e7a41b15ce
gnu: Remove python2-pytest-warnings.
...
* gnu/packages/check.scm (python2-pytest-warnings): Delete variable.
2022-05-31 14:52:26 -04:00
55fc0947d4
gnu: Remove python2-parameterized.
...
* gnu/packages/check.scm (python2-parameterized): Delete variable.
* gnu/packages/patches/python2-parameterized-docstring-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): De-register it.
2022-05-31 14:52:26 -04:00
0837d0aaf1
gnu: Remove python2-fastlmm.
...
* gnu/packages/machine-learning.scm (python2-fastlmm): Delete variable.
2022-05-31 14:52:25 -04:00
7ebb6b7b2b
gnu: Remove python2-pytest-cache.
...
* gnu/packages/check.scm (python2-pytest-cache): Delete variable.
2022-05-31 14:52:25 -04:00
32ec89285f
gnu: Remove python2-statsmodels.
...
* gnu/packages/statistics.scm (python2-statsmodels): Delete variable.
2022-05-31 14:52:25 -04:00
46ef39b4be
gnu: Remove python2-html5lib.
...
* gnu/packages/python-web.scm (python2-html5lib): Delete variable.
(python-html5lib-0.9, python2-html5lib-0.9): Likewise.
2022-05-31 14:52:25 -04:00
b3c7d69fa0
gnu: Remove python2-pandas.
...
* gnu/packages/python-science.scm (python2-pandas): Delete variable.
(python-pandas): Delete related python2-variant property.
2022-05-31 14:52:25 -04:00
1db8080591
gnu: ocrodjvu: Use a Python 3 compatible fork.
...
* gnu/packages/djvu.scm (ocrodjvu)[source]: Update URL to Python 3 fork.
[inputs]: Use new style. Remove python2-subprocess32. Replace all other
Python 2 inputs by their Python 3 equivalent. Add python-future and
python-regex.
[arguments]: Use gexps, and adjust accordingly, using this-package-input and
search-input-file.
2022-05-31 14:52:24 -04:00
1c865e8e1c
gnu: Remove python2-scikit-learn.
...
* gnu/packages/machine-learning.scm (python2-scikit-learn): Delete variable.
(python-scikit-learn)[properties]: Remove the python2-variant property.
2022-05-31 14:52:24 -04:00
dc514a5164
gnu: Remove python2-pytest-pep8.
...
* gnu/packages/check.scm (python2-pytest-pep8): Delete variable.
2022-05-31 14:52:24 -04:00
716b5bd9d9
gnu: Remove python2-hiredis.
...
* gnu/packages/databases.scm (python2-hiredis): Delete variable.
2022-05-31 14:52:24 -04:00
bef8185d08
gnu: Remove python2-pymysql.
...
* gnu/packages/databases.scm (python2-pymysql): Delete variable.
2022-05-31 14:52:24 -04:00
e9121c2dda
gnu: Remove python2-pyodbc-c.
...
* gnu/packages/databases.scm (python2-pyodbc-c): Delete variable.
2022-05-31 14:52:24 -04:00
25e4ddd849
gnu: Remove python2-py2neo.
...
* gnu/packages/databases.scm (python2-py2neo): Delete variable.
2022-05-31 14:52:23 -04:00
3ad04860d5
gnu: Remove python2-apsw.
...
* gnu/packages/databases.scm (python2-apsw): Delete variable.
2022-05-31 14:52:23 -04:00
f503181ffb
gnu: Remove python2-ccm.
...
* gnu/packages/databases.scm (python2-ccm): Delete variable.
2022-05-31 14:52:23 -04:00
80963d9b0f
gnu: Remove python2-peewee.
...
* gnu/packages/databases.scm (python2-peewee): Delete variable.
2022-05-31 14:52:23 -04:00
5ed4cfb924
gnu: Remove python2-trollius-redis.
...
* gnu/packages/databases.scm (python2-trollius-redis): Delete variable.
2022-05-31 14:52:23 -04:00
1aab8a5114
gnu: Remove python2-redis.
...
* gnu/packages/databases.scm (python2-redis): Delete variable.
2022-05-31 14:52:22 -04:00
466d81aae4
gnu: Remove python2-neo4j-driver.
...
* gnu/packages/databases.scm (python2-neo4j-driver): Delete variable.
2022-05-31 14:52:22 -04:00
99d5c9b54a
gnu: Remove nmoldyn.
...
* gnu/packages/chemistry.scm (nmoldyn): Delete variable.
2022-05-31 14:52:22 -04:00
dbac9f890e
gnu: Remove domainfinder.
...
* gnu/packages/chemistry.scm (domainfinder): Delete variable.
2022-05-31 14:52:22 -04:00
be6740df96
gnu: Remove python2-nose-randomly.
...
* gnu/packages/check.scm (python2-nose-randomly): Delete variable.
2022-05-31 14:52:22 -04:00
6e763df31c
gnu: Remove python2-pytest-subtesthack.
...
* gnu/packages/check.scm (python2-pytest-subtesthack): Delete variable.
2022-05-31 14:52:21 -04:00
af6d88c803
gnu: Remove python2-pytest-flakes.
...
* gnu/packages/check.scm (python2-pytest-flakes): Delete variable.
2022-05-31 14:52:21 -04:00
2abde9b927
gnu: Remove python2-cov-core.
...
* gnu/packages/check.scm (python2-cov-core): Delete variable.
2022-05-31 14:52:21 -04:00
f9d31d90ec
gnu: Remove python2-discover.
...
* gnu/packages/check.scm (python2-discover): Delete variable.
2022-05-31 14:52:21 -04:00
359a0b6c2e
gnu: Remove python2-flexmock.
...
* gnu/packages/check.scm (python2-flexmock): Delete variable.
2022-05-31 14:52:21 -04:00
ae2f3bed76
gnu: Remove python2-minimock.
...
* gnu/packages/check.scm (python2-minimock): Delete variable.
2022-05-31 14:52:20 -04:00
2af19eb9b5
gnu: Remove python2-rednose.
...
* gnu/packages/check.scm (python2-rednose): Delete variable.
2022-05-31 14:52:20 -04:00
4178b304ab
gnu: Remove python2-python-paramunittest.
...
* gnu/packages/check.scm (python2-python-paramunittest): Delete variable.
2022-05-31 14:52:20 -04:00
099c5a90e4
gnu: Remove python2-pytest-capturelog.
...
* gnu/packages/check.scm (python2-pytest-capturelog): Delete variable.
2022-05-31 14:52:20 -04:00
94447313e8
gnu: Remove python2-nose2.
...
* gnu/packages/check.scm (python2-nose2): Delete variable.
2022-05-31 14:52:20 -04:00
dc0da7e56f
gnu: Remove python2-testlib.
...
* gnu/packages/check.scm (python2-testlib): Delete variable.
2022-05-31 14:52:19 -04:00
dc612d54fd
gnu: Remove python2-pytest-catchlog.
...
* gnu/packages/check.scm (python2-pytest-catchlog): Delete variable.
2022-05-31 14:52:19 -04:00
4746f9fc63
gnu: Remove python2-nose-timer.
...
* gnu/packages/check.scm (python2-nose-timer): Delete variable.
2022-05-31 14:52:19 -04:00
ddec4b81d6
gnu: Remove transmission-remote-cli.
...
* gnu/packages/bittorrent.scm (transmission-remote-cli): Delete variable.
2022-05-31 14:52:19 -04:00
c30ab2c0b4
gnu: Remove pyicoteo.
...
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31 14:52:19 -04:00
ba09192168
gnu: Remove python2-pbcore.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31 14:52:19 -04:00
8287979669
gnu: Remove python2-pyfaidx.
...
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31 14:52:18 -04:00
850bd0c329
gnu: Remove python2-screed.
...
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31 14:52:18 -04:00
a94bc7798a
gnu: Remove miso.
...
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31 14:52:18 -04:00
23e133a907
gnu: Remove python2-warpedlmm.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31 14:52:18 -04:00
bb35b50adc
gnu: Remove poretools.
...
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31 14:52:18 -04:00
bcdd45be6f
gnu: Remove python2-dendropy.
...
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31 14:52:17 -04:00
d2c971e67b
gnu: Remove bamm.
...
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31 14:52:17 -04:00
1010c05800
gnu: Remove python2-pybedtools.
...
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31 14:52:17 -04:00
725b562962
gnu: Remove python2-htseq.
...
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31 14:52:17 -04:00
8bcb07d089
gnu: Remove pepr.
...
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31 14:52:17 -04:00
3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b.
...
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam.
[home-page]: Update URL.
2022-05-31 14:52:16 -04:00
d29d50a556
gnu: Remove python2-pybigwig.
...
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31 14:52:16 -04:00
98c4f97d18
gnu: Remove ribodiff.
...
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31 14:52:16 -04:00
9f4c958d62
gnu: Remove grit.
...
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31 14:52:16 -04:00
7963e12568
gnu: Remove python2-fastalite.
...
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-31 14:52:16 -04:00
fd4668b111
gnu: Remove python2-pyaudio.
...
* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
2022-05-31 14:52:15 -04:00
1a60e11a98
gnu: Remove raul-devel.
...
* gnu/packages/audio.scm (raul-devel): Delete variable.
2022-05-31 14:52:15 -04:00
94e8f2b9b5
gnu: Remove raul.
...
* gnu/packages/audio.scm (raul): Delete variable.
2022-05-31 14:52:15 -04:00
a5a84babb9
gnu: Remove ingen.
...
* gnu/packages/music.scm (ingen): Delete variable.
2022-05-31 14:52:15 -04:00
cfce386aba
gnu: Remove python2-pyalsaaudio.
...
* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
2022-05-31 14:52:15 -04:00
cd46c8c34b
gnu: Remove graphios.
...
* gnu/packages/admin.scm (graphios): Delete variable.
2022-05-31 14:52:14 -04:00
74641c7f66
gnu: Remove python2-langkit.
...
* gnu/packages/ada.scm (python2-langkit): Delete variable.
2022-05-31 14:52:14 -04:00
787a026f00
gnu: Remove python-pytest-runner-2.
...
* gnu/packages/check.scm (python-pytest-runner-2): Delete variable.
(python2-pytest-runner): Likewise.
2022-05-31 14:52:14 -04:00
20432b839b
gnu: icecat: Update to 91.10.0-guix0-preview1 [security fixes].
...
Includes fixes for CVE-2022-31736, CVE-2022-31737, CVE-2022-31738,
CVE-2022-31739, CVE-2022-31740, CVE-2022-31741, CVE-2022-31742, and
CVE-2022-31747.
* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
2022-05-31 14:12:31 -04:00
be85c4d40f
gnu: ungoogled-chromium: Update to 102.0.5005.61-3.
...
* gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest.
(%ungoogled-origin): Update hash.
2022-05-31 19:54:04 +02:00
2c4c504272
gnu: python-sip-4: Update to 4.19.25.
...
* gnu/packages/qt.scm (python-sip-4): Update to 4.19.25.
2022-05-31 20:45:05 +03:00
d11d27e2e4
gnu: guile-ac-d-bus: Run test suite.
...
* gnu/packages/patches/guile-ac-d-bus-fix-tests.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[source]: Apply patch.
[phases]{check}: New phase.
[native-inputs]: Add bash-minimal.
2022-05-31 11:20:28 -04:00
34c8558af2
gnu: guile-ac-d-bus: Build and install info manual.
...
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[arguments]: Use gexps.
[phases]{build-doc, install-doc}: New phases.
[native-inputs]: Add texinfo.
2022-05-31 11:20:28 -04:00
07909eb092
gnu: python-distributed: Update to 2022.05.2.
...
* gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2.
[arguments]: Remove 'sanity-check phase; adjust 'check phase.
[propagated-inputs]: Add python-urllib3.
[native-inputs]: Add python-pytest-timeout and python-flaky.
2022-05-31 15:18:22 +02:00
3d5144db5a
gnu: r-haven: Fix build.
...
* gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase.
Reported-by: Jonas Freimuth.
2022-05-31 15:18:22 +02:00
098d0012f5
gnu: python-fsspec: Update to 2022.5.0.
...
* gnu/packages/python-xyz.scm (python-fsspec): Update to 2022.5.0.
2022-05-31 15:18:22 +02:00
8b680b00d4
image: Add fat32 support.
...
* gnu/build/image.scm (make-vfat-image): Pass fs-bits as an argument and force
1kb logical sector size only if "ESP" flag is set.
(make-partition-image): Add "fat32" partition type, support explicit "fat16"
type with vfat alias.
* gnu/system/image.scm (partition->dos-type partition): Return file system IDs
for "fat16" and "fat32" partitions.
(partition->gpt-type partition): Ditto.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-05-31 14:51:13 +02:00
6169c582d1
gnu: emacs-helpful: Update to 0.19
...
* gnu/packages/patches/emacs-helpful-docstring-test.patch: New file.
* gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.19.
[source]: Use the patch.
* gnu/local.mk (dist_patch_DATA): Register the patch.
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-05-31 06:16:18 +02:00
b8fc3403d3
gnu: gandi.cli: Fix by downgrading python-click.
...
* gnu/packages/python-xyz.scm (python-click-7): New variable.
* gnu/packages/networking.scm (gandi.cli)[inputs]: Depend on python-click-7.
2022-05-30 22:18:21 +01:00
f12d08c6d2
gnu: python-click@8: Remove redundant package.
...
The python-click package is already version 8.
* gnu/packages/python-xyz.scm (python-click-8): Remove variable.
(python-proselint)[propagated-inputs]: Depend on python-click.
2022-05-30 22:18:12 +01:00
0bcd28e58c
gnu: python-scanpy: Update to 1.9.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
2022-05-30 23:09:46 +02:00
ca2516f065
gnu: python-leidenalg: Update to 0.8.10.
...
* gnu/packages/graph.scm (python-leidenalg): Update to 0.8.10.
[arguments]: Patch setup.py.
[native-inputs]: Remove python-setuptools; add python-setuptools-scm.
2022-05-30 23:09:46 +02:00
7c8f3dfa34
gnu: python-dask: Update to 2022.05.2.
...
* gnu/packages/python-xyz.scm (python-dask): Update to 2022.05.2.
2022-05-30 23:09:46 +02:00
1257c4c663
gnu: Add python-session-info.
...
* gnu/packages/python-xyz.scm (python-session-info): New variable.
2022-05-30 23:09:46 +02:00
216fb59b9b
gnu: non-sequencer: Update to 1.9.5-5.257ec59.
...
* gnu/packages/music.scm (non-sequencer): Update to 1.9.5-5.257ec59.
[source]: Use fork as old repository is defunct; use git-file-name and
git-version.
[arguments]: Remove python-2; add phase to replace bundled waf.
[native-inputs]: Add python-waf.
(non-session-manager)[native-inputs]: Add python-waf.
(non-mixer)[inputs]: Add lv2 and lilv.
[native-inputs]: Add python-waf.
(non-timeline)[native-inputs]: Add python-waf.
2022-05-30 23:09:46 +02:00
df43e8d45c
gnu: quodlibet: Correct wrappers.
...
* gnu/packages/music.scm (quodlibet)[#:phases]: Rename ‘wrap-gi-typelib’ to
‘wrap-extra-paths’. Use ‘=’ for GI_TYPELIB_PATH. Add
‘GST_PLUGIN_SYSTEM_PATH’ with suffix binding.
2022-05-30 21:28:53 +02:00
fed51b2614
gnu: calceph: Add 'release-monitoring-url' property.
...
* gnu/packages/astronomy.scm (calceph)[properties]: New field.
2022-05-30 16:34:41 +02:00
d730bbbbb3
gnu: Add calceph.
...
* gnu/packages/astronomy.scm (calceph): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
8d5b27cae9
gnu: emacs-vterm: Update to 0.0.1-1.b447235.
...
* gnu/packages/emacs-xyz.scm (emacs-vterm): Update to 0.0.1-1.b447235.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
5e5e37fbc4
gnu: rspamd: Update to 3.2
...
* gnu/packages/mail.scm (rspamd): Update to 3.2
I also added a new build option, that changes the LOCAL_CONFDIR variable to
/etc/rspamd. This allows for rspamd configuration via the /etc/rspamd/local.d
and override.d directories, which by default were located in the PREFIX which
is in /gnu/store.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
b67fd51902
gnu: pre-commit: Update to 2.19.0.
...
* gnu/packages/version-control.scm (pre-commit): Update to 2.19.0.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
38f3d38ead
gnu: xpad: Update to 5.8.0.
...
* gnu/packages/gnome.scm (xpad): Update to 5.8.0.
[inputs]: Replace gtksourceview-3 with gtksourceview.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
092ee35155
gnu: casync: Update to 99559cd1.
...
* gnu/packages/sync.scm (casync): Update to 99559cd1.
[source]: Remove patch.
[arguments]: Fix installation.
[native-inputs]: Add python.
[inputs]: Add eudev.
* gnu/packages/patches/casync-renameat2-declaration.patch: Delete file.
* gnu/local.mk: Remove it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:40 +02:00
7d8f6a5db5
gnu: rsync: Update to 3.2.4.
...
* gnu/packages/rsync.scm (rsync): Update to 3.2.4.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:39 +02:00
3f31525546
gnu: GCC: Add cross environment variables patch to GCC 12.
...
* gnu/packages/patches/gcc-12-cross-environment-variables.patch : New file.
* gnu/local.mk (dist_patch_DATA): Add
gcc-12-cross-environment-variables.patch.
* gnu/packages/cross-base.scm (cross-gcc)[source](patches): Apply the patch.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-30 16:34:39 +02:00
56dddd05e8
gnu: emacs-w3m: Update to 20220508.2259.
...
* gnu/packages/emacs-xyz.scm (emacs-w3m): Update to 20220508.2259.
[source]: Switch to 'git-fetch'.
2022-05-30 16:34:39 +02:00
7750f220be
gnu: tor: Record the file name of 'torsocks' in 'torify'.
...
* gnu/packages/tor.scm (tor)[arguments]: Add 'adjust-torify' phase.
[inputs]: Add TORSOCKS.
2022-05-30 16:34:39 +02:00
281bf72745
gnu: r-lmom: Update to 2.9.
...
* gnu/packages/statistics.scm (r-lmom): Update to 2.9.
2022-05-30 15:35:04 +02:00
eba783130f
gnu: r-chron: Update to 2.3-57.
...
* gnu/packages/statistics.scm (r-chron): Update to 2.3-57.
2022-05-30 15:34:59 +02:00
85e77d93ac
gnu: r-tree: Update to 1.0-42.
...
* gnu/packages/cran.scm (r-tree): Update to 1.0-42.
2022-05-30 15:34:52 +02:00
440bd1b617
gnu: r-parameters: Update to 0.18.1.
...
* gnu/packages/cran.scm (r-parameters): Update to 0.18.1.
2022-05-30 15:34:46 +02:00
0880acbcb5
gnu: r-clue: Update to 0.3-61.
...
* gnu/packages/cran.scm (r-clue): Update to 0.3-61.
2022-05-30 15:34:39 +02:00
7815efe731
gnu: r-cobs: Update to 1.3-5.
...
* gnu/packages/cran.scm (r-cobs): Update to 1.3-5.
2022-05-30 15:34:34 +02:00
56373df33a
gnu: r-gee: Update to 4.13-23.
...
* gnu/packages/cran.scm (r-gee): Update to 4.13-23.
2022-05-30 15:34:28 +02:00
d3cb071050
gnu: r-qpdf: Update to 1.2.0.
...
* gnu/packages/cran.scm (r-qpdf): Update to 1.2.0.
[source]: Remove trailing #T from snippet.
[arguments]: Remove trailing #T from 'configure phase.
[inputs]: Add libjpeg-turbo.
2022-05-30 15:30:47 +02:00
bfcae1efbb
gnu: r-batchelor: Update to 1.12.1.
...
* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.1.
2022-05-30 15:16:35 +02:00
d2a9142852
gnu: gcc-9: Update to 9.5.0.
...
* gnu/packages/gcc.scm (gcc-9): Update to 9.5.0.
2022-05-30 15:28:04 +03:00
dc26d0f94e
gnu: hello: Update to 2.12.1.
...
* gnu/packages/base.scm (hello): Update to 2.12.1.
2022-05-30 15:28:04 +03:00
a037815f62
gnu: nss: Skip tests on riscv64-linux.
...
* gnu/packages/nss.scm (nss)[arguments]: Skip tests when building for
riscv64-linux.
2022-05-30 15:26:17 +03:00
19e1045352
gnu: nss: Adjust make-flags for riscv64-linux.
...
* gnu/packages/nss.scm (nss)[arguments]: When building for riscv64-linux
don't build the binaries with gtest.
2022-05-30 15:18:17 +03:00
69b27be15d
gnu: Add rust-serde-regex-1.
...
* gnu/packages/crates-io.scm (rust-serde-regex-1): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:53 +03:00
6ec464ced7
gnu: rust-nom-7: Update to 7.1.1.
...
* gnu/packages/crates-io.scm (rust-nom-7): Update to 7.1.1.
[arguments]: In cargo-inputs replace rust-minimal-lexical-0.1 with 0.2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:52 +03:00
4f5a71d5b7
gnu: Add rust-minimal-lexical-0.2.
...
* gnu/packages/crates-io.scm (rust-minimal-lexical-0.2): New variable.
(rust-minimal-lexical-0.1): Inherit from rust-minimal-lexical-0.2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:52 +03:00
4b18cb437a
gnu: Add rust-located-yaml-0.2.
...
* gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:51 +03:00
30cf5284b2
gnu: Add rust-pretty-0.11.
...
* gnu/packages/crates-io.scm (rust-pretty-0.11) New variable.
(rust-pretty-0.5): Inherit from rust-pretty-0.11.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:51 +03:00
acada2580f
gnu: Add rust-nom-locate-4.
...
* gnu/packages/crates-io.scm (rust-nom-locate-4): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30 11:13:50 +03:00
4259a6516a
gnu: virtuoso-ose: Register patch.
...
This is a follow-up to 48efbde7a9
2022-05-30 10:42:47 +03:00
1a8519dd01
gnu: yt-dlp: Remove trailing #t.
...
* gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from
snippet.
[arguments]: Remove trailing #t from phases.
2022-05-30 10:41:28 +03:00
d56506aad5
gnu: yt-dlp: Update to 2022.05.18.
...
* gnu/packages/video.scm (yt-dlp): Update to 2022.05.18.
[inputs]: Add python-brotli and python-certifi.
2022-05-30 10:41:28 +03:00
e5dd864e68
gnu: links: Update to 2.27.
...
* gnu/packages/web-browsers.scm (links): Update to 2.27.
2022-05-30 10:41:25 +03:00
48efbde7a9
gnu: virtuoso-ose: Update to 7.2.7.
...
* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen
after applying the patch below.
* gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch:
New file.
2022-05-30 09:03:02 +02:00
7f63a6aefc
gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes].
...
Includes fixes for CVE-2022-1529 and CVE-2022-1802.
* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
2022-05-29 23:21:41 -04:00
acb08304c8
gnu: Add python-gpy.
...
* gnu/packages/python-science.scm (python-gpy): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:06 +02:00
6400f08d07
gnu: Add python-paramz.
...
* gnu/packages/python-science.scm (python-paramz): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
6dacd15381
gnu: Add python-climin.
...
* gnu/packages/python-science.scm (python-climin): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
3d1b2bc740
gnu: wla-dx: Update to 10.1.
...
* gnu/packages/assembly.scm (wla-dx): Update to 10.1.
[native-inputs]: Use new style.
[arguments]: Add custom 'check phase to run run_tests.sh.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
98e2f4fbeb
gnu: openjdk: Update to 17.0.3.
...
* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
2022-05-29 22:57:19 +02:00
d1f4b6dc83
gnu: python-translate-toolkit: Update to 3.6.2.
...
* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to
3.6.2.
2022-05-29 22:20:15 +02:00
31a9d8677c
gnu: python-user-agents: Update to 2.2.0.
...
* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
2022-05-29 21:30:45 +02:00
92a83f38b5
gnu: python-ua-parser: Update to 0.10.0.
...
* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
2022-05-29 21:30:16 +02:00
e8b2219152
gnu: lagrange: Update to 1.13.6.
...
* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6.
[source]: Adjust snippet to remove another bundled library.
2022-05-29 19:26:47 +03:00
9cd22702b8
gnu: wget: Update to 1.21.3.
...
* gnu/packages/wget.scm (wget): Update to 1.21.3.
2022-05-29 16:31:59 +03:00
1ed40eee39
gnu: mutt: Update to 2.2.5.
...
* gnu/packages/mail.scm (mutt): Update to 2.2.5.
2022-05-29 16:31:59 +03:00
46ed423e28
gnu: git-annex: Update to 10.20220525.
...
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
2022-05-29 16:31:59 +03:00
e4fe344a5c
gnu: nmap: Honor tests? flag.
...
* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor
the #:tests? flag.
2022-05-29 16:31:09 +03:00
50970a28b7
gnu: wgetpaste: Remove trailing #t from phases.
...
* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from
phases.
2022-05-29 16:31:09 +03:00
c62be7d530
gnu: wgetpaste: Add missing input.
...
* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
2022-05-29 16:23:48 +03:00
69af8a6837
gnu: telescope: Update to 0.8.1.
...
* gnu/packages/web-browsers.scm (telescope): Update to 0.8.1.
[home-page]: Update to new upstream home-page.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-29 16:10:34 +03:00
d540e686ef
gnu: Add pbuilder.
...
* gnu/packages/debian.scm (pbuilder): New variable.
2022-05-29 16:01:02 +03:00
b456086c65
gnu: apostrophe: Build with correct webkitgtk.
...
* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-29 15:53:48 +03:00
e640da33f3
Merge branch 'wip-r'
2022-05-29 11:49:03 +02:00
89e9262012
gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993.
...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
2022-05-29 11:44:09 +02:00
926fcb488b
gnu: clang-from-llvm: Fix building on riscv64-linux.
...
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for
riscv64-linux add configure-flags and make-flags to ensure linking with
'-latomic'.
2022-05-29 08:46:17 +03:00
a5f4c03df1
gnu: Add r-scmap.
...
* gnu/packages/bioconductor.scm (r-scmap): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29 00:43:05 +02:00
cb115ba722
gnu: pigx-sars-cov-2: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
2022-05-29 00:39:19 +02:00
df3e5cfa05
gnu: pigx-bsseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
2022-05-29 00:34:29 +02:00
b64f4a1245
gnu: pigx-scrnaseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
2022-05-29 00:29:19 +02:00
add551f651
gnu: pigx-chipseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
2022-05-29 00:18:48 +02:00
a4b90009c7
gnu: Add r-googlevis.
...
* gnu/packages/cran.scm (r-googlevis): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29 00:01:47 +02:00
f383838a09
services: elogind: When started by dbus-daemon, wait for the Shepherd service.
...
Fixes <https://issues.guix.gnu.org/55444 >.
Previously shepherd and dbus-daemon would race to start elogind. In
some cases (for instance if one logs in quickly enough on the tty),
dbus-daemon would "win" and start elogind before shepherd has had a
chance to do it. Consequently, shepherd would fail to start elogind and
mark it as stopped and disabled, in turn preventing services that depend
on it such as 'xorg-server' from starting.
* gnu/services/desktop.scm (elogind-dbus-service): Rewrite to refer to a
wrapper that waits for the 'elogind' Shepherd service.
2022-05-28 23:23:36 +02:00
b04ae71def
services: herd: Add 'wait-for-service'.
...
* gnu/services/herd.scm (wait-for-service): New procedure.
2022-05-28 23:23:36 +02:00
66bfe55848
gnu: Add r-msdata.
...
* gnu/packages/bioconductor.scm (r-msdata): New variable.
2022-05-28 23:19:48 +02:00
79158a5624
gnu: r-tcgabiolinksgui-data: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
2022-05-28 23:19:48 +02:00
9d538de266
gnu: r-curatedtcgadata: Update to 1.18.0.
...
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
2022-05-28 23:19:47 +02:00
1c4d0fc9a9
gnu: r-gagedata: Update to 2.34.0.
...
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
2022-05-28 23:19:47 +02:00
c56b553e97
gnu: r-affydata: Update to 1.44.0.
...
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
2022-05-28 23:19:47 +02:00
e06ee7a745
gnu: r-all: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
2022-05-28 23:19:47 +02:00
15e10974ef
gnu: r-hsmmsinglecell: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
2022-05-28 23:19:47 +02:00
3ff4e48e85
gnu: r-pasilla: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0.
[propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown.
[native-inputs]: Add r-knitr.
2022-05-28 23:19:47 +02:00
4f2ac5f19f
gnu: r-genomationdata: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
d24b0702b6
gnu: r-genelendatabase: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
2022-05-28 23:19:47 +02:00
7a58c9af46
gnu: r-copyhelper: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
e437cf10a4
gnu: r-chromstardata: Update to 1.22.0.
...
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
2022-05-28 23:19:47 +02:00
1413f9f214
gnu: r-celldex: Update to 1.6.0.
...
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
2022-05-28 23:19:46 +02:00
3ce819d563
gnu: r-biscuiteerdata: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
2022-05-28 23:19:46 +02:00
ccb66a16a0
gnu: r-arrmdata: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
2022-05-28 23:19:46 +02:00
9db43e4979
gnu: r-aneufinderdata: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
2022-05-28 23:19:46 +02:00
c89eb68ede
gnu: r-adductdata: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
2022-05-28 23:19:46 +02:00
7feae8098c
gnu: r-pfam-db: Update to 3.15.0.
...
* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0.
2022-05-28 23:19:46 +02:00
5efae7b049
gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.15.0.
...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.15.0.
[propagated-inputs]: Add r-annotationdbi.
2022-05-28 23:19:46 +02:00
8ee1246a38
gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4.
...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4.
2022-05-28 23:19:46 +02:00
3d93251ea5
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update to 1.4.3.
...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): Update to 1.4.3.
2022-05-28 23:19:46 +02:00
549a9e6f6a
gnu: r-leidenbase: Update to 0.1.9.
...
* gnu/packages/bioconductor.scm (r-leidenbase): Update to 0.1.9.
2022-05-28 23:19:46 +02:00
319fa58dac
gnu: r-phyloseq: Update to 1.40.0.
...
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.40.0.
2022-05-28 23:19:45 +02:00
e0be852a1e
gnu: r-tximeta: Update to 1.14.0.
...
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.0.
2022-05-28 23:19:45 +02:00
e290d834d9
gnu: r-tricycle: Update to 1.4.0.
...
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.4.0.
[propagated-inputs]: Add r-ggnewscale.
2022-05-28 23:19:45 +02:00
5ec7143f69
gnu: r-tcgabiolinks: Update to 2.24.1.
...
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.1.
2022-05-28 23:19:45 +02:00
a4f03b0a55
gnu: r-biscuiteer: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.10.0.
[propagated-inputs]: Add r-iranges.
2022-05-28 23:19:45 +02:00
6f31f4618a
gnu: r-omnipathr: Update to 3.4.0.
...
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.4.0.
[propagated-inputs]: Add r-withr.
2022-05-28 23:19:45 +02:00
b1c215755a
gnu: r-dmrseq: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.16.0.
2022-05-28 23:19:45 +02:00
4ab8327ba4
gnu: r-bsseq: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.32.0.
2022-05-28 23:19:45 +02:00
397bdc4329
gnu: r-biotmle: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.20.0.
2022-05-28 23:19:45 +02:00
4b3f9a16f2
gnu: r-biotip: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.10.0.
[propagated-inputs]: Remove r-hmisc; add r-scran.
2022-05-28 23:19:45 +02:00
e8e3d333f0
gnu: r-bioqc: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.24.0.
2022-05-28 23:19:44 +02:00
dba6a33e3d
gnu: r-bionetstat: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.0.
2022-05-28 23:19:44 +02:00
8fe9bcf0a4
gnu: r-bionet: Update to 1.56.0.
...
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.56.0.
2022-05-28 23:19:44 +02:00
f5262fa4ed
gnu: r-bionero: Update to 1.4.0.
...
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.4.0.
2022-05-28 23:19:44 +02:00
3391ff6ddb
gnu: r-biomvrcns: Update to 1.36.0.
...
* gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.36.0.
2022-05-28 23:19:44 +02:00
7fe83026b7
gnu: r-biomvcclass: Update to 1.64.0.
...
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.64.0.
2022-05-28 23:19:44 +02:00
a3a8109fe8
gnu: r-mvcclass: Update to 1.70.0.
...
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.70.0.
2022-05-28 23:19:44 +02:00
eb18527e5f
gnu: r-biomformat: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.24.0.
2022-05-28 23:19:44 +02:00
12ee563b41
gnu: r-biodb: Update to 1.4.0.
...
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.0.
2022-05-28 23:19:44 +02:00
259c003f02
gnu: r-biocdockermanager: Update to 1.8.0.
...
* gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.8.0.
2022-05-28 23:19:43 +02:00
6766fbb003
gnu: r-biocthis: Update to 1.6.0.
...
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.6.0.
2022-05-28 23:19:43 +02:00
b007802e4b
gnu: r-basilisk: Update to 1.8.0.
...
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.8.0.
2022-05-28 23:19:43 +02:00
90e56ba6e3
gnu: r-basilisk-utils: Update to 1.8.0.
...
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.8.0.
2022-05-28 23:19:43 +02:00
5d2c07021c
gnu: r-dir-expiry: Update to 1.4.0.
...
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.4.0.
2022-05-28 23:19:43 +02:00
3c65a7d577
gnu: r-genetclassifier: Update to 1.36.0.
...
* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.36.0.
2022-05-28 23:19:43 +02:00
c4f8b5759a
gnu: r-minet: Update to 3.54.0.
...
* gnu/packages/bioconductor.scm (r-minet): Update to 3.54.0.
2022-05-28 23:19:43 +02:00
395f152b92
gnu: r-biobtreer: Update to 1.8.0.
...
* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.8.0.
2022-05-28 23:19:43 +02:00
24c13f9d64
gnu: r-bgeedb: Update to 2.22.0.
...
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.0.
2022-05-28 23:19:43 +02:00
00025cdd23
gnu: r-bgeecall: Update to 1.12.1.
...
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.12.1.
2022-05-28 23:19:43 +02:00
460680ef90
gnu: r-beclear: Update to 2.12.0.
...
* gnu/packages/bioconductor.scm (r-beclear): Update to 2.12.0.
[propagated-inputs]: Remove r-outliers; add r-dixontest.
2022-05-28 23:19:42 +02:00
64c3498d9f
gnu: r-megadepth: Update to 1.6.0.
...
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.6.0.
2022-05-28 23:19:42 +02:00
c2a8c4c248
gnu: r-ballgown: Update to 2.28.0.
...
* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.28.0.
2022-05-28 23:19:42 +02:00
d57d65a628
gnu: r-sushi: Update to 1.34.0.
...
* gnu/packages/bioconductor.scm (r-sushi): Update to 1.34.0.
2022-05-28 23:19:42 +02:00
Maxim Cournoyer
Mark H Weaver
Marius Bakke
Efraim Flashner
Ricardo Wurmus
Pavel Shlyak
yarl baudig
Pierre Langlois
Liliana Marie Prikler
Ludovic Courtès
Sharlatan Hellseher
Kyle Meyer
ykonai
jgart
Rene Saavedra
Greg Hogan
Morgan Smith
Evgenii Lepikhin
Roel Janssen
Wiktor Zelazny
Felix Gruber
Danny Milosavljevic
Julien Lepiller
cage
Mădălin Ionel Patrașcu