c5ffc9b65d
gnu: plantuml: Update to 1.2022.3.
...
* gnu/packages/uml.scm (plantuml): Update to 1.2022.3.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 17:52:19 +03:00
05e68f31ba
gnu: python-velocyto: Set cache directory for Numba.
...
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
2022-03-31 16:02:21 +02:00
8f3dc994bb
gnu: wfmash: Enable test suite.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
2022-03-31 16:29:34 +03:00
1ca9d9e194
gnu: Add wfmash.
...
* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:53 +03:00
8524904e08
gnu: atomic-queue: Do not look for boost when cross-compiling.
...
* gnu/packages/cpp.scm (atomic-queue)[arguments]: When cross-compiling, add a
do-not-check-for-boost phase.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:53 +03:00
a83918837e
gnu: atomic-queue: Run tests correctly.
...
* gnu/packages/cpp.scm (atomic-queue)[arguments]: In the check phase, run
tests instead of returning a function to run them.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
7d331dd203
gnu: htslib: Add bzip2 and xz to inputs.
...
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
973ee1c91d
gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux.
...
* gnu/packages/maths.scm (gsl)[arguments]: Force an autotools bootstrap
when cross-compiling to riscv64-linux.
[native-inputs]: Add autoconf, automake and libtool when cross-compiling
to riscv64-linux.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
a69a44bf59
gnu: python-loompy: Update to 3.0.7.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
2022-03-31 14:37:58 +02:00
38b2026515
gnu: Add python-numpy-groupies.
...
* gnu/packages/python-science.scm (python-numpy-groupies): New variable.
2022-03-31 14:37:58 +02:00
668d52a815
gnu: Add riscv-pk.
...
* gnu/packages/virtualization.scm (riscv-pk): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 15:20:11 +03:00
9afad0c16e
gnu: spike: Substitute path to dtc instead of wrapping executables.
...
* gnu/packages/virtualization.scm (spike)[arguments]: Delete the wrap-binary
phase. Add a configure-dtc-path phase that substitutes the absolute path to
dtc.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 15:20:08 +03:00
dda555fead
gnu: python-anndata: Update to 0.8.0.
...
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.8.0.
[arguments]: Remove build phase 'relax-dependency-requirements.
2022-03-31 10:36:31 +02:00
ea403bf290
gnu: python-h5py: Update to 3.6.0.
...
* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0.
[arguments]: Set HDF5_DIR variable instead of patching files.
2022-03-31 10:36:31 +02:00
967d5fd5c2
gnu: python2-h5py: Detach version and source from python-h5py.
...
* gnu/packages/python-xyz.scm (python2-h5py): Override source and version
field.
(python-h5py)[properties]: Record python2-variant.
2022-03-31 10:36:31 +02:00
ecb2603046
gnu: weechat: Update to 3.5.
...
* gnu/packages/irc.scm (weechat): Update to 3.5.
[inputs]: Add zstd:lib.
2022-03-30 20:52:14 +03:00
cb00a5fd85
gnu: msmtp: Update to 1.8.20.
...
* gnu/packages/mail.scm (msmtp): Update to 1.8.20.
2022-03-30 20:24:55 +03:00
96a1d6b7a0
gnu: ncdu-2: Update to 2.1.1.
...
* gnu/packages/ncdu.scm (ncdu-2): Update to 2.1.1.
2022-03-30 19:58:29 +03:00
693212087d
gnu: ncdu2: Set upstream name.
...
* gnu/packages/ncdu.scm (ncdu-2)[properties]: New field.
2022-03-30 19:58:29 +03:00
1c2da66035
gnu: anonip: Update to 1.1.0.
...
* gnu/packages/web.scm (anonip): Update to 1.1.0.
[source]: Fetch from git.
[arguments]: Run tests with pytest.
[native-inputs]: Add python-pytest and python-pytest-cov.
2022-03-30 15:33:22 +02:00
643d05eb20
lsof: Prevent mass-rebuild.
...
* gnu/packages/lsof.scm (lsof): Set LINUX_CONF_CC variable only when
cross-compiling.
2022-03-30 14:40:04 +02:00
2387adf600
gnu: lbzip2: Fix cross-compilation.
...
* gnu/packages/compression.scm (lbzip2)[arguments]: Search (or
native-inputs inputs) for gnulib-tool.py.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-03-30 12:34:36 +02:00
a006b7d347
gnu: lsof: Fix cross-compilation.
...
* gnu/packages/lsof (lsof)[arguments]: Add LINUX_CONF_CC environment
variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-03-30 11:50:58 +02:00
457999ce36
gnu: Mutt: Update to 2.2.2.
...
* gnu/packages/mail.scm (mutt): Update to 2.2.2.
2022-03-29 23:33:07 -04:00
1d62b15dc1
gnu: linux-libre 4.9: Update to 4.9.309.
...
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.309.
(linux-libre-4.9-pristine-source): Update hash.
2022-03-29 13:40:14 -04:00
555b2b0bd0
gnu: linux-libre 4.14: Update to 4.14.274.
...
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.274.
(linux-libre-4.14-pristine-source): Update hash.
2022-03-29 13:40:14 -04:00
ef57c59046
gnu: linux-libre 4.19: Update to 4.19.237.
...
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.237.
(linux-libre-4.19-pristine-source): Update hash.
2022-03-29 13:40:14 -04:00
5721cb284a
gnu: linux-libre 5.4: Update to 5.4.188.
...
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.188.
(linux-libre-5.4-pristine-source): Update hash.
2022-03-29 13:40:14 -04:00
ded6beb9a7
gnu: linux-libre 5.10: Update to 5.10.109.
...
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.109.
(linux-libre-5.10-pristine-source): Update hash.
2022-03-29 13:40:13 -04:00
916b333e86
gnu: linux-libre 5.15: Update to 5.15.32.
...
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.32.
(linux-libre-5.15-pristine-source): Update hash.
2022-03-29 13:40:13 -04:00
c2a141156e
gnu: linux-libre 5.16: Update to 5.16.18.
...
* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.18.
(linux-libre-5.16-pristine-source): Update hash.
2022-03-29 13:40:13 -04:00
89af5cd2a9
gnu: linux-libre 5.17: Update to 5.17.1.
...
* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.1.
(linux-libre-5.17-pristine-source): Update hash.
2022-03-29 13:40:13 -04:00
4b8500e7cb
gnu: gmid: Update to 1.8.2.
...
* gnu/packages/web.scm (gmid): Update to 1.8.2.
[native-inputs]: Remove which.
Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-29 12:53:26 -04:00
6c317e02ee
gnu: git-annex: Update to 10.20220322.
...
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220322.
[inputs]: Add ghc-http-client-restricted.
Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-29 12:53:26 -04:00
e59069fe2b
gnu: Add ghc-http-client-restricted.
...
* gnu/packages/haskell-web.scm (ghc-http-client-restricted): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-29 12:53:26 -04:00
f40c72327e
gnu: ghc-http-client-tls: Update to 0.3.6.1.
...
* gnu/packages/haskell-web.scm (ghc-http-client-tls): Update to 0.3.6.1.
Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-29 12:53:26 -04:00
d2984784fd
gnu: ghc-http-client: Update to 0.7.11.
...
* gnu/packages/haskell-web.scm (ghc-http-client): Update to 0.7.11.
[inputs]: Add ghc-iproute.
Signed-off-by: Leo Famulari <leo@famulari.name>
2022-03-29 12:53:25 -04:00
591007f7d1
gnu: r-signac: Update to 1.6.0-2.458e647.
...
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 17:40:17 +02:00
977a33139e
gnu: plink-ng: Update to 2.00a3-20220315.
...
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29 15:33:55 +02:00
d710f01957
gnu: Add r-cytobackbone.
...
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 14:03:44 +02:00
6d5964e804
gnu: pigx-sars-cov2-ww: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
847acc3206
gnu: pigx-rnaseq: Update to 0.0.20.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
3b0c9e4c20
gnu: kpeoplevcard: Use mirror URI.
...
* gnu/packages/kde-pim.scm (kpeoplevcard)[source]: Use kde mirror URI.
2022-03-29 14:43:21 +03:00
d9710380a4
gnu: pulseaudio-qt: Use mirror URI.
...
* gnu/packages/kde-frameworks.scm (pulseaudio-qt)[source]: Use kde
mirror URI.
2022-03-29 14:43:20 +03:00
67213a2759
download: Use https for main KDE source.
...
* guix/download.scm (%mirrors)[kde]: Use https URIs for main KDE mirrors.
* tests/lint.scm ("mirror-url: kde suggestion"): New test.
2022-03-29 14:43:14 +03:00
53b04339fe
gnu: neovim: Update to 0.6.1.
...
* gnu/packages/vim.scm (neovim): Update to 0.6.1.
Build neovim with LuaJIT in the supported platforms.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-29 11:56:52 +02:00
1e2a25579c
gnu: Add tree-sitter.
...
* gnu/packages/text-editors.scm (tree-sitter): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-29 11:56:49 +02:00
5cabe24e56
gnu: Add xfce4-dict.
...
* gnu/packages/xfce.scm (xfce4-dict): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-29 11:36:15 +02:00
ddfebdab86
gnu: poezio: Update to 0.13.2.
...
* gnu/packages/messaging.scm (poezio): Update to 0.13.2.
[arguments]: Remove trailing boolean and use new style.
[inputs]: Remove unused python input.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-29 11:30:25 +02:00
39b27a17ec
gnu: openmpi: Update to 4.1.2
...
* gnu/packages/mpi.scm (openmpi): Update to 4.1.2
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-03-29 11:27:21 +02:00
Collin J. Doering
Ricardo Wurmus
Efraim Flashner
Arun Isaac
Mathieu Othacehe
Brian Kubisiak
Leo Famulari
cage
Kyle Meyer
Mădălin Ionel Patrașcu
Luis Henrique Gomes Higino
Feng Shu
jgart
Philippe SWARTVAGHER