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Author SHA1 Message Date
Maxim Cournoyer 8795ce8673
gnu: Add python-black. 
* gnu/packages/python.scm (python-black): New variable.
 2018-09-12 22:16:23 -04:00
Maxim Cournoyer 7e846d07e8
gnu: Add python-toml. 
* gnu/packages/python.scm (python-toml): New variables.
 2018-09-12 22:16:23 -04:00
Maxim Cournoyer 4bd8f4f302
gnu: python-jedi: Update to 0.12.1. 
* gnu/packages/python.scm (python-jedi): Update to 0.12.1.
[propagated-inputs]: Move python-parso here, as it is required at run time.
 2018-09-12 22:16:18 -04:00
Danny Milosavljevic 614cfd5c54
gnu: Add rust@1.20.0. 
* gnu/packages/rust.scm (rust-1.20): New variable.
 2018-09-13 00:25:01 +02:00
Danny Milosavljevic 3763e7716c
gnu: rust@1.19.0: Remove superfluous install-file call. 
* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[build]: Remove
superfluous install-file call.
 2018-09-12 23:17:42 +02:00
Danny Milosavljevic 5a3fcf5b44
gnu: rust@1.19.0: Install rustdoc. 
* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[install]: Install
rustdoc.
 2018-09-12 23:17:42 +02:00
Danny Milosavljevic 0bcd1bc778
gnu: rust@1.19.0: Use match-lambda directly. 
Follow-up to 3159ef7c99.

* gnu/packages/rust.scm (rust-1.19)[arguments]<#:phases>[build]: Use
match-lambda directly.
 2018-09-12 23:17:42 +02:00
Nils Gillmann f006237c54
gnu: gnurl: Update to 7.61.1. 
* gnu/packages/gnunet.scm (gnurl): Update to 7.61.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-12 16:02:39 -04:00
Leo Famulari ff9008d8de
gnu: Zsh: Remove workaround required for Zsh 5.6. 
This is a followup to commit 5a5d3e3563.

* gnu/packages/shells.scm (zsh)[arguments]: Remove substitutions in 'patch-test'
phase.
 2018-09-12 15:21:42 -04:00
Pierre Neidhardt 4fa7f29f2a
gnu: emacs-hl-todo: Update to 1.9.0. 
* gnu/packages/emacs.scm (emacs-hl-todo): Update to 1.9.0.
 2018-09-12 19:51:26 +02:00
Ricardo Wurmus 4a89bdd196
gnu: python-scikit-learn: Update to 0.19.2. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.19.2.
[source]: Fetch from git.
[arguments]: Run tests before installation; replace "check" phase, add
"build-ext" phase; delete "reset-gzip-timestamps" phase.
[native-inputs]: Add python-pytest and python-pandas; remove python-nose.
 2018-09-12 19:35:02 +02:00
Pierre Neidhardt b002809f84
gnu: Add emacs-blimp. 
* gnu/packages/emacs.scm (emacs-blimp): New variable.
 2018-09-12 19:34:17 +02:00
Pierre Neidhardt 320105eadb
gnu: Add emacs-org-web-tools. 
* gnu/packages/emacs.scm (emacs-org-web-tools): New variable.
 2018-09-12 19:34:17 +02:00
Pierre Neidhardt 9c208f38f2
gnu: Add emacs-youtube-dl. 
* gnu/packages/emacs.scm (emacs-youtube-dl): New variable.
 2018-09-12 19:34:14 +02:00
Tobias Geerinckx-Rice acd4da3f29
gnu: libfilezilla: Update to 0.13.1. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.1.
 2018-09-12 16:44:08 +02:00
Tobias Geerinckx-Rice bec13d872d
gnu: sg3-utils: Update to 1.43. 
* gnu/packages/scsi.scm (sg3-utils): Update to 1.43.
[license]: Add bsd-2.
 2018-09-12 16:44:08 +02:00
Tobias Geerinckx-Rice 0f304ba73e
gnu: syslinux: Use HTTPS home page. 
* gnu/packages/bootloaders.scm (syslinux)[home-page]: Use HTTPS.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 60d8db74c6
gnu: syslinux: Use INVOKE. 
* gnu/packages/bootloaders.scm (syslinux)[arguments]: Substitute INVOKE
for SYSTEM*.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 5a5d3e3563
gnu: zsh: Update to 5.6.1. 
* gnu/packages/shells.scm (zsh): Update to 5.6.1.
 2018-09-12 16:09:38 +02:00
Tobias Geerinckx-Rice 4dbef67102
gnu: zsh: Use HTTPS. 
* gnu/packages/shells.scm (zsh)[source, home-page]: Use HTTPS.
 2018-09-12 16:09:37 +02:00
Tobias Geerinckx-Rice c8749b0250
gnu: Add perl-mock-config. 
* gnu/packages/perl-check.scm (perl-mock-config): New public variable.
 2018-09-12 16:09:37 +02:00
Efraim Flashner b2c8d31ff6
gnu: perl-moosex-getopt: Update to 0.73. 
* gnu/packages/perl.scm (perl-moosex-getopt): Update to 0.73.
[native-inputs]: Add perl-module-build-tiny, perl-path-tiny,
perl-test-needs.
 2018-09-12 10:28:47 +03:00
Eric Bavier bbe46a4af5
mpi: Factorize openmpi setup build phase. 
* gnu/packages/mpi.scm (%openmpi-setup): New variable.
* gnu/packages/maths.scm (scalapack, slepc-openmpi, mumps-openmpi)
(superlu-dist, p4est, petsc-openmpi, hypre-openmpi, elemental)
(sundials-openmpi, arpack-ng-openmpi)[arguments]: Use it in #:phases.
 2018-09-11 20:29:04 -05:00
Eric Bavier 5882078e8c
font-fantasque-sans: Upgrade to 1.7.2. 
* gnu/packages/fonts.scm (font-fantasque-sans): Upgrade to 1.7.2.
[native-inputs]: Add zip.
[arguments]: Add 'xrange->range phase for python3 compatibility.  Adjust
install phase to work with newly generated font variants.
 2018-09-11 20:29:03 -05:00
Pierre Neidhardt 2b0820bf0d
gnu: emacs-helm: Update to 3.0. 
* gnu/packages/emacs.scm (emacs-helm): Update to 3.0.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt ee0d184502
gnu: Add emacs-hackernews. 
* gnu/packages/emacs.scm (emacs-hackernews): New variable.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt bd8f74dfbe
gnu: emacs-evil-collection: Update to 20180911. 
* gnu/packages/emacs.scm (emacs-evil-collection): Update to 20180911.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt ac9e307740
gnu: emacs-magit-todos: Update to 1.1. 
* gnu/packages/emacs.scm (emacs-magit-todos): Update to 1.1.
 2018-09-11 23:53:35 +02:00
Pierre Neidhardt 475e16578f
gnu: emacs-helm-system-packages: Update to 1.10.1. 
* gnu/packages/emacs.scm (emacs-helm-system-packages): Update to 1.10.1.
 2018-09-11 23:53:35 +02:00
Jan Nieuwenhuizen 4a67079f71
gnu: mes: Oops, use mirror://gnu download url. 
* gnu/packages/mes.scm (mes): Oops, use mirror://gnu download url.
 2018-09-11 22:34:02 +02:00
Tobias Geerinckx-Rice a855117c59
gnu: snakemake: Update home page. 
* gnu/packages/python.scm (snakemake)[home-page]: Update.
 2018-09-11 21:12:43 +02:00
Tobias Geerinckx-Rice 9b83c15afe
gnu: snakemake: Update to 5.2.2. 
* gnu/packages/python.scm (snakemake): Update to 5.2.2.
 2018-09-11 21:03:08 +02:00
Tobias Geerinckx-Rice a93de1ae9e
gnu: obnam: Add deprecation warning. 
* gnu/packages/backup.scm (obnam)[synopsis, description]: Note its
retirement.
 2018-09-11 21:03:07 +02:00
Tobias Geerinckx-Rice cd1e138cc6
gnu: unbound: Update to 1.8.0. 
* gnu/packages/dns.scm (unbound): Update to 1.8.0.
 2018-09-11 21:03:07 +02:00
Tobias Geerinckx-Rice 702a87f2d1
gnu: perl-dbd-mysql: Update to 4.047. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.047.
[arguments]: Add 'skip-library-detection' phase.
 2018-09-11 21:03:07 +02:00
Jonathan Brielmaier 52b0a352c3
gnu: libreoffice: Update to 6.1.0.3. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.0.3.
[source]: Correct indenting.
[inputs]: Add libnumbertext and python-lxml.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:30 +02:00
Jonathan Brielmaier aeba7d4650
gnu: Add libnumbertext. 
* gnu/packages/libreoffice.scm (libnumbertext): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:30 +02:00
Paul Garlick aa82260bc0
gnu: arpack-ng-openmpi: Fix build. 
* gnu/packages/maths.scm (arpack-ng-openmpi)[arguments]: Add
'set-test-environment phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:29 +02:00
Tim Gesthuizen d2fe71b04d
gnu: Add emacs-irony-mode. 
* gnu/packages/emacs.scm (emacs-irony-mode): New variable.
(emacs-irony-mode-server): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 17:46:28 +02:00
Ludovic Courtès 8539eb5c46
gnu: jupyter-guile-kernel: Add dependencies to the search path. 
This allows:

  guix environment --ad-hoc jupyter jupyter-guile-kernel \
    -- jupyter notebook

to work out-of-the-box.

* gnu/packages/guile.scm (jupyter-guile-kernel)[arguments]: In
'install-kernel' phase, add '-L' and '-C' flags to 'kernel.json'.
[propagated-inputs]: Remove.
[inputs]: Add GUILE-JSON and GUILE-SIMPLE-ZMQ.
 2018-09-11 17:46:28 +02:00
Ludovic Courtès 828fa94d7a
gnu: guile-simple-zmq, jupyter-guile-kernel: Update to 5bb66a0 and a7db924. 
* gnu/packages/guile.scm (guile-simple-zmq): Update to 5bb66a0.
(jupyter-guile-kernel): Update to a7db924.
 2018-09-11 17:46:28 +02:00
Mădălin Ionel Patrașcu 01af264dcb
gnu: Add r-svgui. 
* gnu/packages/cran.scm (r-svgui): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-11 17:27:10 +02:00
Marius Bakke f6b7ccc9f9
gnu: spice: Update to 0.14.1 [fixes CVE-2018-10873]. 
* gnu/packages/spice.scm (spice): Update to 0.14.1.
[source](uri): Update to new "spice-server" subdirectory.
[native-inputs]: Add GLIB-NETWORKING and GSETTINGS-DESKTOP-SCHEMAS.
[arguments]: Remove configure-flag which is now off even when celt is
available.  Add phase to set $SSL_CERT_FILE.
 2018-09-11 14:12:53 +02:00
Marius Bakke 41a659d2ec
gnu: usbredir: Update to 0.8.0. 
* gnu/packages/spice.scm (usbredir): Update to 0.8.0.
[source]: Use URL-FETCH.
[native-inputs]: Remove AUTOCONF, AUTOMAKE and LIBTOOL.
[arguments]: Remove.
 2018-09-11 14:12:53 +02:00
Leo Famulari b4ff75b507
gnu: syncthing: Update to 0.14.50. 
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.50.
 2018-09-11 03:24:46 -04:00
Leo Famulari e76709f71f
gnu: go-github-com-syncthing-notify: Update to 0.0.0-2.b76b458. 
* gnu/packages/syncthing.scm (go-github-com-syncthing-notify): Update to
0.0.0-2.b76b458.
 2018-09-11 03:24:42 -04:00
Leo Famulari 091ef8c97e
gnu: VLC: Update to 3.0.4. 
* gnu/packages/video.scm (vlc): Update to 3.0.4.
 2018-09-10 19:24:51 -04:00
Leo Famulari 5d9c28f117
gnu: git: Update to 2.19.0. 
* gnu/packages/version-control.scm (git): Update to 2.19.0.
(cgit)[inputs]: Use the source of Git 2.18.0.
 2018-09-10 19:02:45 -04:00
pimi cbb0edd1be
gnu: Add r-abd. 
* gnu/packages/cran.scm (r-abd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
pimi 6c6ce2d088
gnu: Add r-mosaic. 
* gnu/packages/cran.scm (r-mosaic): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
pimi 2f195b6f23
gnu: Add r-mosaicdata. 
* gnu/packages/cran.scm (r-mosaicdata): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-11 00:14:58 +02:00
Ricardo Wurmus d54145c38a
gnu: guitarix: Update to 0.37.3. 
* gnu/packages/audio.scm (guitarix): Update to 0.37.3.
[inputs]: Add curl.
 2018-09-10 23:58:14 +02:00
Thorsten Wilms 029de52fe9
gnu: guitarix-lv2: Use correct configure flag. 
* gnu/packages/audio.scm (guitarix-lv2)[arguments]: Change configure flag.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 23:58:14 +02:00
Tobias Geerinckx-Rice 2740549754
gnu: kakoune: Use HTTPS home page. 
* gnu/packages/text-editors.scm (kakoune)[home-page]: Use HTTPS.
 2018-09-10 22:54:36 +02:00
Tobias Geerinckx-Rice b38827096f
gnu: mcrl2: Use HTTPS home page. 
* gnu/packages/maths.scm (mcrl2)[home-page]: Use HTTPS.
 2018-09-10 22:54:36 +02:00
Tobias Geerinckx-Rice 4105f13bb5
gnu: tor: Update to 0.3.4.8. 
* gnu/packages/tor.scm (tor): Update to 0.3.4.8.
 2018-09-10 22:54:35 +02:00
Tobias Geerinckx-Rice 695775b138
gnu: kakoune: Update to 2018.09.04. 
* gnu/packages/text-editors.scm (kakoune): Update to 2018.09.04.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice 4b41568fa5
gnu: python-binaryornot: Update to 0.4.4. 
* gnu/packages/python.scm (python-binaryornot): Update to 0.4.4.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice 86788cb0c9
gnu: python-parse: Update to 1.8.4. 
* gnu/packages/python.scm (python-parse): Update to 1.8.4.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice c0ea7f5ff4
gnu: python-parse: Mark up description. 
* gnu/packages/python.scm (python-parse)[description]: Use @code{}.
 2018-09-10 22:15:20 +02:00
Tobias Geerinckx-Rice cc12ac58a2
gnu: python-jedi: Update to 0.12.1. 
* gnu/packages/python.scm (python-jedi): Update to 0.12.1.
[synopsis, description]: Adjust to expanded functionality.
 2018-09-10 22:15:19 +02:00
Tobias Geerinckx-Rice 7a6eaf5ca9
gnu: python-parso: Update to 0.3.1. 
* gnu/packages/python.scm (python-parso): Update to 0.3.1.
 2018-09-10 22:15:19 +02:00
Tobias Geerinckx-Rice d56eee862b
gnu: qtractor: Update to 0.9.2. 
* gnu/packages/music.scm (qtractor): Update to 0.9.2.
[arguments]: Remove obsolete Qt 5.11 workaround.
 2018-09-10 22:15:19 +02:00
Leo Famulari 875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang). 
This is a followup to commit 98d6543f86.

* gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust
accordingly.
 2018-09-10 15:44:32 -04:00
Marius Bakke c5e4b4cc8f
gnu: Add libabigail. 
* gnu/packages/elf.scm (libabigail): New public variable.
 2018-09-10 20:27:42 +02:00
Marius Bakke fc449407fe
gnu: python-debian: Update home page. 
* gnu/packages/python.scm (python-debian)[home-page]: Set to source
repository.
 2018-09-10 20:27:42 +02:00
Marius Bakke 418ec0adc9
gnu: python-libarchive-c: Update to 2.8. 
* gnu/packages/python.scm (python-libarchive-c): Update to 2.8.
[arguments]: Replace 'check' phase.
[native-inputs]: Add PYTHON-MOCK and PYTHON-PYTEST.
 2018-09-10 20:27:42 +02:00
Marius Bakke ba0052e8ae
gnu: python-tlsh: Update to 3.4.5. 
* gnu/packages/python.scm (python-tlsh): Update to 3.4.5.
 2018-09-10 20:27:42 +02:00
Marius Bakke 8fe059bf6c
gnu: python-cryptography: Update to 2.3.1. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.3.1.
 2018-09-10 20:27:42 +02:00
Tobias Geerinckx-Rice 2424d5e56c
gnu: cloc: Update source hash. 
The upstream tarball was modified in place. The only changes are:

  --- /gnu/store/5v39h6zjs33hj5dm2yggz5qk0mva00bs-cloc-1.78.tar.gz
  +++ /gnu/store/pm5ghks76vv6awv3969yvi7qxqfnfs1l-cloc-1.78.tar.gz
  ├── filetype from file(1)
  │ @@ -1 +1 @@
  │ -gzip compressed data, last modified: Fri Sep  7 18:22:49 2018, from Unix
  │ +gzip compressed data, last modified: Sat Sep  8 14:09:43 2018, from Unix
  │   --- 5v39h6zjs33hj5dm2yggz5qk0mva00bs-cloc-1.78.tar
  ├── +++ pm5ghks76vv6awv3969yvi7qxqfnfs1l-cloc-1.78.tar
  │ ├── file list
  │ │ @@ -1,13 +1,13 @@
  │ │  -rwxrwxr-x 0 al (1000) al (1000) 545021 2018-09-07 18:21:22 cloc-1.78/cloc
  │ │  -rwxrwxr-x 0 al (1000) al (1000)   1818 2018-09-07 18:21:22 cloc-1.78/sqlite_formatter
  │ │ -drwxrwxr-x 0 al (1000) al (1000)      0 2018-09-07 18:21:22 cloc-1.78/Unix/
  │ │ --rwxrwxr-x 0 al (1000) al (1000) 498571 2018-09-07 18:21:22 cloc-1.78/Unix/cloc
  │ │ +drwxrwxr-x 0 al (1000) al (1000)      0 2018-09-08 14:09:23 cloc-1.78/Unix/
  │ │ +-rwxrwxr-x 0 al (1000) al (1000) 498537 2018-09-08 14:09:22 cloc-1.78/Unix/cloc
  │ │  -rwxrwxr-x 0 al (1000) al (1000)  32382 2018-09-07 18:21:22 cloc-1.78/Unix/t/00_C.t
  │ │  -rwxrwxr-x 0 al (1000) al (1000)  12614 2018-09-07 18:21:22 cloc-1.78/Unix/t/01_opts.t
  │ │  -rw-rw-r-- 0 al (1000) al (1000)    862 2018-09-07 18:21:22 cloc-1.78/Unix/README
  │ ├── cloc-1.78/Unix/cloc
  │ │ @@ -1,8 +1,7 @@
  │ │ -#!/usr/local/perl/5.28.0/bin/perl
  │ │  #!/usr/bin/env perl

* gnu/packages/code.scm (cloc)[source]: Update sha256 hash.
 2018-09-10 20:20:00 +02:00
Leo Famulari 254844f22d
gnu: nano: Update to 3.0. 
* gnu/packages/nano.scm (nano): Update to 3.0.
 2018-09-10 13:54:29 -04:00
Mark H Weaver eb07a6f898
gnu: linux-libre: Update to 4.18.7. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.7.
(%linux-libre-hash): Update hash.
 2018-09-10 13:25:54 -04:00
Mark H Weaver c727ed05ac
gnu: linux-libre@4.14: Update to 4.14.69. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.69.
(%linux-libre-4.14-hash): Update hash.
 2018-09-10 13:24:01 -04:00
Mark H Weaver 176999f18e
gnu: linux-libre@4.9: Update to 4.9.126. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.126.
 2018-09-10 13:23:20 -04:00
Mark H Weaver d7e9bd15fa
gnu: linux-libre@4.4: Update to 4.4.155. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.155.
 2018-09-10 13:22:35 -04:00
Tobias Geerinckx-Rice 98184e566c
gnu: gnome-mpv: Update to 0.15. 
* gnu/packages/video.scm (gnome-mpv): Update to 0.15.
 2018-09-10 18:22:00 +02:00
Tobias Geerinckx-Rice 37a2ea118d
gnu: fortify-headers: Update to 1.0. 
* gnu/packages/suckless.scm (fortify-headers): Update to 1.0.
 2018-09-10 18:22:00 +02:00
Tobias Geerinckx-Rice 7c8b1bf664
gnu: python-genshi: Update to 0.7.1. 
* gnu/packages/python-web.scm (python-genshi): Update to 0.7.1.
[source]: Use GIT-FETCH and GIT-FILE-NAME. Remove patches.
* gnu/packages/patches/python-genshi-add-support-for-python-3.4-AST.patch,
gnu/packages/patches/python-genshi-buildable-on-python-2.7.patch,
gnu/packages/patches/python-genshi-disable-speedups-on-python-3.3.patch,
gnu/packages/patches/python-genshi-fix-tests-on-python-3.5.patch,
gnu/packages/patches/python-genshi-isstring-helper.patch,
gnu/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch:
Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2018-09-10 18:21:59 +02:00
Tobias Geerinckx-Rice 83397e0786
gnu: python-sockjs-tornado: Update to 1.0.5. 
* gnu/packages/python-web.scm (python-sockjs-tornado): Update to 1.0.5.
 2018-09-10 18:21:59 +02:00
Tobias Geerinckx-Rice 1f7fe26f83
gnu: python-sockjs-tornado: Edit synopsis & description. 
* gnu/packages/python-web.scm (python-sockjs-tornado)[synopsis]
[description]: Pick nits.
 2018-09-10 18:21:59 +02:00
Pjotr Prins 98d6543f86
gnu: Rename ldc.scm to dlang.scm. 
* gnu/packages/ldc.scm: Rename to...
* gnu/packages/dlang.scm: ... this.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
 2018-09-10 17:47:52 +02:00
Pjotr Prins 633e8aab69
gnu: ldc: Update to 1.10.0. 
* gnu/packages/ldc.scm (ldc): Update to 1.10.0.
[native-inputs]: Switch to LLVM and CLANG.
(ldc-bootstrap)[synopsis, description]: Tweak.
* gnu/packages/patches/ldc-disable-phobos-tests.patch: New file.
* gnu/packages/patches/ldc-1.7.0-disable-phobos-tests.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-10 17:47:52 +02:00
Benjamin Slade f80d6ea251
gnu: Add hstr. 
* gnu/packages/shellutils.scm (hstr): New variable.
 2018-09-10 17:47:52 +02:00
Alex Kost 8a8662d286
gnu: emacs-guix: Update to 0.5. 
* gnu/packages/emacs.scm (emacs-guix): Update to 0.5.
[propagated-inputs]: Add 'guile-gcrypt'.
[arguments]: Adjust #:configure-flags accordingly.
 2018-09-10 18:38:32 +03:00
Alex Kost fdf68c232d
gnu: emacs-build-farm: Update to 0.2.1. 
* gnu/packages/emacs.scm (emacs-build-farm): Update to 0.2.1.
Change source from gitlab to notabug.
 2018-09-10 18:38:32 +03:00
Alex Kost 5d78cf0b6c
gnu: emacs-bui: Update to 1.2.0. 
* gnu/packages/emacs.scm (emacs-bui): Update to 1.2.0.
Change source from github to notabug.
 2018-09-10 18:38:32 +03:00
Ricardo Wurmus 5bfa7510d1
gnu: Add python-pygenometracks. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1189c7f1b0
gnu: Add python-hicexplorer. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 5bb9e0af8d
gnu: Add python-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 80f4db91b1
gnu: Add python-pyfaidx. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1f41f01c14
gnu: Add python-pypairix. 
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a9d496b353
gnu: Add python-intervaltree. 
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a6a7156aa9
gnu: Add python-dask. 
* gnu/packages/python.scm (python-dask): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 035989c403
gnu: Add python-partd. 
* gnu/packages/python.scm (python-partd): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus c27a9d8a88
gnu: Add python-blosc. 
* gnu/packages/python.scm (python-blosc): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus b2b8226244
gnu: Add python-locket. 
* gnu/packages/python.scm (python-locket): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 930ba31d20
gnu: Add python-cloudpickle. 
* gnu/packages/python.scm (python-cloudpickle): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 3d352cb9cf
gnu: Add python-sortedcontainers. 
* gnu/packages/python.scm (python-sortedcontainers): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 098cb1e9c4
gnu: Add python-cytoolz. 
* gnu/packages/python.scm (python-cytoolz): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 7cd51cd28e
gnu: Add python-toolz. 
* gnu/packages/python.scm (python-toolz): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus 943a4cb601
gnu: Add python-multiprocess. 
* gnu/packages/python.scm (python-multiprocess): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus fc62567251
gnu: Add python-dill. 
* gnu/packages/python.scm (python-dill): New variable.
 2018-09-10 16:50:25 +02:00
Tobias Geerinckx-Rice 82d5c7c6de
gnu: python-typing: Update to 3.6.6. 
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
 2018-09-10 15:29:13 +02:00
Tobias Geerinckx-Rice 419aa05e1b
gnu: tinyproxy: Update to 1.10.0. 
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0.
[native-inputs]: Remove asciidoc.
 2018-09-10 15:29:12 +02:00
Tobias Geerinckx-Rice f6c8a97a04
gnu: spectrwm: Update to 3.2.0. 
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0.
[arguments]: Remove 'fix-freetype-include' phase.
 2018-09-10 15:29:12 +02:00
Mădălin Ionel Patrașcu 57d70dbabc
gnu: Add yad. 
* gnu/packages/gtk.scm (yad): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 14:45:15 +02:00
Ludovic Courtès 94b3b6041d
gnu: hpcguix-web: Update to 53e09ea. 
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
 2018-09-10 12:18:14 +02:00
Alex Vong d930374014
gnu: youtube-dl: Update to 2018.08.04. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
 2018-09-10 11:31:34 +02:00
Leo Famulari de15ff1a6c
gnu: Add asignify. 
* gnu/packages/crypto.scm (asignify): New variable.
 2018-09-09 20:05:47 -04:00
Leo Famulari d4bd2453ec
gnu: certbot: Update to 0.27.1. 
* gnu/packages/tls.scm (python-acme): Update to 0.27.1.
[arguments]: Use invoke.
(certbot): Update to 0.27.1.
[native-inputs]: Use python-sphinx-1.6.
 2018-09-09 18:52:04 -04:00
Leo Famulari ced98c7e89
gnu: libgd: Fix CVE-2018-{5711,1000222}. 
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd/fixed): New variable.
* gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
 2018-09-09 18:13:19 -04:00
Ricardo Wurmus 45350539aa
gnu: r-chron: Update to 2.3-53. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus 35c076e619
gnu: r-chippeakanno: Update to 3.14.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
 2018-09-09 22:26:02 +02:00
Roel Janssen c36d972531
gnu: Update texmaker to 5.0.2. 
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
 2018-09-09 21:59:08 +02:00
Marius Bakke 0084744b3a
gnu: ghostscript: Update replacement to 9.24 [security fixes]. 
The following CVEs are fixed with this release: CVE-2018-15908,
CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509,
CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539,
CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543.

* gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file.
* gnu/packages/patches/ghostscript-CVE-2018-16509.patch,
gnu/packages/patches/ghostscript-bug-699708.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24.
[source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and
'ghostscript-runpath.patch'.  Add 'ghostscript-CVE-2018-16509.patch' and
'ghostscript-bug-699708.patch'.
[arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output
directory.
 2018-09-09 16:43:11 +02:00
Marius Bakke 910a20e2b8
gnu: jbig2dec: Replace with 0.15 [security fixes]. 
* gnu/packages/image.scm (jbig2dec-0.15): New public variable.
(jbig2dec)[replacement]: New field.
 2018-09-09 16:43:11 +02:00
Marius Bakke a617fd55df
gnu: OpenBLAS: Update source URI. 
* gnu/packages/maths.scm (openblas)[source](uri): Use the more stable
SourceForge mirror.
 2018-09-09 16:43:11 +02:00
Marius Bakke 1448fa2547
gnu: openal: Update to 1.19.0. 
* gnu/packages/audio.scm (openal): Update to 1.19.0.
 2018-09-09 16:43:11 +02:00
Marius Bakke e9c1492f66
gnu: glm: Update to 0.9.9.1. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.1.
 2018-09-09 16:43:10 +02:00
Marius Bakke 91b3a6d4db
gnu: msmtp: Remove unneeded input. 
* gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required
when using OpenSSL (or GnuTLS sans IDN support).
 2018-09-09 16:43:10 +02:00
Marius Bakke 37f9cfae43
gnu: msmtp: Update to 1.8.0. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.0.
 2018-09-09 16:43:10 +02:00
Marius Bakke 249846bfde
gnu: libsoup: Update to 2.64.0. 
* gnu/packages/gnome.scm (libsoup): Update to 2.64.0.
[inputs]: Add LIBPSL.
 2018-09-09 16:43:10 +02:00
Marius Bakke 617cf5de92
gnu: mpfr: Update home page. 
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
 2018-09-09 16:43:10 +02:00
Marius Bakke 81bf0fd0d4
gnu: julia: Update objconv input. 
* gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which
does not have a stable URL.  Add a file name and use HTTPS while at it.
 2018-09-09 16:43:10 +02:00
Tobias Geerinckx-Rice b64e67ad40
gnu: cloc: Update to 1.78. 
* gnu/packages/code.scm (cloc): Update to 1.78.
[source]: Update URI.
 2018-09-09 15:01:55 +02:00
Tobias Geerinckx-Rice c2311644a5
gnu: signify: Update to 24. 
* gnu/packages/crypto.scm (signify): Update to 24.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb105673b8
gnu: musl: Update to 1.1.20. 
* gnu/packages/musl.scm (musl): Update to 1.1.20.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb5e06a35e
gnu: perl-pegex: Update to 0.67. 
* gnu/packages/perl.scm (perl-pegex): Update to 0.67.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice 9ad80992d0
gnu: perl-config-autoconf: Update to 0.317. 
* gnu/packages/perl.scm (perl-config-autoconf): Update to 0.317.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 15dbc911f6
gnu: perl-extutils-installpaths: Update to 0.012. 
* gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.012.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 4e77b75e11
gnu: perl-extutils-helpers: Update to 0.026. 
* gnu/packages/perl.scm (perl-extutils-helpers): Update to 0.026.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 748e6e1271
gnu: perl-getopt-long-descriptive: Update to 0.103. 
* gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.103.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 04fc0b9489
gnu: perl-namespace-clean: Update to 0.27. 
* gnu/packages/perl.scm (perl-namespace-clean): Update to 0.27.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 49e63e3884
gnu: perl-datetime: Update to 1.50. 
* gnu/packages/perl.scm (perl-datetime): Update to 1.50.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 2d32a6572d
gnu: perl-params-validate: Update to 1.29. 
* gnu/packages/perl.scm (perl-params-validate): Update to 1.29.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice a0fad0374e
gnu: links: Update to 2.17. 
* gnu/packages/web-browsers.scm (links): Update to 2.17.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice b9114ccbad
gnu: aircrack-ng: Update to 1.3. 
* gnu/packages/networking.scm (aircrack-ng): Update to 1.3.
[native-inputs]: Add autoconf, automake, libtool, and which.
[inputs]: Add libpcap.
[arguments]: Use conventional --options in #:configure-flags.
Restore ‘configure’ phase. Add ‘patch-evalrev’ and customise ‘bootstrap’
phases. Simplify ‘absolutize-tools’ phase.
 2018-09-09 14:50:34 +02:00
Tobias Geerinckx-Rice 6930ea33c9
gnu: aircrack-ng: Use HTTPS. 
* gnu/packages/networking.scm (aircrack-ng)[source, home-page]: Use HTTPS.
 2018-09-09 14:50:34 +02:00
宋文武 d7f99b3b76
gnu: perl: Improve description. 
Fixes <https://bug.gnu.org/32650>.

* gnu/packages/perl.scm (perl)[description]: Use description from 'perlintro'.
 2018-09-09 19:11:52 +08:00
Jan Nieuwenhuizen c665774a1c
gnu: mes: Update to 0.17.1. 
* gnu/packages/patches/mes-nyacc-0.86.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0.
(nyacc-for-mes): Remove.
 2018-09-08 20:36:30 +02:00
Jan Nieuwenhuizen 445ecce923
gnu: nyacc: Update to 0.86.0. 
* gnu/packages/patches/nyacc-binary-literals.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch.
 2018-09-08 20:36:30 +02:00
Benjamin Slade 39b5d8fd9d
gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl. 
* gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New
variables.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2018-09-08 13:41:10 -04:00
Mark H Weaver 090e3768e8
gnu: linux-libre: Update to 4.18.6. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6.
(%linux-libre-hash): Update hash.
 2018-09-07 21:05:14 -04:00
Mark H Weaver 4be8fdd3cc
gnu: linux-libre@4.14: Update to 4.14.68. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68.
(%linux-libre-4.14-hash): Update hash.
 2018-09-07 21:03:03 -04:00
Mark H Weaver ddb419ce04
gnu: linux-libre@4.9: Update to 4.9.125. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125.
 2018-09-07 21:02:30 -04:00
Mark H Weaver 48d17ba1d3
gnu: linux-libre@4.4: Update to 4.4.154. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154.
 2018-09-07 21:01:48 -04:00
Ludovic Courtès 9f1f200c04
gnu: diffoscope: Update to 100. 
* gnu/packages/package-management.scm (diffoscope): Update to 100.
 2018-09-07 17:59:16 +02:00
Ludovic Courtès afdd1555c4
gnu: indent: Add version 2.2.12. 
* gnu/packages/code.scm (indent-2.2.12): New variable.
 2018-09-07 17:57:04 +02:00
Ludovic Courtès 6b4f99102c
gnu: gdb: Update to 8.2. 
* gnu/packages/gdb.scm (gdb): Update to 8.2.
 2018-09-07 17:55:55 +02:00
Ludovic Courtès 15214828a5
gnu: guile-json: Update to 1.2.0. 
* gnu/packages/guile.scm (guile-json): Update to 1.2.0.
[license]: Change to GPL3+.
 2018-09-07 17:55:51 +02:00
pimi 214452ffd3
gnu: Add r-ggformula. 
* gnu/packages/cran.scm (r-ggformula): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi c61f7bc543
gnu: Add r-mosaiccore. 
* gnu/packages/cran.scm (r-mosaiccore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 77b33e0ede
gnu: Add r-ggstance. 
gnu/packages/cran.scm (r-ggstance): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 12da2a5e58
gnu: Add r-abctools. 
* gnu/packages/cran.scm (r-abctools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi cadc10a513
gnu: Add r-abcrf. 
* gnu/packages/cran.scm (r-abcrf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 40c10917bc
gnu: Add r-abcp2. 
* gnu/packages/cran.scm (r-abcp2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Alex Branham 12498b59e7
gnu: emacs-ess: Update to 17.11. 
* gnu/packages/emacs.scm (emacs-ess): Update to 17.11
[url]: Use github for https
[snippet]: update julia-mode substitution, only build info doc, bypass failing test
[propagated-inputs]: Add emacs-julia-mode
[description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS)
[arguments]: Remove 'set-home' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Tobias Geerinckx-Rice 0012e0dd56
gnu: knot: Update to 2.7.2. 
* gnu/packages/dns.scm (knot): Update to 2.7.2.
 2018-09-07 03:01:40 +02:00
Leo Famulari 91cc2a38de
gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}]. 
* gnu/packages/networking.scm (wireshark): Update to 2.6.3.
 2018-09-06 17:05:42 -04:00
Leo Famulari 1e066f0706
gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618]. 
* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1.
(curl-7.61.0): Replace variable with ...
(curl-7.61.1): ... new variable.
 2018-09-06 17:02:52 -04:00
Kei Kebreau 21f5f351fb
gnu: libgme: Update to 0.6.2. 
* gnu/packages/music.scm (libgme): Update to 0.6.2.
[native-inputs]: Add gcc-4.9.
 2018-09-06 11:01:52 -04:00
Eric Brown f66be84d08
gnu: gfortran, gcc-objc, gcc-objc++: Add version 8. 
* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-06 11:12:40 +02:00
Ludovic Courtès b290a631a0
gnu: guile-present: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.
 2018-09-06 10:49:42 +02:00
Ludovic Courtès 89874fd156
gnu: guile-charting: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.
 2018-09-06 10:48:44 +02:00
Ludovic Courtès b3ca2d8883
gnu: hpcguix-web: Update to 9ff40fc. 
* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.
 2018-09-06 10:46:07 +02:00
Ludovic Courtès 96d6c41dfa
gnu: guile-commonmark: Install .go files to libdir. 
* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).
 2018-09-06 10:43:01 +02:00
Ricardo Wurmus d53aeeafcc
Add missing use-modules clause. 
This is a follow-up to commit 5dfe491290.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
 2018-09-06 04:53:32 +02:00
Tobias Geerinckx-Rice 79b283e433
gnu: ccache: Update to 3.4.3. 
* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice d83477adf9
gnu: font-fira-code: Update to 1.205. 
* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice a5c70c2e0e
gnu: libmpdclient: Update to 2.15. 
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
 2018-09-06 02:33:47 +02:00
Ricardo Wurmus 00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. 
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus f33a4748b7
gnu: r-modelmetrics: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 0d279d607a
gnu: r-robustbase: Update to 0.93-2. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 8e499d756a
gnu: r-rann: Update to 2.6. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 314e8e763f
gnu: r-ggthemes: Update to 4.0.1. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus e5db6890ad
gnu: r-ztable: Update to 0.2.0. 
* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus f0519c8fae
gnu: r-zoo: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 8da236a377
gnu: r-gtools: Update to 3.8.1. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c28d8d8db0
gnu: r-kernlab: Update to 0.9-27. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c0608f815c
gnu: r-adaptivesparsity: Update to 1.6. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a207bca2ad
gnu: r-codedepends: Move from cran to bioconductor. 
* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus caaec88651
gnu: r-ggpubr: Update to 0.1.8. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a9b02ddd73
gnu: r-codedepends: Update to 0.6.5. 
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5.
[propagated-inputs]: Add r-graph.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 2e6909baf0
gnu: r-later: Update to 0.7.4. 
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 12132229b0
gnu: r-maptools: Update to 0.9-3. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 7a96c4e0a0
gnu: r-fnn: Update to 1.1.2.1. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 19950821d7
gnu: r-heatmaply: Update to 0.15.2. 
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 1fe9919a57
gnu: r-tsa: Update to 1.2. 
* gnu/packages/cran.scm (r-tsa): Update to 1.2.
[propagated-inputs]: Remove r-tseries.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus be5642eb69
gnu: r-statnet-common: Update to 4.1.4. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus e32368c130
gnu: r-metap: Update to 1.0. 
* gnu/packages/cran.scm (r-metap): Update to 1.0.
[propagated-inputs]: Add r-rdpack.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus d97d98e142
gnu: r-tinytex: Update to 0.8. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 6f5b157e3d
gnu: r-pillar: Update to 1.3.0. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0.
[propagated-inputs]: Add r-fansi.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 69bf449bf1
gnu: r-xts: Update to 0.11-0. 
* gnu/packages/cran.scm (r-xts): Update to 0.11-0.
[native-inputs]: Remove.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 1b3b2a72ee
gnu: r-mice: Update to 3.3.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus a7265593d3
gnu: r-pan: Update to 1.6. 
* gnu/packages/cran.scm (r-pan): Update to 1.6.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e7630cc931
gnu: r-jomo: Update to 2.6-4. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4.
[propagated-inputs]: Add r-ordinal.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b8f6e2f82a
gnu: Add r-ordinal. 
* gnu/packages/cran.scm (r-ordinal): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus dc66835226
gnu: Add r-ucminf. 
* gnu/packages/cran.scm (r-ucminf): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 45c156bf81
gnu: r-broom: Update to 0.5.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.0.
[propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove
r-plyr and r-psych.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2d2b95d151
gnu: r-ipred: Update to 0.9-7. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus c73752cac5
gnu: r-pls: Update to 2.7-0. 
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b00e8ae771
gnu: r-glue: Update to 1.3.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b72de5b3f6
gnu: r-callr: Update to 3.0.0. 
* gnu/packages/cran.scm (r-callr): Update to 3.0.0.
[propagated-inputs]: Add r-base64enc.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e3c1e93e35
gnu: r-reprex: Update to 0.2.0. 
* gnu/packages/cran.scm (r-reprex): Update to 0.2.0.
[propagated-inputs]: Add r-clipr, r-rlang, and r-withr.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2cdd9d4f83
gnu: r-reticulate: Update to 1.10. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.10.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus cb96d81be4
gnu: r-doby: Update to 4.6-2. 
* gnu/packages/cran.scm (r-doby): Update to 4.6-2.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 589bd1c426
gnu: Add r-flextable. 
* gnu/packages/cran.scm (r-flextable): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 78f2c08c0b
gnu: r-rmarkdown: Use latest version of Pandoc. 
* gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus f9f4578ba0
Revert "gnu: ghc-tasty: Update to 1.1.0.3." 
This reverts commit 3ad6b89090.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 90708323a1
Revert "gnu: ghc-base-compat: Update to 0.10.4." 
This reverts commit 0fa2c552fc.

We may not upgrade base-compat at this point because we haven't upgraded the
default GHC yet.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 0fd7d59dc3
gnu: Add r-moonbook. 
* gnu/packages/cran.scm (r-moonbook): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus aaed237d1b
gnu: Add r-nortest. 
* gnu/packages/cran.scm (r-nortest): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 1f560b9cdb
gnu: Add r-sjmisc. 
* gnu/packages/cran.scm (r-sjmisc): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus cfc0631433
gnu: Add r-sjlabelled. 
* gnu/packages/cran.scm (r-sjlabelled): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus de059e4bd3
gnu: Add r-prediction. 
* gnu/packages/cran.scm (r-prediction): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus bfee9ce88f
gnu: Add r-snakecase. 
* gnu/packages/cran.scm (r-snakecase): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus c183fa2688
gnu: Add r-officer. 
* gnu/packages/cran.scm (r-officer): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 5dbe7aa920
gnu: r-googlesheets: Update to 0.3.0. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.3.0.
[propagated-inputs]: Add r-tibble.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 88cb7aa9e7
gnu: r-plotly: Update to 4.8.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.8.0.
[propagated-inputs]: Add r-promises and r-rlang.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 195eec737c
gnu: r-matrixstats: Update to 0.54.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.54.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e2a2c3378e
gnu: r-r-rsp: Update to 0.43.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.43.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus eefa7c7f3d
gnu: r-r-utils: Update to 2.7.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.7.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e926159eb3
gnu: r-e1071: Update to 1.7-0. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2aafa73a94
gnu: r-xml: Update to 3.98-1.16. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.16.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 41f6685388
gnu: r-rcpparmadillo: Update to 0.9.100.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.100.5.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 19cb93be55
gnu: r-git2r: Update to 0.23.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.23.0.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2848c52c5e
gnu: r-roxygen2: Update to 6.1.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.0.
[propagated-inputs]: Add r-pkgload and r-purrr.
[native-inputs]: Add r-knitr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 9b7e8df85b
gnu: r-ade4: Update to 1.7-13. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-13.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 7f38b31ecb
gnu: r-xtable: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-xtable): Update to 1.8-3.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 6b02569f1d
gnu: r-dbplyr: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.2.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3299bc1c5e
gnu: r-yaml: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.2.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2a96a093ec
gnu: r-evaluate: Update to 0.11. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.11.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3bf390279d
gnu: r-scales: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-scales): Update to 1.0.0.
[propagated-inputs]: Remove r-dichromat and r-plyr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 97c81cc174
gnu: r-stringi: Update to 1.2.4. 
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e362be8e89
gnu: Add r-pkgload. 
* gnu/packages/cran.scm (r-pkgload): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 4f8247b54b
gnu: Add r-pkgbuild. 
* gnu/packages/cran.scm (r-pkgbuild): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 1ec1989f80
gnu: r-httpuv: Update to 1.4.5. 
* gnu/packages/web.scm (r-httpuv): Update to 1.4.5.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus f077174178
gnu: r-scran: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 8e44ff0c0d
gnu: r-scater: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e69c07e61a
gnu: r-hdf5array: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 16527f1cbc
gnu: r-ggbio: Update to 1.28.5. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 70daf9362b
gnu: r-biovizbase: Update to 1.28.2. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3c55304688
gnu: r-edaseq: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus eb251fe524
gnu: r-igraph: Update to 1.2.2. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus c273bcdfce
gnu: r-diffusionmap: Update to 1.1-0.1. 
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 6f6aef80e3
gnu: r-seurat: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 07bd90ce90
gnu: r-msnbase: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 4ee8c37cca
gnu: r-maldiquant: Update to 1.18. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 48b21f8b6b
gnu: r-seqminer: Update to 6.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus a02340058c
gnu: r-biocparallel: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 1d56c79f86
gnu: r-genomicranges: Update to 1.32.6. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 688cb08527
gnu: r-limma: Update to 3.36.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 33a103a543
gnu: r-variantannotation: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 1adf4596a6
gnu: r-edger: Update to 3.22.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 5728d9c6c0
gnu: r-iranges: Update to 2.14.11. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 3c04375614
gnu: r-biocviews: Update to 1.48.3. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 65050163e0
gnu: r-chippeakanno: Update to 3.14.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 88e4ed55d6
gnu: Add r-clipr. 
* gnu/packages/cran.scm (r-clipr): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 6a8469755c
gnu: Add r-rdpack. 
* gnu/packages/cran.scm (r-rdpack): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus dd954dd743
gnu: Add r-gbrd. 
* gnu/packages/cran.scm (r-gbrd): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 53718658d2
gnu: Add r-polynom. 
* gnu/packages/cran.scm (r-polynom): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 356230da4a
gnu: Add r-fansi. 
* gnu/packages/cran.scm (r-fansi): New variable.
 2018-09-05 20:03:03 +02:00
Ludovic Courtès 3b0153bd82
gnu: guix-daemon: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
made Guile-Gcrypt a hard dependency.

* gnu/packages/package-management.scm (guix-daemon)[inputs]: Add
GUILE-GCRYPT.
 2018-09-05 15:48:04 +02:00
Ludovic Courtès 7903f00a74
gnu: cuirass: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
added a hard dependency of Guix on Guile-Gcrypt.

* gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, use 'string-join' to compute
'mods'.  Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take
objects from lib/guile/X.Y/site-ccache.
 2018-09-05 15:35:54 +02:00
Ludovic Courtès 5e3082df1c
gnu: guile-fibers: Install .go files to "…/site-ccache". 
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
 2018-09-05 15:35:54 +02:00
Eric Bavier 3f5e6ccf9b
slepc: Upgrade to 3.9.2. 
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
 2018-09-05 08:10:38 -05:00
Eric Bavier c15be1280e
petsc: Upgrade to 3.9.3. 
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3.
[arguments]: Remove unnecessary configure flags.
 2018-09-05 08:10:37 -05:00
Eric Bavier a3a99e27bb
petsc: Move example code to "examples" output. 
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
 2018-09-05 08:10:37 -05:00
Eric Bavier b26e4f26ff
gnu: Add SUNDIALS. 
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
 2018-09-05 08:10:31 -05:00
Alex Vong 296f091b48
gnu: packages: mp3: Use HTTPS where possible. 
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS.
(libid3tag)[home-page]: Likewise.
(mp3info)[source, home-page]: Likewise.
(mpg123)[source]: Likewise.
(libmpcdec)[source, home-page]: Likewise.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Alex Vong 998100e6e8
gnu: eyed3: Update home page. 
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Ludovic Courtès 53166aec98
gnu: guix: Update to 3d43017. 
* gnu/packages/package-management.scm (guix): Update to 3d43017.
 2018-09-05 14:31:48 +02:00
Ludovic Courtès 185948b8a8
gnu: xorg: Fix typo. 
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
 2018-09-05 13:57:43 +02:00
Ricardo Wurmus 4fd2622df8
gnu: python-tables: Update to 3.4.4. 
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 8afdeb8751
gnu: python-pybigwig: Update to 0.3.12. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 0d7974c376
gnu: libbigwig: Update to 0.4.2. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus ca1dc4c76a
gnu: nss-pam-ldapd: Update to 0.9.10. 
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
 2018-09-05 11:44:52 +02:00
Rutger Helling fefe17b088
gnu: dolphin-emu: Update to commit 5f0d825. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
 2018-09-05 10:23:20 +02:00
Leo Famulari fcf4841c0e
gnu: Zsh: Patch some tests that began failing in 5.6. 
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting
them.
 2018-09-04 18:34:01 -04:00
Leo Famulari 95681e5586
gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}]. 
* gnu/packages/shells.scm (zsh): Update to 5.6.
[arguments]: Skip some tests.
 2018-09-04 18:10:53 -04:00
Ludovic Courtès ca71942445
Switch to Guile-Gcrypt. 
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)

* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt.  Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
 #:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions  Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules.  Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
 2018-09-04 17:25:11 +02:00
Alex Vong 1bf758767d
gnu: Add emacs-picpocket. 
* gnu/packages/emacs.scm (emacs-picpocket): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:39:43 +02:00
Paul Garlick 71ca16b58d
gnu: petsc-openmpi: Configure with support for hdf5 data format. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add
hdf5-parallel-openmpi.
[arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib'
flags.  Add 'set-test-environment' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:22:48 +02:00
Jonathan Brielmaier b50658fe8a
gnu: kicad: Update to 5.0.0. 
* gnu/packages/engineering.scm (kicad): Update to 5.0.0.
[source]: Change from git to url-fetch.
[arguments]: Remove now unneeded build version parameter.
[inputs]: Add opencascade-oce.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:02:59 +02:00
Arun Isaac 906a396bff
gnu: ghc-zlib: Enable tests. 
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building
with newer tasty.
[native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and
ghc-tasty-quickcheck.
 2018-09-04 17:31:09 +05:30
Arun Isaac 6300ba5b66
gnu: ghc-integer-logarithms: Allow building with newer tasty. 
* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building
with newer tasty.
 2018-09-04 15:24:32 +05:30
Arun Isaac 8374cc4b05
gnu: ghc-tasty-ant-xml: Update to 1.1.4. 
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml): Update to 1.1.4.
 2018-09-04 15:21:56 +05:30
Arun Isaac 3ad6b89090
gnu: ghc-tasty: Update to 1.1.0.3. 
* gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3.
[inputs]: Add ghc-wcwidth.
(ghc-attoparsec-bootstrap, ghc-integer-logarithms-bootstrap,
ghc-scientific-bootstrap): New variables.
(ghc-wcwidth)[inputs]: Replace ghc-attoparsec with ghc-attoparsec-bootstrap.
(ghc-scientific)[inputs]: Replace ghc-integer-logarithms with
ghc-integer-logarithms-bootstrap.
(ghc-attoparsec)[inputs]: Replace ghc-scientific with
ghc-scientific-bootstrap.
 2018-09-04 12:15:17 +05:30
Arun Isaac 9c4b522f15
gnu: Add ghc-wcwidth. 
* gnu/packages/haskell.scm (ghc-wcwidth): New variable.
 2018-09-04 12:15:10 +05:30
Ludovic Courtès fd95f37f36
Revert "gnu: perl: Add support for cross-compilation" 
This reverts commit 5108c18e7e, which was
accidentally committed.
 2018-09-03 23:49:12 +02:00
Raphaël Mélotte 5108c18e7e
gnu: perl: Add support for cross-compilation 
* gnu/packages/perl.scm (perl): use cross-libc when cross-compiling

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:41:08 +02:00
Benjamin Slade 38fe6449c0
gnu: Add transset-df. 
* gnu/packages/xorg.scm (transset-df): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:40:23 +02:00
Marius Bakke c702749dfd
gnu: arpack-ng: Update to 3.6.2. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.2.
 2018-09-03 19:09:01 +02:00
Marius Bakke 91bb495b85
gnu: arpack-ng: Drop redundant phase. 
* gnu/packages/maths.scm (arpack-ng)[arguments]: Remove.
 2018-09-03 19:09:01 +02:00
Marius Bakke 1f7d142000
gnu: python-matplotlib: Update to 2.2.3. 
* gnu/packages/python.scm (python-matplotlib): Update to 2.2.3.
 2018-09-03 19:09:00 +02:00
Marius Bakke cbd7c65709
gnu: ppp: Return #t from all phases. 
* gnu/packages/samba.scm (ppp)[arguments]: Return #t from phase.
 2018-09-03 18:58:47 +02:00
Marius Bakke 84aa18ff7f
gnu: re2: Update to 2018-09-01. 
* gnu/packages/regex.scm (re2): Update to 2018-09-01.
 2018-09-03 18:58:47 +02:00
Marius Bakke fcde1d27bb
gnu: openexr: Update to 2.3.0. 
* gnu/packages/graphics.scm (openexr): Update to 2.3.0.
[source](uri): Change to new download location.
[source](snippet): Remove workaround.
[source](patches): Remove.
* gnu/packages/patches/openexr-missing-samples.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-03 18:58:47 +02:00
Marius Bakke 1ae2c577a6
gnu: ilmbase: Update to 2.3.0. 
* gnu/packages/graphics.scm (ilmbase): Update to 2.3.0.
[source](uri): Change to new download location.
 2018-09-03 18:58:46 +02:00
Marius Bakke 9156206199
gnu: simplescreenrecorder: Build against modular Qt. 
* gnu/packages/video.scm (simplescreenrecorder)[inputs]: Remove QT.  Add
QTBASE and QTX11EXTRAS.
 2018-09-03 18:58:46 +02:00
Marius Bakke 65e686d6cb
Merge branch 'security-updates' 2018-09-03 18:58:20 +02:00
Efraim Flashner a5896da34e
gnu: gnu-pw-mgr: Update to 2.4.2. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.4.2.
 2018-09-03 19:34:24 +03:00
Tobias Geerinckx-Rice 38a8cd329d
gnu: python-nbxmpp: Update to 0.6.7. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.7.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice b619b7f67b
gnu: libircclient: Update to 1.10. 
* gnu/packages/messaging.scm (libircclient): Update to 1.10.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice cfcfc6ab62
Fix some typos. 
* doc/guix.texi (Sound Services, DNS Services): Fix typos.
* gnu/packages/cpp.scm (json-modern-cxx)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-fancy-narrow)[synopsis, description]:
Likewise. Edit & mark up while we're here.
* gnu/packages/mail.scm (alot)[synopsis, description]: Ditto.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice fb458bf3bc
gnu: sudo: Update to 1.8.25. 
* gnu/packages/admin.scm (sudo): Update to 1.8.25.
 2018-09-03 18:21:42 +02:00
Efraim Flashner 0cc6447669
gnu: python-efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (python-efl): Update to 1.21.0.
[source]: Don't use pypi source.
[arguments]: Delete network tests.
 2018-09-03 17:32:44 +03:00
Efraim Flashner 290bef39f6
gnu: efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (efl): Update to 1.21.0.
 2018-09-03 17:32:44 +03:00
Ricardo Wurmus 02ddafef55
gnu: python-scipy: Disable broken tests. 
* gnu/packages/python.scm (python-scipy)[arguments]: Skip two broken tests.
 2018-09-03 13:49:32 +02:00
Rutger Helling 26baaaf49b
gnu: c-toxcore: Update to 0.2.7. 
* gnu/packages/messaging.scm (c-toxcore): Update to 0.2.7.
 2018-09-03 08:22:51 +02:00
Rutger Helling aa613d71ec
gnu: openrct2: Update to 0.2.1. 
* gnu/packages/games.scm (openrct2-objects): Update to 1.0.6.
* gnu/packages/games.scm (openrct2): Update to 0.2.1.
 2018-09-03 08:22:50 +02:00
Efraim Flashner 647465ace9
gnu: jellyfish: Update to 2.2.10. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
 2018-09-03 08:32:33 +03:00
Oleg Pykhalov 3910977823
gnu: monitoring.scm: Fix copyright line. 
This is a follow-up to ead46692ec.
 2018-09-02 19:18:16 +03:00
Alex Vong 2bd6ed9e4c
gnu: haskell-mode: Fix test failure. 
Fixes <https://bugs.gnu.org/31726>.

Thanks to Jack Hill <jackhill@jackhill.us> for exploring different solutions
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31726>.

* gnu/packages/patches/haskell-mode-unused-variables.patch,
gnu/packages/patches/haskell-mode-make-check.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/emacs.scm (haskell-mode)[source]: Use them.
[arguments]: Adjust 'pre-build' phase to embed file name.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 17:06:43 +02:00
Konrad Hinsen b21a55a9f2
gnu: emacs-helpful: Update to 0.13. 
* gnu/packages/emacs.scm (emacs-helpful): Update to 0.13.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:58:06 +02:00
Konrad Hinsen 351b6463af
gnu: emacs-elisp-refs: Update to 1.3. 
* gnu/packages/emacs.scm (emacs-elisp-refs): Update to 1.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:56:22 +02:00
Rutger Helling 87284c6b48
gnu: wine-staging: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging): Update to 3.15.
 2018-09-02 08:53:03 +02:00
Rutger Helling ab2e38e206
gnu: wine-staging-patchset-data: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.15.
 2018-09-02 08:53:03 +02:00
宋文武 9bf98520f2
gnu: rosegarden: Update to 18.06. 
* gnu/packages/music.scm (rosegarden): Update to 18.06.
[home-page]: Use HTTPS.
 2018-09-02 13:18:28 +08:00
Danny Milosavljevic 24d298b459
gnu: rust: Move rust-1.19 down. 2018-09-02 00:22:53 +02:00
Danny Milosavljevic 3159ef7c99
gnu: rust: Bootstrap (only) Rust 1.19.0 by mrustc. 
* gnu/packages/patches/rust-1.19-mrustc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rust.scm (rust-1.19)[source]: Add patch
"rust-1.19-mrustc.patch".
[arguments]<#:modules>: New field.
<#:phases>[patch-cargo-tomls]: New phase.
<#:phases>[build]: Modify.
<#:phases>[install]: Modify.
[native-inputs]: Replace rust-bootstrap by mrustc.
(rust-1.23)[native-inputs]: New field.
[arguments]<#:phases>: Delete phase "patch-cargo-tomls".
 2018-09-02 00:09:34 +02:00
Manuel Graf a0a273c1ee
gnu: Add perftest. 
* gnu/packages/linux.scm (perftest): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-01 17:51:29 -04:00
Julien Lepiller 37a0f47073
gnu: Add ruby-jekyll-paginate-v2. 
* gnu/packages/ruby.scm (ruby-jekyll-paginate-v2): New variable.
 2018-09-01 23:09:14 +02:00
Julien Lepiller 49e1dde53f
gnu: Add jekyll. 
* gnu/packages/ruby.scm (jekyll): New variable.
 2018-09-01 23:09:09 +02:00
Julien Lepiller 3729611379
gnu: Add ruby-pathutil. 
* gnu/packages/ruby.scm (ruby-pathutil): New variable.
 2018-09-01 23:09:06 +02:00
Julien Lepiller 49395112c4
gnu: Add ruby-forwardable-extended. 
* gnu/packages/ruby.scm (ruby-forwardable-extended): New variable.
 2018-09-01 23:09:04 +02:00
Julien Lepiller a13d451e18
gnu: Add ruby-liquid. 
* gnu/packages/ruby.scm (ruby-liquid): New variable.
 2018-09-01 23:09:02 +02:00
Julien Lepiller f1ec4d7611
gnu: Add ruby-mercenary. 
* gnu/packages/ruby.scm (ruby-mercenary): New variable.
 2018-09-01 23:09:00 +02:00
Julien Lepiller f8ae2ee528
gnu: Add ruby-safe-yaml. 
* gnu/packages/ruby.scm (ruby-safe-yaml): New variable.
 2018-09-01 23:08:58 +02:00
Julien Lepiller 73bfc125ef
gnu: Add ruby-heredoc-unindent. 
* gnu/packages/ruby.scm (ruby-heredoc-unindent): New variable.
 2018-09-01 23:08:56 +02:00
Julien Lepiller 2e072e37aa
gnu: Add ruby-hashie. 
* gnu/packages/ruby.scm (ruby-hashie): New variable.
 2018-09-01 23:08:55 +02:00
Julien Lepiller 2c5028bd97
gnu: Add ruby-rouge-2. 
* gnu/packages/ruby.scm (ruby-rouge-2): New variable.
 2018-09-01 23:08:53 +02:00
Julien Lepiller 4ce0414bca
gnu: Add ruby-rouge. 
* gnu/packages/ruby.scm (ruby-rouge): New variable.
 2018-09-01 23:08:46 +02:00
Julien Lepiller 5e2f74bdb8
gnu: Add ruby-em-websocket. 
* gnu/packages/ruby.scm (ruby-em-websocket): New variable.
 2018-09-01 23:08:44 +02:00
Julien Lepiller fa0063bcf4
gnu: Add ruby-http-parser.rb. 
* gnu/packages/ruby.scm (ruby-http-parser.rb): New variable.
 2018-09-01 23:08:42 +02:00
Julien Lepiller 0312706955
gnu: Add ruby-kramdown. 
* gnu/packages/ruby.scm (ruby-kramdown): New variable.
 2018-09-01 23:08:40 +02:00
Julien Lepiller 197ca8ecd2
gnu: Add ruby-prawn-table. 
* gnu/packages/ruby.scm (ruby-prawn-table): New variable.
 2018-09-01 23:08:38 +02:00
Julien Lepiller 7ad8dd086c
gnu: Add ruby-prawn. 
* gnu/packages/ruby.scm (ruby-prawn): New variable.
 2018-09-01 23:08:36 +02:00
Julien Lepiller 37fbced73c
gnu: Add ruby-yard. 
* gnu/packages/ruby.scm (ruby-yard): New variable.
 2018-09-01 23:08:34 +02:00
Julien Lepiller 770e3b535e
gnu: Add ruby-pdf-core. 
* gnu/packages/ruby.scm (ruby-pdf-core): New variable.
 2018-09-01 23:08:31 +02:00
Julien Lepiller 461fb8598e
gnu: Add ruby-pdf-inspector. 
* gnu/packages/ruby.scm (ruby-pdf-inspector): New variable.
 2018-09-01 23:08:29 +02:00
Julien Lepiller abbe629c6a
gnu: Add ruby-pdf-reader. 
* gnu/packages/ruby.scm (ruby-pdf-reader): New variable.
 2018-09-01 23:08:27 +02:00
Julien Lepiller 00d71efca6
gnu: Add ruby-morecane. 
* gnu/packages/ruby.scm (ruby-morecane): New variable.
 2018-09-01 23:08:10 +02:00
Julien Lepiller 83d9f67221
gnu: Add ruby-cane. 
* gnu/packages/ruby.scm (ruby-cane): New variable.
 2018-09-01 23:08:06 +02:00
Julien Lepiller 3224a5a84a
gnu: Add ruby-parallel. 
* gnu/packages/ruby.scm (ruby-parallel): New variable.
 2018-09-01 23:08:04 +02:00
Julien Lepiller ceac6f6f5b
gnu: Add ruby-jekyll-watch. 
* gnu/packages/ruby.scm (ruby-jekyll-watch): New variable.
 2018-09-01 23:08:02 +02:00
Julien Lepiller 88ed727fc5
gnu: Add ruby-listen-3.0. 
* gnu/packages/ruby.scm (ruby-listen-3.0): New variable.
 2018-09-01 23:08:00 +02:00
Julien Lepiller 5e242cb44c
gnu: Add ruby-jekyll-sass-converter. 
* gnu/packages/ruby.scm (ruby-jekyll-sass-converter): New variable.
 2018-09-01 23:07:58 +02:00
Julien Lepiller f00f449223
gnu: Add ruby-sass. 
* gnu/packages/ruby.scm (ruby-sass): New variable.
 2018-09-01 23:07:56 +02:00
Julien Lepiller 6456beef01
gnu: Add ruby-sass-spec. 
* gnu/packages/ruby.scm (ruby-sass-spec): New variable.
 2018-09-01 23:07:54 +02:00
Julien Lepiller ddc3a66798
gnu: Add ruby-diffy. 
* gnu/packages/ruby.scm (ruby-diffy): New variable.
 2018-09-01 23:07:52 +02:00
Julien Lepiller 0c8eedc153
gnu: Add ruby-terminfo. 
* gnu/packages/ruby.scm (ruby-terminfo): New variable.
 2018-09-01 23:07:50 +02:00
Julien Lepiller 18077ffc46
gnu: Add ruby-sass-listen. 
* gnu/packages/ruby.scm (ruby-sass-listen): New variable.
 2018-09-01 23:07:48 +02:00
Julien Lepiller 6bba8ecf7b
gnu: Add ruby-rdoc. 
* gnu/packages/ruby.scm (ruby-rdoc): New variable.
 2018-09-01 23:07:46 +02:00
Julien Lepiller f22c038799
gnu: Add ruby-command-line-reporter-3. 
* gnu/packages/ruby.scm (ruby-command-line-reporter-3): New variable.
 2018-09-01 23:07:44 +02:00
Julien Lepiller 78b9c291f6
gnu: Add ruby-command-line-reporter. 
* gnu/packages/ruby.scm (ruby-command-line-reporter): New variable.
 2018-09-01 23:07:42 +02:00
Julien Lepiller 9c7f15c048
gnu: Add ruby-colorator. 
* gnu/packages/ruby.scm (ruby-colorator): New variable.
 2018-09-01 23:07:39 +02:00
Julien Lepiller 6f2c4efb56
gnu: Add ruby-addressable. 
* gnu/package/ruby.scm (ruby-addressable): New variable.
 2018-09-01 23:07:37 +02:00
Julien Lepiller 0d16905b60
gnu: Add ruby-public-suffix. 
* gnu/packages/ruby.scm (ruby-public-suffix): New variable.
 2018-09-01 23:07:35 +02:00
Julien Lepiller afb7a3e8d5
gnu: ruby-ttfunk: Update to 1.5.1. 
* gnu/packages/ruby.scm (ruby-ttfunk): Update to 1.5.1.
 2018-09-01 23:07:32 +02:00
Julien Lepiller ef381322d5
gnu: ruby-activesupport: Update to 5.2.1. 
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.2.1.
 2018-09-01 23:07:30 +02:00
Julien Lepiller cbb50182ad
gnu: ruby-i18n: Update to 1.1.0. 
* gnu/packages/ruby.scm (ruby-i18n): Update to 1.1.0.
 2018-09-01 23:07:28 +02:00
Julien Lepiller 352b5d7e74
gnu: Add ruby-concurrent. 
* gnu/packages/ruby.scm (ruby-concurrent): New variable.
 2018-09-01 23:07:06 +02:00
Oleg Pykhalov ead46692ec
gnu: Add zabbix-agentd and zabbix-server. 
* gnu/packages/monitoring.scm (zabbix-agentd, zabbix-server): New variables.
 2018-09-01 19:01:36 +03:00
Marius Bakke e59588482b
gnu: nss, nss-certs: Update to 3.39 [fixes CVE-2018-12384]. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.39.
* gnu/packages/certs.scm (nss-certs): Likewise.
 2018-09-01 13:26:13 +02:00
Marius Bakke 7ea90c217f
gnu: nspr: Update to 4.20. 
* gnu/packages/gnuzilla.scm (nspr): Update to 4.20.
 2018-09-01 13:23:39 +02:00
Leo Famulari ea59f0487b
gnu: Remove Krita 3. 
Krita 3 fails to build with Qt 5.11.1. Since it's also unmaintained upstream,
remove it.

* gnu/packages/kde.scm (krita-3): Remove variable.
 2018-09-01 02:09:53 -04:00
Leo Famulari fd67d793c2
gnu: Krita: Build with libraw 0.18. 
Fixes <https://bugs.gnu.org/32467>.

Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

* gnu/packages/photo.scm (libraw-0.18): New variable.
* gnu/packages/kde.scm (krita)[inputs]: Use libraw-0.18.
 2018-09-01 02:09:52 -04:00
Leo Famulari 7ce9eaf013
gnu: Krita: Update to 4.1.1. 
* gnu/packages/kde.scm (krita): Update to 4.1.1.
 2018-09-01 02:09:52 -04:00
Leo Famulari d84a887a5f
gnu: libksysguard: Update to 5.13.4. 
* gnu/packages/kde.scm (libksysguard): Update to 5.13.4.
 2018-09-01 02:09:52 -04:00
Leo Famulari 600f1ad8e6
gnu: KDE: Update to 5.49.0. 
Fixes <https://bugs.gnu.org/32013>.

* gnu/packages/kde-frameworks.scm (attica, baloo, bluez-qt, breeze-icons,
extra-cmake-modules, kactivities, kactivities-stats, kapidox, karchive, kauth,
kbookmarks, kcmutils, kcodecs, kcompletion, kconfig, kconfigwidgets,
kcoreaddons, kcrash, kdbusaddons, kde-framework-integration, kdeclarative, kded,
kdesignerplugin, kdesu, kdewebkit, kdnssd, kdoctools, kemoticons, kfilemetadata,
kglobalaccel, kguiaddons, ki18n, kiconthemes, kidletime, kimageformats, kinit,
kio, kirigami, kitemmodels, kitemview, kjobwidgets, knewstuff, knotification,
knotifyconfig, kpackage, kparts, kpeople, kplotting, kpty, krunner, kservice,
ksyntaxhighlighting, ktexteditor, ktextwidgets, kunitcoversion, kwallet,
kwayland, kwidgetsaddons, kwindowsystem, kxmlgui, kxmlrpcclient,
modemmanager-qt, networkmanager-qt, oxygen-icons, plasma-framework, prison,
qqc2-desktop-style, solid, sonnet, threadweaver): Update to 5.49.0.
(extra-cmake-modules)[arguments]: Remove obsolete workaround.
(attica)[arguments]: Disable some new tests.

Co-authored-by: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 2018-09-01 02:09:49 -04:00
Eric Bavier 220458b098
gnu: hypre: Update to 2.14.0. 
* gnu/packages/maths.scm (hypre): Update to 2.14.0
 2018-08-31 10:08:00 -05:00
Ricardo Wurmus 9ce2f07ab6
gnu: python-matplotlib: Use python-pyqt-without-qtwebkit. 
* gnu/packages/python.scm (python-matplotlib)[propagated-inputs]: Replace
python-pyqt with python-pyqt-without-qtwebkit.
 2018-08-31 16:37:56 +02:00
Ricardo Wurmus 0e2d6d2698
gnu: Add python-pyqt-without-qtwebkit. 
* gnu/packages/qt.scm (python-pyqt-without-qtwebkit): New variable.
 2018-08-31 16:37:56 +02:00
Rutger Helling 0b6678cd44
gnu: retroarch: Update to 1.7.4. 
* gnu/packages/emulators.scm (retroarch): Update to 1.7.4.
 2018-08-31 08:25:45 +02:00
Nicolas Goaziou be4c63f484
gnu: mame: Update to 0.201. 
* gnu/packages/emulators.scm (mame): Update to 0.201.
[arguments]: Remove unnecessary fix.
 2018-08-31 07:04:17 +02:00
Tobias Geerinckx-Rice 0c048c11a4
gnu: cmocka: Update to 1.1.2. 
* gnu/packages/check.scm (cmocka): Update to 1.1.2.
 2018-08-30 19:29:08 +02:00
Tobias Geerinckx-Rice 8a68b71d99
gnu: keyutils: Update to 1.5.11. 
* gnu/packages/crypto.scm (keyutils): Update to 1.5.11.
[inputs]: Add mit-krb5.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice d6d9ca1017
gnu: Don't use unstable tarballs in (packages opencl). 
* gnu/packages/opencl.scm (opencl-clhpp, clinfo, beignet, pocl)
[source]: Use GIT-FETCH and GIT-FILE-NAME.
(pocl)[arguments]: Remove ‘remove-headers’ phase.
(make-opencl-headers)[source]: Use GIT-FILE-NAME.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 8294362688
gnu: Add pipewalker. 
* gnu/packages/games.scm (pipewalker): New public variable.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 6e8c75b884
gnu: Add msr-tools. 
* gnu/packages/hardware.scm (msr-tools): New public variable.
 2018-08-30 19:28:10 +02:00
Tobias Geerinckx-Rice aadd1d241c
gnu: Add ddcutil. 
* gnu/packages/hardware.scm: New file.
(ddcutil): New public variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add the new file.
 2018-08-30 19:28:10 +02:00
Marius Bakke 7693f678d1
gnu: pango: Replace with 1.42.4. 
Fixes <https://bugs.gnu.org/32594>.

* gnu/packages/gtk.scm (pango)[replacement]: New field.
(pango-1.42.4): New public variable.
 2018-08-30 18:57:10 +02:00
Marius Bakke 883832b480
gnu: appstream-glib: Update to 0.7.12. 
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.12.
 2018-08-30 18:44:57 +02:00
Marius Bakke 4c13cb36f8
gnu: GnuPG: Update to 2.2.10. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.10.
 2018-08-30 18:44:57 +02:00
Marius Bakke e50c727878
gnu: rng-tools: Update to 6.4. 
* gnu/packages/linux.scm (rng-tools): Update to 6.4.
 2018-08-30 18:44:57 +02:00
Marius Bakke d3c1075c14
gnu: samba: Update to 4.8.5. 
* gnu/packages/samba.scm (samba): Update to 4.8.5.
 2018-08-30 18:44:57 +02:00
Marius Bakke 652940d060
gnu: ldb: Update to 1.3.6. 
* gnu/packages/samba.scm (ldb): Update to 1.3.6.
 2018-08-30 18:44:57 +02:00