Browse Source

Merge branch 'master' into core-updates

Conflicts:
	gnu/local.mk
	gnu/packages/backup.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/guile.scm
	gnu/packages/lisp.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/web.scm
	gnu/packages/xorg.scm
gn-latest-20200725
Marius Bakke 1 year ago
parent
commit
8bf8cd9b85
No known key found for this signature in database GPG Key ID: A2A06DF2A33A54FA
69 changed files with 6316 additions and 867 deletions
  1. +4
    -3
      doc/guix-cookbook.texi
  2. +11
    -4
      doc/guix.texi
  3. +2
    -1
      gnu/local.mk
  4. +6
    -8
      gnu/packages/admin.scm
  5. +8
    -0
      gnu/packages/aspell.scm
  6. +2
    -2
      gnu/packages/astronomy.scm
  7. +2
    -2
      gnu/packages/audio.scm
  8. +40
    -1
      gnu/packages/backup.scm
  9. +277
    -1
      gnu/packages/bioconductor.scm
  10. +156
    -13
      gnu/packages/bioinformatics.scm
  11. +4
    -4
      gnu/packages/chromium.scm
  12. +64
    -1
      gnu/packages/compression.scm
  13. +346
    -81
      gnu/packages/cran.scm
  14. +3608
    -333
      gnu/packages/crates-io.scm
  15. +2
    -2
      gnu/packages/cups.scm
  16. +15
    -13
      gnu/packages/databases.scm
  17. +7
    -4
      gnu/packages/diffoscope.scm
  18. +173
    -19
      gnu/packages/emacs-xyz.scm
  19. +11
    -0
      gnu/packages/emacs.scm
  20. +1
    -1
      gnu/packages/game-development.scm
  21. +3
    -2
      gnu/packages/gnome.scm
  22. +2
    -2
      gnu/packages/gsasl.scm
  23. +37
    -0
      gnu/packages/hardware.scm
  24. +36
    -16
      gnu/packages/linphone.scm
  25. +6
    -6
      gnu/packages/linux.scm
  26. +117
    -23
      gnu/packages/lisp-xyz.scm
  27. +19
    -22
      gnu/packages/lisp.scm
  28. +56
    -19
      gnu/packages/machine-learning.scm
  29. +6
    -6
      gnu/packages/magic-wormhole.scm
  30. +40
    -1
      gnu/packages/maths.scm
  31. +2
    -2
      gnu/packages/mpd.scm
  32. +5
    -2
      gnu/packages/music.scm
  33. +15
    -0
      gnu/packages/openldap.scm
  34. +15
    -4
      gnu/packages/openstack.scm
  35. +2
    -2
      gnu/packages/package-management.scm
  36. +14
    -0
      gnu/packages/patches/emacs-telega-test-env.patch
  37. +34
    -1
      gnu/packages/python-science.scm
  38. +86
    -26
      gnu/packages/python-web.scm
  39. +236
    -49
      gnu/packages/python-xyz.scm
  40. +133
    -5
      gnu/packages/radio.scm
  41. +50
    -1
      gnu/packages/rust-apps.scm
  42. +47
    -1
      gnu/packages/sphinx.scm
  43. +51
    -36
      gnu/packages/statistics.scm
  44. +26
    -0
      gnu/packages/tex.scm
  45. +2
    -2
      gnu/packages/text-editors.scm
  46. +3
    -3
      gnu/packages/valgrind.scm
  47. +154
    -1
      gnu/packages/video.scm
  48. +22
    -9
      gnu/packages/vpn.scm
  49. +41
    -17
      gnu/packages/web.scm
  50. +77
    -18
      gnu/packages/wm.scm
  51. +38
    -0
      gnu/packages/xdisorg.scm
  52. +62
    -0
      gnu/packages/xorg.scm
  53. +6
    -7
      gnu/services.scm
  54. +2
    -1
      gnu/services/docker.scm
  55. +20
    -21
      gnu/system.scm
  56. +2
    -1
      gnu/system/file-systems.scm
  57. +2
    -4
      gnu/system/linux-container.scm
  58. +5
    -4
      gnu/tests/install.scm
  59. +5
    -11
      gnu/tests/reconfigure.scm
  60. +1
    -3
      guix/channels.scm
  61. +8
    -6
      guix/import/crate.scm
  62. +36
    -0
      guix/profiles.scm
  63. +3
    -4
      guix/scripts/edit.scm
  64. +16
    -17
      guix/scripts/pack.scm
  65. +5
    -3
      guix/scripts/substitute.scm
  66. +12
    -11
      tests/crate.scm
  67. +1
    -1
      tests/gem.scm
  68. +12
    -1
      tests/profiles.scm
  69. +4
    -3
      tests/pypi.scm

+ 4
- 3
doc/guix-cookbook.texi View File

@ -13,6 +13,7 @@ Copyright @copyright{} 2019 Efraim Flashner@*
Copyright @copyright{} 2019 Pierre Neidhardt@*
Copyright @copyright{} 2020 Oleg Pykhalov@*
Copyright @copyright{} 2020 Matthew Brooks@*
Copyright @copyright{} 2020 Marcin Karpezo@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@ -1575,7 +1576,7 @@ available for inclusion into the initrd.
@cindex stumpwm
You could install StumpWM with a Guix system by adding
@code{stumpwm-checkout} and optionally @code{`(,stumpwm-checkout "lib")}
@code{stumpwm} and optionally @code{`(,stumpwm "lib")}
packages to a system configuration file, e.g.@: @file{/etc/config.scm}.
An example configuration can look like this:
@ -1586,7 +1587,7 @@ An example configuration can look like this:
(operating-system
;; …
(packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
(packages (append (list sbcl stumpwm `(,stumpwm "lib"))
%base-packages)))
@end lisp
@ -1601,7 +1602,7 @@ module @code{sbcl-stumpwm-ttf-fonts}, adding it to Guix system packages:
(operating-system
;; …
(packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
(packages (append (list sbcl stumpwm `(,stumpwm "lib"))
sbcl-stumpwm-ttf-fonts font-dejavu %base-packages)))
@end lisp


+ 11
- 4
doc/guix.texi View File

@ -63,7 +63,7 @@ Copyright @copyright{} 2018, 2019 Florian Pelz@*
Copyright @copyright{} 2018 Laura Lazzati@*
Copyright @copyright{} 2018 Alex Vong@*
Copyright @copyright{} 2019 Josh Holland@*
Copyright @copyright{} 2019 Diego Nicola Barbato@*
Copyright @copyright{} 2019, 2020 Diego Nicola Barbato@*
Copyright @copyright{} 2019 Ivan Petkov@*
Copyright @copyright{} 2019 Jakob L. Kreuze@*
Copyright @copyright{} 2019 Kyle Andrews@*
@ -5118,7 +5118,7 @@ guix pack -f squashfs bash guile emacs geiser
@noindent
The result is a SquashFS file system image that can either be mounted or
directly be used as a file system container image with the
@uref{https://singularity.lbl.gov, Singularity container execution
@uref{https://www.sylabs.io/docs/, Singularity container execution
environment}, using commands like @command{singularity shell} or
@command{singularity exec}.
@ -8830,7 +8830,7 @@ $ guix environment --no-grafts -C foo --ad-hoc strace gdb
Here, @command{guix environment -C} creates a container and spawns a new
shell in it (@pxref{Invoking guix environment}). The @command{--ad-hoc
strace gdb} part adds the @command{strace} and @command{gdb} commands to
the container, which would may find handy while debugging. The
the container, which you may find handy while debugging. The
@option{--no-grafts} option makes sure we get the exact same
environment, with ungrafted packages (@pxref{Security Updates}, for more
info on grafts).
@ -16289,6 +16289,13 @@ This is the type for the @uref{https://www.pulseaudio.org/, PulseAudio}
sound server. It exists to allow system overrides of the default settings
via @code{pulseaudio-configuration}, see below.
@quotation Warning
This service overrides per-user configuration files. If you want
PulseAudio to honor configuraton files in @file{~/.config/pulse} you
have to unset the environment variables @code{PULSE_CONFIG} and
@code{PULSE_CLIENTCONFIG} in your @file{~/.bash_profile}.
@end quotation
@quotation Warning
This service on its own does not ensure, that the @code{pulseaudio} package
exists on your machine. It merely adds configuration files for it, as
@ -26592,7 +26599,7 @@ like
@lisp
(bootloader
(grub-configuration
(bootloader-configuration
;; @dots{}
(theme (grub-theme
(inherit %default-theme)


+ 2
- 1
gnu/local.mk View File

@ -10,7 +10,7 @@
# Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
# Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
# Copyright © 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
# Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2016, 2017, 2018, 2019, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
# Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
# Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
@ -875,6 +875,7 @@ dist_patch_DATA = \
%D%/packages/patches/emacs-magit-log-format-author-margin.patch \
%D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \
%D%/packages/patches/emacs-source-date-epoch.patch \
%D%/packages/patches/emacs-telega-test-env.patch \
%D%/packages/patches/emacs-undohist-ignored.patch \
%D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch \
%D%/packages/patches/emacs-zones-called-interactively.patch \


+ 6
- 8
gnu/packages/admin.scm View File

@ -152,24 +152,22 @@
(list "--enable-sudo=yes")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-sudo-path
(lambda* (#:key inputs #:allow-other-keys)
(add-after 'unpack 'patch-file-names
(lambda _
(substitute* "configure.ac"
(("supath=`which su 2>/dev/null`")
"supath=/run/setuid-programs/su")
(("sudopath=`which sudo 2>/dev/null`")
(string-append "sudopath="
(string-append (assoc-ref inputs "sudo")
"/bin/sudo"))))
"sudopath=/run/setuid-programs/sudo"))
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
("autogen" ,autogen)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
(inputs
`(("glib" ,glib)
("gtk+" ,gtk+-2)
("sudo" ,sudo)))
("gtk+" ,gtk+-2)))
(synopsis "Graphical front end for @command{su}")
(description
"Ktsuss stands for ``Keep the @command{su} simple, stupid''.


+ 8
- 0
gnu/packages/aspell.scm View File

@ -8,6 +8,7 @@
;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
;;;
;;; This file is part of GNU Guix.
;;;
@ -289,6 +290,13 @@ dictionaries, including personal ones.")
(base32
"0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
(define-public aspell-dict-pl
(aspell-dictionary "pl" "Polish"
#:version "0.51-0"
#:sha256
(base32
"1a3ccji6k5gys7l3ilr2lh5pzxgzb7ipc5vb737svl6nqgdy8757")))
(define-public aspell-dict-pt-br
(aspell-dictionary "pt_BR" "Brazilian Portuguese"
#:version "20131030-12-0"


+ 2
- 2
gnu/packages/astronomy.scm View File

@ -157,7 +157,7 @@ programs for the manipulation and analysis of astronomical data.")
(define-public stellarium
(package
(name "stellarium")
(version "0.19.3")
(version "0.20.1")
(source
(origin
(method url-fetch)
@ -165,7 +165,7 @@ programs for the manipulation and analysis of astronomical data.")
"/releases/download/v" version
"/stellarium-" version ".tar.gz"))
(sha256
(base32 "0p92rgclag0nkic9gk3p9vclb8xx9hv4zlgyij6cyh43s7c1avhp"))))
(base32 "034jkrdaaamvbrkfwi3qcl6h8hwfnw2nvf7a82faj55rskcpnkhm"))))
(build-system cmake-build-system)
(inputs
`(("qtbase" ,qtbase)


+ 2
- 2
gnu/packages/audio.scm View File

@ -1979,14 +1979,14 @@ significantly faster and have minimal dependencies.")
(define-public lv2
(package
(name "lv2")
(version "1.16.0")
(version "1.18.0")
(source (origin
(method url-fetch)
(uri (string-append "http://lv2plug.in/spec/lv2-"
version ".tar.bz2"))
(sha256
(base32
"1ppippbpdpv13ibs06b0bixnazwfhiw0d0ja6hx42jnkgdyp5hyy"))))
"0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target


+ 40
- 1
gnu/packages/backup.scm View File

@ -11,10 +11,11 @@
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -37,6 +38,7 @@
#:use-module (guix git-download)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system python)
@ -64,6 +66,7 @@
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
@ -987,6 +990,42 @@ precious backup space.
@end itemize")
(license license:bsd-2)))
(define-public zbackup
(package
(name "zbackup")
(version "1.4.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zbackup/zbackup.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "14l1kyxg7pccpax3d6qcpmdycb70kn3fxp1a59w64hqy2493hngl"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f)) ;no test
(inputs
`(("lzo" ,lzo)
("libressl" ,libressl)
("protobuf" ,protobuf)
("xz" ,xz)
("zlib" ,zlib)))
(home-page "http://zbackup.org")
(synopsis "Versatile deduplicating backup tool")
(description
"ZBackup is a globally-deduplicating backup tool, based on the
ideas found in Rsync. Feed a large @file{.tar} into it, and it will
store duplicate regions of it only once, then compress and optionally
encrypt the result. Feed another @file{.tar} file, and it will also
re-use any data found in any previous backups. This way only new
changes are stored, and as long as the files are not very different,
the amount of storage required is very low. Any of the backup files
stored previously can be read back in full at any time. The program
is format-agnostic, so you can feed virtually any files to it.")
(license license:gpl2+)))
(define-public burp
(package
(name "burp")


+ 277
- 1
gnu/packages/bioconductor.scm View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
@ -493,6 +493,30 @@ annotations for the genome of the model mouse Mus musculus.")
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-bsgenome-hsapiens-ucsc-hg38
(package
(name "r-bsgenome-hsapiens-ucsc-hg38")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
version 'annotation))
(sha256
(base32
"1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
(synopsis "Full genome sequences for Homo sapiens")
(description
"This package provides full genome sequences for Homo sapiens (Human)
as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-ensdb-hsapiens-v75
(package
(name "r-ensdb-hsapiens-v75")
@ -718,6 +742,30 @@ annotations.")
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
(define-public r-ideoviz
(package
(name "r-ideoviz")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
"0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)))
(home-page "https://bioconductor.org/packages/IdeoViz/")
(synopsis "Plots data along a chromosomal ideogram")
(description "This package provides functions to plot data associated with
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
@ -811,6 +859,32 @@ performing parallel computations on multicore machines.")
Disease Ontology.")
(license license:artistic2.0)))
(define-public r-pasilla
(package
(name "r-pasilla")
(version "1.14.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://bioconductor.org/packages/release/data/experiment"
"/src/contrib/pasilla_" version ".tar.gz"))
(sha256
(base32
"0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocstyle" ,r-biocstyle)
("r-dexseq" ,r-dexseq)
("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)))
(home-page "https://www.bioconductor.org/packages/pasilla/")
(synopsis "Data package with per-exon and per-gene read counts")
(description "This package provides per-exon and per-gene read counts
computed for selected genes from RNA-seq data that were presented in the
article 'Conservation of an RNA regulatory map between Drosophila and mammals'
by Brooks et al., Genome Research 2011.")
(license license:lgpl2.1+)))
(define-public r-pfam-db
(package
(name "r-pfam-db")
@ -995,6 +1069,63 @@ examples' of Affymetrix data, unlike the artificial examples included in the
package @code{affy}.")
(license license:gpl2+)))
(define-public r-coverageview
(package
(name "r-coverageview")
(version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
"0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)
("r-rsamtools" ,r-rsamtools)))
(home-page "https://bioconductor.org/packages/CoverageView/")
(synopsis "Coverage visualization package for R")
(description "This package provides a framework for the visualization of
genome coverage profiles. It can be used for ChIP-seq experiments, but it can
be also used for genome-wide nucleosome positioning experiments or other
experiment types where it is important to have a framework in order to inspect
how the coverage distributed across the genome.")
(license license:artistic2.0)))
(define-public r-cummerbund
(package
(name "r-cummerbund")
(version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
"1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-fastcluster", r-fastcluster)
("r-ggplot2" ,r-ggplot2)
("r-gviz" ,r-gviz)
("r-plyr" ,r-plyr)
("r-reshape2" ,r-reshape2)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/cummeRbund/")
(synopsis "Analyze Cufflinks high-throughput sequencing data")
(description "This package allows for persistent storage, access,
exploration, and manipulation of Cufflinks high-throughput sequencing
data. In addition, provides numerous plotting functions for commonly
used visualizations.")
(license license:artistic2.0)))
(define-public r-curatedtcgadata
(package
(name "r-curatedtcgadata")
@ -2533,6 +2664,41 @@ and regression inferences from RNA-sequencing data.")
gene and isoform level using RNA-seq data")
(license license:artistic2.0)))
(define-public r-karyoploter
(package
(name "r-karyoploter")
(version "1.12.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
"03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-regioner" ,r-regioner)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-rsamtools" ,r-rsamtools)
("r-memoise" ,r-memoise)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
("r-s4vectors" ,r-s4vectors)
("r-biovizbase" ,r-biovizbase)
("r-digest" ,r-digest)
("r-bezier" ,r-bezier)
("r-bamsignals" ,r-bamsignals)
("r-annotationdbi" ,r-annotationdbi)
("r-variantannotation" ,r-variantannotation)))
(home-page "https://bioconductor.org/packages/karyoploteR/")
(synopsis "Plot customizable linear genomes displaying arbitrary data")
(description "This package creates karyotype plots of arbitrary genomes and
offers a complete set of functions to plot arbitrary data on them. It mimicks
many R base graphics functions coupling them with a coordinate change function
automatically mapping the chromosome and data coordinates into the plot
coordinates.")
(license license:artistic2.0)))
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
@ -3972,6 +4138,78 @@ database (e.g. JASPAR). It can also be used to visualize motifs, motif
distributions, modules and filter motifs.")
(license license:gpl2)))
(define-public r-motifdb
(package
(name "r-motifdb")
(version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MotifDb" version))
(sha256
(base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-iranges" ,r-iranges)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-splitstackshape" ,r-splitstackshape)))
(home-page "https://www.bioconductor.org/packages/MotifDb/")
(synopsis "Annotated collection of protein-DNA binding sequence motifs")
(description "This package provides more than 2000 annotated position
frequency matrices from nine public sources, for multiple organisms.")
(license license:artistic2.0)))
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
(version "2.0.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
(base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
`(("r-grimport" ,r-grimport)
("r-stringr" ,r-stringr)
("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-variantannotation" ,r-variantannotation)
("r-biocparallel" ,r-biocparallel)
("r-motifstack" ,r-motifstack)
("r-gviz" ,r-gviz)
("r-matrixstats" ,r-matrixstats)
("r-tfmpvalue" ,r-tfmpvalue)
("r-motifdb" ,r-motifdb)))
(home-page "https://www.bioconductor.org/packages/motifbreakR/")
(synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
(description "This package allows biologists to judge in the first place
whether the sequence surrounding the polymorphism is a good match, and in
the second place how much information is gained or lost in one allele of
the polymorphism relative to another. This package gives a choice of
algorithms for interrogation of genomes with motifs from public sources:
@enumerate
@item a weighted-sum probability matrix;
@item log-probabilities;
@item weighted by relative entropy.
@end enumerate
This package can predict effects for novel or previously described variants in
public databases, making it suitable for tasks beyond the scope of its original
design. Lastly, it can be used to interrogate any genome curated within
Bioconductor.")
(license license:gpl2+)))
(define-public r-motifstack
(package
(name "r-motifstack")
@ -6368,6 +6606,44 @@ and parameters of which are trained on a set of aligned reads and a reference
genome sequence.")
(license license:lgpl3)))
(define-public r-snplocs-hsapiens-dbsnp144-grch37
(package
(name "r-snplocs-hsapiens-dbsnp144-grch37")
(version "0.99.20")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
version 'annotation))
(sha256
(base32
"1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
(build-system r-build-system)
;; As this package provides little more than a very large data file it
;; doesn't make sense to build substitutes.
(arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-bsgenome" ,r-bsgenome)
("r-biostrings" ,r-biostrings)))
(home-page
"https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
(synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
(description "This package provides SNP locations and alleles for Homo
sapiens extracted from NCBI dbSNP Build 144. The source data files used for
this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
the mitochondrion chromosome. Therefore, the SNPs in this package can be
injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
correct position but this injection will exclude chrM (i.e. nothing will be
injected in that sequence).")
(license license:artistic2.0)))
(define-public r-reqon
(package
(name "r-reqon")


+ 156
- 13
gnu/packages/bioinformatics.scm View File

@ -3,7 +3,7 @@
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@ -2334,6 +2334,62 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
files. The code was previously part of the cutadapt tool.")
(license license:expat)))
(define-public python-deeptoolsintervals
(package
(name "python-deeptoolsintervals")
(version "0.1.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "deeptoolsintervals" version))
(sha256
(base32
"1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
(build-system python-build-system)
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/deeptools/deeptools_intervals")
(synopsis "Create GTF-based interval trees with associated meta-data")
(description
"This package provides a Python module creating/accessing GTF-based
interval trees with associated meta-data. It is primarily used by the
@code{deeptools} package.")
(license license:expat)))
(define-public python-deeptools
(package
(name "python-deeptools")
(version "3.4.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "deepTools" version))
(sha256
(base32
"1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
(build-system python-build-system)
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-numpydoc" ,python-numpydoc)
("python-py2bit" ,python-py2bit)
("python-pybigwig" ,python-pybigwig)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-deeptoolsintervals" ,python-deeptoolsintervals)
("python-plotly" ,python-plotly)))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
of data that are now routinely generated from DNA sequencing centers.
@code{deepTools} contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard bedGraph
and bigWig file formats, that allow comparison between different files. Finally,
using such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for functional
annotations of the genome.")
;; The file deeptools/cm.py is licensed under the BSD license. The
;; remainder of the code is licensed under the MIT license.
(license (list license:bsd-3 license:expat))))
(define-public cutadapt
(package
(name "cutadapt")
@ -4886,14 +4942,24 @@ files and writing bioinformatics applications.")
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2)) ; requires Python 2.7
`(#:python ,python-2 ; requires Python 2.7
#:tests? #f ; test data are not included
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-weave
(lambda _
(substitute* "warpedlmm/util/linalg.py"
(("from scipy import linalg, weave")
"from scipy import linalg\nimport weave"))
#t)))))
(propagated-inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-matplotlib" ,python2-matplotlib)
("python-fastlmm" ,python2-fastlmm)
("python-pandas" ,python2-pandas)
("python-pysnptools" ,python2-pysnptools)))
("python-pysnptools" ,python2-pysnptools)
("python-weave" ,python2-weave)))
(native-inputs
`(("python-mock" ,python2-mock)
("python-nose" ,python2-nose)
@ -9102,6 +9168,46 @@ samples into a single report. It contains modules for a large number of
common bioinformatics tools.")
(license license:gpl3+)))
(define-public variant-tools
(package
(name "variant-tools")
(version "3.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vatlab/varianttools.git")
;; There is no tag corresponding to version 3.1.2
(commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
(file-name (git-file-name name version))
(sha256
(base32
"12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
(build-system python-build-system)
(inputs
`(("boost" ,boost)
("c-blosc" ,c-blosc)
("gsl" ,gsl)
("hdf5" ,hdf5)
("hdf5-blosc" ,hdf5-blosc)
("python-cython" ,python-cython)
("zlib" ,zlib)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-pycurl" ,python-pycurl)
("python-pyzmq" ,python-pyzmq)
("python-scipy" ,python-scipy)
("python-tables" ,python-tables)))
(home-page "https://vatlab.github.io/vat-docs/")
(synopsis "Analyze genetic variants from Next-Gen sequencing studies")
(description
"Variant tools is a tool for the manipulation, annotation,
selection, simulation, and analysis of variants in the context of next-gen
sequencing analysis. Unlike some other tools used for next-gen sequencing
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")
@ -9660,13 +9766,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(define-public r-seurat
(package
(name "r-seurat")
(version "3.1.4")
(version "3.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
"1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@ -9688,7 +9794,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
("r-patchwork" ,r-patchwork)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
@ -10634,14 +10739,14 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
(version "1.14.3")
(version "1.14.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
"1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
"0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@ -13152,7 +13257,7 @@ version does count multisplits.")
(define-public minimap2
(package
(name "minimap2")
(version "2.10")
(version "2.17")
(source
(origin
(method url-fetch)
@ -13161,7 +13266,7 @@ version does count multisplits.")
"minimap2-" version ".tar.bz2"))
(sha256
(base32
"080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
"0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
@ -13208,6 +13313,42 @@ cases include:
@end enumerate\n")
(license license:expat)))
(define-public miniasm
(package
(name "miniasm")
(version "0.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/lh3/miniasm/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "miniasm" bin)
(install-file "minidot" bin)))))))
(home-page "https://github.com/lh3/miniasm")
(synopsis "Ultrafast de novo assembly for long noisy reads")
(description "Miniasm is a very fast OLC-based de novo assembler for noisy
long reads. It takes all-vs-all read self-mappings (typically by minimap) as
input and outputs an assembly graph in the GFA format. Different from
mainstream assemblers, miniasm does not have a consensus step. It simply
concatenates pieces of read sequences to generate the final unitig sequences.
Thus the per-base error rate is similar to the raw input reads.")
(license license:expat)))
(define-public r-circus
(package
(name "r-circus")
@ -13366,14 +13507,14 @@ in RNA-seq data.")
(define-public python-scanpy
(package
(name "python-scanpy")
(version "1.4.5.1")
(version "1.4.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(sha256
(base32
"14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j"))))
"0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -13383,6 +13524,7 @@ in RNA-seq data.")
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
@ -13399,8 +13541,8 @@ in RNA-seq data.")
("python-h5py" ,python-h5py)
("python-igraph" ,python-igraph)
("python-joblib" ,python-joblib)
("python-louvain" ,python-louvain)
("python-legacy-api-wrap" ,python-legacy-api-wrap)
("python-louvain" ,python-louvain)
("python-matplotlib" ,python-matplotlib)
("python-natsort" ,python-natsort)
("python-networkx" ,python-networkx)
@ -13413,6 +13555,7 @@ in RNA-seq data.")
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
`(("python-pytest" ,python-pytest)


+ 4
- 4
gnu/packages/chromium.scm View File

@ -248,8 +248,8 @@ from forcing GEXP-PROMISE."
#:system system
#:guile-for-build guile)))
(define %chromium-version "81.0.4044.122")
(define %ungoogled-revision "31d6e60c96481599b42072b4489e4468280198e3")
(define %chromium-version "81.0.4044.129")
(define %ungoogled-revision "c2a89fb6b5b559c826796c811741fa8ed3e11de8")
(define %debian-revision "debian/81.0.4044.92-1")
(define package-revision "0")
(define %package-version (string-append %chromium-version "-"
@ -264,7 +264,7 @@ from forcing GEXP-PROMISE."
%chromium-version ".tar.xz"))
(sha256
(base32
"0ahqh3vmzbpai4xwn7qybgw9phc8ssjdvfc7384mxqk9swqgv7qg"))))
"1ls663s1f74p912x42qp3zcvm17kmjiv1ij6yy1c14gdhcpmjx7z"))))
(define %ungoogled-origin
(origin
@ -275,7 +275,7 @@ from forcing GEXP-PROMISE."
(string-take %ungoogled-revision 7)))
(sha256
(base32
"1pj2vmzb2fagvypjsjn2kqf5n5k8vnhbisyb0snr6wqvpv09x0vv"))))
"0bbr4a2gkgm3ykdgpj8x58sd3dwam6qkifhzfs2997681g7b2v2q"))))
(define %debian-origin
(origin


+ 64
- 1
gnu/packages/compression.scm View File

@ -4,7 +4,7 @@
;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@ -27,6 +27,7 @@
;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -52,6 +53,7 @@
#:use-module (guix build-system cmake)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@ -2126,3 +2128,64 @@ independent. Supported formats are 7z, ARJ, bzip2, gzip, LHA, lzma, lzop,
RAR, RPM, DEB, tar, and ZIP. It cannot perform functions for archives, whose
archiver is not installed.")
(license license:gpl2+)))
(define-public tarsplitter
(package
(name "tarsplitter")
(version "2.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/AQUAOSOTech/tarsplitter.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"17qkg95r97kcrs17b0mcqswx99280ni47j5yx8xa7nl3bdhm6325"))))
(build-system go-build-system)
(arguments
`(#:import-path "github.com/AQUAOSOTech/tarsplitter"
#:install-source? #f
#:phases
(modify-phases %standard-phases
(add-after 'install 'install-documentation
(lambda* (#:key import-path outputs #:allow-other-keys)
(let* ((source (string-append "src/" import-path))
(out (assoc-ref outputs "out"))
(doc (string-append out "/share/doc/" ,name "-" ,version)))
(with-directory-excursion source
(install-file "README.md" doc))
#t))))))
(home-page "https://github.com/AQUAOSOTech/tarsplitter")
(synopsis "Multithreaded tar utility")
(description
"Archive huge numbers of files, or split massive tar archives into smaller
chunks.")
(license license:expat)))
(define-public c-blosc
(package
(name "c-blosc")
(version "1.18.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Blosc/c-blosc.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ywq8j70149859vvs19wgjq89d6xsvvmvm2n1dmkzpchxgrvnw70"))))
(build-system cmake-build-system)
(home-page "https://blosc.org")
(synopsis "Blocking, shuffling and lossless compression library")
(description
"Blosc is a high performance compressor optimized for binary data. It has
been designed to transmit data to the processor cache faster than the
traditional, non-compressed, direct memory fetch approach via a
@code{memcpy()} system call. Blosc is meant not only to reduce the size of
large datasets on-disk or in-memory, but also to accelerate memory-bound
computations.")
;; Blosc itself is released under BSD-3 but it incorporates code under
;; other non-copyleft licenses.
(license license:bsd-3)))

+ 346
- 81
gnu/packages/cran.scm View File

@ -2,7 +2,7 @@
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@ -83,6 +83,25 @@
#:use-module (gnu packages web)
#:use-module (gnu packages xorg))
(define-public r-bezier
(package
(name "r-bezier")
(version "1.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "bezier" version))
(sha256
(base32
"1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/bezier/")
(synopsis "Bezier curve and spline toolkit")
(description
"This package is a toolkit for working with Bezier curves and splines.
The package provides functions for point generation, arc length estimation,
degree elevation and curve fitting.")
(license license:gpl2+)))
(define-public r-clipr
(package
(name "r-clipr")
@ -102,6 +121,36 @@
the system clipboards.")
(license license:gpl3)))
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
(version "0.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
"0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
("r-mass" ,r-mass)
("r-plyr" ,r-plyr)
("r-polynom" ,r-polynom)
("r-splus2r" ,r-splus2r)
("r-tibble" ,r-tibble)
("r-xts" ,r-xts)
("r-zoo" ,r-zoo)))
(home-page "https://www.r4photobiology.info/")
(synopsis "Miscellaneous Extensions to @code{ggplot2}")
(description "This package provides extensions to @code{ggplot2},
respecting the grammar of its graphics paradigm.")
(license license:gpl2+)))
(define-public r-oenb
(package
(name "r-oenb")
@ -177,6 +226,30 @@ legends.")
control over dimensions and appearance.")
(license license:gpl2+)))
(define-public r-ecp
(package
(name "r-ecp")
(version "3.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "ecp" version))
(sha256
(base32
"11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ecp/")
(synopsis "Multiple change-point analysis of multivariate data")
(description
"This package implements various procedures for finding multiple
change-points. Two methods make use of dynamic programming and pruning, with
no distributional assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods are included.
All methods return the set of estimated change-points as well as other summary
information.")
(license license:gpl2+)))
(define-public r-ellipsis
(package
(name "r-ellipsis")
@ -449,6 +522,27 @@ small, reproducible, and runnable examples on code-oriented websites or email.
such as copy/paste from an R session.")
(license license:expat)))
(define-public r-reordercluster
(package
(name "r-reordercluster")
(version "1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "ReorderCluster" version))
(sha256
(base32
"0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gplots" ,r-gplots)
("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ReorderCluster")
(synopsis "Reordering the dendrogram according to the class labels")
(description "This package provides tools for performing the leaf reordering
for the dendrogram that preserves the hierarchical clustering result and at the
same time tries to group instances from the same class together.")
(license license:gpl3+)))
(define-public r-callr
(package
(name "r-callr")
@ -1027,13 +1121,13 @@ application framework for R, making it easy to create attractive dashboards.")
(define-public r-shinyfiles
(package
(name "r-shinyfiles")
(version "0.7.5")
(version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyFiles" version))
(sha256
(base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
(base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
(properties `((upstream-name . "shinyFiles")))
(build-system r-build-system)
(propagated-inputs
@ -1677,13 +1771,13 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
(version "1.0.6")
(version "1.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
(base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@ -1910,17 +2004,19 @@ multi-dimensional data.")
(define-public r-powerlaw
(package
(name "r-powerlaw")
(version "0.70.4")
(version "0.70.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "poweRlaw" version))
(sha256
(base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
(base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
(properties `((upstream-name . "poweRlaw")))
(build-system r-build-system)
(propagated-inputs
`(("r-vgam" ,r-vgam)))
`(("r-pracma" ,r-pracma)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/csgillespie/poweRlaw")
(synopsis "Tools for the analysis of heavy tailed distributions")
(description
@ -2029,14 +2125,14 @@ any subsequent lookup as it keeps the hash table in memory.")
(define-public r-ff
(package
(name "r-ff")
(version "2.2-14")
(version "2.2-14.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ff" version))
(sha256
(base32
"1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
"1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
(build-system r-build-system)
(propagated-inputs `(("r-bit" ,r-bit)))
(home-page "http://ff.r-forge.r-project.org/")
@ -2176,14 +2272,14 @@ plot networks.")
(define-public r-proxy
(package
(name "r-proxy")
(version "0.4-23")
(version "0.4-24")
(source
(origin
(method url-fetch)
(uri (cran-uri "proxy" version))
(sha256
(base32
"17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
"0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/proxy")
(synopsis "Distance and similarity measures")
@ -2293,14 +2389,14 @@ quantile mixture from L-moments and trimmed L-moments.")
(define-public r-distillery
(package
(name "r-distillery")
(version "1.0-6")
(version "1.0-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "distillery" version))
(sha256
(base32
"1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
"0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
(build-system r-build-system)
(home-page "https://ral.ucar.edu/staff/ericg/")
(synopsis "Functions for confidence intervals and object information")
@ -2400,6 +2496,27 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
;; Any version of the LGPL.
(license license:lgpl3+)))
(define-public r-inum
(package
(name "r-inum")
(version "1.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "inum" version))
(sha256
(base32
"16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)))
(home-page "https://cran.r-project.org/web/packages/inum/")
(synopsis "Interval and enum-type representation of vectors")
(description
"This package provides an enum-type representation of vectors and
representation of intervals, including a method of coercing variables
in data frames.")
(license license:gpl2)))
(define-public r-bdsmatrix
(package
(name "r-bdsmatrix")
@ -3105,14 +3222,14 @@ by base R methods related to model fitting.")
(define-public r-broom
(package
(name "r-broom")
(version "0.5.5")
(version "0.5.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
"0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
"0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@ -3124,6 +3241,8 @@ by base R methods related to model fitting.")
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/broom")
(synopsis "Convert statistical analysis objects into tidy data frames")
(description
@ -3926,14 +4045,14 @@ timeout. It can also poll several processes at once.")
(define-public r-tsp
(package
(name "r-tsp")
(version "1.1-9")
(version "1.1-10")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSP" version))
(sha256
(base32
"183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
"0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
(properties `((upstream-name . "TSP")))
(build-system r-build-system)
(propagated-inputs `(("r-foreach" ,r-foreach)))
@ -4195,14 +4314,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
(version "0.21")
(version "0.22")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
"088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
"0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@ -6456,14 +6575,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
(version "0.8.2")
(version "0.8.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
"0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
"0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@ -6965,14 +7084,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
(define-public r-rootsolve
(package
(name "r-rootsolve")
(version "1.8.2")
(version "1.8.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rootSolve" version))
(sha256
(base32
"0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
"0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
(properties `((upstream-name . "rootSolve")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@ -7313,14 +7432,14 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
(version "3.0-12")
(version "3.1-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
"0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
"010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@ -8324,14 +8443,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
(version "1.4.5")
(version "1.4.6")
(source
(origin
(method url-fetch)