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Author SHA1 Message Date
Tobias Geerinckx-Rice 0971f8bd88
gnu: Remove r-biocinstaller. 
It requires R < 3.6 and is no longer supported.

* gnu/packages/bioinformatics.scm (r-biocinstaller): Define as
deprecated in favour of r-biocmanager.
 2019-07-08 16:13:11 +02:00
Tobias Geerinckx-Rice 1042e3481d
gnu: r-xbioc: Update to 0.1.16-1.6ff0670. 
This is needed to deprecate r-biocinstaller, which is no longer
distributed.

* gnu/packages/bioinformatics.scm (r-xbioc): Update to 0.1.16-1.6ff0670.
[propagated-inputs]: Replace deprecated r-biocinstaller with
r-biocmanager.
 2019-07-08 16:11:55 +02:00
Tobias Geerinckx-Rice ddfb62807d
gnu: cmh: Fix build. 
This follows up on commit 1de48e8f8a.

* gnu/packages/algebra.scm (fplll-4-cmh): New variable.
(cmh)[inputs]: Use it.
 2019-07-08 15:48:07 +02:00
Tobias Geerinckx-Rice 69e3512b7c
gnu: libomp: Download over HTTPS. 
* gnu/packages/llvm.scm (libomp)[source]: Use HTTPS.
 2019-07-08 15:33:35 +02:00
Tobias Geerinckx-Rice e2170c3192
gnu: libomp: Fix source hash. 
This is a follow-up to commit c5296e205b,
which updated llvm.

* gnu/packages/llvm.scm (libomp)[source]: Fix hash.
 2019-07-08 15:33:35 +02:00
Tobias Geerinckx-Rice 61242625ad
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.7. 
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.7.
 2019-07-08 15:33:35 +02:00
Joseph LaFreniere 377b0501c4
gnu: Add emacs-polymode-org. 
* gnu/packages/emacs-xyz.scm (emacs-polymode-org): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-08 13:05:56 +02:00
Joseph LaFreniere 85630d8042
gnu: emacs-polymode: Update to 0.2. 
* gnu/packages/emacs-xyz.scm (emacs-polymode): Update to 0.2.
[source]: Change URL of Git repository to Polymode GitHub project.
[homepage]: Change URL to polymode GitHub project.
[description]: Realign text.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-08 13:05:56 +02:00
ison 88a29b5cd3
gnu: i3blocks: Update to ec050e7. 
* gnu/packages/wm.scm (i3blocks): Update to ec050e7.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-08 13:05:56 +02:00
Pierre Langlois a55dd25d3e
gnu: dosfstools: Enable compat symlinks. 
Enable compatibility symlinks to provide commands such as `mkfs.vfat`.

* gnu/packages/disk.scm (dosfstools)[arguments]: Pass
"--enable-compat-symlinks" to configure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-08 13:05:56 +02:00
Pierre Langlois b9a1d74de5
gnu: wireservice: New wireservice-package macro. 
Replace the parent 'base-package' variable with a 'wireservice-package' macro
that includes all common package fields.

* gnu/packages/wireservice.scm (base-package): Delete.
(wireservice-package): New macro.
(python-leather, python-agate, python-agate-sql, python-agate-dbf,
python-agate-excel): Use wireservice-package.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-08 13:05:55 +02:00
Efraim Flashner c7b757c46c
gnu: gama: Update to 2.06. 
* gnu/packages/gps.scm (gama): Update to 2.06.
 2019-07-08 10:38:23 +03:00
Vagrant Cascadian d335ef51d7
gnu: diffoscope: Update to 116. 
* gnu/packages/package-management (diffoscope): Update to 116.
 2019-07-07 18:57:28 -07:00
Pierre Langlois bf187d92e3
gnu: Add csvkit. 
* gnu/packages/wireservice.scm (csvkit): New variable.
* gnu/packages/patches/csvkit-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois 213b05f04e
gnu: Add python-agate-excel. 
* gnu/packages/wireservice.scm (python-agate-excel): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois f1122a2c91
gnu: Add python-agate-dbf. 
* gnu/packages/wireservice.scm (python-agate-dbf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois 9b2850c845
gnu: Add python-agate-sql. 
* gnu/packages/wireservice.scm (python-agate-sql): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois dc835e75ce
gnu: Add python-agate. 
* gnu/packages/wireservice.scm (python-agate): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois 451742bcf6
gnu: Add python-leather. 
* gnu/packages/wireservice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois edeb04bfb7
gnu: Add python-dbfread. 
* gnu/packages/python-xyz.scm (python-dbfread): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois 450d5dc289
gnu: Add python-crate. 
* gnu/packages/databases.scm (python-crate): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:20 +02:00
Pierre Langlois 0d5b7ea11f
gnu: Add python-pytimeparse. 
* gnu/packages/time.scm (python-pytimeparse): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Pierre Langlois 6543bc80b4
gnu: Add python-slugify. 
* gnu/packages/python-web.scm (python-slugify): New variable.
* gnu/packages/patches/python-slugify-depend-on-unidecode.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung e41ba8606f
gnu: Add emacs-moe-theme-el. 
* gnu/packages/emacs-xyz.scm (emacs-moe-theme-el): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung ae429e48d1
gnu: emacs-goto-chg: Update to 1.7.3-1.1829a13. 
* gnu/packages/emacs-xyz.scm (emacs-goto-chg): Update to 1.7.3-1.1829a13.
[origin]: Use GIT-FETCH and GIT-REFERENCE.
[home-page]: Update.
[inputs]: Add emacs-undo-tree.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung 81d1baafdb
gnu: emacs-hydra: Update to 0.15.0. 
* gnu/packages/emacs-xyz.scm (emacs-hydra): Update to 0.15.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung b453637f1b
gnu: Add emacs-lpy. 
* gnu/packages/emacs-xyz.scm (emacs-lpy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung 55a0b2a08d
gnu: emacs-md4rd: Update to 0.3.1. 
* gnu/packages/emacs-xyz.scm (emacs-md4rd): Update to 0.3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:19 +02:00
Brian Leung 26150eac73
gnu: emacs-zoutline: Update to 0.2.0. 
* gnu/packages/emacs-xyz.scm (emacs-zoutline): Update to 0.2.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 9f6dca4de3
gnu: emacs-restclient: Update to 0-2.422ee8d. 
* gnu/packages/emacs-xyz.scm (emacs-restclient): Update to 0-2.422ee8d.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung fa71034115
gnu: emacs-disk-usage: Don't use unstable tarball. 
* gnu/packages/emacs-xyz.scm (emacs-disk-usage)[source]: Use GIT-FETCH and GIT-FILE-NAME.
[home-page] Move to usual location.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 8330715878
gnu: emacs-fish-completion: Don't use unstable tarball. 
* gnu/packages/emacs-xyz.scm (emacs-fish-completion)[source]: Use GIT-FETCH
  and GIT-FILE-NAME.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 846d83482f
gnu: emacs-company-restclient: Update to 0.3.0. 
* gnu/packages/emacs-xyz.scm (emacs-company-restclient): Update to 0.3.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 1fd2886ca7
gnu: emacs-skewer-mode: Update to 1.8.0. 
* gnu/packages/emacs-xyz.scm (emacs-skewer-mode): Update to 1.8.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 9ee3be1bd5
gnu: emacs-simple-httpd: Update to 1.5.1. 
* gnu/packages/emacs-xyz.scm (emacs-simple-httpd): Update to 1.5.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:18 +02:00
Brian Leung 1c9ea5aaa4
gnu: emacs-git-timemachine: Update to 4.10. 
* gnu/packages/emacs-xyz.scm (emacs-git-timemachine): Update to 4.10.
[propagated-inputs] Add emacs-transient.
[source] Use GIT-FETCH and GIT-REFERENCE.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-07-07 15:48:17 +02:00
Rutger Helling aad6596294
gnu: wine-staging: Update to 4.12.1. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.12.1.
* gnu/packages/wine.scm (wine-staging): Update to 4.12.1.
 2019-07-07 13:51:06 +02:00
Christopher Baines d029afdd2d
gnu: Update lollypop to 1.1.3.1. 
* gnu/packages/gnome.scm (lollypop): Update to 1.1.3.1.
[inputs]: Add python-pil.
 2019-07-07 12:24:19 +01:00
Marius Bakke c72647fbae
gnu: xpad: Build against gtksourceview@3. 
* gnu/packages/gnome.scm (xpad)[inputs]: Change GTKSOURCEVIEW to GTKSOURCEVIEW-3.
 2019-07-06 20:43:00 +02:00
Marius Bakke 4ed252c332
gnu: jsoncpp: Update to 1.9.0. 
* gnu/packages/serialization.scm (jsoncpp): Update to 1.9.0.
 2019-07-06 18:49:52 +02:00
Marius Bakke f1818f96a3
gnu: jsoncpp: Fetch sources through git. 
* gnu/packages/serialization.scm (jsoncpp)[source]: Switch to GIT-FETCH.
 2019-07-06 18:48:56 +02:00
Marius Bakke f4d562b008
gnu: libraw: Update to 0.19.3. 
* gnu/packages/photo.scm (libraw): Update to 0.19.3.
 2019-07-06 18:44:15 +02:00
Marius Bakke e9cb6edd06
gnu: python-soupsieve: Update to 1.9.2. 
* gnu/packages/python-xyz.scm (python-soupsieve): Update to 1.9.2.
 2019-07-06 18:39:17 +02:00
Brian Leung e39d4933d1
gnu: python-setuptools: Update to 41.0.1. 
* gnu/packages/python-xyz.scm (python-setuptools): Update to 41.0.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2019-07-06 18:26:02 +02:00
Marius Bakke 5bef0f108c
gnu: python-olefile: Update to 0.46. 
* gnu/packages/python-xyz.scm (python-olefile): Update to 0.46.
[source]: Switch to release tarball instead of git snapshot.
 2019-07-06 18:26:02 +02:00
Ludovic Courtès 8dfb0c969e
tests: encrypted-root-os: Increase root partition size. 
1.2G had become slightly too small on x86_64.

* gnu/tests/install.scm (%encrypted-root-installation-script): Increase
root partition size to 1.3G.
 2019-07-06 16:17:24 +02:00
Ludovic Courtès c3ab921eed
ci: 'channel-build-system' honors the target system. 
Fixes a bug made evident e79281be105b16153c375af5506db31fd1e32698: the
x86_64-linux derivation of 'current-guix' would be cached and reused for
i686-linux, leading to test
failures.

Namely, /run/current-system/profile/bin/guix would have an x86_64
binary in its shebang, and thus it would end up being interpreted by
/bin/sh, which would fail like this:

  + guix --version
  /run/current-system/profile/bin/guix: line 2: !#: command not found
  /run/current-system/profile/bin/guix: line 3: syntax error near unexpected token `set!'
  /run/current-system/profile/bin/guix: line 3: `(begin (set! %load-path …

See <https://ci.guix.gnu.org/build/1431119/details>.

* gnu/ci.scm (channel-build-system)[build]: Pass #:system to
'run-with-store'.
 2019-07-06 16:17:24 +02:00
Rutger Helling 403f2189aa
gnu: wine-staging: Update to 4.12. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.12.
* gnu/packages/wine.scm (wine-staging): Update to 4.12.
 2019-07-06 10:47:51 +02:00
Ludovic Courtès 935e79af61
linux-container: Mount a new /dev/pts instance in the container. 
Fixes <https://bugs.gnu.org/36463>.
Reported by Steffen Rytter Postas <nc@scalehost.eu>.

* gnu/build/linux-container.scm (mount-file-systems): When /dev/ptmx
exists on the host, explicitly mount a new instance of devpts and make
/dev/ptmx a symlink to /dev/pts/ptmx.
 2019-07-06 00:26:58 +02:00
Nicolas Goaziou c356e5f7a0
gnu: grammalecte: Update to 1.2. 
* gnu/packages/dictionaries.scm (grammalecte): Update to 1.2.
 2019-07-06 00:10:44 +02:00