2a360cf6ac
gnu: Add r-wavetiling.
...
* gnu/packages/bioconductor.scm (r-wavetiling): New variable.
2019-09-15 22:54:21 +02:00
f5349b4d5a
gnu: Add r-genomegraphs.
...
* gnu/packages/bioconductor.scm (r-genomegraphs): New variable.
2019-09-15 22:51:52 +02:00
4c63eeb8a4
gnu: Add r-oligo.
...
* gnu/packages/bioconductor.scm (r-oligo): New variable.
2019-09-15 22:50:31 +02:00
d6a5d9b24f
gnu: Add r-affxparser.
...
* gnu/packages/bioconductor.scm (r-affxparser): New variable.
2019-09-15 22:50:25 +02:00
df8576e5c9
gnu: Add r-variantfiltering.
...
* gnu/packages/bioconductor.scm (r-variantfiltering): New variable.
2019-09-15 22:41:03 +02:00
fc3719cc0f
gnu: Add r-shinythemes.
...
* gnu/packages/cran.scm (r-shinythemes): New variable.
2019-09-15 22:40:25 +02:00
41b8b05c9e
gnu: Add r-shinytree.
...
* gnu/packages/cran.scm (r-shinytree): New variable.
2019-09-15 22:33:50 +02:00
4112ff7e74
gnu: Add js-requirejs.
...
* gnu/packages/javascript.scm (js-requirejs): New variable.
2019-09-15 21:19:53 +02:00
bb0024dc69
gnu: Add r-reqon.
...
* gnu/packages/bioconductor.scm (r-reqon): New variable.
2019-09-15 21:07:57 +02:00
e5dfcd8e26
gnu: Add r-seqbias.
...
* gnu/packages/bioconductor.scm (r-seqbias): New variable.
2019-09-15 21:07:56 +02:00
12105c6c3a
gnu: Add r-affycoretools.
...
* gnu/packages/bioconductor.scm (r-affycoretools): New variable.
2019-09-15 20:58:26 +02:00
01c7ba9982
gnu: Add r-oligoclasses.
...
* gnu/packages/bioconductor.scm (r-oligoclasses): New variable.
2019-09-15 20:58:26 +02:00
15184fb386
gnu: Add r-reportingtools.
...
* gnu/packages/bioconductor.scm (r-reportingtools): New variable.
2019-09-15 20:58:25 +02:00
83b4209122
gnu: Add r-pfam-db.
...
* gnu/packages/bioconductor.scm (r-pfam-db): New variable.
2019-09-15 20:57:26 +02:00
4ca2d6c1a6
gnu: Add r-affycontam.
...
* gnu/packages/bioconductor.scm (r-affycontam): New variable.
2019-09-15 20:53:27 +02:00
5094aa9472
gnu: Add r-affycompatible.
...
* gnu/packages/bioconductor.scm (r-affycompatible): New variable.
2019-09-15 20:53:21 +02:00
5cf940de21
gnu: Add r-affycomp.
...
* gnu/packages/bioconductor.scm (r-affycomp): New variable.
2019-09-15 20:53:14 +02:00
53b1e10f23
gnu: Add r-affydata.
...
* gnu/packages/bioconductor.scm (r-affydata): New variable.
2019-09-15 20:53:01 +02:00
853211a51b
gnu: Add r-timeseriesexperiment.
...
* gnu/packages/bioconductor.scm (r-timeseriesexperiment): New variable.
2019-09-15 20:42:41 +02:00
739b2d10f0
gnu: Add r-wavcluster.
...
* gnu/packages/bioconductor.scm (r-wavcluster): New variable.
2019-09-15 20:41:01 +02:00
d77e69e9e1
gnu: r-spam: Update to 2.3-0.
...
* gnu/packages/cran.scm (r-spam): Update to 2.3-0.
2019-09-15 16:15:37 +02:00
e48e476f41
gnu: r-feather: Update to 0.3.5.
...
* gnu/packages/cran.scm (r-feather): Update to 0.3.5.
2019-09-15 16:15:37 +02:00
21fc601295
gnu: emacs-zerodark-theme: Update to 4.6.
...
* gnu/packages/emacs-xyz.scm (emacs-zerodark-theme): Update to 4.6.
[source]: Update to new source uri.
2019-09-15 15:29:18 +03:00
991c44109f
gnu: Add yubico-pam.
...
* gnu/packages/authentication.scm (yubico-pam): New variable.
2019-09-15 09:28:24 +02:00
9eac315069
gnu: r-delayedmatrixstats: Update to 1.6.1.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
2019-09-14 23:39:39 +02:00
82e343d14a
gnu: r-rhdf5lib: Update to 1.6.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
2019-09-14 23:39:25 +02:00
cd25e29616
gnu: r-rtracklayer: Update to 1.44.4.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
2019-09-14 23:39:20 +02:00
146f0ba5d1
gnu: r-genomicranges: Update to 1.36.1.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
2019-09-14 23:39:12 +02:00
7f518ef70b
gnu: r-s4vectors: Update to 0.22.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
2019-09-14 23:39:08 +02:00
11f973e093
gnu: r-mixomics: Update to 6.8.4.
...
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.4.
2019-09-14 23:39:03 +02:00
f8fb5b75c9
gnu: r-gtrellis: Update to 1.16.1.
...
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.1.
2019-09-14 23:38:58 +02:00
ec0270b1e9
gnu: r-regioner: Update to 1.16.4.
...
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.4.
2019-09-14 23:38:51 +02:00
cd75c487c8
gnu: Add emacs-elixir-mode.
...
* gnu/packages/emacs-xyz.scm (emacs-elixir-mode): New variable.
2019-09-14 19:44:40 +02:00
fda8ed0eb1
gnu: wine-staging: Update to 4.16.
...
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.16.
* gnu/packages/wine.scm (wine-staging): Update to 4.16.
2019-09-14 13:01:28 +02:00
981dcc3b0c
gnu: r-tidyr: Update to 1.0.0.
...
* gnu/packages/statistics.scm (r-tidyr): Update to 1.0.0.
[propagated-inputs]: Add r-ellipsis, r-lifecycle, and r-vctrs.
2019-09-14 00:37:47 +02:00
17f3960f28
gnu: r-diffusionmap: Update to 1.2.0.
...
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.2.0.
2019-09-14 00:37:46 +02:00
fd399b7a83
gnu: r-seqinr: Update to 3.6-1.
...
* gnu/packages/cran.scm (r-seqinr): Update to 3.6-1.
2019-09-14 00:37:46 +02:00
f5b1354fdb
gnu: Add r-lifecycle.
...
* gnu/packages/cran.scm (r-lifecycle): New variable.
2019-09-14 00:37:46 +02:00
cd3ba9c8c7
gnu: r-huge: Update to 1.3.3.
...
* gnu/packages/cran.scm (r-huge): Update to 1.3.3.
2019-09-14 00:37:46 +02:00
ac50956f31
gnu: r-tidytree: Update to 0.2.7.
...
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.7.
2019-09-14 00:37:46 +02:00
aef5e2aadd
gnu: r-activity: Update to 1.3.
...
* gnu/packages/cran.scm (r-activity): Update to 1.3.
[propagated-inputs]: Add r-insol.
2019-09-14 00:37:46 +02:00
d72da21d54
gnu: r-sjplot: Update to 2.7.1.
...
* gnu/packages/cran.scm (r-sjplot): Update to 2.7.1.
2019-09-14 00:37:46 +02:00
664e15ed8f
gnu: r-sjstats: Update to 0.17.6.
...
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.6.
[propagated-inputs]: Add r-parameters.
2019-09-14 00:37:46 +02:00
28110e6842
gnu: r-emmeans: Update to 1.4.1.
...
* gnu/packages/cran.scm (r-emmeans): Update to 1.4.1.
2019-09-14 00:37:46 +02:00
3ab3f7f3bb
gnu: r-sjlabelled: Update to 1.1.1.
...
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.1.
2019-09-14 00:37:46 +02:00
4557f44755
gnu: r-circlize: Update to 0.4.8.
...
* gnu/packages/cran.scm (r-circlize): Update to 0.4.8.
2019-09-14 00:37:46 +02:00
a1f4399438
gnu: r-httpuv: Update to 1.5.2.
...
* gnu/packages/cran.scm (r-httpuv): Update to 1.5.2.
2019-09-14 00:37:46 +02:00
5ad9da9ab3
gnu: Add r-insol.
...
* gnu/packages/cran.scm (r-insol): New variable.
2019-09-14 00:37:46 +02:00
a0244ef000
gnu: Add r-rgdal.
...
* gnu/packages/cran.scm (r-rgdal): New variable.
2019-09-14 00:37:46 +02:00
a5a79dd0b8
gnu: Add r-parameters.
...
* gnu/packages/cran.scm (r-parameters): New variable.
2019-09-14 00:37:45 +02:00
18a613fb29
gnu: gnujump: Add desktop file.
...
This fixes bug#37069.
* gnu/packages/games.scm (gnujump)[arguments]: Add custom
'create-desktop-entry phase to install a desktop file.
2019-09-13 17:07:16 +03:00
dbb0b06eb4
gnu: tipp10: Fix path in desktop entry.
...
* gnu/packages/patches/tipp10-fix-compiling.patch: Remove changes to
hardcode executable path.
2019-09-13 17:07:13 +03:00
0746c33eff
gnu: gmsh: Update home page.
...
This addresses a 'guix lint' warning.
* gnu/packages/maths.scm (gmsh)[home-page]: Update to avoid URL
redirection.
2019-09-13 14:53:57 +01:00
f61f424d5b
gnu: mcron: Update to 1.1.2.
...
* gnu/packages/guile-xyz.scm (mcron): Update to 1.1.2.
[arguments]: Remove custom 'set-timezone phase.
[native-inputs]: Add autoconf, automake, help2man, texinfo.
[inputs]: Remove ed, which.
2019-09-13 16:02:31 +03:00
f0e149752a
gnu: shellutils.scm: Sort module inputs.
...
* gnu/packages/shellutils.scm: Sort module inputs alphabetically.
2019-09-13 15:39:43 +03:00
8ebd56ea75
gnu: Add zsh-autosuggestions.
...
* gnu/packages/shellutils.scm (zsh-autosuggestions): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-09-13 15:39:34 +03:00
9c4cb1ef4c
gnu: Add ruby-rspec-wait.
...
* gnu/packages/ruby.scm (ruby-rspec-wait): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-09-13 15:39:28 +03:00
f69f37d54a
gnu: Add sh-z shell tool
...
* gnu/packages/shellutils.scm (sh-z): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-13 10:50:11 +02:00
a00a3132c7
gnu: Thunar: Update to 1.8.9.
...
* gnu/packages/xfce.scm (thunar): Update to 1.8.9.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-13 10:50:11 +02:00
ba05be2249
gnu: openblas: Set 'NUM_THREADS'.
...
Until now, OpenBLAS would use at most the N threads, where N is the
number of cores that happened to be available on the build
machine (typically N=8).
* gnu/packages/maths.scm (openblas/fixed-num-threads): New variable.
(openblas)[replacement]: New field.
(openblas-ilp64): Use 'package/inherit'.
2019-09-13 10:50:11 +02:00
5ad0a45221
gnu: python-matplotlib-documentation: Add missing input.
...
* gnu/packages/python-xyz.scm (python-matplotlib-documentation)[native-inputs]:
Add python-sphinx-copybutton.
(python2-matplotlib-documentation)[native-inputs]: Remove
python-sphinx-copybutton.
2019-09-13 00:44:57 +02:00
bcb22b3624
gnu: Add python-sphinx-copybutton.
...
* gnu/packages/sphinx.scm (python-sphinx-copybutton): New variable.
2019-09-13 00:44:57 +02:00
5ea654cfe0
gnu: python-matplotlib: Update to 3.1.1.
...
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.1.1.
[native-inputs]: Remove python-nose; add python-pytest and unzip; add
jquery-ui.
[arguments]: Add build phases "fix-and-disable-failing-tests" and
"install-jquery-ui", and move the "check" phase after the "install" phase;
use the default backend in setup.cfg.
(python2-matplotlib): Keep at version 2.2.3.
(python-matplotlib-documentation)[arguments]: Remove "check" phase.
2019-09-13 00:44:57 +02:00
16fddf17f5
gnu: Add r-assertr.
...
* gnu/packages/cran.scm (r-assertr): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-09-13 00:44:57 +02:00
86ce3691e1
gnu: emacs-interactive-align: Update to 0.4.2.
...
* gnu/packages/emacs-xyz.scm (emacs-interactive-align): Update to 0.4.2.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-12 23:23:47 +02:00
2151e04c1a
gnu: Add emacs-doom-themes.
...
* gnu/packages/emacs-xyz.scm (emacs-doom-themes): New variable.
Co-authored-by: Brett Gilio <brettg@posteo.net>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-12 23:22:19 +02:00
d236cd16a7
linux-container: "run-container" scripts shows the container's PID.
...
* gnu/build/linux-container.scm (call-with-container): Add
#:process-spawned-hook and honor it.
* gnu/system/linux-container.scm (container-script)[script]:
Define 'explain' and pass it as #:process-spawned-hook'.
2019-09-12 23:07:43 +02:00
3d8424a5ad
services: Fix /usr/bin/env special file target.
...
This is a followup to a916215597
2019-09-12 23:07:42 +02:00
da966a7a3d
linux-container: Exclude more services when sharing networking with the host.
...
* gnu/system/linux-container.scm (containerized-operating-system)[useless-services]:
Add more services to the list when SHARED-NETWORK? is true.
2019-09-12 23:07:42 +02:00
5ccec77176
file-systems: Add /var/run/nscd to '%network-file-mappings'.
...
This allows containers created by "guix environment -CN" or by
"guix system container -N" to talk to the host nscd.
* gnu/system/file-systems.scm (%network-file-mappings): Add
"/var/run/nscd".
* gnu/build/shepherd.scm (default-mounts)[nscd-socket]: Remove.
* gnu/system/linux-container.scm (container-script)[nscd-run-directory]
[nscd-mapping, nscd-os, nscd-specs]: Remove.
[script]: Filter out from SPECS bind-mounts where the device does not
exist.
* guix/scripts/environment.scm (launch-environment/container)
[optional-mapping->fs]: New procedure.
[mappings]: Remove %NETWORK-FILE-MAPPINGS.
[file-systems]: Add %NETWORK-FILE-MAPPINGS here, filtered through
'optional-mapping->fs'.
2019-09-12 23:07:42 +02:00
abed5df777
gnu: gmsh: Fetch source from Git.
...
* gnu/packages/maths.scm (gmsh)[source]: Switch to GIT-FETCH.
2019-09-12 16:21:31 +01:00
e2fb29b792
gnu: python-pytest-virtualenv: Enable tests.
...
* gnu/packages/python-check.scm (python-pytest-virtualenv)
[phases]{patch-virtualenv-executable}: New phase.
[propagated-inputs]: Move python-virtualenv from here...
[inputs]: ...to here.
2019-09-13 00:10:35 +09:00
01a53e0b37
gnu: python-pathpy: Add a missing propagated input.
...
This fixes the build of 'python-pytest-shutil', amongst others.
* gnu/packages/python-xyz.scm (python-pathpy)[propagated-inputs]: Add
python-importlib-metadata.
2019-09-13 00:09:50 +09:00
237d4cf73c
gnu: gfbgraph: Don't use NAME in source URI.
...
* gnu/packages/gnome.scm (gfbgraph)[source]: Hard-code NAME.
2019-09-12 16:16:44 +02:00
7faed56c44
gnu: openconnect: Update to 8.05 [fixes CVE-2019-16239].
...
* gnu/packages/vpn.scm (openconnect): Update to 8.05.
2019-09-12 16:16:44 +02:00
8b35c8cd61
gnu: hypre: Update texlive-union.
...
* gnu/packages/maths.scm (hypre)[native-inputs]: Replace texlive-generic-xypic
and texlive-fonts-xypic with texlive-xypic; add texlive-cm to the
texlive-union.
2019-09-12 12:10:05 +02:00
63d57404b3
gnu: texlive-xypic: Install all files.
...
Reported by numerobis on the #guix IRC channel.
* gnu/packages/tex.scm (texlive-xypic)[source]: Install "tex/generic/xypic"
files.
[arguments]: Remove #:tex-directory.
2019-09-12 12:10:05 +02:00
4913828bb1
gnu: python-language-server: Update to 0.28.3-1.c3cab77.
...
* gnu/packages/python-xyz.scm (python-language-server): Update to 0.28.3-1.c3cab77.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2019-09-12 09:47:48 +09:00
412153bbaf
gnu: r-bsgenome-celegans-ucsc-ce6: Permit substitution.
...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6)[arguments]:
Remove field.
2019-09-11 23:59:28 +02:00
86ced7b271
gnu: r-bsgenome-celegans-ucsc-ce6: Use bioconductor-uri.
...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6)[source]: Use
BIOCONDUCTOR-URI.
2019-09-11 23:58:52 +02:00
0f272518ec
gnu: python-ipython-documentation: Make reproducible.
...
Fixes <https://bugs.gnu.org/37373/ >.
* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Add phase
"make-docs-reproducible" to remove timestamps from documentation generated in
dependent python-ipython-documentation package.
2019-09-11 23:30:49 +02:00
6f2f7bc88a
gnu: recode: Don't use NAME in source URI.
...
* gnu/packages/textutils.scm (recode)[source]: Hard-code NAME.
2019-09-11 22:56:04 +02:00
5ca1900ba5
gnu: recode: Update to 3.7.5.
...
* gnu/packages/textutils.scm (recode): Update to 3.7.5.
[native-inputs]: Use python@3 and python-cython@3.
2019-09-11 22:56:04 +02:00
3b14974706
gnu: glslang: Use GIT-FILE-NAME.
...
* gnu/packages/vulkan.scm (glslang)[source]: Use GIT-FILE-NAME.
2019-09-11 22:56:04 +02:00
97e53dccc0
gnu: nghttp2: Don't use NAME in source URI.
...
* gnu/packages/web.scm (nghttp2)[source]: Hard-code NAME.
2019-09-11 22:56:04 +02:00
bfebc73a74
gnu: neofetch: Update to 6.1.0.
...
* gnu/packages/admin.scm (neofetch): Update to 6.1.0.
2019-09-11 22:56:04 +02:00
e8cfac22c7
gnu: youtube-dl: Update to 2019.09.12.
...
* gnu/packages/video.scm (youtube-dl): Update to 2019.09.12.
2019-09-11 21:03:02 +02:00
cf065aba1e
gnu: openssl: Update to 1.1.1d [fix CVE-2019-{1547,1549,1552,1563}].
...
* gnu/packages/tls.scm (openssl-next): Update to 1.1.1d.
2019-09-11 18:30:22 +02:00
5df412bfe6
services: libvirtd: Use '/run/current-system/profile/bin' as PATH.
...
This is a followup to ef640db2f5
2019-09-11 23:12:02 +08:00
ae9b6dba19
gnu: foo2zjs: Update to 20190909.
...
* gnu/packages/cups.scm (foo2zjs): Update to 20190909.
2019-09-11 16:30:15 +02:00
d1c9684753
gnu: workrave: Correct the types of inputs used.
...
* gnu/packages/gnome.scm (workrave)[propagated-inputs]: Move them all to...
[inputs]: ...here.
[native-inputs]: Move libxscrnsaver to the 'inputs' field.
2019-09-11 22:07:13 +09:00
aa51d92cdb
gnu: workrave: Update to version 1.10.34.
...
* gnu/packages/gnome.scm (workrave): Update version and hash strings.
[inputs]: Remove python-cheetah.
[native-inputs]: Add boost, python-3 and python-jinja2; remove the "bin"
output of glib.
2019-09-11 22:07:12 +09:00
7dc4b2a728
gnu: emacs-debbugs: Update to 0.19.
...
* gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.19.
2019-09-11 14:44:15 +02:00
373546123e
gnu: emacs-smart-mode-line: Update to 2.13.
...
* gnu/packages/emacs-xyz.scm (emacs-smart-mode-line): Update to 2.13.
2019-09-11 14:43:57 +02:00
28123c01d1
gnu: guile-json: Use "mirror://savannah" URL.
...
* gnu/packages/guile.scm (guile-json, guile-json-3): Change URL to
mirror://savannah.
2019-09-11 14:08:34 +02:00
4e0299194d
gnu: guile-json: Update to 3.2.0.
...
* gnu/packages/guile.scm (guile-json-3): Update to 3.2.0.
2019-09-11 14:08:34 +02:00
9abc58d3ef
gnu: guile-gcrypt: Update to 0.2.0.
...
* gnu/packages/gnupg.scm (guile-gcrypt): Update to 0.2.0.
2019-09-11 14:08:33 +02:00
ef640db2f5
gnu: libvirt: Don't wrap with PATH.
...
This reverts commit 903e051a71https://bugs.gnu.org/31365 >. The full path of the 'ip' command is already
embedded, and we want to search 'qemu' in PATH.
* gnu/packages/virtualization.scm (libvirt): Remove 'wrap-libvirtd phase. Add
configure flags to run qemu as 'nobody:kvm'.
* gnu/services/virtualization.scm (libvirt-service-type): Add 'qemu' to the
system profile.
2019-09-11 19:15:30 +08:00
e135ef9686
gnu: emacs-elpy: Update to 1.31.0.
...
* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1.31.0.
2019-09-11 18:10:21 +09:00
296e1aea65
gnu: python-jedi: Update to 0.15.1 and re-enable tests.
...
* gnu/packages/python-xyz.scm (python-jedi): Update to 0.15.1; re-enable
tests.
2019-09-11 18:10:20 +09:00
Ricardo Wurmus