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Author SHA1 Message Date
Paul Garlick f52de1e17f
gnu: Add perl-cgi-formbuilder. 
* gnu/packages/web.scm (perl-cgi-formbuilder): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-06-08 20:27:30 +08:00
Mark H Weaver 0b2fd1600f
gnu: linux-libre@4.9: Update to 4.9.107. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.107.
 2018-06-07 23:38:28 -04:00
Mark H Weaver b09dc3b911
gnu: linux-libre@4.4: Update to 4.4.136. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.136.
 2018-06-07 23:37:46 -04:00
Tobias Geerinckx-Rice 20860819d6
gnu: ruby-asciidoctor: Update description. 
Synchronise with upstream README.

* gnu/packages/ruby.scm (ruby-asciidoctor)[description]: Add PDF.
 2018-06-07 23:58:26 +02:00
Tobias Geerinckx-Rice 4ee41a6ac1
gnu: inxi: Fix up synopsis & description. 
* gnu/packages/admin.scm (inxi)[synopsis]: Fix typo.
[description]: Use @code{}.
 2018-06-07 23:58:26 +02:00
Tobias Geerinckx-Rice 7a83eb37ad
gnu: libngspice: Update to 28. 
* gnu/packages/engineering.scm (libngspice): Update to 28.
 2018-06-07 23:58:25 +02:00
Tobias Geerinckx-Rice ec425ca3a6
gnu: libngspice: Use C-locale date format. 
* gnu/packages/engineering.scm (libngspice): Use a more standard
(C-locale) date format when forging timestamps.
 2018-06-07 23:57:39 +02:00
Tobias Geerinckx-Rice 10ee03c1df
gnu: python-pyxdg: Return #t from phases. 
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Substitute
INVOKE for SYSTEM*.
 2018-06-07 23:57:39 +02:00
Tobias Geerinckx-Rice 5f82a9d5cc
gnu: seabios: Return #t from all phases. 
* gnu/packages/firmware.scm (seabios)[arguments]: Return #t from
the ‘install’ phase.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice edf075987c
gnu: gnuastro: Add TIFF support. 
This adds ~3.6 MiB (3.6%) to gnuastro's now-103.9 MiB closure.

* gnu/packages/astronomy.scm (gnuastro)[inputs]: Add libtiff and zlib.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice 33031faa4e
gnu: xmlsec: Update to 1.2.26. 
* gnu/packages/xml.scm (xmlsec): Update to 1.2.26.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice 6d727bf4c7
gnu: xcalib: Update to 0.10. 
* gnu/packages/xdisorg.scm (xcalib): Update to 0.10.
[home-page]: Switch to new upstream.
[source]: Use GIT-FETCH.  Add xcalib-update-man-page.patch.
[build-system]: Switch to CMAKE-BUILD-SYSTEM.
[arguments]: Remove the old build system's arguments.
[inputs]: Add libxrandr.
 2018-06-07 23:57:38 +02:00
Tobias Geerinckx-Rice d35135fa9e
gnu: perl-net-http: Update to 6.18. 
* gnu/packages/web.scm (perl-net-http): Update to 6.18.
 2018-06-07 23:57:37 +02:00
Tobias Geerinckx-Rice c727262d5f
gnu: perl-cgi: Update to 4.38. 
* gnu/packages/web.scm (perl-cgi): Update to 4.38.
 2018-06-07 23:57:37 +02:00
Danny Milosavljevic 5e88194661
gnu: qucs: Patch bootstrapping scripts. 
* gnu/packages/engineering.scm (qucs)[arguments]<#:phases>[patch-bootstrap]:
New phase.
 2018-06-07 23:23:40 +02:00
Theodoros Foradis 394b89ae04
gnu: qucs-s: Update to 0.0.20. 
* gnu/packages/engineering.scm (qucs-s): Update to 0.0.20.
[arguments]: Modify patch-paths phase to work with version 0.0.20.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis fc3c88ec9c
gnu: lapack-3.5: Delete package. 
* gnu/packages/maths.scm (lapack-3.5): Delete package.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis ac04601a82
gnu: xyce-serial: Update to 6.8. 
* gnu/packages/engineering.scm (xyce-serial): Update to 6.8.
[inputs]: Replace lapack-3.5 with lapack.
* gnu/packages/engineering.scm (xyce-prallel):
[arguments]: Update configure flags to work with 6.8 version.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis d73482b408
gnu: trilinos-serial-xyce: Update to 12.12.1. 
* gnu/packages/engineering.scm (trilinos-serial-xyce): Update to 12.12.1.
[arguments]: Add delete-tribits phase.
[inputs]: Replace lapack-3.5 with lapack.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis ecf8d2a935
gnu: libngspice: Update to 27. 
* gnu/packages/engineering.scm (libngspice): Update to 27.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:40 +02:00
Theodoros Foradis 4f12a62d18
gnu: qucs: Build from git to fix bug. 
* gnu/packages/engineering.scm (qucs): Add TODO comment.
[source]: Use git commit b4f27d9.
[native-inputs]: Add autoconf, automake, flex and bison.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-06-07 23:23:34 +02:00
Ricardo Wurmus bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
 2018-06-07 22:51:00 +02:00
Ricardo Wurmus e67acae706
gnu: Add r-ggseqlogo. 
* gnu/packages/cran.scm (r-ggseqlogo): New variable.
 2018-06-07 22:51:00 +02:00
Rutger Helling 8ec919404f
gnu: Add deprecated-package vulkan-icd-loader. 
* gnu/packages/vulkan.scm (vulkan-icd-loader): New variable.
 2018-06-07 13:34:13 +02:00
Efraim Flashner bb63502f0b
gnu: ovmf: Simplify build. 
* gnu/packages/firmware.scm (ovmf)[arguments]: Change custom 'build-ia32
phase to replace 'build. Remove unneeded substitutions in 'configure,
'build and 'build-x64. Shorten 'build and 'build-x64 phases.
 2018-06-07 12:20:47 +03:00
Ricardo Wurmus 6d095c4cab
gnu: star: Update to 2.6.0c. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 54179e2463
gnu: libreoffice: Update to 6.0.5.1. 
* gnu/packages/patches/libreoffice-icu.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.0.5.1.
[source]: Add patch.
[inputs]: Add libepubgen and libqxp.
[arguments]: Adjust "prepare-src" phase.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus e47e1f3311
gnu: orcus: Update to 0.13.4. 
* gnu/packages/libreoffice.scm (orcus): Update to 0.13.4.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus a3f2425e5d
gnu: ixion: Update to 0.13.0. 
* gnu/packages/libreoffice.scm (ixion): Update to 0.13.0.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 4e4dcd476e
gnu: Add libqxp. 
* gnu/packages/libreoffice.scm (libqxp): New variable.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus 38be0f4245
gnu: Add libepubgen. 
* gnu/packages/libreoffice.scm (libepubgen): New variable.
 2018-06-07 11:09:54 +02:00
Adam Zimmerman d6dd64af37
gnu: opensmtpd: Fix crash on table authentication. 
* gnu/packages/patches/opensmtpd-fix-crash.patch: New patch.
* gnu/packages/mail.scm (opensmtpd)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2018-06-07 03:57:42 +02:00
Tobias Geerinckx-Rice 6acc671bef
gnu: jbig2dec: Update source and home page URIs. 
The old downloads.ghostscript.com returns a bogus 200 response, while
the new home page lists a different source.

Reported by Gábor Boskovits <boskovits@gmail.com>.

* gnu/packages/image.scm (jbig2dec)[source, home-page]: Update URIs.
 2018-06-07 03:57:41 +02:00
Nicolas Goaziou 4a007e2db9
gnu: scribus: Fix build. 
* gnu/packages/scribus.scm (scribus)[arguments]: Re-introduce fix for
  "ImportError: No module named _sysconfigdata_nd".
 2018-06-07 00:30:13 +02:00
Ricardo Wurmus 116ca65b58
Merge branch 'master' into core-updates 2018-06-06 22:43:37 +02:00
Nicolas Goaziou 25133ca172
gnu: colobot: Update to 0.1.11.1-alpha. 
* gnu/packages/games.scm (colobot): Update to 0.1.11.1-alpha.
[native-inputs]: Update "colobot-data" and "colobot-music" to 0.1.11.1-alpha.
 2018-06-06 19:16:21 +02:00
Nicolas Goaziou 89a651964a
gnu: scribus: Add "libzmf" dependency 
* gnu/packages/scribus.scm (scribus)[inputs]: Add "libzmf".
 2018-06-06 18:34:45 +02:00
Nicolas Goaziou fec8d80cd1
gnu: scribus: Update to 1.5.4. 
* gnu/packages/scribus.scm (scribus): Update to 1.5.4.
[source]: Remove patches.
[arguments]: Remove `patch-source' phase.
 2018-06-06 18:33:38 +02:00
Rutger Helling e6fcf903ec
gnu: vulkan-loader: Update URL and change name. 
* gnu/packages/emulators.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/games.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/video.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/vulkan.scm (vulkan-loader): Rename from 'vulkan-icd-loader' to
'vulkan-loader'. Update URL and hash.
* gnu/packages/wine.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
 2018-06-06 16:48:47 +02:00
Rutger Helling 7ea56cdec0
gnu: you-get: Update to 0.4.1077. 
* gnu/packages/video.scm (you-get): Update to 0.4.1077.
 2018-06-06 14:39:24 +02:00
Rutger Helling c7a2f7b999
gnu: diffoscope: Update to 95. 
* gnu/packages/package-management.scm (diffoscope): Update to 95.
 2018-06-06 14:39:24 +02:00
Rutger Helling 89fc8aef8c
gnu: epiphany: Update to 3.28.2.1. 
* gnu/packages/gnome.scm (epiphany): Update to 3.28.2.1.
 2018-06-06 14:39:24 +02:00
Rutger Helling f9036105e6
gnu: gnome-disk-utility: Update to 3.28.3. 
* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.28.3.
 2018-06-06 14:39:23 +02:00
Rutger Helling 9cf329aecc
gnu: gnome-terminal: Update to 3.28.2. 
* gnu/packages/gnome.scm (gnome-terminal): Update to 3.28.2.
 2018-06-06 14:39:23 +02:00
Rutger Helling 6a29c8d344
gnu: gedit: Update to 3.28.1. 
* gnu/packages/gnome.scm (gedit): Update to 3.28.1.
 2018-06-06 14:39:23 +02:00
Ricardo Wurmus e32db0fa0f
gnu: vigra: Disable broken test. 
* gnu/packages/image.scm (vigra)[arguments]: Add phase "disable-broken-test";
enable parallel build.
 2018-06-06 13:15:21 +02:00
Rutger Helling c648781cec
gnu: lynx: Update to 2.8.9dev.19. 
* gnu/packages/web-browsers.scm (lynx): Update to 2.8.9dev.19.
 2018-06-06 12:46:40 +02:00
Efraim Flashner 73c0e477e5
gnu: esmtp: Replace 'bootstrap phase. 
* gnu/packages/mail.scm (esmtp)[arguments]: Use custom 'autoconf phase
to replace default 'bootstrap phase.
 2018-06-06 13:11:50 +03:00
Efraim Flashner a34dfa249c
gnu: can-utils: Remove 'bootstrap phase. 
* gnu/packages/networking.scm (can-utils)[arguments]: Remove unnecessary
'bootstrap phase.
 2018-06-06 13:11:47 +03:00
Tobias Geerinckx-Rice 37b561e4ed
gnu: gerbv: Update to 2.6.2. 
* gnu/packages/engineering.scm (gerbv): Update to 2.6.2.
[arguments]: Remove ‘autoconf’ phase...
[native-inputs]: ...and remove its dependencies.
 2018-06-06 06:12:23 +02:00
Tobias Geerinckx-Rice d193903e0c
gnu: linsmith: Update to 0.99.31. 
* gnu/packages/engineering.scm (linsmith): Update to 0.99.31.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 6e3d48c207
gnu: linsmith: Use HTTPS home page. 
* gnu/packages/engineering.scm (linsmith)[home-page]: Use HTTPS.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 3b295d3f4b
gnu: python-lmdb: Update to 0.94. 
* gnu/packages/databases.scm (python-lmdb): Update to 0.94.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice fcf29a7fbb
gnu: debootstrap: Update to 1.0.101. 
* gnu/packages/debian.scm (debootstrap): Update to 1.0.101.
 2018-06-06 06:12:22 +02:00
Tobias Geerinckx-Rice 1a16b925f2
gnu: tomb: Update to 2.5. 
* gnu/packages/crypto.scm (tomb): Update to 2.5.
[inputs, arguments]: Add util-linux for ‘findmnt’.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 115af78e32
gnu: cfitsio: Update to 3.450. 
* gnu/packages/astronomy.scm (cfitsio): Update to 3.450.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 9566bb82e5
gnu: gnuastro: Update to 0.6. 
* gnu/packages/astronomy.scm (gnuastro): Update to 0.6.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 60b0c25222
gnu: wcslib: Fix build. 
* gnu/packages/astronomy.scm (wcslib)[arguments]: Skip the default
‘install-license-files’ phase.  Don't build or test in parallel.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice 4f12e5cc7c
gnu: inxi: Update to 3.0.11-1. 
* gnu/packages/admin.scm (inxi): Update to 3.0.11-1.
 2018-06-06 06:12:21 +02:00
Tobias Geerinckx-Rice b740a30527
gnu: inxi: Use GIT-FETCH. 
* gnu/packages/admin.scm (inxi)[source]: Use GIT-FETCH.
[native-inputs]: Remove tar.
[arguments]: Adjust accordingly.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 55f5556e24
gnu: inxi: Fix man page location. 
* gnu/packages/admin.scm (inxi)[arguments]: Install man page to
/share/man instead of /share/doc/man.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice bba082a1f8
gnu: ruby-asciidoctor: Use HTTPS home page. 
* gnu/packages/ruby.scm (ruby-asciidoctor)[home-page]: Use HTTPS.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 9933a8e739
gnu: ruby-asciidoctor: Update to 1.5.7.1. 
* gnu/packages/ruby.scm (ruby-asciidoctor): Update to 1.5.7.1.
 2018-06-06 06:12:20 +02:00
Tobias Geerinckx-Rice 24a2622712
gnu: ruby-eventmachine: Use working home page. 
* gnu/packages/ruby.scm (ruby-eventmachine)[home-page]: Update URI.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice c207fa5e6c
gnu: ruby-eventmachine: Update to 1.2.7. 
* gnu/packages/ruby.scm (ruby-eventmachine): Update to 1.2.7.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice 58021db4d2
gnu: ruby-connection-pool: Update to 2.2.2. 
* gnu/packages/ruby.scm (ruby-connection-pool): Update to 2.2.2.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice 15dd85f0c3
gnu: linkchecker: Update to 9.4.0. 
* gnu/packages/web.scm (linkchecker): Update to 9.4.0.
[source]: Use GIT-FETCH.
[inputs]: Add python2-dnspython and python2-pyxdg.
[arguments]: Remove ‘remove-python-requests-version’ phase.
[license]: Remove licences of unbundled inputs.
 2018-06-06 06:12:19 +02:00
Tobias Geerinckx-Rice fe04975281
gnu: xf86-input-wacom: Update to 0.36.1. 
* gnu/packages/xdisorg.scm (xf86-input-wacom): Update to 0.36.1.
[source]: Update URI.
 2018-06-06 06:12:18 +02:00
Tobias Geerinckx-Rice 0ac68e7268
gnu: libwacom: Update to 0.30. 
* gnu/packages/xdisorg.scm (libwacom): Update to 0.30.
[source]: Update URI.
 2018-06-06 06:12:18 +02:00
Tobias Geerinckx-Rice 81dc1d1220
gnu: libwacom, xf86-input-wacom: Update home page. 
‘The Linux Wacom Project has moved.’
-- <http://linuxwacom.sourceforge.net/wiki>

* gnu/packages/xdisorg.scm (libwacom, xf86-input-wacom)[home-page]:
Update URI.
 2018-06-06 06:12:18 +02:00
Leo Famulari d83c9fcb7b
gnu: darktable: Update to 2.4.4. 
* gnu/packages/photo.scm (darktable): Update to 2.4.4.
 2018-06-06 00:05:54 -04:00
Leo Famulari f83eadd2ad
gnu: Update Syncthing to 0.14.48. 
*  gnu/packages/syncthing.scm (syncthing): Update to 0.14.48.
 2018-06-05 20:35:52 -04:00
Leo Famulari a624be49a2
gnu: go-github-com-chmduquesne-rollinghash-adler32: Update to 0.0.0-2.abb8cba. 
* gnu/packages/syncthing.scm (go-github-com-chmduquesne-rollinghash-adler32):
Update to 0.0.0-2.abb8cba.
 2018-06-05 20:35:49 -04:00
Ricardo Wurmus ca8de35e90
Merge branch 'master' into core-updates 2018-06-05 23:44:11 +02:00
Ricardo Wurmus 42639cc980
gnu: qtractor: Update to 0.9.1. 
* gnu/packages/music.scm (qtractor): Update to 0.9.1.
[arguments]: Add phase "fix-build-with-qt-5.11".
 2018-06-05 23:43:12 +02:00
Mark H Weaver db89d31876
gnu: linux-libre: Update to 4.17. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.
(%linux-libre-hash): Update hash.
* gnu/packages/aux-files/linux-libre/4.16-arm.conf,
gnu/packages/aux-files/linux-libre/4.16-arm64.conf,
gnu/packages/aux-files/linux-libre/4.16-i686.conf,
gnu/packages/aux-files/linux-libre/4.16-x86_64.conf: Delete files.
* gnu/packages/aux-files/linux-libre/4.17-arm.conf,
gnu/packages/aux-files/linux-libre/4.17-arm64.conf,
gnu/packages/aux-files/linux-libre/4.17-i686.conf,
gnu/packages/aux-files/linux-libre/4.17-x86_64.conf: New files.
* Makefile.am (AUX_FILES): Adjust accordingly.
 2018-06-05 17:21:03 -04:00
Mark H Weaver 704051b258
gnu: linux-libre@4.14: Update to 4.14.48. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.48.
(%linux-libre-4.14-hash): Update hash.
 2018-06-05 17:20:57 -04:00
Mark H Weaver 4418c59005
gnu: linux-libre@4.9: Update to 4.9.106. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.106.
 2018-06-05 17:20:53 -04:00
Ricardo Wurmus b4a145fa71
gnu: yoshimi: Update to 1.5.8. 
* gnu/packages/music.scm (yoshimi): Update to 1.5.8.
 2018-06-05 23:18:10 +02:00
Efraim Flashner 396aab8e69
gnu: freedoom: Fix compilation. 
* gnu/packages/games.scm (freedoom)[arguments]: Remove 'bootstrap phase.
 2018-06-05 22:53:48 +03:00
Efraim Flashner d88884fa3b
gnu: arc-theme: Replace bootstrap phase. 
* gnu/packages/gmome.scm (arc-theme)[arguments]: Replace 'boostrap phase
with a custom phase.
 2018-06-05 22:53:45 +03:00
Efraim Flashner f1c6de3735
gnu: tilda: Replace bootstrap phase. 
* gnu/packages/terminals.scm (tilda)[arguments]: Remove custom
'bootstrap phase and use it to replace default bootstrap phase.
 2018-06-05 22:10:49 +03:00
Ricardo Wurmus 909301591d
gnu: Add sjcount. 
* gnu/packages/bioinformatics.scm (sjcount): New variable.
 2018-06-05 15:42:44 +02:00
宋文武 97f6e9133a
services: Add dnsmasq-service-type. 
* gnu/services/dns.scm (dnsmasq-service-type): New variable.
(<dnsmasq-configuration>): New record type.
(dnsmasq-shepherd-service): New procedure.
* doc/guix.texi (DNS Services): Document it.
 2018-06-05 20:05:31 +08:00
Ricardo Wurmus a64e30ed9e
gnu: Remove duplicate definition of r-heatmaply. 
* gnu/packages/cran.scm (r-heatmaply): Remove duplicate.
 2018-06-05 13:59:54 +02:00
Ricardo Wurmus d0f3427433
gnu: Remove duplicate definition of r-heatmaply. 
* gnu/packages/cran.scm (r-heatmaply): Remove duplicate.
 2018-06-05 13:59:15 +02:00
Ricardo Wurmus 1ee581973a
gnu: r-heatmaply: Add r-knitr. 
* gnu/packages/cran.scm (r-heatmaply)[propagated-inputs]: Add r-knitr.
 2018-06-05 13:51:27 +02:00
Ricardo Wurmus 6da3aa3763
gnu: r-heatmaply: Add r-knitr. 
* gnu/packages/cran.scm (r-heatmaply)[propagated-inputs]: Add r-knitr.
 2018-06-05 13:50:29 +02:00
Ricardo Wurmus e53152c72d
gnu: dropseq-tools: Remove failing phase. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 13:12:13 +02:00
Ricardo Wurmus 0c68f7fd9b
gnu: java-bouncycastle: Disable tests. 
* gnu/packages/java.scm (java-bouncycastle)[arguments]: Disable tests.
 2018-06-05 12:49:41 +02:00
Ricardo Wurmus 9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
 2018-06-05 11:26:34 +02:00
Ricardo Wurmus 1f94ba9408
gnu: java-picard: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 11:26:08 +02:00
Ricardo Wurmus 1ed386fc26
gnu: java-cisd-jhdf5: Delete failing build phase. 
* gnu/packages/java.scm (java-cisd-jhdf5)[arguments]: Delete build phase
"generate-jar-indices".
 2018-06-05 11:17:03 +02:00
Ricardo Wurmus a993ad833e
gnu: java-picard-1.113: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
 2018-06-05 11:15:21 +02:00
Ricardo Wurmus e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
 2018-06-05 11:14:38 +02:00
Ricardo Wurmus d7e6fb6d7e
Merge branch 'master' into core-updates 2018-06-05 11:09:39 +02:00
Ricardo Wurmus 71c495c941
gnu: r-rtracklayer: Update to 1.40.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus fb8c17baef
gnu: r-ranger: Update to 0.10.1. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.10.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus c9a879ed54
gnu: r-np: Update to 0.60-8. 
* gnu/packages/cran.scm (r-np): Update to 0.60-8.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 83d5c2e106
gnu: t-series: Update to 0.10-45. 
* gnu/packages/cran.scm (t-series): Update to 0.10-45.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus c152c6b361
gnu: r-ksamples: Update to 1.2-8. 
* gnu/packages/cran.scm (r-ksamples): Update to 1.2-8.
 2018-06-05 10:40:42 +02:00
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