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Author SHA1 Message Date
Ricardo Wurmus d19e0690b9
gnu: r-methylkit: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 0da6afa286
gnu: r-bamsignals: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 66ece08d05
Merge branch 'master' into core-updates 2018-06-05 09:59:27 +02:00
Tobias Geerinckx-Rice 4bf0a1f8d1
gnu: p11-kit: Update to 0.23.12. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.12.
 2018-06-05 03:19:48 +02:00
Mark H Weaver 8b71684a20
gnu: elfutils: Disable test suite on MIPS. 
* gnu/packages/elf.scm (elfutils)[arguments]: Add (#:tests? #f) on MIPS.
 2018-06-04 21:19:35 -04:00
Tobias Geerinckx-Rice 46fce96881
gnu: beets: Return #t from phases. 
* gnu/packages/music.scm (beets)[arguments]: Substitute INVOKE for
SYSTEM* and return #t from all phases.
 2018-06-05 03:19:26 +02:00
Tobias Geerinckx-Rice 123f86d898
gnu: nano: Update to 2.9.8. 
* gnu/packages/nano.scm (nano): Update to 2.9.8.
 2018-06-05 03:18:46 +02:00
Tobias Geerinckx-Rice 0d35a95417
gnu: python-pycurl: Update to 7.43.0.2. 
* gnu/packages/python-web.scm (python-pycurl): Update to 7.43.0.2.
 2018-06-05 03:18:46 +02:00
Tobias Geerinckx-Rice 4682d48363
gnu: fvwm: Update to 2.6.8. 
* gnu/packages/fvwm.scm (fvwm): Update to 2.6.8.
 2018-06-05 03:01:17 +02:00
Tobias Geerinckx-Rice f7b53e6855
gnu: perl-parse-yapp: Update to 1.21. 
* gnu/packages/perl.scm (perl-parse-yapp): Update to 1.21.
 2018-06-05 03:01:17 +02:00
Tobias Geerinckx-Rice b5dfccd7b6
gnu: perl-text-balanced: Update to 2.03. 
* gnu/packages/perl.scm (perl-text-balanced): Update to 2.03.
[source]: Update URI.
 2018-06-05 03:01:16 +02:00
Tobias Geerinckx-Rice 971b8381ff
gnu: perl-posix-strftime-compiler: Update to 0.42. 
* gnu/packages/perl.scm (perl-posix-strftime-compiler): Update to
0.42.
 2018-06-05 03:01:07 +02:00
Tobias Geerinckx-Rice 27f89be5c9
gnu: perl-moosex-methodattributes: Update to 0.31. 
* gnu/packages/perl.scm (perl-moosex-methodattributes): Update to
0.31.
 2018-06-05 03:00:58 +02:00
Tobias Geerinckx-Rice 91cb6eaf52
gnu: perl-module-install: Update to 1.19. 
* gnu/packages/perl.scm (perl-module-install): Update to 1.19.
[source]: Update URI.
 2018-06-05 01:31:32 +02:00
Tobias Geerinckx-Rice ed2e354b79
gnu: perl-memoize-expirelru: Update to 0.56. 
* gnu/packages/perl.scm (perl-memoize-expirelru): Update to 0.56.
[source]: Update URI.
 2018-06-05 01:31:32 +02:00
Tobias Geerinckx-Rice 01c6607af9
gnu: ccid, pcsc-lite: Move away from alioth.debian.org. 
* gnu/packages/security-token.scm (ccid, pcsc-lite)[source, home-page]:
Update upstream URI.
 2018-06-04 18:27:59 +02:00
Rutger Helling 19b662ea7c
gnu: ranger: Enable image support. 
* gnu/packages/disk.scm (ranger)[inputs]: Add 'w3m'.
[arguments]: Add wrapper for W3MIMGDISPLAY_PATH environment variable.
 2018-06-04 16:35:03 +02:00
Tobias Geerinckx-Rice fd17434249
gnu: lz4: Use HTTPS home page. 
* gnu/packages/compression.scm (lz4)[home-page]: Use HTTPS.
 2018-06-04 15:35:48 +02:00
Tobias Geerinckx-Rice b6315bc0d2
gnu: thermald: Update to 1.7.2. 
* gnu/packages/admin.scm (thermald): Update to 1.7.2.
[arguments]: Remove Upstart kluge as promised.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice 49d85a19fb
gnu: pdfgrep: Update to 2.1.1. 
* gnu/packages/pdf.scm (pdfgrep): Update to 2.1.1.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice e1345dec67
gnu: lxqt-build-tools: Update to 0.5.0. 
* gnu/packages/lxqt.scm (lxqt-build-tools): Update to 0.5.0.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice 12eadf5649
gnu: perl-libintl-perl: Update to 1.29. 
* gnu/packages/perl.scm (perl-libintl-perl): Update to 1.29.
 2018-06-04 15:35:47 +02:00
Tobias Geerinckx-Rice a0b9612fc9
gnu: perl-hash-multivalue: Update to 0.16. 
* gnu/packages/perl.scm (perl-hash-multivalue): Update to 0.16.
[source]: Update URI.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice 92299d669a
gnu: perl-file-pushd: Update to 1.016. 
* gnu/packages/perl.scm (perl-file-pushd): Update to 1.016.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice cf25329661
gnu: perl-exception-class: Update to 1.44. 
* gnu/packages/perl.scm (perl-exception-class): Update to 1.44.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice 4f6c01e78a
gnu: perl-datetime-timezone: Update to 2.19. 
* gnu/packages/perl.scm (perl-datetime-timezone): Update to 2.19.
 2018-06-04 15:35:46 +02:00
Tobias Geerinckx-Rice a1b16662bc
gnu: perl-test-without-module: Update to 0.20. 
* gnu/packages/perl-check.scm (perl-test-without-module): Update to 0.20.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice e40ab7382e
gnu: perl-datetime: Update to 1.49. 
* gnu/packages/perl.scm (perl-datetime): Update to 1.49.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice 854cf20647
gnu: perl-context-preserve: Update to 0.03. 
* gnu/packages/perl.scm (perl-context-preserve): Update to 0.03.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice 30c070d1ae
gnu: perl-class-load-xs: Update to 0.10. 
* gnu/packages/perl.scm (perl-class-load-xs): Update to 0.10.
[native-inputs]: Replace perl-test-requires with perl-test-needs.
Add perl-test-without-module.
 2018-06-04 15:35:45 +02:00
Tobias Geerinckx-Rice d2fe431870
gnu: perl-class-load: Update to 0.24. 
* gnu/packages/perl.scm (perl-class-load): Update to 0.24.
[native-inputs]: Replace perl-test-requires with perl-test-needs.
Add perl-test-without-module.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice d017dfaaf3
gnu: sent: Say ‘plain text’. 
‘Plaintext’ is a crypto term.  ‘Slideshow’ is apparently acceptable.

* gnu/packages/suckless.scm (sent)[synopsis, description]: Add spaces.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice 4ae9274ae9
gnu: snd: Version documentation directory. 
* gnu/packages/audio.scm (snd)[arguments]: Install documentation to the
conventional location.  Remove redundant MKDIR-P.  Align cosmetically.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice 84979374c2
gnu: acpica: Update to 20180531. 
* gnu/packages/admin.scm (acpica): Update to 20180531.
 2018-06-04 15:35:44 +02:00
Tobias Geerinckx-Rice a052d5ab0d
gnu: isync: Add SASL support. 
This adds ~5.5 MiB (7.5%) to isync's now-78.6 MiB closure.

* gnu/packages/mail.scm (isync)[inputs]: Add CYRUS-SASL.
 2018-06-04 15:35:43 +02:00
Ludovic Courtès 7394e264fc
gnu: perf: Work around GCC bug. 
Works around <https://bugs.gnu.org/31708>.

* gnu/packages/patches/perf-gcc-ice.patch: New patch.
* gnu/packages/linux.scm (perf)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-06-04 14:03:54 +02:00
Ludovic Courtès 831f07a009
gnu: signing-party: Update to commit d6f2296. 
* gnu/packages/gnupg.scm (signing-party): Update to commit d6f2296.
[home-page]: Change to salsa.debian.org.
[source]: Use git-fetch.
[arguments]: Remove 'change-directory' phase.  In 'configure' phase,
modify 'gpgwrap/Makefile' instead of 'gpgwrap/src/Makefile'.
 2018-06-04 14:03:54 +02:00
Ricardo Wurmus 32da38d572
Merge branch 'master' into core-updates 2018-06-04 11:25:48 +02:00
Efraim Flashner c0e7a52996
gnu: python-pyqt: Update to 5.10.1. 
* gnu/packages/qt.scm (python-pyqt): Update to 5.10.1.
[inputs]: Remove qtwebkit.
[arguments]: Add custom phase to fix compilation with Qt 5.11.
 2018-06-04 11:06:00 +03:00
Efraim Flashner 9cdd868450
gnu: python-sip: Update to 4.19.8. 
* gnu/packages/qt.scm (python-sip): Update to 4.19.8.
 2018-06-04 11:05:57 +03:00
Efraim Flashner d53e5b366d
gnu: gcompris-qt: Update to 0.91. 
* gnu/packages/education.scm (gcompris-qt): Update to 0.91.
[arguments]: Add custom phase to fix building with Qt 5.11.
 2018-06-03 19:11:27 +03:00
Efraim Flashner 68ddfb2e8d
gnu: quassel: Fix building with Qt 5.11. 
* gnu/packages/irc.scm (quassel)[sources]: Add patch. Return #t from
snippet.
* gnu/packages/patches/quassel-qt-5.11.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2018-06-03 15:49:50 +03:00
Rutger Helling 4edc431b0f
gnu: w3m: Enable image support. 
* gnu/packages/w3m.scm (w3m)[inputs]: Add gdk-pixbuf, libx11.
 2018-06-03 13:01:41 +02:00
Efraim Flashner 6f5c67d725
gnu: keepassxc: Fix compilation with Qt 5.11. 
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add custom
'patch-sources phase to include missing headers.
 2018-06-03 12:46:11 +03:00
Mark H Weaver 0c0431f9ce
Merge branch 'master' into core-updates 2018-06-03 03:36:47 -04:00
Mark H Weaver 2c790226d2
gnu: rust: Fix build for armhf and mips64el. 
This is a followup to commit 514026d7de.

* gnu/packages/rust.scm (nix-system->gnu-triplet-for-rust): New variable.
(rust-bootstrap, mrustc, rust-1.23): Use 'nix-system->gnu-triplet-for-rust'
instead of 'nix-system->gnu-triplet'.
 2018-06-03 03:36:13 -04:00
Efraim Flashner 0ec430f795
gnu: xxd: Remove all inherited inputs. 
* gnu/packages/vim.scm (xxd)[inputs]: New field, don't inherit from vim.
 2018-06-02 23:34:56 +03:00
Efraim Flashner aa75dadab8
gnu: vim: Update to 8.1.0026. 
* gnu/packages/vim.scm (vim): Update to 8.1.0026.
[arguments]: Update substitute list on custom 'patch-config-files phase.
[inputs]: Remove inetutils.
 2018-06-02 23:34:37 +03:00
Efraim Flashner 2d4fdb707e
gnu: xxd: Return true from all phases. 
* gnu/packages/vim.scm (xxd)[arguments]: Return '#t' from custom 'chdir
phase.
 2018-06-02 22:34:23 +03:00
Pierre Neidhardt 15dcd292df
gnu: Add emacs-fish-completion. 
* gnu/packages/emacs.scm (emacs-fish-completion): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:52 +02:00
Pierre Neidhardt e374010923
gnu: Add emacs-evil-org. 
* gnu/packages/emacs.scm (emacs-evil-org): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt ac85107c9f
gnu: Add emacs-evil-multiedit. 
* gnu/packages/emacs.scm (emacs-evil-multiedit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt e1e09bcb43
gnu: Add emacs-evil-mu4e. 
* gnu/packages/emacs.scm (emacs-evil-mu4e): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt c6c1f0bf41
gnu: Add emacs-evil-magit. 
* gnu/packages/emacs.scm (emacs-evil-magit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Pierre Neidhardt 22deb03439
gnu: Add emacs-evil-ediff. 
* gnu/packages/emacs.scm (emacs-evil-ediff): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-02 16:02:51 +02:00
Ludovic Courtès f52ef55e2b
gnu: guile-json: Update to 1.0.1. 
* gnu/packages/guile.scm (guile-json): Update to 1.0.1.
[source]: Switch to github.com.  Adjust 'snippet' to modify
'configure.ac' and 'Makefile.am'.
[native-inputs]: Add AUTOCONF and AUTOMAKE.
 2018-06-02 15:29:38 +02:00
Ricardo Wurmus e0f8970357
Merge branch 'master' into core-updates 2018-06-02 13:44:43 +02:00
Ricardo Wurmus 92963798a6
gnu: r-scater: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
 2018-06-02 13:42:05 +02:00
Ricardo Wurmus 83402242ea
gnu: r-mvtnorm: Update to 1.0-8. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-8.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 7799a01ef1
gnu: r-rgraphviz: Update to 2.24.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.24.0.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus d7e3299987
gnu: r-scran: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fd613234b7
gnu: r-beachmat: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e9c417361e
gnu: r-rhdf5lib: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bbcd19fb4d
gnu: r-ensembldb: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 19adb89854
gnu: r-dirichletmultinomial: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d3fb2ad834
gnu: r-complexheatmap: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d1463f1b0c
gnu: r-genomicfiles: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 1ba126e0e4
gnu: r-gage: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 419e438d52
gnu: r-keggrest: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 15cc1a6867
gnu: r-fastseg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 646439c7e3
gnu: r-annotationhub: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 6fd71f1b6a
gnu: r-biobase: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e51afc63b7
gnu: r-genomicranges: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus c2401d06c5
gnu: r-xvector: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 0a465e5694
gnu: r-limma: Update to 3.36.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d358a5a0c1
gnu: r-variantannotation: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 4639025284
gnu: r-edger: Update to 3.22.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 953c8b18f8
gnu: r-genomeinfodb: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 8b44c28f5d
gnu: r-iranges: Update to 2.14.10. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 33cd15fa84
gnu: r-s4vectors: Update to 0.18.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 607acf3194
gnu: r-dnacopy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 3679a2fec4
gnu: r-bioccheck: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus dc6c168ac1
gnu: r-biocstyle: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5f52b692a
gnu: r-biocviews: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 97af51ef40
gnu: r-biocinstaller: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5907a44e1
gnu: r-biocgenerics: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9370b8ee9f
gnu: r-grohmm: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 712fe39680
gnu: r-systempiper: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus eabe78faca
gnu: r-shortread: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9da8e275ca
gnu: r-gostats: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus d8410d6610
gnu: r-category: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00