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Author SHA1 Message Date
Arun Isaac
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
Arun Isaac
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
Ricardo Wurmus
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
Ricardo Wurmus
38b2026515
gnu: Add python-numpy-groupies. 
* gnu/packages/python-science.scm (python-numpy-groupies): New variable.
 2022-03-31 14:37:58 +02:00
Arun Isaac
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
Arun Isaac
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
693212087d
gnu: ncdu2: Set upstream name. 
* gnu/packages/ncdu.scm (ncdu-2)[properties]: New field.
 2022-03-30 19:58:29 +03:00
Ricardo Wurmus
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
Mathieu Othacehe
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
Brian Kubisiak
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
Brian Kubisiak
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
cage
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
Kyle Meyer
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
Kyle Meyer
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
Kyle Meyer
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
Kyle Meyer
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
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Luis Henrique Gomes Higino
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
Luis Henrique Gomes Higino
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
Feng Shu
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
jgart
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
Philippe SWARTVAGHER
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
Ludovic Courtès
2ae2a15b07
gnu: slurm: Install libpmi2. 
* gnu/packages/parallel.scm (slurm)[source](snippet): Let PMI2 through.
[arguments]: In phase 'install-libpmi', install "contribs/pmi2".
[license]: Add 'non-copyleft'.
 2022-03-29 11:26:58 +02:00
jgart
779acb0ba1
gnu: mercury: Remove trailing #T from phases and snippet. 
* gnu/packages/mercury.scm (mercury)[arguments]<#:phases>: Remove trailing #T.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-29 11:17:46 +02:00
jgart
c116376542
gnu: python-livereload: Update to 2.6.3. 
* gnu/packages/python-web.scm (python-livereload): Update to 2.6.3.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-29 10:59:07 +02:00
jgart
6d0d176580
gnu: solfege: Remove trailing booleans. 
* gnu/packages/music.scm (solfege): Remove trailing booleans.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-29 10:56:33 +02:00
jgart
a1c11cc652
gnu: python-port-for: Remove trailing boolean. 
* gnu/packages/python-web.scm (python-port-for)[arguments]: Remove trailing
boolean from lambda function.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-29 10:55:02 +02:00
Brian Kubisiak
db7b8d1c9a
gnu: dnsmasq: Fix cross-compilation. 
* gnu/packages/dns.scm (dnsmasq)[arguments]: Use PKG-CONFIG-FOR-TARGET.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-29 10:52:45 +02:00