Commit graph

56631 commits

Author SHA1 Message Date
Ricardo Wurmus
103de43c67
gnu: r-umap: Update to 0.2.5.0.
* gnu/packages/cran.scm (r-umap): Update to 0.2.5.0.
[native-inputs]: Add r-knitr.
2020-03-09 08:51:40 +01:00
Ricardo Wurmus
ea20989d87
gnu: r-rcppannoy: Update to 0.0.16.
* gnu/packages/cran.scm (r-rcppannoy): Update to 0.0.16.
[native-inputs]: Remove r-knitr.
2020-03-09 08:51:40 +01:00
Ricardo Wurmus
207ba868a3
gnu: r-quantmod: Update to 0.4-16.
* gnu/packages/cran.scm (r-quantmod): Update to 0.4-16.
2020-03-09 08:51:40 +01:00
Ricardo Wurmus
bcbcd17d45
gnu: r-vcd: Update to 1.4-6.
* gnu/packages/cran.scm (r-vcd): Update to 1.4-6.
2020-03-09 08:51:40 +01:00
Ricardo Wurmus
fec7f576b4
gnu: r-ggrepel: Update to 0.8.2.
* gnu/packages/cran.scm (r-ggrepel): Update to 0.8.2.
2020-03-09 08:51:36 +01:00
Christopher Baines
af96c1e0e4
services: cuirass: Allow passing extra command line options.
This is so that the options supported by the service configuration don't have
to always be changed. Generally though all options should be explicitly
supported and documented, so this is mostly to facilitate experimentation.

* gnu/services/cuirass.scm (<cuirass-configuration>): Add an extra-options
field.
(cuirass-shepherd-service): Pass the extra options to the shepherd servvices.
* doc/guix.texi (Continuous Integration): Document it.
2020-03-08 23:46:11 +00:00
Christopher Baines
d8ab68b929
services: guix-data-service: Allow passing extra options.
This is so that the options supported by the service configuration don't have
to always be changed. Generally though all options should be explicitly
supported and documented, so this is mostly to facilitate experimentation.

* gnu/services/guix.scm (<guix-data-service-configuration>): Add extra-options
and extra-process-jobs-options to the record type.
(guix-data-service-shepherd-services): Handle these new configuration record
fields.
* doc/guix.texi (Guix Data Service): Document these new options.
2020-03-08 23:35:03 +00:00
Christopher Baines
67d21e2b08
gnu: guix-data-service: Update to 0.0.1-18.18eb9df.
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-18.18eb9df.
(inputs, native-inputs): Switch to using the Guile 3 package variants where
applicable.
2020-03-08 23:35:00 +00:00
Jakub Kądziołka
94d57ba339
gnu: python-virtualenv: Update to 20.0.8.
* gnu/packages/python-xyz.scm (python-virtualenv): Update to 20.0.8.
  [arguments]: Remove the now-redundant 'disable-failing-test phase.
  [native-inputs]: Add python-setuptools and python-setuptools-scm.
  [inputs]: Add python-{appdirs, distlib, filelock, six,
  importlib-metadata}.
2020-03-09 00:20:49 +01:00
Jakub Kądziołka
6e79208954
gnu: python-xyz: Add python-filelock.
* gnu/packages/python-xyz.scm (python-filelock): New variable.
2020-03-09 00:20:47 +01:00
Jakub Kądziołka
f2a6483084
gnu: python-xyz: Add python-distlib.
* gnu/packages/python-xyz.scm (python-distlib): New variable.
2020-03-09 00:20:46 +01:00
Ricardo Wurmus
830eac9c27
gnu: ngless: Update to 1.1.0.
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08 23:37:09 +01:00
Ricardo Wurmus
3f68f76eaf
gnu: Add jack-select.
* gnu/packages/music.scm (jack-select): New variable.
2020-03-08 23:13:11 +01:00
Ricardo Wurmus
46a864e7c1
gnu: taxtastic: Update to 0.8.11.
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
2020-03-08 22:50:16 +01:00
Ludovic Courtès
d6d0e10b3d
gnu: guile-next: Revert to 3.0.0.
Guile 3.0.1 segfaults while building guix-system-tests.drv on
and "guile3.0-guix" on x86_64-linux.

* gnu/packages/guile.scm (guile-next): Revert to 3.0.0.
(guile-3.0):
2020-03-08 22:15:54 +01:00
Roel Janssen
3d33ca27b2
gnu: Add perl-config-inifiles.
* gnu/packages/perl.scm (perl-config-inifiles): New variable.
2020-03-08 21:50:44 +01:00
Roel Janssen
d0ca79e53d
gnu: Add perl-attribute-util.
* gnu/packages/perl.scm (perl-attribute-util): New variable.
2020-03-08 21:50:32 +01:00
Efraim Flashner
30acf2f959
gnu: Add font-opendyslexic.
* gnu/packages/fonts.scm (font-opendyslexic): New variable.
(font-open-dyslexic): Mark as deprecated package.
2020-03-08 22:42:33 +02:00
Ludovic Courtès
e5059c95aa
gnu: beep: Remove dependency on GCC 8.
* gnu/packages/terminals.scm (beep)[native-inputs]: Remove.
2020-03-08 21:21:57 +01:00
Vincent Legoll
1d91680c84
gnu: beep: Update to 1.4.9.
* gnu/packages/terminals.scm (beep): Update to 1.4.9.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08 21:21:57 +01:00
Jack Hill
f6713b55a1
services: certbot: Add server option.
* gnu/services/certbot.scm (certbot-configuration): Add server option.
(certbot-command): Use server option.
(certbot-actication): Use server option.
(certbot-nginx-server-configurations): Use server option.
* doc/guix.texi (Certificate Services): Document server option.

Co-authored-by: Tobias Geerinckx-Rice <me@tobias.gr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08 21:21:57 +01:00
Brice Waegeneire
9ef37e81d6
system: Export 'operating-system' missing fields.
* gnu/system.scm: Export 'operating-system-firmware',
'operating-system-keyboard-layout',
'operating-system-name-service-switch', 'operating-system-pam-services',
'operating-system-setuid-programs', 'operating-system-skeletons',
'operating-system-sudoers-file', 'operating-system-swap-devices'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-08 21:21:57 +01:00
Ludovic Courtès
1a30351bf3
gnu: guile-next: Update to 3.0.1.
* gnu/packages/guile.scm (guile-3.0): Update to 3.0.1.  Use "mirror://" URL.
2020-03-08 21:21:57 +01:00
Mathieu Othacehe
9a2f99f42f
gexp: Default to current target.
* guix/gexp.scm (lower-object): Set target argument to 'current by default and
look for the current target system at bind time if needed,
(gexp->file): ditto,
(gexp->script): ditto,
(lower-gexp): make sure lowered extensions are not cross-compiled.

* tests/gexp.scm: Add cross-compilation test-cases for gexp->script and
gexp->file with a target passed explicitely and with a default target.
2020-03-08 20:28:31 +01:00
Mathieu Othacehe
5d52d10661
store: Add set-current-target procedure.
* guix/store.scm (set-current-target): New exported procedure.
2020-03-08 20:28:31 +01:00
Ricardo Wurmus
c32897b6e4
gnu: r-robust: Update to 0.5-0.0.
* gnu/packages/statistics.scm (r-robust): Update to 0.5-0.0.
2020-03-08 16:02:04 +01:00
Ricardo Wurmus
7b2acf1508
gnu: r-rapidjsonr: Update to 1.2.0.
* gnu/packages/cran.scm (r-rapidjsonr): Update to 1.2.0.
2020-03-08 16:02:04 +01:00
Ricardo Wurmus
dc30cc0300
gnu: r-atacseqqc: Update to 1.10.3.
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.10.3.
[native-inputs]: Add r-knitr.
2020-03-08 16:02:04 +01:00
Hartmut Goebel
6434f9b634
gnu: Reword and extend descriptions for some KDE packages.
* gnu/packages/kde-multimedia.scm (libkcompatdisc)[description]: Extend.
* gnu/packages/kde-pim.scm (akonadi-search, kalarmcal, kdemailimporter,
  kdepim-apps-libs, kidentitymanagement, kldap, kmailtransport, kmbox, kmime,
  kontactinterface, kpimtextedit)[description]: Reword and extend.
  (ktnef, kpimcommon, libkdepim)[synopsis, description]: Reword and extend.
  (kmailtransport)[synopsis]: Fix space.
* gnu/packages/kde-systemtools.scm (khelpcenter)[description]: Extend.
2020-03-08 14:06:00 +01:00
Martin Becze
1eb3b2b666
gnu: Add emacs-org-journal.
* gnu/packages/emacs-xyz.scm (emacs-org-journal): New Variable.
2020-03-08 11:19:16 +01:00
Roel Janssen
e2ca10a46f
gnu: python-umap-learn: Fix build.
* gnu/packages/machine-learning.scm (python-umap-learn): Add python-joblib to
  run the test suite.
2020-03-08 10:20:22 +01:00
Maxim Cournoyer
5fdc5b2d57
services: nfs: Run rpc.mountd in foreground.
Fixes <https://bugs.gnu.org/39708>.

Shepherd doesn't keep track of processes that fork themselves and would
disable the process after restarting it a couple times.

* gnu/services/nfs.scm (nfs-shepherd-services): Invoke rpc.mountd with the
'--foreground' option.
2020-03-08 00:26:02 -05:00
Leo Famulari
be3908fa14
gnu: QEMU: Fix CVE-2020-8608.
* gnu/packages/patches/qemu-CVE-2020-8608.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/virtualization.scm (qemu)[source]: Use it.
2020-03-07 16:37:25 -05:00
Lars-Dominik Braun
83ac7cb42b
gnu: brotli: Remove package
Same package is provided by google-brotli.

* gnu/packages/compression.scm (brotli): Redefine as a deprecated alias
for "google-brotli".

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07 22:30:06 +01:00
Lars-Dominik Braun
d9476a3700
gnu: woff2: Update to 1.0.2
* gnu/packages/fontutils.scm (woff2): Update to 1.0.2 and switch to cmake
* gnu/packages/patches/woff2-libbrotli.patch: Remove
* gnu/local.mk (dist_patch_DATA): Remove patch

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07 22:30:06 +01:00
Vincent Legoll
74ff08e6b8
gnu: ccache: Fix indentation
* gnu/packages/ccache.scm (ccache): Fix indentation

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07 22:30:06 +01:00
Vincent Legoll
9eb456b8c7
gnu: ccache: Update to 3.7.7.
gnu/packages/ccache.scm (ccache): Update to 3.7.7, update homepage
to ccache.dev, get source code from github, remove fortran 77 from
description.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-07 22:30:06 +01:00
Ludovic Courtès
24a4a635fd
gnu: eudev: Add variant with corrected Btrfs rules.
Discussed at <https://bugs.gnu.org/39926>.

* gnu/packages/linux.scm (eudev/btrfs-fix): New variable.
* gnu/services/base.scm (<udev-configuration>)[udev]: Default to it.
(udev-service): Likewise for #:udev.
2020-03-07 22:30:00 +01:00
Ludovic Courtès
8ab060b68b
gnu: guile: Add 2.2.7.
* gnu/packages/guile.scm (guile-2.2.7): New variable.
(guile-2.2/bug-fix): Redefine as a deprecated alias for GUILE-2.2.7.
* gnu/packages/admin.scm (shepherd)[native-inputs, inputs]: Use GUILE-2.2.7.
* gnu/packages/patches/guile-finalization-crash.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
2020-03-07 22:29:44 +01:00
Nicolas Goaziou
2519e4cba8
gnu: emacs-xr: Update to 1.17.
* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.17.
2020-03-07 21:42:45 +01:00
Nicolas Goaziou
f61b980f5d
gnu: emacs-relint: Update to 1.15.
* gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.15.
2020-03-07 21:41:06 +01:00
Ricardo Wurmus
1c9e3e9f36
gnu: r-dplyr: Update to 0.8.5.
* gnu/packages/statistics.scm (r-dplyr): Update to 0.8.5.
[native-inputs]: Add r-knitr.
2020-03-07 20:03:55 +01:00
Ricardo Wurmus
667f799641
gnu: r-survival: Update to 3.1-11.
* gnu/packages/statistics.scm (r-survival): Update to 3.1-11.
2020-03-07 20:03:43 +01:00
Ricardo Wurmus
d8545835bd
gnu: r-lifecycle: Update to 0.2.0.
* gnu/packages/cran.scm (r-lifecycle): Update to 0.2.0.
[native-inputs]: Add r-knitr.
2020-03-07 20:03:32 +01:00
Ricardo Wurmus
a97c648c61
gnu: r-covr: Update to 3.5.0.
* gnu/packages/cran.scm (r-covr): Update to 3.5.0.
[native-inputs]: Add r-knitr.
2020-03-07 20:03:21 +01:00
Ricardo Wurmus
4882fcd292
gnu: r-pscl: Update to 1.5.5.
* gnu/packages/cran.scm (r-pscl): Update to 1.5.5.
2020-03-07 20:03:11 +01:00
Ricardo Wurmus
15d3ac75ce
gnu: r-mosaic: Add r-knitr.
* gnu/packages/cran.scm (r-mosaic)[native-inputs]: Add r-knitr.
2020-03-07 20:02:52 +01:00
Ricardo Wurmus
c68c7e2fbf
gnu: r-insight: Update to 0.8.2.
* gnu/packages/cran.scm (r-insight): Update to 0.8.2.
[native-inputs]: Add r-knitr.
2020-03-07 20:02:35 +01:00
Ricardo Wurmus
491ce4f083
gnu: r-heatmaply: Add r-knitr.
* gnu/packages/cran.scm (r-heatmaply)[native-inputs]: Add r-knitr.
2020-03-07 20:02:14 +01:00
Ricardo Wurmus
d56553edc3
gnu: r-methylkit: Add r-knitr.
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07 19:42:34 +01:00