party/libaom/source/libaom/third_party/vector" ;Expat
"third_party/libaom/source/libaom/third_party/x86inc" ;ISC
+ "third_party/libjxl" ;ASL2.0
"third_party/libgav1" ;ASL2.0
"third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2
"third_party/libjingle_xmpp" ;BSD-3
@@ -239,7 +241,6 @@
"third_party/rnnoise" ;BSD-3
"third_party/ruy" ;ASL2.0
"third_party/s2cellid" ;ASL2.0
- "third_party/schema_org" ;CC-BY-SA3.0
"third_party/securemessage" ;ASL2.0
"third_party/shell-encryption" ;ASL2.0
"third_party/skia" ;BSD-3
@@ -274,6 +275,7 @@
"third_party/wayland-protocols" ;Expat
"third_party/web-animations-js" ;ASL2.0
"third_party/webdriver" ;ASL2.0
+ "third_party/webgpu-cts" ;BSD-3
"third_party/webrtc" ;BSD-3
"third_party/webrtc/common_audio/third_party/ooura" ;Non-copyleft
"third_party/webrtc/common_audio/third_party/spl_sqrt_floor" ;Public domain
@@ -320,14 +322,14 @@
(string-append "ungoogled-chromium-" category "-" name))))
(sha256 (base32 hash))))
-(define %chromium-version "90.0.4430.212")
+(define %chromium-version "91.0.4472.77")
(define %debian-revision "debian/90.0.4430.85-1")
-(define %ungoogled-revision "90.0.4430.85-1-11-g3184907")
+;; Note: use 'git describe --long' even for exact tags to placate the
+;; custom version format for ungoogled-chromium.
+(define %ungoogled-revision "91.0.4472.77-1-0-g6802c88")
(define %debian-patches
- (list (debian-patch "fixes/missing-includes.patch"
- "1f0drxp1cy76g71rkkzxxbwixn03yn9b0q22vb0mb6h2qk6cw92q")
- (debian-patch "fixes/nomerge.patch"
+ (list (debian-patch "fixes/nomerge.patch"
"0lybs2b5gk08j8cr6vjrs9d3drd7qfw013z2r0y00by8dnpm74i3")
(debian-patch "system/nspr.patch"
"1gdirn1k1i841l8zp8xgr95kl16b5nx827am9rcxj8sfkm8hgkn3")
@@ -344,7 +346,7 @@
(file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
(sha256
(base32
- "18xfwgkw3xarxcgnzvyv70h4icyqh3k8lfx6fvhp7fsr6x20sai0"))))
+ "1jfmmkw1y4rcjfgsm7b4v2lrgd3sks5qpajvq0djflbhkpsqxfk0"))))
(define %guix-patches
(list (local-file
@@ -399,6 +401,11 @@
(format #t "Replacing GN files...~%")
(force-output)
+ ;; XXX: Chromium no longer relies on overriding ICU's UCHAR_TYPE,
+ ;; but the unbundling code was not updated. Remove for M92.
+ (substitute* "build/linux/unbundle/icu.gn"
+ (("\"UCHAR_TYPE=uint16_t\",")
+ ""))
(substitute* "tools/generate_shim_headers/generate_shim_headers.py"
;; The "is_official_build" configure option enables certain
;; release optimizations like those used in the commercial
@@ -481,7 +488,7 @@
%chromium-version ".tar.xz"))
(sha256
(base32
- "17nmhrkl81qqvzbh861k2mmifncx4wg1mv1fmn52f8gzn461vqdb"))
+ "0c8vj3gq3nmb7ssiwj6875g0a8hcprss1a4gqw9h7llqywza9ma5"))
(modules '((guix build utils)))
(snippet (force ungoogled-chromium-snippet))))
(build-system gnu-build-system)
@@ -630,6 +637,12 @@
(("include \"third_party/lcms/include/lcms2\\.h\"")
"include \"lcms2.h\""))
+ ;; Add missing include statement.
+ (substitute* "third_party/pdfium/core/fxcodec/png/png_decoder.cpp"
+ (("#include \"core/fxcodec/fx_codec.h\"" all)
+ (string-append all
+ "\n#include \"core/fxcodec/fx_codec_def.h\"")))
+
(substitute*
"third_party/breakpad/breakpad/src/common/linux/libcurl_wrapper.h"
(("include \"third_party/curl")
@@ -852,7 +865,7 @@
("glib" ,glib)
("gtk+" ,gtk+)
("harfbuzz" ,harfbuzz)
- ("icu4c" ,icu4c-68)
+ ("icu4c" ,icu4c-69)
("lcms" ,lcms)
("libevent" ,libevent)
("libffi" ,libffi)
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 62f197c2f9..e3918fb724 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -73,8 +73,8 @@
(file-name (string-append name "-" version "-checkout")))))))
(define-public cuirass
- (let ((commit "31fd4d4fe107d86f5e202510e177726a1f49e828")
- (revision "17"))
+ (let ((commit "21202760c0d15c99b69ef235ff129ab9cb478186")
+ (revision "25"))
(package
(name "cuirass")
(version (git-version "1.0.0" revision commit))
@@ -87,7 +87,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "08phqr0sfi6hkzrqhqsh9ri9434sd41qg1b5vijbadgsj1ql33rw"))))
+ "1bzzycz7jmmrph730p8d3q2h76ab6i8j72wblm3w0szf8vimcqfk"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -141,7 +141,7 @@
(guix (assoc-ref inputs "guix"))
(deps (list avahi gcrypt json zmq squee git bytes
fibers zlib matd tls mail guix))
- (guile (assoc-ref %build-inputs "guile"))
+ (guile (assoc-ref inputs "guile"))
(effective
(read-line
(open-pipe* OPEN_READ
diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm
index 01996591c7..e643cc58f9 100644
--- a/gnu/packages/cluster.scm
+++ b/gnu/packages/cluster.scm
@@ -3,6 +3,7 @@
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2021 Dion Mendel <guix@dm9.info>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -33,6 +34,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages sphinx)
+ #:use-module (gnu packages sqlite)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages tls))
@@ -186,7 +188,7 @@ independently or together to provide resilient infrastructures.")
(define-public libraft
(package
(name "libraft")
- (version "0.9.11")
+ (version "0.10.1")
(home-page "https://github.com/canonical/raft")
(source (origin
(method git-fetch)
@@ -195,7 +197,7 @@ independently or together to provide resilient infrastructures.")
(file-name (git-file-name name version))
(sha256
(base32
- "00rsq4z9nykmf7r5rlpv1y6bvckcmg3zv57vh1h681y5pij6cch1"))))
+ "18idj53vnl5fx1ja1zlp8kiwmdxgwjxsi88rdql0pbh0484b92a3"))))
(arguments '(#:configure-flags '("--enable-uv")
#:phases
(modify-phases %standard-phases
@@ -220,3 +222,42 @@ that, a pluggable interface defines the I/O implementation for networking
(send/receive RPC messages) and disk persistence (store log entries and
snapshots).")
(license license:asl2.0)))
+
+(define-public libdqlite
+ (package
+ (name "libdqlite")
+ (version "1.7.0")
+ (home-page "https://github.com/canonical/dqlite")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "15cg8yl3n7lcg0qyg0byciz8v6y200ghmzzkwpdzggy3m6c168wl"))))
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-failing-tests
+ (lambda _
+ (substitute* "Makefile.am"
+ ;; Test client/query sometimes fails.
+ ;; The actual tested asserts succeed, but there appears to be a
+ ;; race condition when tearing down the test server.
+ ((".*test_client.c.*") "")))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("libraft" ,libraft)
+ ("libuv" ,libuv)))
+ (propagated-inputs
+ `(("sqlite" ,sqlite))) ; dqlite.h includes sqlite3.h
+ (build-system gnu-build-system)
+ (synopsis "Distributed SQLite")
+ (description "dqlite is a C library that implements an embeddable and replicated
+SQL database engine with high-availability and automatic failover.")
+ (license license:lgpl3)))
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 64816a30c0..cc91bcfaa4 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -864,7 +864,15 @@ time for compression ratio.")
"squashfs" version ".tar.gz"))
(sha256
(base32
- "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9"))))
+ "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Fix build with -fno-common (default in GCC 10).
+ ;; Remove for squashfs-tools > 4.4.
+ (substitute* "squashfs-tools/mksquashfs.h"
+ (("struct cache \\*bwriter_buffer" all)
+ (string-append "extern " all)))))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -1008,7 +1016,7 @@ tarballs.")
(define-public libjcat
(package
(name "libjcat")
- (version "0.1.7")
+ (version "0.1.8")
(source
(origin
(method git-fetch)
@@ -1018,7 +1026,7 @@ tarballs.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "110c8h3p7m4ibrfvgja592z7j5h88qqanllxsvmxkjz3b129i02r"))))
+ (base32 "18qkyg19r7fxzv93kar5n808n3582ygjmqwa7rnyg5y4b6hnwihl"))))
(build-system meson-build-system)
(native-inputs
`(("gobject-introspection" ,gobject-introspection)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8709cd21fa..2e7e9041c6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,7 +33,6 @@
;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
-;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -351,6 +350,54 @@ easier.")
for authoring journal articles and conference submissions.")
(license license:gpl3)))
+(define-public r-benchmarkmedata
+ (package
+ (name "r-benchmarkmedata")
+ (version "1.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "benchmarkmeData" version))
+ (sha256
+ (base32
+ "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-tibble" ,r-tibble)))
+ (home-page "https://github.com/csgillespie/benchmarkme-data")
+ (synopsis "Data set for the @code{benchmarkme} package")
+ (description "This package contains the data set for the crowd-sourced
+benchmarks from running the @code{benchmarkme} package.")
+ (license license:gpl2+)))
+
+(define-public r-benchmarkme
+ (package
+ (name "r-benchmarkme")
+ (version "1.0.7")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "benchmarkme" version))
+ (sha256
+ (base32
+ "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-benchmarkmedata" ,r-benchmarkmedata)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-httr" ,r-httr)
+ ("r-matrix" ,r-matrix)
+ ("r-tibble" ,r-tibble)))
+ (home-page "https://csgillespie.github.io/benchmarkme/")
+ (synopsis "Crowd-sourced system benchmarks")
+ (description "This package provides functionality to benchmark your CPU
+and compare against other CPUs. Also provides functions for obtaining system
+specifications, such as RAM, CPU type, and R version.")
+ (license license:gpl2+)))
+
(define-public r-bezier
(package
(name "r-bezier")
@@ -671,6 +718,28 @@ provides methods for automatically determining breaks and labels for axes and
legends.")
(license license:expat)))
+(define-public r-pacman
+ (package
+ (name "r-pacman")
+ (version "0.5.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "pacman" version))
+ (sha256
+ (base32
+ "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-remotes" ,r-remotes)))
+ (home-page "https://github.com/trinker/pacman")
+ (synopsis "Package Management Tool")
+ (description "This package provides tools to more conveniently perform
+tasks associated with add-on packages. @code{pacman} conveniently wraps
+library and package related functions and names them in an intuitive and
+consistent fashion. It seeks to combine functionality from lower level
+functions which can speed up workflow.")
+ (license license:gpl2)))
+
(define-public r-pheatmap
(package
(name "r-pheatmap")
@@ -1130,6 +1199,29 @@ without affecting the current R process at all. This package does exactly
that.")
(license license:expat)))
+(define-public r-depmixs4
+ (package
+ (name "r-depmixs4")
+ (version "1.5-0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "depmixS4" version))
+ (sha256
+ (base32
+ "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
+ (propagated-inputs
+ `(("r-nnet" ,r-nnet)
+ ("r-nlme" ,r-nlme)
+ ("r-mass" ,r-mass)
+ ("r-rsolnp" ,r-rsolnp)))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/depmixS4/")
+ (synopsis "Dependent Mixture Models")
+ (description "This package fits latent (hidden) Markov models on mixed
+categorical and continuous (time series) data, otherwise known as dependent
+mixture models.")
+ (license license:gpl2+)))
+
(define-public r-readxl
(package
(name "r-readxl")
@@ -1157,6 +1249,36 @@ the embedded @code{RapidXML} C++ library.")
;; 'rapidxml' which is Boost.
(license (list license:gpl3 license:bsd-2 license:boost1.0))))
+(define-public r-model4you
+ (package
+ (name "r-model4you")
+ (version "0.9-7")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "model4you" version))
+ (sha256
+ (base32
+ "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-formula" ,r-formula)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-partykit" ,r-partykit)
+ ("r-sandwich" ,r-sandwich)
+ ("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/model4you/")
+ (synopsis "Stratified and personalised models based on trees and forests")
+ (description
+ "This package provides procedures for model-based trees for subgroup
+analyses in clinical trials and model-based forests for the estimation and
+prediction of personalised treatment effects. Currently partitioning of linear
+models, @code{lm()}, generalised linear models, @code{glm()}, and
+Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
+supported for the trees and a test for parameter heterogeneity is provided for
+the personalised models.")
+ (license license:gpl2+)))
+
(define-public r-modelr
(package
(name "r-modelr")
@@ -1204,6 +1326,28 @@ and make inference with discrete time and discrete space hidden Markov
models.")
(license license:gpl2+)))
+(define-public r-hiddenmarkov
+ (package
+ (name "r-hiddenmarkov")
+ (version "1.8-13")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "HiddenMarkov" version))
+ (sha256
+ (base32
+ "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
+ (synopsis "Hidden markov models for R")
+ (description "This package contains functions for the analysis of Discrete
+Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
+Poisson Process. It includes functions for simulation, parameter estimation,
+and the Viterbi algorithm. The algorithms are based of those of Walter
+Zucchini.")
+ (license license:gpl2+)))
+
(define-public r-httpuv
(package
(name "r-httpuv")
@@ -1307,6 +1451,29 @@ documents that can be converted to HTML files (e.g., R Markdown) under a given
directory.")
(license license:expat)))
+(define-public r-howmany
+ (package
+ (name "r-howmany")
+ (version "0.3-1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "howmany" version))
+ (sha256
+ (base32
+ "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/howmany/")
+ (synopsis "Lower bound for the number of correct rejections")
+ (description "When testing multiple hypotheses simultaneously, this package
+provides functionality to calculate a lower bound for the number of correct
+rejections (as a function of the number of rejected hypotheses), which holds
+simultaneously -with high probability- for all possible number of rejections.
+As a special case, a lower bound for the total number of false null hypotheses
+can be inferred. Dependent test statistics can be handled for multiple tests
+of associations. For independent test statistics, it is sufficient to provide
+a list of p-values.")
+ (license license:gpl2+)))
+
(define-public r-htmltools
(package
(name "r-htmltools")
@@ -2894,6 +3061,26 @@ attaching it. This is a key part of the @code{devtools} package as it allows
you to rapidly iterate while developing a package.")
(license license:gpl3)))
+(define-public r-pvclust
+ (package
+ (name "r-pvclust")
+ (version "2.2-0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "pvclust" version))
+ (sha256
+ (base32
+ "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/shimo-lab/pvclust")
+ (synopsis
+ "Hierarchical clustering with P-values via multiscale bootstrap resampling")
+ (description "This package provides an implementation of multiscale bootstrap
+resampling for assessing the uncertainty in hierarchical cluster analysis. It
+provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
+value for each cluster in a dendrogram.")
+ (license license:gpl2+)))
+
(define-public r-rcpp
(package
(name "r-rcpp")
@@ -2939,6 +3126,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
safely be interrupted from R.")
(license license:expat)))
+(define-public r-rcppnumerical
+ (package
+ (name "r-rcppnumerical")
+ (version "0.4-0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "RcppNumerical" version))
+ (sha256
+ (base32
+ "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)))
+ (home-page "https://github.com/yixuan/RcppNumerical")
+ (synopsis"Numerical computing libraries integration with @code{Rcpp}")
+ (description "This package provides a collection of libraries for numerical
+computing (numerical integration, optimization, etc.) and their integration
+with @code{Rcpp}.")
+ (license license:gpl2+)))
+
(define-public r-bindr
(package
(name "r-bindr")
@@ -3288,6 +3496,25 @@ statistical functions and other utilities to ease their usage.")
quantities.")
(license license:expat)))
+(define-public r-princurve
+ (package
+ (name "r-princurve")
+ (version "2.1.6")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "princurve" version))
+ (sha256
+ (base32
+ "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/rcannood/princurve")
+ (synopsis "Fit a principal curve in arbitrary dimension")
+ (description "This package provides procedures for fitting a principal
+curve to a data matrix in arbitrary dimensions.")
+ (license license:gpl2)))
+
(define-public r-reshape
(package
(name "r-reshape")
@@ -3584,14 +3811,14 @@ which should be seen for details.")
(define-public r-extremes
(package
(name "r-extremes")
- (version "2.1")
+ (version "2.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "extRemes" version))
(sha256
(base32
- "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
+ "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as"))))
(properties `((upstream-name . "extRemes")))
(build-system r-build-system)
(propagated-inputs
@@ -3653,13 +3880,13 @@ by Li, Brown, Huang, and Bickel")
(define-public r-inline
(package
(name "r-inline")
- (version "0.3.18")
+ (version "0.3.19")
(source (origin
(method url-fetch)
(uri (cran-uri "inline" version))
(sha256
(base32
- "0fpcfwbhfg1lhkqc0gdqv2sq64r3ljld7piy34vv0nimq30xi2fc"))))
+ "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/inline")
(synopsis "Functions to inline C, C++, Fortran function calls from R")
@@ -3843,14 +4070,14 @@ functions from LINPACK.")
(define-public r-fitdistrplus
(package
(name "r-fitdistrplus")
- (version "1.1-3")
+ (version "1.1-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "fitdistrplus" version))
(sha256
(base32
- "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
+ "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -5058,6 +5285,44 @@ Friendly and is now the main support package for a new book, \"Discrete Data
Analysis with R\" by Michael Friendly and David Meyer (2015).")
(license license:gpl2)))
+(define-public r-vcfr
+ (package
+ (name "r-vcfr")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "vcfR" version))
+ (sha256
+ (base32
+ "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-dplyr" ,r-dplyr)
+ ("r-magrittr" ,r-magrittr)
+ ("r-memuse" ,r-memuse)
+ ("r-pinfsc50" ,r-pinfsc50)
+ ("r-rcpp" ,r-rcpp)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-vegan" ,r-vegan)
+ ("r-viridislite" ,r-viridislite)))
+ (home-page "https://github.com/knausb/vcfR")
+ (synopsis "Manipulate and visualize VCF data")
+ (description "This package facilitates easy manipulation of variant call
+format (VCF) data. Functions are provided to rapidly read from and write to
+VCF files. Once VCF data is read into R, a parser function extracts matrices
+of data. This information can then be used for quality control or other
+purposes. Additional functions provide visualization of genomic data. Once
+processing is complete data may be written to a VCF file. It also may be
+converted into other popular R objects. This package provides a link between
+VCF data and familiar R software.")
+ (license license:gpl3)))
+
(define-public r-ica
(package
(name "r-ica")
@@ -5535,6 +5800,25 @@ columns of data using the full range of colours provided by modern
terminals.")
(license license:gpl3)))
+(define-public r-pinfsc50
+ (package
+ (name "r-pinfsc50")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "pinfsc50" version))
+ (sha256
+ (base32
+ "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
+ (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
+ (description "This package contains genomic data for the plant pathogen
+Phytophthora infestans. It includes a variant file, a sequence file and an
+annotation file. This package is intended to be used as example data for
+packages that work with genomic data.")
+ (license license:gpl2+)))
+
(define-public r-uuid
(package
(name "r-uuid")
@@ -5557,14 +5841,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.31")
+ (version "0.32")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p"))))
+ "17y20kb5xgmz77n4rrkqmcm0cnjwfi4mn84h6zabij76b8cjiykh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -6280,6 +6564,30 @@ fixed values. Other functions include a custom @code{geom}, and helper
functions to enforce symmetric scales or add tags to facetted plots.")
(license license:gpl3)))
+(define-public r-heatmap3
+ (package
+ (name "r-heatmap3")
+ (version "1.1.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "heatmap3" version))
+ (sha256
+ (base32
+ "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fastcluster" ,r-fastcluster)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://cran.r-project.org/web/packages/heatmap3/")
+ (synopsis "Improved heatmap package")
+ (description
+ "This package provides an improved heatmap package. It is completely
+compatible with the original R function @code{heatmap}, and provides more
+powerful and convenient features.")
+ (license license:gpl2+)))
+
(define-public r-heatmaply
(package
(name "r-heatmaply")
@@ -6561,14 +6869,14 @@ and within plot factors interact.")
(define-public r-signal
(package
(name "r-signal")
- (version "0.7-6")
+ (version "0.7-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "signal" version))
(sha256
(base32
- "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
+ "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
(build-system r-build-system)
(propagated-inputs `(("r-mass" ,r-mass)))
(native-inputs `(("gfortran" ,gfortran)))
@@ -6948,14 +7256,14 @@ misclassification probabilities of different models.")
(define-public r-zip
(package
(name "r-zip")
- (version "2.1.1")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "zip" version))
(sha256
(base32
- "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
+ "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/zip")
(synopsis "Cross-platform Zip compression")
@@ -7882,14 +8190,14 @@ steps and provides ggplot2-based elegant data visualization.")
(define-public r-fansi
(package
(name "r-fansi")
- (version "0.4.2")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fansi" version))
(sha256
(base32
- "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
+ "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
@@ -8064,14 +8372,14 @@ implemented in bibutils.")
(define-public r-rdpack
(package
(name "r-rdpack")
- (version "2.1.1")
+ (version "2.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
- "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
+ "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
@@ -8316,14 +8624,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.14.0")
+ (version "0.14.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "1zkifkj2qg9vdv26z4qvi81qv9l1cqyrq3ihdpacpax80plkgdln"))))
+ "0af15kqz4kiyi5p4qi748hvdw462vdwigzyykh1k7vj6gacn2xqf"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -8913,13 +9221,13 @@ based on index arrays and simple triplet representations, respectively.")
(define-public r-manipulatewidget
(package
(name "r-manipulatewidget")
- (version "0.10.1")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "manipulateWidget" version))
(sha256
- (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
+ (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj"))))
(properties
`((upstream-name . "manipulateWidget")))
(build-system r-build-system)
@@ -8931,7 +9239,10 @@ based on index arrays and simple triplet representations, respectively.")
("r-knitr" ,r-knitr)
("r-miniui" ,r-miniui)
("r-shiny" ,r-shiny)
+ ("r-shinyjs" ,r-shinyjs)
("r-webshot" ,r-webshot)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
(synopsis "Add even more interactivity to interactive charts")
(description
@@ -10261,14 +10572,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "07iw3faprf98mncymbjbmfm2yi294yiwdg30xlql5sfx12qbf6r0"))))
+ "02sh1q6f2ik56w348pfkg4a8jvdn3a31r7d8mzg7zq3sv7lmvqwl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@@ -10497,14 +10808,14 @@ differentiation.")
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.9.0")
+ (version "0.10.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "0msr24ymnazpaz8s9qs5v3xn1i9984p98lr9x4qq9cxgx34rm9h0"))))
+ "1qr51mag5wf44h4sygkn5arsirpqdanf039cg6fxmyw83k51fi2v"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@@ -10581,14 +10892,14 @@ results using @code{ggplot2}.")
(define-public r-effectsize
(package
(name "r-effectsize")
- (version "0.4.4-1")
+ (version "0.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "effectsize" version))
(sha256
(base32
- "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb"))))
+ "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf"))))
(properties `((upstream-name . "effectsize")))
(build-system r-build-system)
(propagated-inputs
@@ -10608,13 +10919,13 @@ conversion of indices such as Cohen's d, r, odds, etc.")
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.8.7")
+ (version "2.8.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
- (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
+ (base32 "050aarycgzy1n8ad67pj09s8k7s7xk6dicg0kjg0ivlkyyq0shqz"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
@@ -11187,14 +11498,14 @@ the interfaces between R and C++.")
(define-public r-mvabund
(package
(name "r-mvabund")
- (version "4.1.9")
+ (version "4.1.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "mvabund" version))
(sha256
(base32
- "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
+ "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -11301,21 +11612,21 @@ al. (2016)).")
(define-public r-weights
(package
(name "r-weights")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "weights" version))
(sha256
(base32
- "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
+ "1sq8ls5idspddn8m2c8n2107lgx53kbach8vgjrhqx1mc6xfvrvw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gdata" ,r-gdata)
("r-hmisc" ,r-hmisc)
+ ("r-lme4" ,r-lme4)
("r-mice" ,r-mice)))
- (home-page
- "https://cran.r-project.org/web/packages/weights/")
+ (home-page "https://cran.r-project.org/web/packages/weights/")
(synopsis "Weighting and weighted statistics")
(description "This package Provides a variety of functions for producing
simple weighted statistics, such as weighted Pearson's correlations, partial
@@ -11531,13 +11842,13 @@ isosurfaces.")
(define-public r-ks
(package
(name "r-ks")
- (version "1.12.0")
+ (version "1.13.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ks" version))
(sha256
- (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
+ (base32 "0zi7yixz3hvqvb5fxipkxprk5p4irr61csd3k6scsxqyhrb5ffls"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fnn" ,r-fnn)
@@ -11548,7 +11859,8 @@ isosurfaces.")
("r-mgcv" ,r-mgcv)
("r-multicool" ,r-multicool)
("r-mvtnorm" ,r-mvtnorm)
- ("r-plot3d" ,r-plot3d)))
+ ("r-plot3d" ,r-plot3d)
+ ("r-pracma" ,r-pracma)))
(home-page "https://www.mvstat.net/tduong/")
(synopsis "Kernel smoothing")
(description
@@ -11997,13 +12309,13 @@ maps.")
(define-public r-tidytree
(package
(name "r-tidytree")
- (version "0.3.3")
+ (version "0.3.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytree" version))
(sha256
- (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
+ (base32 "0bqsb0zplkqkx2mp8kpanadkds4kwwvdrc07lp0qzwqqzaxq5xa3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
@@ -12385,6 +12697,89 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
Touzet and Varre (2007).")
(license license:gpl2)))
+(define-public r-rncl
+ (package
+ (name "r-rncl")
+ (version "0.8.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "rncl" version))
+ (sha256
+ (base32
+ "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-progress" ,r-progress)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/fmichonneau/rncl")
+ (synopsis "Interface to the Nexus class library")
+ (description "This package provides an interface to the Nexus class
+library which allows parsing of NEXUS, Newick and other phylogenetic tree
+ file formats. It provides elements of the file that can be used to build
+ phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
+@code{phylo4(d)}. This functionality is demonstrated with
+@code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
+ (license license:bsd-2)))
+
+(define-public r-phylobase
+ (package
+ (name "r-phylobase")
+ (version "0.8.10")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "phylobase" version))
+ (sha256
+ (base32
+ "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ade4" ,r-ade4)
+ ("r-ape" ,r-ape)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rncl" ,r-rncl)
+ ("r-rnexml" ,r-rnexml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/fmichonneau/phylobase")
+ (synopsis "Base package for phylogenetic structures and comparative data")
+ (description "This package provides a base @code{S4} class for comparative
+methods, incorporating one or more trees and trait data.")
+ (license license:gpl2+)))
+
+(define-public r-rnexml
+ (package
+ (name "r-rnexml")
+ (version "2.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "RNeXML" version))
+ (sha256
+ (base32
+ "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-lazyeval" ,r-lazyeval)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-stringi" ,r-stringi)
+ ("r-stringr" ,r-stringr)
+ ("r-tidyr" ,r-tidyr)
+ ("r-uuid" ,r-uuid)
+ ("r-xml" ,r-xml)
+ ("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://docs.ropensci.org/RNeXML/")
+ (synopsis "Semantically rich I/O for the NeXML Format")
+ (description "This package provides access to phyloinformatic data in
+NeXML format. The package should add new functionality to R such as the
+possibility to manipulate NeXML objects in more various and refined way
+and compatibility with @code{ape} objects.")
+ (license license:bsd-3)))
+
(define-public r-rnifti
(package
(name "r-rnifti")
@@ -13504,6 +13899,23 @@ Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
(license license:gpl2+)))
+(define-public r-locfdr
+ (package
+ (name "r-locfdr")
+ (version "1.1-8")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "locfdr" version))
+ (sha256
+ (base32
+ "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/locfdr/")
+ (synopsis "Computes local false discovery rates")
+ (description "This package can be used to compute local false
+discovery rates.")
+ (license license:gpl2)))
+
(define-public r-longitudinal
(package
(name "r-longitudinal")
@@ -15493,14 +15905,26 @@ datum transformations.")
(define-public r-spdep
(package
(name "r-spdep")
- (version "1.1-7")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "spdep" version))
- (sha256
- (base32
- "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1"))))
+ (version "1.1-8")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "spdep" version))
+ (sha256
+ (base32
+ "1k82vx58kpn0fwgcpxq2jc3qfffl8wzbgr4cdkxihrfk28kkqh7l"))
+ (snippet
+ '(for-each delete-file '("inst/doc/nb_igraph.html"
+ "inst/doc/nb_igraph.R"
+ "inst/doc/nb_igraph.Rmd"
+ "inst/doc/sids.html"
+ "inst/doc/sids.R"
+ "inst/doc/nb.html"
+ "inst/doc/nb.R"
+ "inst/doc/CO69.html"
+ "inst/doc/CO69.R"
+ "inst/doc/nb_sf.html"
+ "inst/doc/nb_sf.R"
+ "inst/doc/nb_sf.Rmd")))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -17249,6 +17673,116 @@ making it possible to download files over HTTPS across platforms. The
external dependencies. This package has is implemented purely in R.")
(license license:gpl2)))
+(define-public r-aplot
+ (package
+ (name "r-aplot")
+ (version "0.0.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "aplot" version))
+ (sha256
+ (base32
+ "08kqrm9r57l8zgij897wpp428l4i50qfhp7y78r3pk5pjz37bsan"))))
+ (properties `((upstream-name . "aplot")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-patchwork" ,r-patchwork)))
+ (home-page "https://github.com/YuLab-SMU/aplot")
+ (synopsis "Decorate a ggplot with associated information")
+ (description
+ "Users may want to align plots with associated information that requires
+axes to be exactly matched in subplots, e.g. hierarchical clustering with a
+heatmap. This package provides utilities to align associated subplots to a
+main plot at different sides (left, right, top and bottom) with axes exactly
+matched.")
+ (license license:artistic2.0)))
+
+(define-public r-ggnewscale
+ (package
+ (name "r-ggnewscale")
+ (version "0.4.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggnewscale" version))
+ (sha256
+ (base32
+ "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702"))))
+ (properties `((upstream-name . "ggnewscale")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)))
+ (home-page "https://cran.r-project.org/package=ggnewscale")
+ (synopsis "Multiple fill and color scales in ggplot2")
+ (description
+ "This package lets you use multiple fill and color scales in ggplot2.")
+ (license license:gpl3)))
+
+(define-public r-ggpointdensity
+ (package
+ (name "r-ggpointdensity")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggpointdensity" version))
+ (sha256
+ (base32
+ "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
+ (properties
+ `((upstream-name . "ggpointdensity")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)))
+ (home-page "https://github.com/LKremer/ggpointdensity")
+ (synopsis "Cross between a 2D density plot and a scatter plot")
+ (description
+ "This package provides a cross between a 2D density plot and a scatter
+plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
+colored by the number of neighboring points. This is useful to visualize the
+2D-distribution of points in case of overplotting.")
+ (license license:gpl3)))
+
+(define-public r-arrow
+ (package
+ (name "r-arrow")
+ (version "4.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "arrow" version))
+ (sha256
+ (base32
+ "19kzfjxp90ybi1px3r93mfx59nqmnagxr4g73y7iby5blwl1bblc"))))
+ (properties `((upstream-name . "arrow")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-bit64" ,r-bit64)
+ ("r-cpp11" ,r-cpp11)
+ ("r-purrr" ,r-purrr)
+ ("r-r6" ,r-r6)
+ ("r-rlang" ,r-rlang)
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/apache/arrow/")
+ (synopsis "R integration to Apache Arrow")
+ (description
+ "Apache Arrow is a cross-language development platform for in-memory
+data. It specifies a standardized language-independent columnar memory format
+for flat and hierarchical data, organized for efficient analytic operations on
+modern hardware. This package provides an R interface to the Arrow C++
+library.")
+ (license license:asl2.0)))
+
(define-public r-rex
(package
(name "r-rex")
@@ -17709,14 +18243,14 @@ been used in the call to @code{aov}.")
(define-public r-dalex
(package
(name "r-dalex")
- (version "2.2.0")
+ (version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn"))))
+ "184mzby1giismhx4brvrdfl5n5kialyvv8ik18blhchvpy145cwf"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs
@@ -17765,14 +18299,14 @@ annotated biological functions.")
(define-public r-plot3d
(package
(name "r-plot3d")
- (version "1.3")
+ (version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "plot3D" version))
(sha256
(base32
- "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
+ "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
(properties `((upstream-name . "plot3D")))
(build-system r-build-system)
(propagated-inputs `(("r-misc3d" ,r-misc3d)))
@@ -18103,14 +18637,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
(define-public r-leiden
(package
(name "r-leiden")
- (version "0.3.7")
+ (version "0.3.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "leiden" version))
(sha256
(base32
- "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
+ "0sv0j4sgpz8z65vhbpmaglg878jhq52srzf5rpw4vbsbys2807w1"))))
(properties `((upstream-name . "leiden")))
(build-system r-build-system)
(propagated-inputs
@@ -18491,14 +19025,14 @@ in pipelines.")
(define-public r-parameters
(package
(name "r-parameters")
- (version "0.13.0")
+ (version "0.14.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
- "17dlwx9hrl6z2il14nxji0snwsf4sfbp3mv33jbpcw13sani1q81"))))
+ "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@@ -19645,6 +20179,31 @@ introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
(license license:bsd-3)))
+(define-public r-rnmf
+ (package
+ (name "r-rnmf")
+ (version "0.5.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "rNMF" version))
+ (sha256
+ (base32
+ "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-nnls" ,r-nnls)))
+ (home-page "https://cran.r-project.org/web/packages/rNMF/")
+ (synopsis "Robust nonnegative matrix factorization")
+ (description
+ "This package provides an implementation of robust nonnegative matrix
+factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
+dimension data matrix into the product of two low rank nonnegative matrices,
+while detecting and trimming outliers. The main function is @code{rnmf()}.
+The package also includes a visualization tool, @code{see()}, that arranges
+and prints vectorized images.")
+ (license license:gpl2+)))
+
(define-public r-randtoolbox
(package
(name "r-randtoolbox")
@@ -20353,6 +20912,23 @@ modeling often used in @dfn{analytical customer relationship
management} (aCRM).")
(license license:gpl2+)))
+(define-public r-tree
+ (package
+ (name "r-tree")
+ (version "1.0-40")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "tree" version))
+ (sha256
+ (base32
+ "1rr6ws62j9h36f3nl713f8h3ndkh95mv46l055jvgmby5lw1dazz"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/tree/")
+ (synopsis "Classification and regression trees")
+ (description "This package provides procedures to work with classification
+and regression trees.")
+ (license license:gpl2+)))
+
(define-public r-treeclust
(package
(name "r-treeclust")
@@ -20563,14 +21139,14 @@ allowed.")
(define-public r-gdina
(package
(name "r-gdina")
- (version "2.8.0")
+ (version "2.8.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "GDINA" version))
(sha256
(base32
- "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
+ "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4"))))
(properties `((upstream-name . "GDINA")))
(build-system r-build-system)
(propagated-inputs
@@ -21026,14 +21602,14 @@ API; see the package vignette for details.")
(define-public r-actuar
(package
(name "r-actuar")
- (version "3.1-2")
+ (version "3.1-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y"))))
+ "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs `(("r-expint" ,r-expint)))
@@ -21360,14 +21936,14 @@ cluster stability.")
(define-public r-biclust
(package
(name "r-biclust")
- (version "2.0.2")
+ (version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "biclust" version))
(sha256
(base32
- "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
+ "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
(properties `((upstream-name . "biclust")))
(build-system r-build-system)
(propagated-inputs
@@ -21922,14 +22498,14 @@ both exclusive and shared locking.")
(define-public r-archivist
(package
(name "r-archivist")
- (version "2.3.5")
+ (version "2.3.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "archivist" version))
(sha256
(base32
- "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
+ "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
(properties `((upstream-name . "archivist")))
(build-system r-build-system)
(propagated-inputs
@@ -22094,14 +22670,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
(define-public r-forecast
(package
(name "r-forecast")
- (version "8.14")
+ (version "8.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "forecast" version))
(sha256
(base32
- "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
+ "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7"))))
(properties `((upstream-name . "forecast")))
(build-system r-build-system)
(propagated-inputs
@@ -23076,14 +23652,14 @@ and reproducible way.")
(define-public r-rsconnect
(package
(name "r-rsconnect")
- (version "0.8.17")
+ (version "0.8.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "rsconnect" version))
(sha256
(base32
- "0cd2bpc22jam1qxn6yg7yr7xdhsm0jgnm5bm2f3vg5b3c96plxk4"))))
+ "01bj16iggj5fggfa7n312458p8xg30zx2vzfkd8jqcchnbrphfvl"))))
(properties `((upstream-name . "rsconnect")))
(build-system r-build-system)
(propagated-inputs
@@ -24880,6 +25456,26 @@ theory; see @url{Strumbel and Kononenko (2014),
doi.org/10.1007/s10115-013-0679-x} for details.")
(license license:gpl2+)))
+(define-public r-memuse
+ (package
+ (name "r-memuse")
+ (version "4.1-0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "memuse" version))
+ (sha256
+ (base32
+ "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq"))))
+ (properties `((upstream-name . "memuse")))
+ (build-system r-build-system)
+ (home-page "https://github.com/shinra-dev/memuse")
+ (synopsis "Memory Estimation Utilities")
+ (description
+ "This package provides procedures to answer the following questions:
+How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
+your current R session using? How much ram do you even have?")
+ (license license:bsd-2)))
+
(define-public r-metrics
(package
(name "r-metrics")
@@ -25286,17 +25882,41 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic,
Poisson), are some of the many fast functions.")
(license license:gpl2+)))
+(define-public r-rffc
+ (package
+ (name "r-rffc")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://download.r-forge.r-project.org/src/contrib/"
+ "rfFC_" version ".tar.gz"))
+ (sha256
+ (base32
+ "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-randomforest",r-randomforest)))
+ (home-page "https://r-forge.r-project.org/projects/rffc/")
+ (synopsis "Random Forest Feature Contributions")
+ (description "This package provides functions for extracting feature
+contributions from a random forest model from package @code{randomForest}.
+Feature contributions provide detailed information about the relationship
+between data variables and the predicted value returned by random forest
+model.")
+ (license license:gpl2)))
+
(define-public r-clusterr
(package
(name "r-clusterr")
- (version "1.2.4")
+ (version "1.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ClusterR" version))
(sha256
(base32
- "01vgr1mpm7l1lyhril5hm1l72aicqc4iwb0b15ypijb6hwkv7g47"))))
+ "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx"))))
(properties `((upstream-name . "ClusterR")))
(build-system r-build-system)
(propagated-inputs
@@ -25412,6 +26032,35 @@ so that natural sort function arranges a character vector by their numbers,
not digit characters.")
(license license:bsd-3)))
+(define-public r-visdat
+ (package
+ (name "r-visdat")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "visdat" version))
+ (sha256
+ (base32
+ "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
+ ("r-purrr" ,r-purrr)
+ ("r-readr" ,r-readr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://visdat.njtierney.com/")
+ (synopsis "Preliminary Visualisation of Data")
+ (description "This package provides procedures to create preliminary exploratory
+data visualisations of an entire dataset to identify problems or unexpected features
+using @code{ggplot2}.")
+ (license license:expat)))
+
(define-public r-muhaz
(package
(name "r-muhaz")
@@ -26336,14 +26985,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
(define-public r-parsnip
(package
(name "r-parsnip")
- (version "0.1.5")
+ (version "0.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "parsnip" version))
(sha256
(base32
- "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
+ "0qhdh2xdswqy94f4gkdxi1iqm0k794p9y8sdh6mgbd1a86c8ngfs"))))
(properties `((upstream-name . "parsnip")))
(build-system r-build-system)
(propagated-inputs
@@ -26351,6 +27000,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
("r-generics" ,r-generics)
("r-globals" ,r-globals)
("r-glue" ,r-glue)
+ ("r-lifecycle" ,r-lifecycle)
("r-magrittr" ,r-magrittr)
("r-prettyunits" ,r-prettyunits)
("r-purrr" ,r-purrr)
@@ -26795,13 +27445,13 @@ other R users.")
(define-public r-seurat
(package
(name "r-seurat")
- (version "4.0.1")
+ (version "4.0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
+ "1b1wyj4dxjn0hfg09l8z282grdgwgah0czs7pn2ian455x0dphng"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@@ -26923,14 +27573,14 @@ rate speciation and extinction.")
(define-public r-calculus
(package
(name "r-calculus")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "calculus" version))
(sha256
(base32
- "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
+ "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn"))))
(properties `((upstream-name . "calculus")))
(build-system r-build-system)
(propagated-inputs
@@ -27837,14 +28487,14 @@ in same length matches).")
(define-public r-textshape
(package
(name "r-textshape")
- (version "1.7.1")
+ (version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "textshape" version))
(sha256
(base32
- "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
+ "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
(properties `((upstream-name . "textshape")))
(build-system r-build-system)
(propagated-inputs
@@ -28629,35 +29279,6 @@ indicator, a quantitative variable or a survival time.")
;; Any version of the LGPL
(license license:lgpl3+)))
-(define-public r-samr
- (package
- (name "r-samr")
- (version "3.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "samr" version))
- (sha256
- (base32
- "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
- (properties `((upstream-name . "samr")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-gsa" ,r-gsa)
- ("r-impute" ,r-impute)
- ("r-matrixstats" ,r-matrixstats)
- ("r-openxlsx" ,r-openxlsx)
- ("r-shiny" ,r-shiny)
- ("r-shinyfiles" ,r-shinyfiles)))
- (native-inputs `(("gfortran" ,gfortran)))
- (home-page "https://statweb.stanford.edu/~tibs/SAM/")
- (synopsis "Significance analysis of Microarrays")
- (description
- "This is a package for significance analysis of Microarrays for
-differential expression analysis, RNAseq data and related problems.")
- ;; Any version of the LGPL
- (license license:lgpl3+)))
-
(define-public r-randomforestsrc
(package
(name "r-randomforestsrc")
@@ -28683,3 +29304,72 @@ quantile regression and solutions for class imbalanced data. It provides a
fast interface using subsampling and confidence regions for variable
importance.")
(license license:gpl3+)))
+
+(define-public r-contfrac
+ (package
+ (name "r-contfrac")
+ (version "1.1-12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "contfrac" version))
+ (sha256
+ (base32
+ "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
+ (properties `((upstream-name . "contfrac")))
+ (build-system r-build-system)
+ (home-page
+ "https://github.com/RobinHankin/contfrac")
+ (synopsis "Continued Fractions")
+ (description
+ "Various utilities for evaluating continued fractions.")
+ (license license:gpl2)))
+
+(define-public r-elliptic
+ (package
+ (name "r-elliptic")
+ (version "1.4-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "elliptic" version))
+ (sha256
+ (base32
+ "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
+ (properties `((upstream-name . "elliptic")))
+ (build-system r-build-system)
+ (inputs `(("pari-gp" ,pari-gp)))
+ (propagated-inputs `(("r-mass" ,r-mass)))
+ (home-page
+ "https://github.com/RobinHankin/elliptic")
+ (synopsis
+ "Weierstrass and Jacobi Elliptic Functions")
+ (description
+ "A suite of elliptic and related functions including Weierstrass and
+Jacobi forms. Also includes various tools for manipulating and visualizing
+complex functions.")
+ (license license:gpl2)))
+
+(define-public r-hypergeo
+ (package
+ (name "r-hypergeo")
+ (version "1.2-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hypergeo" version))
+ (sha256
+ (base32
+ "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
+ (properties `((upstream-name . "hypergeo")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-contfrac" ,r-contfrac)
+ ("r-desolve" ,r-desolve)
+ ("r-elliptic" ,r-elliptic)))
+ (home-page
+ "https://cran.r-project.org/web/packages/hypergeo/")
+ (synopsis "The Gauss Hypergeometric Function")
+ (description
+ "The Gaussian hypergeometric function for complex numbers.")
+ (license license:gpl2)))
diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm
index e5719f97e4..bc47bf1287 100644
--- a/gnu/packages/crates-graphics.scm
+++ b/gnu/packages/crates-graphics.scm
@@ -10,6 +10,7 @@
;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
;;; Copyright © 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
+;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -32,6 +33,7 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (gnu packages)
+ #:use-module (gnu packages assembly)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages llvm)
@@ -269,6 +271,38 @@ the term library to handle the ANSI nonsense and hence it works on Windows,
Mac, and Unix.")
(license (list license:asl2.0 license:expat))))
+(define-public rust-avif-parse-0.13
+ (package
+ (name "rust-avif-parse")
+ (version "0.13.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "avif-parse" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vylrjq77mpl6flmd85j5f2qimh6vjn03syvq8agb62x56khm0xj"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-bitreader" ,rust-bitreader-0.3)
+ ("rust-byteorder" ,rust-byteorder-1)
+ ("rust-fallible-collections" ,rust-fallible-collections-0.4)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-static-assertions" ,rust-static-assertions-1))
+ #:cargo-development-inputs
+ (("rust-env-logger" ,rust-env-logger-0.8)
+ ("rust-walkdir" ,rust-walkdir-2))))
+ (home-page "https://github.com/kornelski/avif-parse")
+ (synopsis "Parser for AVIF image files")
+ (description "This AVIF parser allows extracting the AV1 payload and alpha
+channel metadata out of AVIF image files. The parser is a fork of Mozilla's
+MP4 parser used in Firefox, so it's designed to be robust and safely handle
+untrusted data.")
+ (license license:mpl2.0)))
+
(define-public rust-avif-serialize-0.6
(package
(name "rust-avif-serialize")
@@ -1915,75 +1949,6 @@ interactive applications.")
("rust-glob" ,rust-glob-0.2)
("rust-term" ,rust-term-0.4))))))
-(define-public rust-rav1e-0.4
- (package
- (name "rust-rav1e")
- (version "0.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (crate-uri "rav1e" version))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32 "02cpgzycfgnflnv8sck6ajasa7abfgdzn6b4jv01sf6r21yfipbq"))))
- (build-system cargo-build-system)
- (arguments
- `(#:skip-build? #t
- #:cargo-inputs
- (("rust-aom-sys" ,rust-aom-sys-0.2)
- ("rust-arbitrary" ,rust-arbitrary-0.4)
- ("rust-arg-enum-proc-macro" ,rust-arg-enum-proc-macro-0.3)
- ("rust-arrayvec" ,rust-arrayvec-0.5)
- ("rust-assert-cmd" ,rust-assert-cmd-1)
- ("rust-av-metrics" ,rust-av-metrics-0.6)
- ("rust-backtrace" ,rust-backtrace-0.3)
- ("rust-bitstream-io" ,rust-bitstream-io-1)
- ("rust-byteorder" ,rust-byteorder-1)
- ("rust-cc" ,rust-cc-1)
- ("rust-cfg-if" ,rust-cfg-if-1)
- ("rust-clap" ,rust-clap-2)
- ("rust-console" ,rust-console-0.14)
- ("rust-criterion" ,rust-criterion-0.3)
- ("rust-crossbeam" ,rust-crossbeam-0.8)
- ("rust-dav1d-sys" ,rust-dav1d-sys-0.3)
- ("rust-fern" ,rust-fern-0.6)
- ("rust-image" ,rust-image-0.23)
- ("rust-interpolate-name" ,rust-interpolate-name-0.2)
- ("rust-itertools" ,rust-itertools-0.10)
- ("rust-ivf" ,rust-ivf-0.1)
- ("rust-libc" ,rust-libc-0.2)
- ("rust-libfuzzer-sys" ,rust-libfuzzer-sys-0.3)
- ("rust-log" ,rust-log-0.4)
- ("rust-nasm-rs" ,rust-nasm-rs-0.2)
- ("rust-noop-proc-macro" ,rust-noop-proc-macro-0.3)
- ("rust-num-derive" ,rust-num-derive-0.3)
- ("rust-num-traits" ,rust-num-traits-0.2)
- ("rust-paste" ,rust-paste-1)
- ("rust-pretty-assertions" ,rust-pretty-assertions-0.6)
- ("rust-rand" ,rust-rand-0.8)
- ("rust-rand-chacha" ,rust-rand-chacha-0.3)
- ("rust-rayon" ,rust-rayon-1)
- ("rust-regex" ,rust-regex-1)
- ("rust-rust-hawktracer" ,rust-rust-hawktracer-0.7)
- ("rust-rustc-version" ,rust-rustc-version-0.3)
- ("rust-scan-fmt" ,rust-scan-fmt-0.2)
- ("rust-serde" ,rust-serde-1)
- ("rust-signal-hook" ,rust-signal-hook-0.3)
- ("rust-simd-helpers" ,rust-simd-helpers-0.1)
- ("rust-thiserror" ,rust-thiserror-1)
- ("rust-toml" ,rust-toml-0.5)
- ("rust-v-frame" ,rust-v-frame-0.2)
- ("rust-vergen" ,rust-vergen-3)
- ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
- ("rust-y4m" ,rust-y4m-0.7))))
- (home-page "https://github.com/xiph/rav1e")
- (synopsis "Fast and safe AV1 encoder")
- (description
- "@code{rav1e} is an AV1 video encoder. It is designed to eventually
-cover all use cases, though in its current form it is most suitable for cases
-where libaom (the reference encoder) is too slow.")
- (license license:bsd-2)))
-
(define-public rust-ravif-0.6
(package
(name "rust-ravif")
@@ -1997,20 +1962,22 @@ where libaom (the reference encoder) is too slow.")
(base32 "1gyc7w1fz3qdk95cdpkj185dm6lskxfp329xm69waxc565fcz9rx"))))
(build-system cargo-build-system)
(arguments
- `(#:skip-build? #t
- #:cargo-inputs
+ `(#:cargo-inputs
(("rust-avif-serialize" ,rust-avif-serialize-0.6)
("rust-imgref" ,rust-imgref-1)
("rust-loop9" ,rust-loop9-0.1)
("rust-num-cpus" ,rust-num-cpus-1)
- ("rust-rav1e" ,rust-rav1e-0.4)
+ ("rav1e" ,rav1e)
("rust-rayon" ,rust-rayon-1)
- ("rust-rgb" ,rust-rgb-0.8))))
+ ("rust-rgb" ,rust-rgb-0.8))
+ #:cargo-development-inputs
+ (("rust-avif-parse" ,rust-avif-parse-0.13))))
+ (native-inputs
+ `(("nasm" ,nasm))) ;for building rav1e
(home-page "https://lib.rs/ravif")
(synopsis "Library for encoding images in AVIF format")
- (description
- "This package is a rav1e-based pure Rust library for encoding images in
-AVIF format.")
+ (description "This package is a rav1e-based pure Rust library for encoding
+images in AVIF format.")
(license license:bsd-3)))
(define-public rust-raw-window-handle-0.3
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index c488a769f6..76c1b2f954 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -16,6 +16,8 @@
;;; Copyright © 2021 aecepoglu <aecepoglu@fastmail.fm>
;;; Copyright © 2021 Zheng Junjie <873216071@qq.com>
;;; Copyright © 2021 Alexandru-Sergiu Marton <brown121407@posteo.ro>
+;;; Copyright © 2021 Antero Mejr <antero@kodmin.com>
+;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -56,6 +58,7 @@
#:use-module (gnu packages pcre)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages rust)
#:use-module (gnu packages rust-apps)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sqlite)
@@ -64,7 +67,8 @@
#:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
- #:use-module (gnu packages xorg))
+ #:use-module (gnu packages xorg)
+ #:use-module (srfi srfi-1))
;;;
;;; Please: Try to add new module packages in alphabetic order.
@@ -1487,14 +1491,14 @@ using AES-NI for high performance.")
(define-public rust-aho-corasick-0.7
(package
(name "rust-aho-corasick")
- (version "0.7.15")
+ (version "0.7.18")
(source
(origin
(method url-fetch)
(uri (crate-uri "aho-corasick" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1rb8gzhljl8r87dpf2n5pnqnkl694casgns4ma0sqzd4zazzw13l"))))
+ (base32 "0vv50b3nvkhyy7x7ip19qnsq11bqlnffkmj2yx2xlyk5wzawydqy"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -1930,23 +1934,23 @@ on every platform.")
"153awzwywmb61xg857b80l63b1x6hifx2pha7lxf6fck9qxwraq8"))))
(arguments '())))
-(define-public rust-arbitrary-0.4
+(define-public rust-arbitrary-1
(package
(name "rust-arbitrary")
- (version "0.4.7")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "arbitrary" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0sa55cynafwzvlhyhfpm3vmi2fydj3ipdj5yfbaif7l56cixfmfv"))))
+ (base32 "14a6r7q9b1kf1m7810p8bcl51q11mrwc5z7fjkz0lx6kdvyk0x13"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-derive-arbitrary" ,rust-derive-arbitrary-0.4))))
- (home-page "https://github.com/nagisa/rust_arbitrary")
+ (("rust-derive-arbitrary" ,rust-derive-arbitrary-1))))
+ (home-page "https://github.com/rust-fuzz/arbitrary")
(synopsis "Trait for generating structured data from unstructured data")
(description
"The @code{Arbitrary} crate lets you construct arbitrary instance of
@@ -1959,6 +1963,22 @@ values. This allows you to combine structure-aware test case generation with
coverage-guided, mutation-based fuzzers.")
(license (list license:expat license:asl2.0))))
+(define-public rust-arbitrary-0.4
+ (package/inherit rust-arbitrary-1
+ (name "rust-arbitrary")
+ (version "0.4.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "arbitrary" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0sa55cynafwzvlhyhfpm3vmi2fydj3ipdj5yfbaif7l56cixfmfv"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-derive-arbitrary" ,rust-derive-arbitrary-0.4))))))
+
(define-public rust-arbitrary-0.2
(package
(inherit rust-arbitrary-0.4)
@@ -2118,6 +2138,31 @@ coverage-guided, mutation-based fuzzers.")
that runs on Argon2.")
(license license:expat)))
+(define-public rust-array-ops-0.1
+ (package
+ (name "rust-array-ops")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "array-ops" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1jn7l9gppp6kr9kgsy22sw5p9cn1jazmqxy296gjwiwz5d11i4fc"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-rand-core" ,rust-rand-core-0.5)
+ ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.4))))
+ (home-page "https://github.com/bodil/array-ops")
+ (synopsis "Automatic method implementations for array data types")
+ (description "This package provides a number of traits with default
+implementations for most of the standard library's methods on array like data
+structures.")
+ (license license:mpl2.0)))
+
(define-public rust-arrayref-0.3
(package
(name "rust-arrayref")
@@ -2195,6 +2240,120 @@ ArrayVec and ArrayString.")
("rust-matches" ,rust-matches-0.1)
("rust-serde-test" ,rust-serde-test-1))))))
+(define-public rust-askama-escape-0.10
+ (package
+ (name "rust-askama-escape")
+ (version "0.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "askama_escape" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ys6wcrkpzygk6r93zd0rhinhy89rraarl0m4afwi023m70hihch"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page "https://github.com/djc/askama")
+ (synopsis
+ "Optimized HTML escaping code, extracted from Askama")
+ (description
+ "This package provides a optimized HTML escaping code, extracted from
+Askama.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-askama-shared-0.11
+ (package
+ (name "rust-askama-shared")
+ (version "0.11.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "askama_shared" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1g3ksf5is0qwx9rd5lxn5gbvxfcpby5gl9cahg26wl1w1xzbg0i5"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-askama-escape" ,rust-askama-escape-0.10)
+ ("rust-humansize" ,rust-humansize-1)
+ ("rust-nom" ,rust-nom-6)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-percent-encoding"
+ ,rust-percent-encoding-2)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-serde-yaml" ,rust-serde-yaml-0.8)
+ ("rust-syn" ,rust-syn-1)
+ ("rust-toml" ,rust-toml-0.5))))
+ (home-page "https://github.com/djc/askama")
+ (synopsis "Shared code for Askama")
+ (description "This package provides a shared code for Askama.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-askama-derive-0.10
+ (package
+ (name "rust-askama-derive")
+ (version "0.10.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "askama_derive" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08jmqb4lq5cvfjjcq7kjk5q4589zlsvc3ld35yfjyf4hqb22aafa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-askama-shared" ,rust-askama-shared-0.11)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-syn" ,rust-syn-1))))
+ (home-page "https://github.com/djc/askama")
+ (synopsis "Procedural macro package for Askama")
+ (description
+ "This package provide procedural macro package for Askama.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-askama-0.10
+ (package
+ (name "rust-askama")
+ (version "0.10.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "askama" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0d1iwywdgw3nba2iphayw8sfm3s8m9izwnhfar707qa7ds5p766j"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-askama-derive" ,rust-askama-derive-0.10)
+ ("rust-askama-escape" ,rust-askama-escape-0.10)
+ ("rust-askama-shared" ,rust-askama-shared-0.11)
+ ("rust-mime" ,rust-mime-0.3)
+ ("rust-mime-guess" ,rust-mime-guess-2))))
+ (home-page "https://github.com/djc/askama")
+ (synopsis
+ "Type-safe, compiled Jinja-like templates for Rust")
+ (description
+ "This package provides a type-safe, compiled Jinja-like templates for Rust.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-as-slice-0.1
(package
(name "rust-as-slice")
@@ -2316,7 +2475,7 @@ standard library.")
(define-public rust-assert-cmd-1
(package
(name "rust-assert-cmd")
- (version "1.0.3")
+ (version "1.0.4")
(source
(origin
(method url-fetch)
@@ -2325,7 +2484,7 @@ standard library.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "15h3wfxn1q7sfcrin4z35x9hgf539f2dhkwz2mq4zswlrmc5nizj"))))
+ "127mhhjbclg63rfhmy0jc382w5x7y6aig0b9rhnyfkbymk0zwmwg"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -3703,6 +3862,25 @@ trace (backtrace) at runtime in a Rust program.")
(license (list license:asl2.0
license:expat))))
+(define-public rust-base32-0.4
+ (package
+ (name "rust-base32")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "base32" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ykwx8jhksqxghfgyw2pzikzjf4n9wqm1x2ww5wqyn68ssf6dki3"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/andreasots/base32")
+ (synopsis "Base32 encoder/decoder for Rust")
+ (description "This library lets you encode and decode in either
+RFC4648 Base32 or in Crockford Base32.")
+ (license (list license:asl2.0 license:expat))))
+
(define-public rust-base58-0.1
(package
(name "rust-base58")
@@ -4417,7 +4595,8 @@ bindings to C and C++ libraries.")
("rust-shlex" ,rust-shlex-0.1))))))
(define-public rust-bindgen-0.49
- (package/inherit rust-bindgen-0.50
+ (package
+ (inherit rust-bindgen-0.50)
(name "rust-bindgen")
(version "0.49.4")
(source
@@ -4687,6 +4866,57 @@ behave like a set of bitflags.")
(build-system cargo-build-system)
(arguments `(#:skip-build? #t))))
+(define-public rust-bitmaps-2
+ (package
+ (name "rust-bitmaps")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bitmaps" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "18k4mcwxl96yvii5kcljkpb8pg5j4jj1zbsdn26nsx4r83846403"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-typenum" ,rust-typenum-1))
+ #:cargo-development-inputs
+ (("rust-proptest", rust-proptest-0.9)
+ ("rust-proptest-derive", rust-proptest-derive-0.1))))
+ (home-page "https://github.com/bodil/bitmaps")
+ (synopsis "Fixed size compact boolean array in Rust")
+ (description "This crate provides a convenient and efficient way of
+declaring and working with fixed size bitmaps in Rust.")
+ (license license:mpl2.0)))
+
+(define-public rust-bitreader-0.3
+ (package
+ (name "rust-bitreader")
+ (version "0.3.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bitreader" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "06wlzf8ra7k8ya0m71dq0kxbaalaan48dymairn9q8s4gld1hy4i"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-cfg-if" ,rust-cfg-if-1))))
+ (home-page "https://github.com/irauta/bitreader")
+ (synopsis "Individual bits reader from a slice of bytes")
+ (description "BitReader helps reading individual bits from a slice of
+bytes. You can read an arbitrary numbers of bits from the byte slice, for
+example 13 bits at once. The reader internally keeps track of position within
+the buffer.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-bitstream-io-1
(package
(name "rust-bitstream-io")
@@ -5950,7 +6180,8 @@ little-endian.")
(("rust-serde" ,rust-serde-1))))))
(define-public rust-bytes-0.4
- (package/inherit rust-bytes-0.5
+ (package
+ (inherit rust-bytes-0.5)
(name "rust-bytes")
(version "0.4.12")
(source
@@ -6048,6 +6279,29 @@ little-endian.")
exposed as Reader/Writer streams.")
(license (list license:expat license:asl2.0))))
+(define-public rust-bytesize-1
+ (package
+ (name "rust-bytesize")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bytesize" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1nl2j2bi9nk3q564jhyb77947wdv5ch54r14gjv4c59s563qd8c1"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-serde" ,rust-serde-1))))
+ (home-page "https://github.com/hyunsik/bytesize/")
+ (synopsis "Human-readable byte count representation library for Rust")
+ (description "ByteSize is an utility for human-readable byte count
+representation, with support for both SI and binary units.")
+ (license license:asl2.0)))
+
(define-public rust-bzip2-0.3
(package
(inherit rust-bzip2-0.4)
@@ -6499,6 +6753,96 @@ remote procedure call protocol")
capabilities")
(license (list license:expat license:asl2.0))))
+(define-public rust-cargo-0.53
+ (package
+ (name "rust-cargo")
+ (version "0.53.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cargo" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "12ns9v4dd8vnvsaqgd897h2zc19w00i5ii3slda653zbhfzm6zna"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(;; The test suite is disabled as the internal 'cargo-test-macro' and
+ ;; 'cargo-test-support' crates are not included in the release.
+ #:tests? #f
+ #:rust ,rust-1.52 ;transitively inherited from rust-sized-chunks
+ #:cargo-inputs
+ (("rust-anyhow" ,rust-anyhow-1)
+ ("rust-atty" ,rust-atty-0.2)
+ ("rust-bytesize" ,rust-bytesize-1)
+ ("rust-cargo-platform" ,rust-cargo-platform-0.1)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-core-foundation" ,rust-core-foundation-0.9)
+ ("rust-crates-io" ,rust-crates-io-0.33)
+ ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8)
+ ("rust-crypto-hash" ,rust-crypto-hash-0.3)
+ ("rust-curl" ,rust-curl-0.4)
+ ("rust-curl-sys" ,rust-curl-sys-0.4)
+ ("rust-env-logger" ,rust-env-logger-0.8)
+ ("rust-filetime" ,rust-filetime-0.2)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-fwdansi" ,rust-fwdansi-1)
+ ("rust-git2" ,rust-git2-0.13)
+ ("rust-git2-curl" ,rust-git2-curl-0.14)
+ ("rust-glob" ,rust-glob-0.3)
+ ("rust-hex" ,rust-hex-0.4)
+ ("rust-home" ,rust-home-0.5)
+ ("rust-humantime" ,rust-humantime-2)
+ ("rust-ignore" ,rust-ignore-0.4)
+ ("rust-im-rc" ,rust-im-rc-15)
+ ("rust-jobserver" ,rust-jobserver-0.1)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-lazycell" ,rust-lazycell-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-libgit2-sys" ,rust-libgit2-sys-0.12)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-memchr" ,rust-memchr-2)
+ ("rust-miow" ,rust-miow-0.3)
+ ("rust-num-cpus" ,rust-num-cpus-1)
+ ("rust-opener" ,rust-opener-0.4)
+ ("rust-openssl" ,rust-openssl-0.10)
+ ("rust-percent-encoding" ,rust-percent-encoding-2)
+ ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.4)
+ ("rust-rand" ,rust-rand-0.8)
+ ("rust-rustc-workspace-hack" ,rust-rustc-workspace-hack-1)
+ ("rust-rustfix" ,rust-rustfix-0.5)
+ ("rust-same-file" ,rust-same-file-1)
+ ("rust-semver" ,rust-semver-0.10)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-ignored" ,rust-serde-ignored-0.1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-shell-escape" ,rust-shell-escape-0.1)
+ ("rust-strip-ansi-escapes" ,rust-strip-ansi-escapes-0.1)
+ ("rust-tar" ,rust-tar-0.4)
+ ("rust-tar" ,rust-tar-0.4)
+ ("rust-tempfile" ,rust-tempfile-3)
+ ("rust-termcolor" ,rust-termcolor-1)
+ ("rust-toml" ,rust-toml-0.5)
+ ("rust-unicode-width" ,rust-unicode-width-0.1)
+ ("rust-unicode-xid" ,rust-unicode-xid-0.2)
+ ("rust-url" ,rust-url-2)
+ ("rust-walkdir" ,rust-walkdir-2)
+ ("rust-winapi" ,rust-winapi-0.3))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("curl" ,curl)
+ ("libssh2" ,libssh2)
+ ("openssl" ,openssl)
+ ("zlib" ,zlib)))
+ (home-page "https://crates.io")
+ (synopsis "Package manager for Rust")
+ (description "Cargo, a package manager for Rust. This package provides
+the library crate of Cargo.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-cargo-metadata-0.9
(package
(name "rust-cargo-metadata")
@@ -6557,6 +6901,29 @@ metadata}.")
(;("rust-docopt" ,rust-docopt-0.8)
("rust-clap" ,rust-clap-2))))))
+(define-public rust-cargo-platform-0.1
+ (package
+ (name "rust-cargo-platform")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cargo-platform" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1mzi60pf0z83qkzqp7jwd61xnqz2b5ydsj7rnnikbgyicd5989h2"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-serde" ,rust-serde-1))))
+ (home-page "https://github.com/rust-lang/cargo")
+ (synopsis "Target platform abstraction for Cargo")
+ (description "This package provides abstractions for the target platforms
+supported by Cargo.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-cargon-0.0
(package
(name "rust-cargon")
@@ -7087,19 +7454,90 @@ traits.")
("rust-libc" ,rust-libc-0.2)
("rust-libloading" ,rust-libloading-0.3))))))
+(define-public rust-clap-derive-3
+ (package
+ (name "rust-clap-derive")
+ (version "3.0.0-beta.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "clap_derive" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "18cn82jhcha7m0nkpi1a03jx8k7aaq5kxfcxnsqpaa8ih5dp23rp"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-heck" ,rust-heck-0.3)
+ ("rust-proc-macro-error"
+ ,rust-proc-macro-error-1)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))))
+ (home-page "https://clap.rs/")
+ (synopsis
+ "Parse command line argument by defining a struct, derive crate")
+ (description
+ "This package provides a parse command line argument by defining a struct,
+derive crate.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-clap-3
+ (package
+ (name "rust-clap")
+ (version "3.0.0-beta.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "clap" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hm1kivw6190rxbfqhdr4hqwlrijvwh90i3d9dyyw0d5k0chdlab"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-atty" ,rust-atty-0.2)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-clap-derive" ,rust-clap-derive-3)
+ ("rust-indexmap" ,rust-indexmap-1)
+ ("rust-os-str-bytes" ,rust-os-str-bytes-2)
+ ("rust-strsim" ,rust-strsim-0.10)
+ ("rust-termcolor" ,rust-termcolor-1)
+ ("rust-terminal-size" ,rust-terminal-size-0.1)
+ ("rust-textwrap" ,rust-textwrap-0.12)
+ ("rust-unicode-width" ,rust-unicode-width-0.1)
+ ("rust-vec-map" ,rust-vec-map-0.8)
+ ("rust-yaml-rust" ,rust-yaml-rust-0.4))
+ #:cargo-development-inputs
+ (("rust-criterion" ,rust-criterion-0.3)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-version-sync" ,rust-version-sync-0.8))))
+ (home-page "https://clap.rs/")
+ (synopsis "Command Line Argument Parser")
+ (description
+ "This package provides a simple to use, efficient, and full-featured
+Command Line Argument Parser.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-clap-2
(package
+ (inherit rust-clap-3)
(name "rust-clap")
(version "2.33.3")
(source
- (origin
- (method url-fetch)
- (uri (crate-uri "clap" version))
- (file-name (string-append name "-" version ".crate"))
- (sha256
- (base32
- "00i065a58987k1sbzqmlz721rw521zcg08jmsh40gi3khp3qmr9p"))))
- (build-system cargo-build-system)
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "clap" version))
+ (file-name (string-append name "-" version ".crate"))
+ (sha256
+ (base32
+ "00i065a58987k1sbzqmlz721rw521zcg08jmsh40gi3khp3qmr9p"))))
(arguments
`(#:cargo-inputs
(("rust-ansi-term" ,rust-ansi-term-0.11)
@@ -7116,11 +7554,6 @@ traits.")
(("rust-lazy-static" ,rust-lazy-static-1)
("rust-regex" ,rust-regex-1)
("rust-version-sync" ,rust-version-sync-0.8))))
- (home-page "https://clap.rs/")
- (synopsis "Command Line Argument Parser")
- (description
- "This package provides a simple to use, efficient, and full-featured
-Command Line Argument Parser.")
(license license:expat)))
(define-public rust-clicolors-control-1
@@ -7661,7 +8094,8 @@ colors.")
(license license:mpl2.0)))
(define-public rust-colored-1.9.1
- (package/inherit rust-colored-1
+ (package
+ (inherit rust-colored-1)
(name "rust-colored")
(version "1.9.1")
(source
@@ -7756,6 +8190,57 @@ combinator.")
and 1.0.")
(license (list license:expat license:asl2.0))))
+(define-public rust-commoncrypto-sys-0.2
+ (package
+ (name "rust-commoncrypto-sys")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "commoncrypto-sys" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ql381ziqh594a7z6m9bvs583lkrhbynk02pmbgp7aj7czs39v8z"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t ;requires the Mac OS library
+ #:cargo-inputs
+ (("rust-clippy" ,rust-clippy-0.0)
+ ("rust-libc" ,rust-libc-0.2))))
+ (home-page "https://github.com/malept/rust-commoncrypto")
+ (synopsis "FFI bindings to Mac OS X's CommonCrypto library")
+ (description "This package is a component of the @code{commoncrypto}
+library which provides Rust FFI bindings and idiomatic wrappers for Mac OS X's
+CommonCrypto library.")
+ (license license:expat)))
+
+(define-public rust-commoncrypto-0.2
+ (package
+ (name "rust-commoncrypto")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "commoncrypto" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "01whnqcziclsj1gwavvqhrw2r5cmwh00j2fbc56iwnm2ddcahmnh"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-clippy" ,rust-clippy-0.0)
+ ("rust-commoncrypto-sys" ,rust-commoncrypto-sys-0.2))))
+ (home-page "https://github.com/malept/rust-commoncrypto")
+ (synopsis "Idiomatic Rust wrappers for Mac OS X's CommonCrypto library")
+ (description "The @{commoncrypto} library provides Rust FFI bindings and
+idiomatic wrappers for Mac OS X's CommonCrypto library.")
+ (license license:expat)))
+
(define-public rust-common-path-1
(package
(name "rust-common-path")
@@ -8797,6 +9282,29 @@ intrinsics.")
(("rust-clap" ,rust-clap-2)
("rust-diff" ,rust-diff-0.1))))))
+(define-public rust-cpufeatures-0.1
+ (package
+ (name "rust-cpufeatures")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cpufeatures" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1j0i97325c2grndsfgnm3lqk0xbyvdl2dbgn8i5dd9yhnmycc07d"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-libc" ,rust-libc-0.2))))
+ (home-page "https://github.com/RustCrypto/utils")
+ (synopsis "Alternative to the @code{is_x86_feature_detected!} macro")
+ (description
+ "Cpufeatures is a lightweight and efficient no-std compatible alternative
+to the @code{is_x86_feature_detected!} macro.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-cpuid-bool-0.1
(package
(name "rust-cpuid-bool")
@@ -8851,6 +9359,39 @@ to @code{is_x86_feature_detected}.")
"Library for retrieving and interacting with the crates.io index.")
(license license:asl2.0)))
+(define-public rust-crates-io-0.33
+ (package
+ (name "rust-crates-io")
+ (version "0.33.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "crates-io" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "147mggf85fz77vsrzsvsxxwid4f4fg30zwfyirx7sl1k7y33hw91"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-anyhow" ,rust-anyhow-1)
+ ("rust-curl" ,rust-curl-0.4)
+ ("rust-percent-encoding" ,rust-percent-encoding-2)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))))
+ (native-inputs
+ `(("curl" ,curl)
+ ("openssl" ,openssl)
+ ("pkg-config" ,pkg-config)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/rust-lang/cargo")
+ (synopsis "Helpers for interacting with @url{crates.io}")
+ (description "This package provides helpers for interacting with
+@url{crates.io}.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-crc-1
(package
(name "rust-crc")
@@ -9813,6 +10354,34 @@ Code (MAC) algorithms.")
algorithms.")
(license (list license:expat license:asl2.0))))
+(define-public rust-crypto-hash-0.3
+ (package
+ (name "rust-crypto-hash")
+ (version "0.3.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "crypto-hash" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1jnxgpk0j29hzcv42viq5dckyfjnxdjsar55366j95zx80i1cxwa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-commoncrypto" ,rust-commoncrypto-0.2)
+ ("rust-hex" ,rust-hex-0.3)
+ ("rust-openssl" ,rust-openssl-0.10)
+ ("rust-winapi" ,rust-winapi-0.3))))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://github.com/malept/crypto-hash")
+ (synopsis "Wrapper for OS-level cryptographic hash functions")
+ (description "This package provides a wrapper for OS-level cryptographic
+hash functions.")
+ (license license:expat)))
+
(define-public rust-cryptovec-0.4
(package
(name "rust-cryptovec")
@@ -11055,17 +11624,17 @@ algorithm which serves to quantify the difference between two colors.")
Rust.")
(license (list license:expat license:asl2.0))))
-(define-public rust-derive-arbitrary-0.4
+(define-public rust-derive-arbitrary-1
(package
(name "rust-derive-arbitrary")
- (version "0.4.7")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "derive_arbitrary" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1rp0z4k0j5ip0bx6dssg97l4q6bakhf6lm5h1lpr3p3kwjsi585i"))))
+ (base32 "0nig0iydva7a9h9i9qyi6an9w5qjafmn3qlzvdqqiw0x2kp824jz"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -11080,6 +11649,18 @@ Rust.")
Instead, enable the @code{derive} feature of the @code{arbitrary} crate.")
(license (list license:expat license:asl2.0))))
+(define-public rust-derive-arbitrary-0.4
+ (package/inherit rust-derive-arbitrary-1
+ (name "rust-derive-arbitrary")
+ (version "0.4.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "derive_arbitrary" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1rp0z4k0j5ip0bx6dssg97l4q6bakhf6lm5h1lpr3p3kwjsi585i"))))))
+
(define-public rust-derive-builder-0.9
(package
(name "rust-derive-builder")
@@ -11576,7 +12157,8 @@ Diesel.")
(license license:expat)))
(define-public rust-difference-1
- (package/inherit rust-difference-2
+ (package
+ (inherit rust-difference-2)
(name "rust-difference")
(version "1.0.0")
(source
@@ -11657,7 +12239,7 @@ diff.")
`(#:skip-build? #t
#:cargo-inputs
(("rust-blobby" ,rust-blobby-0.1)
- ("rust-generic-array" ,rust-generic-array-0.13))))))
+ ("rust-generic-array" ,rust-generic-array-0.12))))))
(define-public rust-digest-0.7
(package
@@ -12124,7 +12706,8 @@ from macros.")
(license (list license:expat license:unlicense))))
(define-public rust-docopt-0.8
- (package/inherit rust-docopt-1
+ (package
+ (inherit rust-docopt-1)
(name "rust-docopt")
(version "0.8.3")
(source
@@ -13304,6 +13887,30 @@ variables.")
"Environment variables utility functions.")
(license license:asl2.0)))
+(define-public rust-envy-0.4
+ (package
+ (name "rust-envy")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "envy" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0rar459p7pl19v6pbx98q3hi2hxfl8q1ndxxw5d4zd9cgway0irz"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-serde" ,rust-serde-1))))
+ (home-page "https://github.com/softprops/envy")
+ (synopsis "Deserialize environment variables into Rust structs")
+ (description
+ "This package provides access to typesafe config structs
+deserialized from environment variables.")
+ (license license:expat)))
+
(define-public rust-erased-serde-0.3
(package
(name "rust-erased-serde")
@@ -13700,6 +14307,34 @@ traits but without the boilerplate.")
"Crate for mimicking simd crate on stable Rust.")
(license (list license:asl2.0 license:expat))))
+(define-public rust-fallible-collections-0.4
+ (package
+ (name "rust-fallible-collections")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fallible_collections" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1sk6ckixvf0pax47qgs8lfd2zi2gmyg1xgk1k7z2qgalhaaidnaa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-hashbrown" ,rust-hashbrown-0.9))))
+ (home-page "https://github.com/vcombey/fallible_collections")
+ (synopsis "Fallible collections implementation in Rust")
+ (description "This library extends the Rust standard collections to return
+a result when an allocation error occurs, ala
+@url{https://github.com/rust-lang/rfcs/blob/master/text/2116-alloc-me-maybe.md,RFC
+2116}. The API currently proposes a fallible interface for @code{Vec},
+@code{Box}, @code{Arc}, @code{Btree} and @code{Rc}, as well as a
+@code{TryClone} trait wich is implemented for primitive Rust traits and a
+fallible format macro.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-failure-0.1
(package
(name "rust-failure")
@@ -14015,7 +14650,7 @@ sparse files.")
(define-public rust-filetime-0.2
(package
(name "rust-filetime")
- (version "0.2.8")
+ (version "0.2.14")
(source
(origin
(method url-fetch)
@@ -14023,14 +14658,14 @@ sparse files.")
(file-name (string-append name "-" version ".crate"))
(sha256
(base32
- "0zfc90802dbw11bx6kmm8zw6r88k7glm4q6l8riqw35an3dd9xhz"))))
+ "1s71cb7hzkk4ahc5j53w8933gnxv2giyj7v0za5hbbk37ahwyd0x"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-cfg-if" ,rust-cfg-if-0.1)
+ (("rust-cfg-if" ,rust-cfg-if-1)
("rust-libc" ,rust-libc-0.2)
- ("rust-redox-syscall" ,rust-redox-syscall-0.1)
+ ("rust-redox-syscall" ,rust-redox-syscall-0.2)
("rust-winapi" ,rust-winapi-0.3))
#:cargo-development-inputs
(("rust-tempfile" ,rust-tempfile-3))))
@@ -15823,6 +16458,32 @@ futures-rs library.")
(description "This package provides a fuzzy matching library in Rust.")
(license license:expat)))
+(define-public rust-fwdansi-1
+ (package
+ (name "rust-fwdansi")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fwdansi" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "027jz2x5fbi6rskic8sd6xx0mn03a7dnhwkpyz8hamg8gxwgbh88"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-memchr" ,rust-memchr-2)
+ ("rust-termcolor" ,rust-termcolor-1))
+ #:cargo-development-inputs
+ (("rust-proptest" ,rust-proptest-0.9))))
+ (home-page "https://github.com/kennytm/fwdansi")
+ (synopsis "ANSI escape codes to termcolor terminal library")
+ (description "This library can be used to forward a byte string with ANSI
+escape codes to a termcolor terminal.")
+ (license license:expat)))
+
(define-public rust-fxhash-0.2
(package
(name "rust-fxhash")
@@ -16552,14 +17213,16 @@ dirty state into your program.")
(define-public rust-git2-0.13
(package
(name "rust-git2")
- (version "0.13.15")
+ (version "0.13.20")
(source
(origin
(method url-fetch)
(uri (crate-uri "git2" version))
- (file-name (string-append name "-" version ".tar.gz"))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0na3vsa44nn1sr6pzscn93w69wbmdih277mm2p3f6kcavb4ngwj4"))))
+ (base32
+ "1fkc2gzcnl4ci3rja9mc5jl2ygl3fkc1fgym3rcwby216ac1x0yr"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -16571,7 +17234,7 @@ dirty state into your program.")
("rust-openssl-sys" ,rust-openssl-sys-0.9)
("rust-url" ,rust-url-2))
#:cargo-development-inputs
- (("rust-paste" ,rust-paste-0.1)
+ (("rust-paste" ,rust-paste-1)
("rust-structopt" ,rust-structopt-0.3)
("rust-time" ,rust-time-0.1))))
(native-inputs
@@ -16650,6 +17313,33 @@ reading and writing git repositories.")
("rust-thread-id" ,rust-thread-id-3)
("rust-time" ,rust-time-0.1))))))
+(define-public rust-git2-curl-0.14
+ (package
+ (name "rust-git2-curl")
+ (version "0.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "git2-curl" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0l1sckmpvhd498c9ji04gkpfkfrpx7c8rabihczsnjx91v5kjdc8"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t ;need rust-civet and others
+ #:cargo-inputs
+ (("rust-curl" ,rust-curl-0.4)
+ ("rust-git2" ,rust-git2-0.13)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-url" ,rust-url-2))))
+ (home-page "https://github.com/rust-lang/git2-rs")
+ (synopsis "Libgit2 HTTP transport backend powered by @code{libcurl}")
+ (description "Backend for an HTTP transport in @code{libgit2}, powered by
+libcurl, which is intended to be used with the @code{git2} crate.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-gjson-0.7
(package
(name "rust-gjson")
@@ -17332,6 +18022,30 @@ of gzip files based on the gzip header implementation in the @code{flate2} crate
IEEE 754-2008 binary16 type.")
(license (list license:expat license:asl2.0))))
+(define-public rust-home-0.5
+ (package
+ (name "rust-home")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "home" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0m3nfcksrj784liji1c5j47dymxw2l7hqy5fj90piadnwvrawmi4"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-winapi" ,rust-winapi-0.3))))
+ (home-page "https://github.com/brson/home")
+ (synopsis "Shared definitions of home directories")
+ (description "This packages provides the definition of @code{home_dir}
+used by @command{cargo} and @command{rustup}, as well as functions to find the
+correct value of @samp{CARGO_HOME} and @samp{RUSTUP_HOME}.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-bat-0.17
(package
(name "rust-bat")
@@ -18313,7 +19027,8 @@ Hash-based Message Authentication Code algorithm} for SHA1.")
("rust-typed-arena" ,rust-typed-arena-1))))))
(define-public rust-html5ever-0.23
- (package/inherit rust-html5ever-0.24
+ (package
+ (inherit rust-html5ever-0.24)
(name "rust-html5ever")
(version "0.23.0")
(source
@@ -18388,7 +19103,8 @@ requests and responses.")
(license (list license:asl2.0 license:expat))))
(define-public rust-http-0.1
- (package/inherit rust-http-0.2
+ (package
+ (inherit rust-http-0.2)
(name "rust-http")
(version "0.1.17")
(source
@@ -18455,7 +19171,8 @@ HTTP request or response body.")
("rust-http" ,rust-http-0.2))))))
(define-public rust-http-body-0.1
- (package/inherit rust-http-body-0.3
+ (package
+ (inherit rust-http-body-0.3)
(name "rust-http-body")
(version "0.1.0")
(source
@@ -19125,6 +19842,74 @@ with hyper.")
#:cargo-development-inputs
(("rust-tokio" ,rust-tokio-0.1))))))
+(define-public rust-hyphenation-commons-0.8
+ (package
+ (name "rust-hyphenation-commons")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "hyphenation_commons" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "089jv1pr718aq0yjfcv6x0zljw9f73jm15khdsydzfln3ci7n4hj"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build?
+ #t
+ #:cargo-inputs
+ (("rust-fst" ,rust-fst-0.4)
+ ("rust-serde" ,rust-serde-1))))
+ (home-page
+ "https://github.com/tapeinosyne/hyphenation")
+ (synopsis
+ "Proemial code for the @code{hyphenation} library")
+ (description
+ "This package provides a proemial code for the @code{hyphenation} library.")
+ (license (list license:asl2.0 license:expat))))
+
+(define-public rust-hyphenation-0.8
+ (package
+ (name "rust-hyphenation")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "hyphenation" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "117h952d2zlpyqmy0kb49wb42rd3l5m5kl3ldfhgygv6lin09b2w"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build?
+ #t
+ #:cargo-inputs
+ (("rust-bincode" ,rust-bincode-1)
+ ("rust-bincode" ,rust-bincode-1)
+ ("rust-fst" ,rust-fst-0.4)
+ ("rust-fst" ,rust-fst-0.4)
+ ("rust-hyphenation-commons"
+ ,rust-hyphenation-commons-0.8)
+ ("rust-hyphenation-commons"
+ ,rust-hyphenation-commons-0.8)
+ ("rust-pocket-resources"
+ ,rust-pocket-resources-0.3)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-unicode-normalization"
+ ,rust-unicode-normalization-0.1))))
+ (home-page
+ "https://github.com/tapeinosyne/hyphenation")
+ (synopsis
+ "Knuth-Liang hyphenation for a variety of languages")
+ (description
+ "This package provides a Knuth-Liang hyphenation for a variety of languages.")
+ (license (list license:asl2.0 license:expat))))
+
(define-public rust-ident-case-1
(package
(name "rust-ident-case")
@@ -20580,7 +21365,7 @@ the jni-bindgen code generator for binding to JVM APIs from Rust.")
(define-public rust-jobserver-0.1
(package
(name "rust-jobserver")
- (version "0.1.19")
+ (version "0.1.22")
(source
(origin
(method url-fetch)
@@ -20589,7 +21374,7 @@ the jni-bindgen code generator for binding to JVM APIs from Rust.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1q2w80v8p2pbfm8ayhjs6zi11a1hp4535z4ck8kg872z8ldnrc37"))))
+ "1zg7p4khibisbvd8b1lqvvni6lr00g49d4bq2zj6m76bs7jmlbwp"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -21390,17 +22175,16 @@ algorithm and related formats (ZLIB, GZIP).")
(define-public rust-libgit2-sys-0.12
(package
(name "rust-libgit2-sys")
- (version "0.12.17+1.1.0")
+ (version "0.12.21+1.1.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "libgit2-sys" version))
- (file-name (string-append name "-" version ".tar.gz"))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0hc89v7kp2b3rbc64cxq024shd85m8vqcs14i3gjclblr9jxzszl"))
- (modules '((guix build utils)))
- (snippet
- '(begin (delete-file-recursively "libgit2") #t))))
+ (base32
+ "09b85x3gpvq0d7v1mhg4f3w1b3skzlpbikrx9j2rwarbsyn1n9w6"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -21466,32 +22250,6 @@ library.")
(snippet
'(begin (delete-file-recursively "libgit2") #t))))))
-(define-public rust-libgit2-sys-0.7
- (package
- (inherit rust-libgit2-sys-0.8)
- (name "rust-libgit2-sys")
- (version "0.7.11")
- (source
- (origin
- (method url-fetch)
- (uri (crate-uri "libgit2-sys" version))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1wcvg2qqra2aviasvqcscl8gb2rnjnd6h998wy5dlmf2bnriqi28"))
- (modules '((guix build utils)))
- (snippet
- '(begin (delete-file-recursively "libgit2") #t))))
- (arguments
- `(#:cargo-inputs
- (("rust-curl-sys" ,rust-curl-sys-0.4)
- ("rust-libc" ,rust-libc-0.2)
- ("rust-libssh2-sys" ,rust-libssh2-sys-0.2)
- ("rust-libz-sys" ,rust-libz-sys-1)
- ("rust-openssl-sys" ,rust-openssl-sys-0.9)
- ("rust-cc" ,rust-cc-1)
- ("rust-pkg-config" ,rust-pkg-config-0.3))))))
-
(define-public rust-libloading-0.6
(package
(name "rust-libloading")
@@ -22411,7 +23169,8 @@ explosion.")
("rust-serde-json" ,rust-serde-json-1))))))
(define-public rust-loom-0.2
- (package/inherit rust-loom-0.3
+ (package
+ (inherit rust-loom-0.3)
(name "rust-loom")
(version "0.2.13")
(source
@@ -22433,7 +23192,8 @@ explosion.")
("rust-serde-json" ,rust-serde-json-1))))))
(define-public rust-loom-0.1
- (package/inherit rust-loom-0.3
+ (package
+ (inherit rust-loom-0.3)
(name "rust-loom")
(version "0.1.1")
(source
@@ -23140,7 +23900,7 @@ unstable -Z self-profile flag.")
(define-public rust-memchr-2
(package
(name "rust-memchr")
- (version "2.3.4")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
@@ -23149,7 +23909,7 @@ unstable -Z self-profile flag.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "098m9clfs495illlw00hv2gg67mhm7jflld3msyclvi5m9xc9q8f"))))
+ "1p478fqf4nia2ma0kv4npb8x1hli0zz6k16517ikb51jkryx8sxi"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -23381,6 +24141,47 @@ for Rust structs.")
(sha256
(base32 "13ir50j549gdz94pds1i7ljnk14d66q5x91s11hncm1pih7jif8c"))))))
+(define-public rust-merge-derive-0.1
+ (package
+ (name "rust-merge-derive")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "merge_derive" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "01wxhi7mqmp34l540wcfb24hb13vcbps4wlynas66bnsfra0g790"))))
+ (build-system cargo-build-system)
+ (home-page "https://sr.ht/~ireas/merge-rs")
+ (synopsis "Derive macro for the merge crate")
+ (description "This crate provides a derive macro for the
+@code{merge::Merge} crate.")
+ (license (list license:asl2.0 license:expat))))
+
+(define-public rust-merge-0.1
+ (package
+ (name "rust-merge")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "merge" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1sck0vhi9lk8a6mgky0rgn842fj7yspywidwbd963nmimf9yzfqh"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-merge-derive" ,rust-merge-derive-0.1)
+ ("rust-num-traits" ,rust-num-traits-0.2))))
+ (home-page "https://sr.ht/~ireas/merge-rs")
+ (synopsis "Rust trait for objects that can be merged")
+ (description "This package provides a merge trait that can be used
+to merge two objects of the same type into one.")
+ (license (list license:asl2.0 license:expat))))
+
(define-public rust-merlin-2
(package
(name "rust-merlin")
@@ -23536,6 +24337,61 @@ based on Rustls and Ring.")
(("rust-sema" ,rust-sema-0.1)
("rust-winit" ,rust-winit-0.19)))))) ; 0.17?
+(define-public rust-twox-hash-1
+ (package
+ (name "rust-twox-hash")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "twox-hash" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ndb4pil758kn0av83jjgq8kkfkwc5lhi5ii7fk5yw96h1wapy04"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-cfg-if" ,rust-cfg-if-0.1)
+ ("rust-digest" ,rust-digest-0.8)
+ ("rust-digest" ,rust-digest-0.9)
+ ("rust-rand" ,rust-rand-0.7)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-static-assertions" ,rust-static-assertions-1))
+ #:cargo-development-inputs
+ (("rust-serde-json" ,rust-serde-json-1))))
+ (home-page "https://github.com/shepmaster/twox-hash")
+ (synopsis "Rust implementation of the XXHash and XXH3 algorithms")
+ (description "This package provides a Rust implementation of the XXHash
+and XXH3 algorithms.")
+ (license license:expat)))
+
+(define-public rust-metrohash-1
+ (package
+ (name "rust-metrohash")
+ (version "1.0.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "metrohash" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0v2hn33ypx79naimfcz58pz46qhj2prawvx1p9abrb72375m799v"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-development-inputs
+ (("rust-fnv" ,rust-fnv-1)
+ ("rust-twox-hash" ,rust-twox-hash-1))))
+ (home-page
+ "https://github.com/arthurprs/metrohash-rs")
+ (synopsis "Rust implementation of the MetroHash hash algorithm")
+ (description "This library is a Rust implementation of MetroHash, a high
+quality, high performance hash algorithm.")
+ (license license:expat)))
+
(define-public rust-meval-0.2
(package
(name "rust-meval")
@@ -25098,6 +25954,96 @@ selectors. You can use the jQuery-like syntax to query and manipulate an HTML
document quickly.")
(license (list license:expat license:asl2.0))))
+(define-public rust-nitrokey-0.9
+ (package
+ (name "rust-nitrokey")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "nitrokey" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0c8mj52ckvy1311vwxs6jpw16b2bihp5cc811isb96j9slcjvsyx"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-lazy_static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-nitrokey-sys" ,rust-nitrokey-sys-3)
+ ("rust-rand_core" ,rust-rand-core-0.5))))
+ (home-page "https://git.sr.ht/~ireas/nitrokey-rs")
+ (synopsis "Rust bindings to libnitrokey")
+ (description
+ "This package provides bindings to libnitrokey for communication
+with Nitrokey devices.")
+ (license license:expat)))
+
+(define-public rust-nitrokey-sys-3
+ (package
+ (name "rust-nitrokey-sys")
+ (version "3.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "nitrokey-sys" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08c3lnb8iqx000jd5rzvrdvv4ihjyw3x3s8q11dw56is0nmjyvws"))))
+ (build-system cargo-build-system)
+ (home-page "https://git.sr.ht/~ireas/nitrokey-sys-rs")
+ (synopsis "Low-level Rust bindings for libnitrokey")
+ (description
+ "This package provides low-level bindings to libnitrokey for
+communication with Nitrokey devices.")
+ (license license:lgpl3)))
+
+(define-public rust-nitrokey-test-0.5
+ (package
+ (name "rust-nitrokey-test")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "nitrokey-test" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "197j9r2s4ydzbqfydza6v31mgcsgd29jpidz4psqawjdm49f8lg6"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("quote" ,rust-quote-1)
+ ("syn" ,rust-syn-1))))
+ (home-page "https://github.com/d-e-s-o/nitrokey-test")
+ (synopsis "Supporting test infrastructure for the nitrokey crate")
+ (description
+ "This package provides supporting test infrastructure for the
+nitrokey crate and others using it.")
+ (license license:gpl3+)))
+
+(define-public rust-nitrokey-test-state-0.1
+ (package
+ (name "rust-nitrokey-test-state")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "nitrokey-test-state" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "00w817kl8q3sna924pzl72ybqljny14rdv1ixlj288fmsqp776x5"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/d-e-s-o/nitrokey-test")
+ (synopsis "State required and used by the nitrokey-test crate")
+ (description "This package provides state required and used by the
+nitrokey-test crate.")
+ (license license:gpl3+)))
+
(define-public rust-nix-0.20
(package
(name "rust-nix")
@@ -26871,6 +27817,29 @@ contents.")
the system.")
(license license:expat)))
+(define-public rust-opener-0.4
+ (package
+ (name "rust-opener")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "opener" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1bpknqvhqkalhmq8n2m97apc0r3y194ppybl1qxay34xr83p848k"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-winapi" ,rust-winapi-0.3))))
+ (home-page "https://github.com/Seeker14491/opener")
+ (synopsis "Open a file or link using the system default program")
+ (description "This crate provides the ability to open a file or link with
+the default program configured on the system.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-openssl-0.10
(package
(name "rust-openssl")
@@ -27098,10 +28067,10 @@ system for OpenSSL.")
PartialOrd types, like floats.")
(license (list license:expat license:asl2.0))))
-(define-public rust-ordered-float-1
+(define-public rust-ordered-float-2
(package
(name "rust-ordered-float")
- (version "1.0.2")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
@@ -27110,10 +28079,12 @@ PartialOrd types, like floats.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0625x96987kspdxbikry5mb7hsf5pdc5bbanxd8wjwqlx0ar71hq"))))
+ "0632g8bacvras6nig1bb1ihgc560476jkrb3is6n542ll86q8vvn"))))
(build-system cargo-build-system)
(arguments
- `(#:cargo-inputs
+ `(#:skip-build?
+ #t
+ #:cargo-inputs
(("rust-num-traits" ,rust-num-traits-0.2)
("rust-serde" ,rust-serde-1))
#:cargo-development-inputs
@@ -27124,6 +28095,21 @@ PartialOrd types, like floats.")
"This package provides wrappers for total ordering on floats in Rust.")
(license license:expat)))
+(define-public rust-ordered-float-1
+ (package
+ (inherit rust-ordered-float-2)
+ (name "rust-ordered-float")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "ordered-float" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0625x96987kspdxbikry5mb7hsf5pdc5bbanxd8wjwqlx0ar71hq"))))))
+
(define-public rust-ordermap-0.3
(package
(name "rust-ordermap")
@@ -27184,6 +28170,30 @@ under its new name.")
"A cross-platform library for opening OS pipes.")
(license license:expat)))
+(define-public rust-os-str-bytes-2
+ (package
+ (name "rust-os-str-bytes")
+ (version "2.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "os_str_bytes" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "11agh8n3x2l4sr3sxvx6byc1j3ryb1g6flb1ywn0qhq7xv1y3cmg"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page
+ "https://github.com/dylni/os_str_bytes")
+ (synopsis
+ "Traits for converting between byte sequences and platform-native strings")
+ (description
+ "This package provides a traits for converting between byte sequences and
+platform-native strings.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-output-vt100-0.1
(package
(name "rust-output-vt100")
@@ -30194,6 +31204,29 @@ macro use case.")
@code{proc_macro_derive} pretend to be @code{proc_macro}.")
(license (list license:expat license:asl2.0))))
+(define-public rust-progressing-3
+ (package
+ (name "rust-progressing")
+ (version "3.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "progressing" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "06sb1cxpkc8lx56s76c95cfljs0513nsnn35wd6w79sblwcxpdwp"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("log" ,rust-log-0.4))))
+ (home-page "https://github.com/dominicparga/progressing")
+ (synopsis "Counting progress-bar for Rust")
+ (description
+ "This package provides a set of text-based, counting
+progress-bars for Rust.")
+ (license license:asl2.0)))
+
(define-public rust-progrs-0.1
(package
(name "rust-progrs")
@@ -30535,7 +31568,8 @@ compliant email address validation.")
("rust-getopts" ,rust-getopts-0.2))))))
(define-public rust-pulldown-cmark-0.0.8
- (package/inherit rust-pulldown-cmark-0.4
+ (package
+ (inherit rust-pulldown-cmark-0.4)
(name "rust-pulldown-cmark")
(version "0.0.8")
(source
@@ -32531,24 +33565,47 @@ functionality.")
(base32
"0av43xxjlinfqklb67rpj217cmaxfjsf8151gs0hbs4hnr5664ck"))))))
+(define-public rust-refpool-0.4
+ (package
+ (name "rust-refpool")
+ (version "0.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "refpool" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0n6b1qpq0fcyzm3nrmiw0z9x4nawy9dklqfr3mb8rp571yw8d7in"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-development-inputs
+ (("rust-criterion" ,rust-criterion-0.3))))
+ (home-page "https://github.com/bodil/refpool")
+ (synopsis "Efficient memory pool with reference counting")
+ (description "@code{refpool} is a re-implementation of Rust's
+@code{std::boxed::Box} and @code{std::rc::Rc} which uses a pool of reusable
+memory to speed up reallocation.")
+ (license license:mpl2.0)))
+
(define-public rust-regex-1
(package
(name "rust-regex")
- (version "1.4.3")
+ (version "1.5.4")
(source
(origin
(method url-fetch)
(uri (crate-uri "regex" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "12llbg82js69mdl50lav4yn1iqlx71ckb18dww467q99w4wi49fr"))))
+ (base32 "0qf479kjbmb582h4d1d6gfl75h0j8aq2nrdi5wg6zdcy6llqcynh"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-aho-corasick" ,rust-aho-corasick-0.7)
("rust-memchr" ,rust-memchr-2)
- ("rust-regex-syntax" ,rust-regex-syntax-0.6)
- ("rust-thread-local" ,rust-thread-local-1))
+ ("rust-regex-syntax" ,rust-regex-syntax-0.6))
#:cargo-development-inputs
(("rust-lazy-static" ,rust-lazy-static-1)
("rust-quickcheck" ,rust-quickcheck-0.8)
@@ -32654,14 +33711,14 @@ uses finite automata and guarantees linear time matching on all inputs.")
(define-public rust-regex-syntax-0.6
(package
(name "rust-regex-syntax")
- (version "0.6.22")
+ (version "0.6.25")
(source
(origin
(method url-fetch)
(uri (crate-uri "regex-syntax" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "10b56ylil35jkb4nwqxm8hbyx3zq7fws0wpydjln165s8xql3sxm"))))
+ (base32 "16y87hz1bxmmz6kk360cxwfm3jnbsxb3x4zw9x1gzz7khic2i5zl"))))
(build-system cargo-build-system)
(home-page "https://github.com/rust-lang/regex")
(synopsis "Regular expression parser")
@@ -32830,14 +33887,14 @@ uses finite automata and guarantees linear time matching on all inputs.")
(define-public rust-reqwest-0.11
(package
(name "rust-reqwest")
- (version "0.11.2")
+ (version "0.11.3")
(source
(origin
(method url-fetch)
(uri (crate-uri "reqwest" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1m12j00if0gj0alhad4r7w0air4j0gqlpiwiqpsxna4l51zha4mz"))))
+ (base32 "097i9z42jq2sn3va3r6pksz3gzffbnr3c4aapk6fhy9rqpxg55i2"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -32881,7 +33938,16 @@ uses finite automata and guarantees linear time matching on all inputs.")
("rust-wasm-bindgen-futures" ,rust-wasm-bindgen-futures-0.4)
("rust-web-sys" ,rust-web-sys-0.3)
("rust-webpki-roots" ,rust-webpki-roots-0.21)
- ("rust-winreg" ,rust-winreg-0.7))))
+ ("rust-winreg" ,rust-winreg-0.7))
+ #:cargo-development-inputs
+ (("rust-brotli" ,rust-brotli-3)
+ ("rust-doc-comment" ,rust-doc-comment-0.3)
+ ("rust-env-logger" ,rust-env-logger-0.8)
+ ("rust-hyper" ,rust-hyper-0.14)
+ ("rust-libflate" ,rust-libflate-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-tokio" ,rust-tokio-1)
+ ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3))))
(home-page "https://github.com/seanmonstar/reqwest")
(synopsis "High level HTTP client library")
(description "This package provides a high level HTTP client library.")
@@ -33151,7 +34217,8 @@ functionality as retain but gives mutable borrow to the predicate.")
("rust-cc" ,rust-cc-1))))))
(define-public rust-ring-0.13
- (package/inherit rust-ring-0.16
+ (package
+ (inherit rust-ring-0.16)
(name "rust-ring")
(version "0.13.5")
(source
@@ -34916,10 +35983,10 @@ rustc compiler.")
"This package provides a tool to manipulate rustdoc comments.")
(license license:asl2.0)))
-(define-public rust-rustfix-0.4
+(define-public rust-rustfix-0.5
(package
(name "rust-rustfix")
- (version "0.4.6")
+ (version "0.5.1")
(source
(origin
(method url-fetch)
@@ -34928,12 +35995,12 @@ rustc compiler.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "01zn0ysnass3mmrhxk90584y713vjfq1x97mi4saac99g9vsql3i"))))
+ "0kkhfab60747zpmn8jwfdwl9a2s4rqiq7yjjfs7yppfwp9s0pigj"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-failure" ,rust-failure-0.1)
+ (("rust-anyhow" ,rust-anyhow-1)
("rust-log" ,rust-log-0.4)
("rust-serde" ,rust-serde-1)
("rust-serde-json" ,rust-serde-json-1))
@@ -34950,6 +36017,25 @@ rustc compiler.")
"Automatically apply the suggestions made by rustc.")
(license (list license:expat license:asl2.0))))
+(define-public rust-rustfix-0.4
+ (package/inherit rust-rustfix-0.5
+ (name "rust-rustfix")
+ (version "0.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "rustfix" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "01zn0ysnass3mmrhxk90584y713vjfq1x97mi4saac99g9vsql3i"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments rust-rustfix-0.5)
+ ((#:cargo-inputs cargo-inputs)
+ `(("rust-failure" ,rust-failure-0.1)
+ ,@(alist-delete "rust-anyhow" cargo-inputs)))))))
+
(define-public rust-rustls-0.19
(package
(name "rust-rustls")
@@ -35112,7 +36198,8 @@ rustc compiler.")
("rust-webpki" ,rust-webpki-0.18))))))
(define-public rust-rustls-0.12
- (package/inherit rust-rustls-0.16
+ (package
+ (inherit rust-rustls-0.16)
(name "rust-rustls")
(version "0.12.0")
(source
@@ -36159,7 +37246,8 @@ Pwrite traits from the scroll crate.")
("rust-untrusted" ,rust-untrusted-0.6))))))
(define-public rust-sct-0.3
- (package/inherit rust-sct-0.6
+ (package
+ (inherit rust-sct-0.6)
(name "rust-sct")
(version "0.3.0")
(source
@@ -36661,6 +37749,33 @@ also have to make sure that the wrapper is dropped from within the original
thread. If any of these constraints is violated, a panic occurs.")
(license (list license:expat license:asl2.0))))
+(define-public rust-seq-macro-0.2
+ (package
+ (name "rust-seq-macro")
+ (version "0.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "seq-macro" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "168y8k344gssy1q0q6napy8cswgl4hyh2kcim9pk3b9wxbx4g7ss"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-development-inputs
+ (("rust-rustversion" ,rust-rustversion-1)
+ ("rust-trybuild" ,rust-trybuild-1))))
+ (home-page
+ "https://github.com/dtolnay/seq-macro")
+ (synopsis
+ "Macro to repeat sequentially indexed copies of a fragment of code")
+ (description
+ "This package provides a macro to repeat sequentially indexed copies of a
+fragment of code.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-sequoia-openpgp-0.9
(package
(name "rust-sequoia-openpgp")
@@ -37182,17 +38297,44 @@ TOML/JSON/MessagePack strings and serializable values.")
("rust-serde-codegen-internals" ,rust-serde-codegen-internals-0.14)
("rust-syn" ,rust-syn-0.11))))))
+(define-public rust-serde-ignored-0.1
+ (package
+ (name "rust-serde-ignored")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "serde_ignored" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0bzz3546g3p01hgwh6jh0gyqdwc28xcp3pir4al2wbsgs4wpsb0w"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-serde" ,rust-serde-1))
+ #:cargo-development-inputs
+ (("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1))))
+ (home-page "https://github.com/dtolnay/serde-ignored")
+ (synopsis "Find ignored keys when deserializing data")
+ (description "Find out about keys that are ignored when deserializing
+data. This crate provides a wrapper that works with any existing Serde
+@code{Deserializer} and invokes a callback on every ignored field.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-serde-json-1
(package
(name "rust-serde-json")
- (version "1.0.61")
+ (version "1.0.64")
(source
(origin
(method url-fetch)
(uri (crate-uri "serde_json" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0nijvxvgcncvd1wbn73zx7q14bdxah0gf2789qd8kdjpa1cv5kjg"))))
+ (base32 "0y9gk3yikncrc0zajmwc0pidr7zfwafawb4gidf6mqyskzf9g7kr"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -38017,7 +39159,7 @@ code is translated from C to Rust using c2rust.")
(define-public rust-sha2-0.9
(package
(name "rust-sha2")
- (version "0.9.3")
+ (version "0.9.5")
(source
(origin
(method url-fetch)
@@ -38026,17 +39168,16 @@ code is translated from C to Rust using c2rust.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1phjvjcvc33xa3xdpxw3a324ksbnrg9qhjnig13z9dwsn8a7m0ps"))))
+ "04lzf4swq6cijvxnc6facr3g72h5v7a5z8lz3xrkf8gxa9bswqmk"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-block-buffer" ,rust-block-buffer-0.9)
("rust-cfg-if" ,rust-cfg-if-1)
- ("rust-cpuid-bool" ,rust-cpuid-bool-0.1)
+ ("rust-cpufeatures" ,rust-cpufeatures-0.1)
("rust-digest" ,rust-digest-0.9)
- ("rust-libc" ,rust-libc-0.2)
("rust-opaque-debug" ,rust-opaque-debug-0.3)
- ("rust-sha2-asm" ,rust-sha2-asm-0.5))
+ ("rust-sha2-asm" ,rust-sha2-asm-0.6))
#:cargo-development-inputs
(("rust-digest" ,rust-digest-0.9)
("rust-hex-literal" ,rust-hex-literal-0.2))))
@@ -38115,27 +39256,40 @@ function family including SHA-224, SHA-256, SHA-384, and SHA-512.")
("rust-generic-array" ,rust-generic-array-0.8)
("rust-sha2-asm" ,rust-sha2-asm-0.3))))))
-(define-public rust-sha2-asm-0.5
+(define-public rust-sha2-asm-0.6
(package
(name "rust-sha2-asm")
- (version "0.5.4")
+ (version "0.6.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "sha2-asm" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0y4n8r4362y2fa6p2j0dgny4zfi194gdf01l6j850n9vf8ha3kwj"))))
+ (base32 "08rp21zv96n8cnwcix177xkdw43zx8dqgfjfwd0gly9hvrl7lfaw"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
- (("rust-cc" ,rust-cc-1)))) ;; build dependency
+ (("rust-cc" ,rust-cc-1)))) ;build dependency
(home-page "https://github.com/RustCrypto/asm-hashes")
(synopsis "Assembly implementation of SHA-2")
(description "This package provides an assembly implementations of hash
functions core functionality.")
(license license:expat)))
+(define-public rust-sha2-asm-0.5
+ (package
+ (inherit rust-sha2-asm-0.6)
+ (name "rust-sha2-asm")
+ (version "0.5.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "sha2-asm" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0y4n8r4362y2fa6p2j0dgny4zfi194gdf01l6j850n9vf8ha3kwj"))))))
+
(define-public rust-sha2-asm-0.3
(package
(inherit rust-sha2-asm-0.5)
@@ -38734,6 +39888,34 @@ variants in pure Rust.")
(description "This package allows for easier formatting of sizes.")
(license (list license:expat license:asl2.0))))
+(define-public rust-sized-chunks-0.6
+ (package
+ (name "rust-sized-chunks")
+ (version "0.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "sized-chunks" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "07ix5fsdnpf2xsb0k5rbiwlmsicm2237fcx7blirp9p7pljr5mhn"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ;requires the "if in const fn" feature
+ #:cargo-inputs
+ (("rust-arbitrary" ,rust-arbitrary-1)
+ ("rust-array-ops" ,rust-array-ops-0.1)
+ ("rust-bitmaps" ,rust-bitmaps-2)
+ ("rust-refpool" ,rust-refpool-0.4)
+ ("rust-typenum" ,rust-typenum-1))))
+ (home-page "https://github.com/bodil/sized-chunks")
+ (synopsis "Efficient sized chunk datatypes")
+ (description "This package provides various fixed length array data types,
+designed for @code{immutable.rs}.")
+ (license license:mpl2.0)))
+
(define-public rust-skeptic-0.9
(package
(name "rust-skeptic")
@@ -40291,18 +41473,19 @@ and write it somewhere that does not easily support them, such as a log
file.")
(license (list license:asl2.0 license:expat))))
-(define-public rust-strsim-0.9
+(define-public rust-strsim-0.10
(package
(name "rust-strsim")
- (version "0.9.3")
+ (version "0.10.0")
(source
- (origin
- (method url-fetch)
- (uri (crate-uri "strsim" version))
- (file-name (string-append name "-" version ".crate"))
- (sha256
- (base32
- "0k497pv882qn3q977ckznm13vxx927g8s1swvcv68j3c1pccwik4"))))
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strsim" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08s69r4rcrahwnickvi0kq49z524ci50capybln83mg6b473qivk"))))
(build-system cargo-build-system)
(home-page "https://github.com/dguo/strsim-rs")
(synopsis "Rust implementations of string similarity metrics")
@@ -40311,6 +41494,20 @@ metrics. It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro,
and Jaro-Winkler.")
(license license:expat)))
+(define-public rust-strsim-0.9
+ (package
+ (inherit rust-strsim-0.10)
+ (name "rust-strsim")
+ (version "0.9.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strsim" version))
+ (file-name (string-append name "-" version ".crate"))
+ (sha256
+ (base32
+ "0k497pv882qn3q977ckznm13vxx927g8s1swvcv68j3c1pccwik4"))))))
+
(define-public rust-strsim-0.8
(package
(inherit rust-strsim-0.9)
@@ -40358,16 +41555,16 @@ and Jaro-Winkler.")
(define-public rust-structopt-0.3
(package
(name "rust-structopt")
- (version "0.3.12")
+ (version "0.3.21")
(source
- (origin
- (method url-fetch)
- (uri (crate-uri "structopt" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "178m7wxnjyy9a8a961z74nazjsg79rfv3gv9g3bykfrrjmqs5yn8"))))
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "structopt" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "136j0lvjmpv5syi751vxg8vb30gfyv4k81x8d18kxrj6xvbsqxsj"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -40378,7 +41575,8 @@ and Jaro-Winkler.")
(home-page "https://github.com/TeXitoi/structopt")
(synopsis "Parse command line argument by defining a struct")
(description
- "Parse command line argument by defining a struct.")
+ "This package parses command lines arguments by defining a Rust
+struct.")
(license (list license:asl2.0 license:expat))))
(define-public rust-structopt-0.2
@@ -40407,31 +41605,31 @@ and Jaro-Winkler.")
(define-public rust-structopt-derive-0.4
(package
- (name "rust-structopt-derive")
- (version "0.4.5")
- (source
- (origin
- (method url-fetch)
- (uri (crate-uri "structopt-derive" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0c04bbzc5bmr2ns6qy35yz55nn3xvlq4dpwxdynnljb9ikhvi21z"))))
- (build-system cargo-build-system)
- (arguments
- `(#:skip-build? #t
- #:cargo-inputs
- (("rust-heck" ,rust-heck-0.3)
- ("rust-proc-macro-error" ,rust-proc-macro-error-0.4)
- ("rust-proc-macro2" ,rust-proc-macro2-1)
- ("rust-syn" ,rust-syn-1)
- ("rust-quote" ,rust-quote-1))))
- (home-page "https://github.com/TeXitoi/structopt")
- (synopsis "Parse command line argument by defining a struct, derive crate")
- (description
- "Parse command line argument by defining a struct, derive crate.")
- (license (list license:asl2.0 license:expat))))
+ (name "rust-structopt-derive")
+ (version "0.4.14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "structopt-derive" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "143gjwvz3s86hwp070km83y25n8kqp5f01kb1dr19f4ilkywvaav"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-heck" ,rust-heck-0.3)
+ ("rust-proc-macro-error" ,rust-proc-macro-error-1)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-syn" ,rust-syn-1)
+ ("rust-quote" ,rust-quote-1))))
+ (home-page "https://github.com/TeXitoi/structopt")
+ (synopsis "Parse command line argument by defining a struct, derive crate")
+ (description
+ "This package provides the derive Rust crate for the structopt crate.")
+ (license license:asl2.0)))
(define-public rust-structopt-derive-0.2
(package
@@ -41959,7 +43157,8 @@ template language.")
("rust-winapi" ,rust-winapi-0.2))))))
(define-public rust-term-0.2
- (package/inherit rust-term-0.4
+ (package
+ (inherit rust-term-0.4)
(name "rust-term")
(version "0.2.14")
(source
@@ -42322,19 +43521,49 @@ for TLS).")
unstable language features.")
(license (list license:expat license:asl2.0))))
+(define-public rust-textwrap-0.12
+ (package
+ (name "rust-textwrap")
+ (version "0.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "textwrap" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "12978qmkl5gcp94lxndpvp9qxq8mxp7hm9xbrw3422dgikchhc10"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-hyphenation" ,rust-hyphenation-0.8)
+ ("rust-terminal-size" ,rust-terminal-size-0.1)
+ ("rust-unicode-width" ,rust-unicode-width-0.1))))
+ (home-page
+ "https://github.com/mgeisler/textwrap")
+ (synopsis "Library for word wrapping, indenting, and dedenting strings")
+ (description
+ "Textwrap is a small library for word wrapping, indenting, and dedenting
+strings. You can use it to format strings (such as help and error messages)
+for display in commandline applications. It is designed to be efficient and
+handle Unicode characters correctly.")
+ (license license:expat)))
+
(define-public rust-textwrap-0.11
(package
+ (inherit rust-textwrap-0.12)
(name "rust-textwrap")
(version "0.11.0")
(source
- (origin
- (method url-fetch)
- (uri (crate-uri "textwrap" version))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk"))))
- (build-system cargo-build-system)
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "textwrap" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk"))))
(arguments
`(#:skip-build? #t
#:cargo-inputs
@@ -42345,15 +43574,7 @@ unstable language features.")
(;("rust-lipsum" ,rust-lipsum-0.6)
("rust-rand" ,rust-rand-0.6)
("rust-rand-xorshift" ,rust-rand-xorshift-0.1)
- ("rust-version-sync" ,rust-version-sync-0.6))))
- (home-page "https://github.com/mgeisler/textwrap")
- (synopsis "Library for word wrapping, indenting, and dedenting strings")
- (description
- "Textwrap is a small library for word wrapping, indenting, and dedenting
-strings. You can use it to format strings (such as help and error messages)
-for display in commandline applications. It is designed to be efficient and
-handle Unicode characters correctly.")
- (license license:expat)))
+ ("rust-version-sync" ,rust-version-sync-0.6))))))
(define-public rust-thin-slice-0.1
(package
@@ -47061,7 +48282,8 @@ untrusted inputs in Rust.")
(license license:isc)))
(define-public rust-untrusted-0.6
- (package/inherit rust-untrusted-0.7
+ (package
+ (inherit rust-untrusted-0.7)
(name "rust-untrusted")
(version "0.6.2")
(source
@@ -47075,7 +48297,7 @@ untrusted inputs in Rust.")
(define-public rust-url-2
(package
(name "rust-url")
- (version "2.2.1")
+ (version "2.2.2")
(source
(origin
(method url-fetch)
@@ -47084,7 +48306,7 @@ untrusted inputs in Rust.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32
- "12qzdzgcvmc5l1fk4psldiipx80423mikb6g4a9qwb322d0rdkcw"))))
+ "132pzpvfvpw33gjlzqd55n5iag9qddzffq8qbp1myfykna1w61x5"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -47475,14 +48697,14 @@ first byte.")
(define-public rust-v-frame-0.2
(package
(name "rust-v-frame")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "v_frame" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0xqf7dynsc6fm94jz3hknwi2n4ch1j7wrs0dd333r1ldniw49rf3"))))
+ (base32 "0ia1j0j1v5zp9bp91imbnbxnv937x3xfpc06nyj96yjfk8zbmxhp"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -47494,10 +48716,9 @@ first byte.")
("rust-serde" ,rust-serde-1)
("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))))
(home-page "https://github.com/xiph/rav1e")
- (synopsis "@code{Video Frame} data structures, part of rav1e")
- (description
- "This package provides @code{Video Frame} data structures, as a part of
-rav1e.")
+ (synopsis "Video Frame data structures, part of rav1e")
+ (description "This package provides @code{Video Frame} data structures, as
+a part of rav1e.")
(license license:bsd-2)))
(define-public rust-value-bag-1
@@ -48682,7 +49903,8 @@ Verification.")
(("rust-base64" ,rust-base64-0.9))))))
(define-public rust-webpki-0.18
- (package/inherit rust-webpki-0.21
+ (package
+ (inherit rust-webpki-0.21)
(name "rust-webpki")
(version "0.18.1")
(source
@@ -48768,7 +49990,8 @@ with webpki.")
(base32 "1d4ss607rgi9pj01zzqa13c1p3m35z314yh6lmjaj4kzvwv5gkci"))))))
(define-public rust-webpki-roots-0.17
- (package/inherit rust-webpki-roots-0.18
+ (package
+ (inherit rust-webpki-roots-0.18)
(name "rust-webpki-roots")
(version "0.17.0")
(source
@@ -48819,7 +50042,8 @@ with webpki.")
("rust-webpki" ,rust-webpki-0.18))))))
(define-public rust-webpki-roots-0.14
- (package/inherit rust-webpki-roots-0.18
+ (package
+ (inherit rust-webpki-roots-0.18)
(name "rust-webpki-roots")
(version "0.14.0")
(source
@@ -50269,6 +51493,52 @@ configuration file and/or environment variables.")
(description "This package provides a Rust XML XPath library.")
(license (list license:expat license:asl2.0))))
+(define-public rust-im-rc-15
+ (package
+ (name "rust-im-rc")
+ (version "15.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "im-rc" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0gsgcs1nn38r40973l6zr1v4d85f4s9qyl32n5f20jphf5z9ba1w"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ;for rust-sized-chunks
+ #:cargo-inputs
+ (("rust-arbitrary" ,rust-arbitrary-0.4)
+ ("rust-bitmaps" ,rust-bitmaps-2)
+ ("rust-proptest" ,rust-proptest-0.9)
+ ("rust-quickcheck" ,rust-quickcheck-0.9)
+ ("rust-rand-core" ,rust-rand-core-0.5)
+ ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.4)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-refpool" ,rust-refpool-0.4)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-sized-chunks" ,rust-sized-chunks-0.6)
+ ("rust-typenum" ,rust-typenum-1)
+ ("rust-version-check" ,rust-version-check-0.9))
+ #:cargo-development-inputs
+ (("rust-metrohash" ,rust-metrohash-1)
+ ("rust-pretty-assertions" ,rust-pretty-assertions-0.6)
+ ("rust-proptest" ,rust-proptest-0.9)
+ ("rust-proptest-derive" ,rust-proptest-derive-0.1)
+ ("rust-rand" ,rust-rand-0.7)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-version-check" ,rust-version-check-0.9))))
+ (home-page "https://docs.rs/crate/im")
+ (synopsis "Fast immutable collection datatypes for Rust")
+ (description "@code{im-rc} provides immutable collection datatypes for
+Rust that are very fast but not thread-safe. A thread-safe (and slower)
+variant of this library is available separately as @code{im}.")
+ (license license:mpl2.0)))
+
(define-public rust-inflections-1
(package
(name "rust-inflections")
@@ -50290,6 +51560,26 @@ configuration file and/or environment variables.")
"High performance inflection transformation library for changing properties of words like the case.")
(license license:expat)))
+(define-public rust-rustc-workspace-hack-1
+ (package
+ (name "rust-rustc-workspace-hack")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "rustc-workspace-hack" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1yx8l58n2vb2ldpi3z1jn4dmi5hnxvikbhpd5lilpdvkl7xd4wgw"))))
+ (build-system cargo-build-system)
+ (home-page "https://crates.io/crates/rustc-workspace-hack")
+ (synopsis "Hack for the compiler's own build system")
+ (description "Hack for the compiler's own build system. It is used by
+@code{cargo}.")
+ (license (list license:expat license:asl2.0))))
+
(define-public skim
(package
(name "skim")
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index b5672cbe50..8848954ab8 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -944,14 +944,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R
(define-public botan
(package
(name "botan")
- (version "2.17.3")
+ (version "2.18.1")
(source (origin
(method url-fetch)
(uri (string-append "https://botan.randombit.net/releases/"
"Botan-" version ".tar.xz"))
(sha256
(base32
- "121vn1aryk36cpks70kk4c4cfic5g0qs82bf92xap9258ijkn4kr"))))
+ "0adf53drhk1hlpfih0175c9081bqpclw6p2afn51cmx849ib9izq"))))
(build-system gnu-build-system)
(arguments
'(#:phases
@@ -976,7 +976,9 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R
(add-before 'check 'library-path-for-tests
(lambda _ (setenv "LD_LIBRARY_PATH" (getcwd))))
(replace 'check
- (lambda _ (invoke "./botan-test"))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (invoke "./botan-test")))))))
(native-inputs
`(("python" ,python-wrapper)
("python-docutils" ,python-docutils)))
@@ -1297,7 +1299,7 @@ Trusted comments are signed, thus verified, before being displayed.")
(define-public libolm
(package
(name "libolm")
- (version "3.2.2")
+ (version "3.2.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1305,7 +1307,7 @@ Trusted comments are signed, thus verified, before being displayed.")
(commit version)))
(sha256
(base32
- "0qji25wiwmkxyfpraxj96c54hyayqmjkvwh0gsy5gb5pz5bp4mcy"))
+ "0bixly6jqpwfx3p37c1qp1j685yg6m429r1nazwh43w4n527bs3y"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
diff --git a/gnu/packages/cryptsetup.scm b/gnu/packages/cryptsetup.scm
index 1b3da5389c..4c4633fe0b 100644
--- a/gnu/packages/cryptsetup.scm
+++ b/gnu/packages/cryptsetup.scm
@@ -35,7 +35,7 @@
(define-public cryptsetup
(package
(name "cryptsetup")
- (version "2.3.5")
+ (version "2.3.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://kernel.org/linux/utils/cryptsetup/v"
@@ -43,7 +43,7 @@
"/cryptsetup-" version ".tar.xz"))
(sha256
(base32
- "1hbhzlv4vbib1da20vnrqaikhxi7ljnchbzrv8v2a4sd8ipr9nff"))))
+ "0pv34l6230ba1i5p0z6zmvfqvv3as0cwn731h2qw4xm53sibg5mj"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -63,14 +63,22 @@
("lvm2" ,lvm2) ; device-mapper
("popt" ,popt)
("util-linux" ,util-linux "lib"))) ;libuuid
- (synopsis "Hard disk encryption tool")
+ (synopsis "Set up transparent encryption of block devices using dm-crypt")
(description
- "LUKS (Linux Unified Key Setup)/Cryptsetup provides a standard on-disk
-encryption format, which does not only facilitate compatibility among
-distributions, but which also provides secure management of multiple user
-passwords. In contrast to existing solutions, LUKS stores all setup necessary
-setup information in the partition header, enabling the users to transport
-or migrate their data seamlessly.")
+ "Cryptsetup is a utility used to conveniently set up disk encryption based
+on the @code{dm-crypt} Linux kernel module. It is most often used to manage
+LUKS volumes but also supports plain dm-crypt volumes and loop-AES, TrueCrypt
+(including VeraCrypt extension), and BitLocker formats.
+
+@acronym{LUKS, Linux Unified Key Setup} is the standard for hard disk encryption
+with the kernel Linux. It provides a standard on-disk-format compatible amongst
+distributions as well as secure management of multiple user passwords. LUKS
+stores all necessary setup information in the partition header to facilitate
+data transport and migration.
+
+The package also includes the @command{veritysetup} and @command{integritysetup}
+utilities to conveniently configure the @code{dm-verity} and @code{dm-integrity}
+block integrity kernel modules.")
(license license:gpl2)
(home-page "https://gitlab.com/cryptsetup/cryptsetup")))
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index de926500ea..1075fe9448 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -53,6 +53,7 @@
(define-public curl
(package
(name "curl")
+ (replacement curl-7.77.0)
(version "7.76.1")
(source (origin
(method url-fetch)
@@ -145,6 +146,20 @@ tunneling, and so on.")
(define-public curl-minimal
(deprecated-package "curl-minimal" curl))
+(define-public curl-7.77.0
+ (package
+ (inherit curl)
+ (version "7.77.0")
+ (source
+ (origin
+ (inherit (package-source curl))
+ (uri (string-append "https://curl.haxx.se/download/curl-"
+ version ".tar.xz"))
+ (patches (search-patches "curl-7.76-use-ssl-cert-env.patch"))
+ (sha256
+ (base32
+ "0jsrc97vbghvljic997r9nypc9qqddcil2lzvv032br8ahn5hr0g"))))))
+
(define-public kurly
(package
(name "kurly")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index bc508aadf4..3d99ef08e6 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -51,6 +51,7 @@
;;; Copyright © 2021 David Larsson <david.larsson@selfhosted.xyz>
;;; Copyright © 2021 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
+;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -2135,14 +2136,14 @@ similar to BerkeleyDB, LevelDB, etc.")
(define-public redis
(package
(name "redis")
- (version "6.0.11")
+ (version "6.2.4")
(source (origin
(method url-fetch)
(uri (string-append "http://download.redis.io/releases/redis-"
version".tar.gz"))
(sha256
(base32
- "0prwqap452m581nyc3cz642d1z3x9nd81896hlqdm3z8238z49y9"))
+ "0vp1d9mlfsppry3nsj9f7bmh9wjgsy3jggp24sac1hhgl43c8cms"))
(modules '((guix build utils)))
(snippet
;; Delete bundled jemalloc, as the package will use the libc one
@@ -2150,8 +2151,8 @@ similar to BerkeleyDB, LevelDB, etc.")
#t))))
(build-system gnu-build-system)
(native-inputs
- `(("procps" ,procps) ; for tests
- ("tcl" ,tcl))) ; for tests
+ `(("procps" ,procps) ; for tests
+ ("tcl" ,tcl))) ; for tests
(arguments
'(#:phases
(modify-phases %standard-phases
@@ -2168,9 +2169,10 @@ similar to BerkeleyDB, LevelDB, etc.")
(lambda _
;; Disable failing tests
(substitute* "tests/test_helper.tcl"
- ((" integration/replication[^-]") "")
- ((" integration/replication-4") "")
- ((" integration/replication-psync") ""))
+ (("integration/failover") "")
+ (("integration/replication-4") "")
+ (("integration/replication-psync") "")
+ (("integration/replication[^-]") ""))
#t)))
#:make-flags `("CC=gcc"
"MALLOC=libc"
@@ -2383,7 +2385,7 @@ database.")
(define-public lmdb
(package
(name "lmdb")
- (version "0.9.28")
+ (version "0.9.29")
(source
(origin
(method git-fetch)
@@ -2392,7 +2394,7 @@ database.")
(commit (string-append "LMDB_" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "012a8bs49cswsnzw7k4piis5b6dn4by85w7a7mai9i04xcjyy9as"))))
+ (base32 "0airps4cd0d91nbgy7hgvifa801snxwxzwxyr6pdv61plsi7h8l3"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index 30995bf986..2b1f7f0ad1 100644
--- a/gnu/packages/dictionaries.scm
+++ b/gnu/packages/dictionaries.scm
@@ -175,11 +175,10 @@ work, such as sentence length and other readability measures.")
(delete 'build)
(delete 'check)
(replace 'install
- (lambda _
+ (lambda* (#:key inputs #:allow-other-keys)
(let ((bindir (string-append
(assoc-ref %outputs "out") "/bin"))
- (wish (string-append
- (assoc-ref %build-inputs "tk")
+ (wish (string-append (assoc-ref inputs "tk")
"/bin/wish8.6"))
(sharedir (string-append
(assoc-ref %outputs "out")
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index b74b9d1b1a..35e4783b2a 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -72,7 +72,7 @@
(define-public diffoscope
(package
(name "diffoscope")
- (version "174")
+ (version "177")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -81,7 +81,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "16nvcvvps2gxr0b9wbfilrn4397cqkcm716zvhlx5hsbq6w6cx08"))))
+ "02np9dq7jnq48lcmz4k1hvwc6xiqgjhrwr1vsbsfw8rxnp9vs0a5"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 006cb8e301..c31afee627 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -552,14 +552,14 @@ and can dramatically shorten the lifespan of the drive if left unchecked.")
(define-public gparted
(package
(name "gparted")
- (version "1.2.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gparted/gparted/gparted-"
version "/gparted-" version ".tar.gz"))
(sha256
- (base32 "06f72hqx5jf2irzsmi7lgpxxj38ncixh0acb4307wyjd4mfp343c"))))
+ (base32 "0amx3hb4rc504nl9i73rgyz0hzhq5x8nkg7lwbk4bsnrblj81hcd"))))
(build-system glib-or-gtk-build-system)
(arguments
;; Tests require access to paths outside the build container, such
@@ -1144,15 +1144,18 @@ of choice for all light thinking Unix addicts!")
(define-public hddtemp
(package
(name "hddtemp")
- (version "0.3-beta15")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://savannah/hddtemp/hddtemp-"
- version
- ".tar.bz2"))
- (sha256
- (base32
- "0nzgg4nl8zm9023wp4dg007z6x3ir60rwbcapr9ks2al81c431b1"))))
+ ;; <https://savannah.nongnu.org/projects/hddtemp/> advertises the project as
+ ;; ‘orphaned/unmaintained’. Use a maintained fork/continuation.
+ (version "0.4.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vitlav/hddtemp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "04kylb2ka0jimi238zpfq1yii2caidpmj3ck51rvxz03y5lpq8fw"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list (string-append
@@ -1161,19 +1164,20 @@ of choice for all light thinking Unix addicts!")
"/share/hddtemp/hddtemp.db"))
#:phases
(modify-phases %standard-phases
+ (add-before 'bootstrap 'delete-autogen.sh
+ (lambda _
+ ;; The default 'bootstrap phase works better.
+ (delete-file "autogen.sh")))
(add-after 'install 'install-db
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((target (string-append (assoc-ref outputs "out")
- "/share/hddtemp/hddtemp.db")))
- (mkdir-p (dirname target))
- (copy-file (assoc-ref inputs "db") target)))))))
- (inputs
- `(("db" ,(origin
- (method url-fetch)
- (uri "mirror://savannah/hddtemp/hddtemp.db")
- (sha256
- (base32 "1fr6qgns6qv7cr40lic5yqwkkc7yjmmgx8j0z6d93csg3smzhhya"))))))
- (home-page "https://savannah.nongnu.org/projects/hddtemp/")
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "data/hddtemp.db"
+ (string-append out "/share/hddtemp"))))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("gettext" ,gettext-minimal)))
+ (home-page "https://github.com/vitlav/hddtemp")
(synopsis "Report the temperature of hard drives from S.M.A.R.T. information")
(description "@command{hddtemp} is a small utility that gives you the
temperature of your hard drive by reading S.M.A.R.T. information (for drives
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 94480c5313..d53c06380a 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -48,13 +48,13 @@
(define-public python-django
(package
(name "python-django")
- (version "3.2.2")
+ (version "3.2.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "Django" version))
(sha256
(base32
- "0gffaabnnpzj0sl3jl7mllvi3gc0jvab6xw2bckvyljwsrd1j78a"))))
+ "15pjwyvrx4n8gi8n51b14wp54bg4jqapr25p52597zn6ikdxijb6"))))
(build-system python-build-system)
(arguments
'(#:phases
@@ -130,13 +130,13 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
(define-public python-django-2.2
(package
(inherit python-django)
- (version "2.2.22")
+ (version "2.2.24")
(source (origin
(method url-fetch)
(uri (pypi-uri "Django" version))
(sha256
(base32
- "0q30zjcmnvwp1v1syn739wapahs2dx784n0yjyypq0cr3kdi88nv"))))
+ "1dvx3x85lggm91x7mpvaf9nmpxyz7r97pbpnmr2k1qfy0c7gyf9k"))))
(native-inputs
`(;; XXX: In 2.2 and 3.0, selenium is required for the test suite.
("python-selenium" ,python-selenium)
@@ -932,7 +932,7 @@ name is purely coincidental.")
(define-public python-django-statici18n
(package
(name "python-django-statici18n")
- (version "1.9.0")
+ (version "2.1.0")
(home-page "https://github.com/zyegfryed/django-statici18n")
(source (origin
(method git-fetch)
@@ -942,7 +942,7 @@ name is purely coincidental.")
(file-name (git-file-name name version))
(sha256
(base32
- "1p3myp2im6c87yc05alh91jyahqws5lcw3zzdsj4dh8lx9s9cgpf"))))
+ "0x0xvfqd40is2ks43d65awgqkx3wk10lvdim15scvbjhkh301b6v"))))
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@@ -1089,14 +1089,13 @@ forms using your favorite CSS framework, without writing template code.")
(define-public python-django-compressor
(package
(name "python-django-compressor")
- (version "2.4")
+ (version "2.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "django_compressor" version))
(sha256
- (base32
- "0kx7bclfa0sxlsz6ka70zr9ra00lks0hmv1kc99wbanx6xhirvfj"))))
+ (base32 "1q0m0hfg7sqmj5km924g4dgy3nx51aszzsprlp6gsin10mv0fn1k"))))
(build-system python-build-system)
(arguments
'(#:phases
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 86185373c4..a0388a1419 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm