jackhill/guix/guix.git
6 years agognu: sudo: Use ‘modify-phases’ syntax.
Tobias Geerinckx-Rice [Mon, 7 Aug 2017 14:26:31 +0000 (16:26 +0200)]
gnu: sudo: Use ‘modify-phases’ syntax.

* gnu/packages/admin.scm (sudo)[arguments]: Use ‘modify-phases’.

6 years agognu: linux-libre: Update to 4.12.5.
Mark H Weaver [Tue, 8 Aug 2017 01:33:03 +0000 (21:33 -0400)]
gnu: linux-libre: Update to 4.12.5.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.5.
(%linux-libre-hash): Update hash.

6 years agognu: linux-libre@4.9: Update to 4.9.41.
Mark H Weaver [Tue, 8 Aug 2017 01:32:13 +0000 (21:32 -0400)]
gnu: linux-libre@4.9: Update to 4.9.41.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.41.

6 years agognu: linux-libre@4.4: Update to 4.4.80.
Mark H Weaver [Tue, 8 Aug 2017 01:31:36 +0000 (21:31 -0400)]
gnu: linux-libre@4.4: Update to 4.4.80.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.80.

6 years agognu: linux-libre@4.1: Update to 4.1.43.
Mark H Weaver [Tue, 8 Aug 2017 01:30:47 +0000 (21:30 -0400)]
gnu: linux-libre@4.1: Update to 4.1.43.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.43.

6 years agognu: ruby-puma: Update to 3.9.1.
Ben Woodcroft [Mon, 7 Aug 2017 08:39:44 +0000 (18:39 +1000)]
gnu: ruby-puma: Update to 3.9.1.

* gnu/packages/ruby.scm (ruby-puma): Update to 3.9.1.
[source]: Remove patch.
[arguments]: Disable tests.
[native-inputs]: Remove field.
* gnu/packages/patches/ruby-puma-ignore-broken-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

6 years agognu: ruby-nokogiri-diff: Update to 0.2.0-1.a38491e4.
Ben Woodcroft [Sun, 6 Aug 2017 06:52:40 +0000 (16:52 +1000)]
gnu: ruby-nokogiri-diff: Update to 0.2.0-1.a38491e4.

* gnu/packages/ruby.scm (ruby-nokogiri-diff): Update to 0.2.0-1.a38491e4.

6 years agognu: ruby-tdiff: Update to 0.3.3-1.b662a604.
Ben Woodcroft [Sun, 6 Aug 2017 06:41:05 +0000 (16:41 +1000)]
gnu: ruby-tdiff: Update to 0.3.3-1.b662a604.

* gnu/packages/ruby.scm: Update to 0.3.3-1.b662a604

6 years agoruby: Replace with ruby-2.4.1.
Ben Woodcroft [Mon, 7 Aug 2017 23:19:22 +0000 (09:19 +1000)]
ruby: Replace with ruby-2.4.1.

* gnu/packages/ruby.scm (ruby-2.4.1): New variable.
(ruby)[replacement]: New field.

6 years agodaemon: Ensure the child stack is aligned on a 16-byte boundary.
Mark H Weaver [Mon, 7 Aug 2017 20:41:03 +0000 (16:41 -0400)]
daemon: Ensure the child stack is aligned on a 16-byte boundary.

* nix/libstore/build.cc (DerivationGoal::startBuilder): When calling 'clone',
ensure that the stack is aligned on a 16-byte boundary.

6 years agoRevert "doc: Suggest running guix-daemon with 'sudo -E'."
Leo Famulari [Mon, 7 Aug 2017 18:09:04 +0000 (14:09 -0400)]
Revert "doc: Suggest running guix-daemon with 'sudo -E'."

This change might not correct, so we revert it for now:

https://lists.gnu.org/archive/html/guix-devel/2017-08/msg00057.html

This reverts commit 6a4364335c967f841b53ed35c22f90445437e4b0.

6 years agognu: propeller-gcc-4: Don't build on aarch64-linux.
Efraim Flashner [Mon, 7 Aug 2017 14:02:04 +0000 (17:02 +0300)]
gnu: propeller-gcc-4: Don't build on aarch64-linux.

* gnu/packages/embedded.scm (propeller-gcc-4)[supported-system]: New field.

6 years agognu: nim: Update to 0.17.0.
Efraim Flashner [Mon, 7 Aug 2017 10:36:11 +0000 (13:36 +0300)]
gnu: nim: Update to 0.17.0.

* gnu/packages/nim.scm (nim): Update to 0.17.0.
[source, home-page]: Use https.
[arguments]: Patch more shebangs, use custom build phase.

6 years agognu: cubicle: Fix evaluation.
Marius Bakke [Sun, 6 Aug 2017 23:52:31 +0000 (01:52 +0200)]
gnu: cubicle: Fix evaluation.

* gnu/packages/maths.scm (cubicle)[native-inputs]: Retrieve WHICH from
(gnu packages base).

6 years agognu: vapoursynth: Don't build on aarch64-linux.
Efraim Flashner [Mon, 7 Aug 2017 04:24:17 +0000 (07:24 +0300)]
gnu: vapoursynth: Don't build on aarch64-linux.

* gnu/packages/video.scm (vapoursynth)[supported-systems]: Remove
aarch64-linux from the supported-systems.

6 years agognu: youtube-dl: Update to 2017.08.06.
Tobias Geerinckx-Rice [Mon, 7 Aug 2017 03:27:39 +0000 (05:27 +0200)]
gnu: youtube-dl: Update to 2017.08.06.

* gnu/packages/video.scm (youtube-dl): Update to 2017.08.06.

6 years agognu: ntfs-3g: Update to 2017.3.23.
Tobias Geerinckx-Rice [Sun, 6 Aug 2017 22:21:11 +0000 (00:21 +0200)]
gnu: ntfs-3g: Update to 2017.3.23.

* gnu/packages/linux.scm (ntfs-3g): Update to 2017.3.23.
[source]: Remove patch.
* gnu/packages/patches/ntfs-3g-CVE-2017-0358.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

6 years agognu: ntfs-3g: Use HTTPS for the home page as well.
Tobias Geerinckx-Rice [Sun, 6 Aug 2017 22:01:43 +0000 (00:01 +0200)]
gnu: ntfs-3g: Use HTTPS for the home page as well.

* gnu/packages/linux.scm (ntfs-3g)[home-page]: Use HTTPS.

6 years agognu: wimlib: Update to 1.12.0.
Tobias Geerinckx-Rice [Sun, 6 Aug 2017 22:34:01 +0000 (00:34 +0200)]
gnu: wimlib: Update to 1.12.0.

* gnu/packages/backup.scm (wimlib): Update to 1.12.0.

6 years agognu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.
Tobias Geerinckx-Rice [Sun, 6 Aug 2017 23:39:21 +0000 (01:39 +0200)]
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place.  It changed back.

This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c.

6 years agognu: khal: Don't propagate vdirsyncer.
Leo Famulari [Sun, 6 Aug 2017 20:57:07 +0000 (16:57 -0400)]
gnu: khal: Don't propagate vdirsyncer.

* gnu/packages/calendar.scm (khal)[propagated-inputs]: Move vdirsyncer ...
[native-inputs]: ... here.

6 years agognu: python-icalendar: Update to 3.11.6.
Leo Famulari [Sun, 6 Aug 2017 20:46:45 +0000 (16:46 -0400)]
gnu: python-icalendar: Update to 3.11.6.

* gnu/packages/python.scm (python-icalendar): Update to 3.11.6.

6 years agognu: mpg123: Update to 1.25.4.
Leo Famulari [Sun, 6 Aug 2017 20:45:19 +0000 (16:45 -0400)]
gnu: mpg123: Update to 1.25.4.

* gnu/packages/mp3.scm (mpg123): Update to 1.25.4.

6 years agognu: freedoom: Update to 0.11.3.
Kei Kebreau [Sun, 6 Aug 2017 18:08:02 +0000 (14:08 -0400)]
gnu: freedoom: Update to 0.11.3.

* gnu/packages/games.scm (freedoom): Update to 0.11.3.
[arguments]: Remove unnecessary "no" phase.

6 years agognu: deutex: Update to 5.0.0.
Kei Kebreau [Sun, 6 Aug 2017 17:44:12 +0000 (13:44 -0400)]
gnu: deutex: Update to 5.0.0.

* gnu/packages/game-development.scm (deutex): Update to 5.0.0.
[source]: Change upstream URI.
[arguments]: Enable tests and restore normal "configure" and "install"
phases.
[native-inputs]: Add asciidoc.

6 years agognu: Add motti.
Efraim Flashner [Mon, 31 Jul 2017 12:26:06 +0000 (15:26 +0300)]
gnu: Add motti.

* gnu/packages/motti.scm (motti): New variable.

6 years agognu: keepassx: Superseded by keepassxc.
Efraim Flashner [Tue, 1 Aug 2017 15:04:43 +0000 (18:04 +0300)]
gnu: keepassx: Superseded by keepassxc.

* gnu/packages/password-utils.scm (keepassx)[properties]: New field.

6 years agognu: Add keepassxc.
Efraim Flashner [Tue, 1 Aug 2017 15:02:40 +0000 (18:02 +0300)]
gnu: Add keepassxc.

* gnu/packages/password-utils.scm (keepassxc): New variable.

6 years agognu: python-efl: Update to 1.20.0.
Efraim Flashner [Sun, 6 Aug 2017 11:36:33 +0000 (14:36 +0300)]
gnu: python-efl: Update to 1.20.0.

* gnu/packages/enlightenment.scm (python-efl): Update to 1.20.0.
[source]: Add alternate source uri.
[arguments]: Enable tests.

6 years agognu: efl: Update to 1.20.1.
Efraim Flashner [Sun, 6 Aug 2017 11:35:48 +0000 (14:35 +0300)]
gnu: efl: Update to 1.20.1.

* gnu/packages/enlightenment.scm (efl): Update to 1.20.1.

6 years agognu: make-u-boot-package: Don't unnecessarily cross-compile.
Efraim Flashner [Sat, 5 Aug 2017 21:13:06 +0000 (00:13 +0300)]
gnu: make-u-boot-package: Don't unnecessarily cross-compile.

* gnu/packages/bootloaders.scm (make-u-boot-package)[native-inputs]: Only
use cross-gcc and cross-binutils if compiling for a different
architecture.
[arguments]: Only use cross compiling make-flags if cross compiling.

6 years agognu: Add python-flask-httpauth.
Danny Milosavljevic [Sun, 6 Aug 2017 11:33:51 +0000 (13:33 +0200)]
gnu: Add python-flask-httpauth.

* gnu/packages/python.scm (python-flask-httpauth, python2-flask-httpauth):
New variables.

6 years agognu: Add font-open-dyslexic.
ng0 [Tue, 1 Aug 2017 10:27:46 +0000 (10:27 +0000)]
gnu: Add font-open-dyslexic.

* gnu/packages/fonts.scm (font-open-dyslexic): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
6 years agognu: gnucash: Update to 2.6.17.
Vasile Dumitrascu [Fri, 4 Aug 2017 10:37:49 +0000 (12:37 +0200)]
gnu: gnucash: Update to 2.6.17.

* gnu/packages/gnucash.scm (gnucash): Update to 2.6.17.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
6 years agognu: libtasn1: Fix CVE-2017-10790.
Leo Famulari [Tue, 25 Jul 2017 19:04:57 +0000 (15:04 -0400)]
gnu: libtasn1: Fix CVE-2017-10790.

* gnu/packages/patches/libtasn1-CVE-2017-10790.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/tls.scm (libtasn1/fixed)[source]: Use it.

6 years agodoc: Suggest running guix-daemon with 'sudo -E'.
Ludovic Courtès [Sat, 5 Aug 2017 21:08:44 +0000 (23:08 +0200)]
doc: Suggest running guix-daemon with 'sudo -E'.

Suggested by Martin H. <maze@strahlungsfrei.de>.

* doc/contributing.texi (Running Guix Before It Is Installed): Suggest
'sudo -E'.

6 years agodaemon: On aarch64, use increments of 16 on the stack.
Efraim Flashner [Sat, 5 Aug 2017 19:36:10 +0000 (22:36 +0300)]
daemon: On aarch64, use increments of 16 on the stack.

* nix/libstore/build.cc (DerivationGoal::startBuilder): When on aarch64,
when calling clone(), increment the stack by 16.

6 years agobuild: Allow mounting of entire disks.
Danny Milosavljevic [Thu, 20 Jul 2017 23:06:46 +0000 (01:06 +0200)]
build: Allow mounting of entire disks.

* gnu/build/file-systems.scm (disk-partitions): Also return entire drives.

6 years agognu: emacs-exwm-x: Do not set DISPLAY.
Feng Shu [Fri, 4 Aug 2017 12:52:16 +0000 (20:52 +0800)]
gnu: emacs-exwm-x: Do not set DISPLAY.

* gnu/packages/emacs.scm (emacs-exwm-x): Do not set DISPLAY. The issue has
been fixed upstream in exwm-0.15.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
6 years agognu: emacs-exwm: Update to 0.15.
Feng Shu [Thu, 3 Aug 2017 13:03:41 +0000 (21:03 +0800)]
gnu: emacs-exwm: Update to 0.15.

* gnu/packages/emacs.scm (emacs-exwm): Update to 0.15.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
6 years agognu: git: Update to 2.14.0.
Marius Bakke [Sat, 5 Aug 2017 12:07:12 +0000 (14:07 +0200)]
gnu: git: Update to 2.14.0.

* gnu/packages/version-control.scm (git): Update to 2.14.0.

6 years agognu: lftp: Update to 4.7.8.
Marius Bakke [Sat, 5 Aug 2017 11:44:03 +0000 (13:44 +0200)]
gnu: lftp: Update to 4.7.8.

* gnu/packages/ftp.scm (lftp): Update to 4.7.8.

6 years agognu: Add cubicle.
Julien Lepiller [Sun, 30 Jul 2017 08:23:08 +0000 (10:23 +0200)]
gnu: Add cubicle.

* gnu/packages/maths.scm (cubicle): New variable.

6 years agoRevert "daemon: Ensure proper alignment on the stack."
Mark H Weaver [Sat, 5 Aug 2017 05:57:25 +0000 (01:57 -0400)]
Revert "daemon: Ensure proper alignment on the stack."

This reverts commit ab4ccc8fcfaf2215d4b33b1376147e4c2c70426a.

6 years agognu: php: Update to 7.1.8.
Julien Lepiller [Thu, 3 Aug 2017 18:14:56 +0000 (20:14 +0200)]
gnu: php: Update to 7.1.8.

* gnu/packages/patches/gd-CVE-2017-7890.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it
* gnu/packages/php.scm (php): Update to 7.1.8.

6 years agognu: Add r-crosstalk.
Ricardo Wurmus [Fri, 4 Aug 2017 09:22:19 +0000 (11:22 +0200)]
gnu: Add r-crosstalk.

* gnu/packages/web.scm (r-crosstalk): New variable.

6 years agognu: Add r-shiny.
Ricardo Wurmus [Thu, 3 Aug 2017 14:04:24 +0000 (16:04 +0200)]
gnu: Add r-shiny.

* gnu/packages/web.scm (r-shiny): New variable.

6 years agognu: Add js-es5-shim.
Ricardo Wurmus [Thu, 3 Aug 2017 13:55:39 +0000 (15:55 +0200)]
gnu: Add js-es5-shim.

* gnu/packages/javascript.scm (js-es5-shim): New variable.

6 years agognu: Add js-selectize.
Ricardo Wurmus [Thu, 3 Aug 2017 13:55:22 +0000 (15:55 +0200)]
gnu: Add js-selectize.

* gnu/packages/javascript.scm (js-selectize): New variable.

6 years agognu: Add js-datatables.
Ricardo Wurmus [Thu, 3 Aug 2017 13:55:05 +0000 (15:55 +0200)]
gnu: Add js-datatables.

* gnu/packages/javascript.scm (js-datatables): New variable.

6 years agognu: Add js-highlight.
Ricardo Wurmus [Thu, 3 Aug 2017 13:54:51 +0000 (15:54 +0200)]
gnu: Add js-highlight.

* gnu/packages/javascript.scm (js-highlight): New variable.

6 years agognu: Add js-strftime.
Ricardo Wurmus [Thu, 3 Aug 2017 13:54:33 +0000 (15:54 +0200)]
gnu: Add js-strftime.

* gnu/packages/javascript.scm (js-strftime): New variable.

6 years agognu: Add js-json2.
Ricardo Wurmus [Thu, 3 Aug 2017 13:54:16 +0000 (15:54 +0200)]
gnu: Add js-json2.

* gnu/packages/javascript.scm (js-json2): New variable.

6 years agognu: Add js-html5shiv.
Ricardo Wurmus [Thu, 3 Aug 2017 13:53:54 +0000 (15:53 +0200)]
gnu: Add js-html5shiv.

* gnu/packages/javascript.scm (js-html5shiv): New variable.

6 years agobuild: Add minify build system.
Ricardo Wurmus [Wed, 2 Aug 2017 20:49:30 +0000 (22:49 +0200)]
build: Add minify build system.

* guix/build-system/minify.scm: New file.
* guix/build/minify-build-system: New file.
* Makefile.am (MODULES): Add new files.
* doc/guix.texi (Build Systems): Document minify-build-system.

6 years agognu: python-lz4: Fix typo in synopsis.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 02:58:19 +0000 (04:58 +0200)]
gnu: python-lz4: Fix typo in synopsis.

* gnu/packages/compression.scm (python-lz4)[synopsis]: Fix typo.

6 years agognu: python-lz4: Update to 0.10.1.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 02:33:28 +0000 (04:33 +0200)]
gnu: python-lz4: Update to 0.10.1.

* gnu/packages/compression.scm (python-lz4): Update to 0.10.1.
[native-inputs]: Add python-setuptools-scm.

6 years agognu: diffoscope: Use HTTPS.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 02:30:11 +0000 (04:30 +0200)]
gnu: diffoscope: Use HTTPS.

* gnu/packages/package-management.scm (diffoscope)[home-page]: Use HTTPS.

6 years agognu: sshoot: Update to 1.2.6.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 02:20:04 +0000 (04:20 +0200)]
gnu: sshoot: Update to 1.2.6.

* gnu/packages/vpn.scm (sshoot): Update to 1.2.6.
[home-page]: Update to new project home.

6 years agognu: fabric: Update to 1.13.2.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 01:46:49 +0000 (03:46 +0200)]
gnu: fabric: Update to 1.13.2.

* gnu/packages/admin.scm (fabric): Update to 1.13.2.  Remove outdated comments.
[source]: Remove ‘patches’.
* gnu/packages/patches/fabric-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

6 years agognu: certbot, python-acme: Update to 0.17.0.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 00:11:37 +0000 (02:11 +0200)]
gnu: certbot, python-acme: Update to 0.17.0.

* gnu/packages/tls.scm (certbot, python-acme, python2-acme): Update to 0.17.0.

6 years agognu: xonsh: Update to 0.5.12.
Tobias Geerinckx-Rice [Fri, 4 Aug 2017 00:06:39 +0000 (02:06 +0200)]
gnu: xonsh: Update to 0.5.12.

* gnu/packages/shells.scm (xonsh): Update to 0.5.12.

6 years agognu: cmark: Update to 0.28.0.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 23:27:14 +0000 (01:27 +0200)]
gnu: cmark: Update to 0.28.0.

* gnu/packages/markup.scm (cmark): Update to 0.28.0.

6 years agognu: thefuck: Update to 3.19.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 23:15:42 +0000 (01:15 +0200)]
gnu: thefuck: Update to 3.19.

* gnu/packages/admin.scm (thefuck): Update to 3.19.

6 years agognu: zerofree: Update to 1.1.0.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 20:27:21 +0000 (22:27 +0200)]
gnu: zerofree: Update to 1.1.0.

* gnu/packages/linux.scm (zerofree): Update to 1.1.0.
[home-page, source]: Update from old, inaccessible location.

6 years agognu: zerofree: Expand description.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 20:26:36 +0000 (22:26 +0200)]
gnu: zerofree: Expand description.

* gnu/packages/linux.scm (zerofree)[description]: Expand.

6 years agognu: zerofree: Use ‘install-file’.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 20:22:43 +0000 (22:22 +0200)]
gnu: zerofree: Use ‘install-file’.

* gnu/packages/linux.scm (zerofree)[arguments]: Simplify install phase,
using ‘install-file’.

6 years agognu: zerofree: Use ‘modify-phases’ syntax.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 20:14:54 +0000 (22:14 +0200)]
gnu: zerofree: Use ‘modify-phases’ syntax.

* gnu/packages/linux.scm (zerofree)[arguments]: Use ‘modify-phases’.

6 years agognu: sshfs-fuse: Update to 2.10.
Tobias Geerinckx-Rice [Thu, 3 Aug 2017 19:55:20 +0000 (21:55 +0200)]
gnu: sshfs-fuse: Update to 2.10.

* gnu/packages/linux.scm (sshfs-fuse): Update to 2.10.

6 years agognu: freerdp: Update to 2.0.0-rc0 [security fixes].
Marius Bakke [Thu, 3 Aug 2017 22:47:07 +0000 (00:47 +0200)]
gnu: freerdp: Update to 2.0.0-rc0 [security fixes].

Fixes CVE-2017-{2834,2835,2836,2837,2838,2839}.

Reported by Leo Famulari in <https://bugs.gnu.org/27939>.

* gnu/packages/rdesktop.scm (freerdp): Update to 2.0.0-rc0.
[source]: Use tarball release. Adjust file-name.
[arguments]: Remove #:phases.

6 years agognu: git: Enable tests.
Marius Bakke [Thu, 3 Aug 2017 21:02:02 +0000 (23:02 +0200)]
gnu: git: Enable tests.

* gnu/packages/version-control.scm (git)[arguments]: Remove #:tests?. Add
'patch-tests' phase.

6 years agognu: gnupg@1.4: Update to 1.4.22 [fixes CVE-2017-7526].
Leo Famulari [Thu, 3 Aug 2017 22:00:45 +0000 (18:00 -0400)]
gnu: gnupg@1.4: Update to 1.4.22 [fixes CVE-2017-7526].

* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.22.

6 years agognu: Add missing references to (gnu packages cran).
Ricardo Wurmus [Thu, 3 Aug 2017 20:14:48 +0000 (22:14 +0200)]
gnu: Add missing references to (gnu packages cran).

This is a follow-up to commit a8cba9dd112528d67a946eee057c838221eb5249.

Reported-by: Efraim Flashner <efraim@flashner.co.il>
6 years agognu: bioinformatics.scm: Use (gnu packages cran) module.
Efraim Flashner [Thu, 3 Aug 2017 18:39:12 +0000 (21:39 +0300)]
gnu: bioinformatics.scm: Use (gnu packages cran) module.

This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.

6 years agovm: Use grub-hybrid's grub-mkrescue.
Danny Milosavljevic [Thu, 20 Jul 2017 23:06:48 +0000 (01:06 +0200)]
vm: Use grub-hybrid's grub-mkrescue.

* gnu/system/vm.scm (system-disk-image): Use grub-hybrid's grub-mkrescue.
* gnu/bootlader/grub.scm (grub-mkrescue-bootloader): New variable.

6 years agognu: r-purrr: Update to 0.2.3.
Ricardo Wurmus [Thu, 3 Aug 2017 15:45:27 +0000 (17:45 +0200)]
gnu: r-purrr: Update to 0.2.3.

* gnu/packages/statistics.scm (r-purrr): Update to 0.2.3.
[propagated-inputs]: Remove r-rcpp and r-lazyeval; add r-rlang.

6 years agognu: r-desc: Update to 1.1.1.
Ricardo Wurmus [Thu, 3 Aug 2017 15:45:10 +0000 (17:45 +0200)]
gnu: r-desc: Update to 1.1.1.

* gnu/packages/statistics.scm (r-desc): Update to 1.1.1.

6 years agognu: r-seqminer: Update to 6.0.
Ricardo Wurmus [Thu, 3 Aug 2017 15:31:50 +0000 (17:31 +0200)]
gnu: r-seqminer: Update to 6.0.

* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.

6 years agognu: r-wgcna: Update to 1.60.
Ricardo Wurmus [Thu, 3 Aug 2017 15:31:27 +0000 (17:31 +0200)]
gnu: r-wgcna: Update to 1.60.

* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.

6 years agognu: r-qtl: Update to 1.41-6.
Ricardo Wurmus [Thu, 3 Aug 2017 15:30:59 +0000 (17:30 +0200)]
gnu: r-qtl: Update to 1.41-6.

* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.

6 years agognu: r-seqinr: Update to 3.4-5.
Ricardo Wurmus [Thu, 3 Aug 2017 15:30:31 +0000 (17:30 +0200)]
gnu: r-seqinr: Update to 3.4-5.

* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.

6 years agognu: r-optparse: Update to 1.4.4.
Ricardo Wurmus [Thu, 3 Aug 2017 15:30:08 +0000 (17:30 +0200)]
gnu: r-optparse: Update to 1.4.4.

* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.

6 years agognu: r-bookdown: Update to 0.4.
Ricardo Wurmus [Thu, 3 Aug 2017 15:29:47 +0000 (17:29 +0200)]
gnu: r-bookdown: Update to 0.4.

* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.

6 years agognu: r-tclust: Update to 1.2-7.
Ricardo Wurmus [Thu, 3 Aug 2017 15:29:20 +0000 (17:29 +0200)]
gnu: r-tclust: Update to 1.2-7.

* gnu/packages/statistics.scm (r-tclust): Update to 1.2-7.

6 years agognu: r-car: Update to 2.1-5.
Ricardo Wurmus [Thu, 3 Aug 2017 15:28:49 +0000 (17:28 +0200)]
gnu: r-car: Update to 2.1-5.

* gnu/packages/statistics.scm (r-car): Update to 2.1-5.

6 years agognu: r-rcppeigen: Update to 0.3.3.3.0.
Ricardo Wurmus [Thu, 3 Aug 2017 15:28:29 +0000 (17:28 +0200)]
gnu: r-rcppeigen: Update to 0.3.3.3.0.

* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.3.0.

6 years agognu: r-pbapply: Update to 1.3-3.
Ricardo Wurmus [Thu, 3 Aug 2017 15:28:01 +0000 (17:28 +0200)]
gnu: r-pbapply: Update to 1.3-3.

* gnu/packages/statistics.scm (r-pbapply): Update to 1.3-3.

6 years agognu: r-vgam: Update to 1.0-4.
Ricardo Wurmus [Thu, 3 Aug 2017 15:27:40 +0000 (17:27 +0200)]
gnu: r-vgam: Update to 1.0-4.

* gnu/packages/statistics.scm (r-vgam): Update to 1.0-4.

6 years agognu: r-mclust: Update to 5.3.
Ricardo Wurmus [Thu, 3 Aug 2017 15:27:10 +0000 (17:27 +0200)]
gnu: r-mclust: Update to 5.3.

* gnu/packages/statistics.scm (r-mclust): Update to 5.3.

6 years agognu: r-flexmix: Update to 2.3-14.
Ricardo Wurmus [Thu, 3 Aug 2017 15:26:37 +0000 (17:26 +0200)]
gnu: r-flexmix: Update to 2.3-14.

* gnu/packages/statistics.scm (r-flexmix): Update to 2.3-14.

6 years agognu: r-fastica: Update to 1.2-1.
Ricardo Wurmus [Thu, 3 Aug 2017 15:26:06 +0000 (17:26 +0200)]
gnu: r-fastica: Update to 1.2-1.

* gnu/packages/statistics.scm (r-fastica): Update to 1.2-1.

6 years agognu: r-cowplot: Update to 0.8.0.
Ricardo Wurmus [Thu, 3 Aug 2017 15:25:45 +0000 (17:25 +0200)]
gnu: r-cowplot: Update to 0.8.0.

* gnu/packages/statistics.scm (r-cowplot): Update to 0.8.0.

6 years agognu: r-rann: Update to 2.5.1.
Ricardo Wurmus [Thu, 3 Aug 2017 15:25:18 +0000 (17:25 +0200)]
gnu: r-rann: Update to 2.5.1.

* gnu/packages/statistics.scm (r-rann): Update to 2.5.1.

6 years agognu: r-statmod: Update to 1.4.30.
Ricardo Wurmus [Thu, 3 Aug 2017 15:24:46 +0000 (17:24 +0200)]
gnu: r-statmod: Update to 1.4.30.

* gnu/packages/statistics.scm (r-statmod): Update to 1.4.30.

6 years agognu: r-gdata: Update to 2.18.0.
Ricardo Wurmus [Thu, 3 Aug 2017 15:24:19 +0000 (17:24 +0200)]
gnu: r-gdata: Update to 2.18.0.

* gnu/packages/statistics.scm (r-gdata): Update to 2.18.0.

6 years agognu: r-sfsmisc: Update to 1.1-1.
Ricardo Wurmus [Thu, 3 Aug 2017 15:23:53 +0000 (17:23 +0200)]
gnu: r-sfsmisc: Update to 1.1-1.

* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-1.

6 years agognu: r-googlesheets: Update to 0.2.2.
Ricardo Wurmus [Thu, 3 Aug 2017 15:23:31 +0000 (17:23 +0200)]
gnu: r-googlesheets: Update to 0.2.2.

* gnu/packages/statistics.scm (r-googlesheets): Update to 0.2.2.

6 years agognu: r-tidyr: Update to 0.6.3.
Ricardo Wurmus [Thu, 3 Aug 2017 15:22:55 +0000 (17:22 +0200)]
gnu: r-tidyr: Update to 0.6.3.

* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.3.

6 years agognu: r-glmnet: Update to 2.0-10.
Ricardo Wurmus [Thu, 3 Aug 2017 15:22:36 +0000 (17:22 +0200)]
gnu: r-glmnet: Update to 2.0-10.

* gnu/packages/statistics.scm (r-glmnet): Update to 2.0-10.

6 years agognu: r-irlba: Update to 2.2.1.
Ricardo Wurmus [Thu, 3 Aug 2017 15:22:07 +0000 (17:22 +0200)]
gnu: r-irlba: Update to 2.2.1.

* gnu/packages/statistics.scm (r-irlba): Update to 2.2.1.