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Author SHA1 Message Date
Ricardo Wurmus
7f4d25f86e
gnu: python2-sphinx: Remove websupport test. 
* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test
file.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
68619cad28
gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2. 
* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to
1.1.2.
[arguments]: Override; delete 'sanity-check phase.
[propagated-inputs]: Override and add python2-six.
(python-sphinxcontrib-websupport)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
a4a7c78f68
gnu: python2-jinja2: Downgrade to 2.11.3 
* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version
supporting Python 2.
(python-jinja2)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Tobias Geerinckx-Rice
852ad65bd4
gnu: fastboot: Fix ‘--version’ output. 
* gnu/packages/android.scm (fastboot)[arguments]: Replace broken
‘git rev-parse’ shell command with the actual package VERSION.

Reported by kwjc on #guix.
 2021-12-08 15:42:33 +01:00
Zhu Zihao
5573d98f81
gnu: rtl8821ce-linux-module: Update to 0.0.0-4-ca204c6. 
Fixes compatibility with linux-libre@5.15:

  […]/source/core/rtw_br_ext.c:20:11: fatal error: net/ipx.h:
  No such file or directory
    #include <net/ipx.h>
             ^~~~~~~~~~~
  compilation terminated.

* gnu/packages/linux.scm (rtl8821ce-linux-module):
Update to 0.0.0-4-ca204c6.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-12-08 15:42:33 +01:00
Ricardo Wurmus
14ed9b049e
gnu: python2-markupsafe: Downgrade to 1.1.1. 
* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1,
because that's the last version to support Python 2.
 2021-12-08 14:43:38 +01:00
Ricardo Wurmus
c8060055de
gnu: ocaml-mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
b835d10d61
gnu: paml: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
2157d82ed3
gnu: paml: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
76b39f03d2
gnu: sambamba: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
62da1b34d1
gnu: discrover: Add texlive-fonts-ec to inputs. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
62e196608c
gnu: discrover: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T
from build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
1f63c46a1c
gnu: tbsp: Update to 1.0.0-2.dc30c03. 
* gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03.
[arguments]: Relax requirement on matplot.  This may turn out to be a mistake.
[inputs]: Replace python-biopython with python-biopython-1.73.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
1f7c06965c
gnu: mantis: Update to 0.1-2.b6979a2. 
* gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2.
[arguments]: Disable the use of SSE4.2 instructions.
[native-inputs]: Build with GCC 7.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
738f22fa06
gnu: imp: Disable tests. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
acfbb53222
gnu: snap-aligner: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
42a7b5215b
gnu: snap-aligner: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T
from 'install phase.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
7c58677a29
gnu: snap-aligner: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS?
option.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
298a8d0b89
gnu: khmer: Cythonize source files. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files.
[arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp
files from Cython sources; add 'build-extensions phase; replace 'check phase.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
9a19e8f609
gnu: cwltool: Update to 3.1.20211107152837. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837.
[arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T
from build phases; fix /bin/sh invocations in test files.
 2021-12-08 14:31:52 +01:00
Guillaume Le Vaillant
ac53cbb368
gnu: monero: Improve check phase. 
* gnu/packages/finance.scm (monero)[arguments]: Take 'tests?' parameter
  into consideration in 'check' phase.
 2021-12-08 13:31:37 +01:00
Guillaume Le Vaillant
3ccf33bbe6
gnu: monero-gui: Update to 0.17.3.0. 
* gnu/packages/finance.scm (monero-gui): Update to 0.17.3.0.
 2021-12-08 13:31:37 +01:00
Guillaume Le Vaillant
107481ea0f
gnu: monero: Update to 0.17.3.0. 
* gnu/packages/finance.scm (monero): Update to 0.17.3.0.
* gnu/packages/patches/monero-use-system-miniupnpc.patch: Update patch.
 2021-12-08 13:31:37 +01:00
Efraim Flashner
c9b42242f9
gnu: python-userspacefs: Update to 2.0.4. 
* gnu/packages/python-xyz.scm (python-userspacefs): Update to 2.0.4.
 2021-12-08 12:34:13 +02:00
Efraim Flashner
f45e304aa4
gnu: python-dropbox: Update to 11.25.0. 
* gnu/packages/file-systems.scm (python-dropbox): Update to 11.25.0.
[propagated-inputs]: Remove python-certifi, python-chardet, and python-urllib3.
 2021-12-08 11:51:03 +02:00
Marius Bakke
ddcec589bc
gnu: lollypop: Update to 1.4.24. 
* gnu/packages/gnome.scm (lollypop): Update to 1.4.24.
[native-inputs]: Remove INTLTOOL and ITSTOOL.  Add GETTEXT-MINIMAL.
 2021-12-08 08:46:28 +01:00
Marius Bakke
2b8b89b7ab
gnu: python-toolz: Update to 0.11.2. 
* gnu/packages/python-xyz.scm (python-toolz): Update to 0.11.2.
 2021-12-08 08:46:28 +01:00
Marius Bakke
6f29d34bb2
gnu: python-django: Update to 3.2.10 [fixes CVE-2021-4442]. 
* gnu/packages/django.scm (python-django): Update to 3.2.10.
 2021-12-08 08:46:28 +01:00
Marius Bakke
b5e69cf6c1
gnu: python-django@2.2: Update to 2.2.25 [fixes CVE-2021-4442]. 
* gnu/packages/django.scm (python-django-2.2): Update to 2.2.25.
 2021-12-08 08:46:28 +01:00
Marius Bakke
cb8d62bd42
gnu: hitch: Update to 1.7.2. 
* gnu/packages/web.scm (hitch): Update to 1.7.2.
 2021-12-08 08:46:28 +01:00
Marius Bakke
ee03b51f6e
gnu: lollypop: Build with libsoup@2. 
* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to
LIBSOUP-MINIMAL-2.
 2021-12-08 08:45:11 +01:00
Marius Bakke
637735da4d
gnu: rhythmbox: Adjust inputs. 
* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to
PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
 2021-12-08 08:45:11 +01:00
Marius Bakke
14bc2ce43a
gnu: labelme: Loosen Python requirements. 
* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it
does not require a specific version of Matplotlib.
 2021-12-08 08:45:11 +01:00
Mark H Weaver
906dd9ff63
gnu: icecat: Update to 91.4.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2021-43536, CVE-2021-43537, CVE-2021-43538,
CVE-2021-43539, CVE-2021-43541, CVE-2021-43542, CVE-2021-43543,
CVE-2021-43545, CVE-2021-43546, and MOZ-2021-0009.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Remove icecat-CVE-2021-43527.patch, which is now included
in upstream icecat.  Update the gnuzilla commit, base version, and hashes.
* gnu/packages/patches/icecat-CVE-2021-43527.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-07 19:09:24 -05:00
Denis 'GNUtoo' Carikli
9e67f2ad41
gnu: Add kiwix-tools. 
* gnu/packages/web.scm (kiwix-tools): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-07 17:28:44 -05:00
Ricardo Wurmus
5fb1ba880f
gnu: newick-utils: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
 2021-12-07 23:27:40 +01:00
Ricardo Wurmus
ed5e6c7502
gnu: blasr: Update to 5.3.5. 
* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
38cf62a236
gnu: blasr: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
d068de0c7d
gnu: blasr-libcpp: Update to 5.3.5. 
* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
b81daed2de
gnu: htseq: Update to 0.12.3. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
6eecbfb9ac
gnu: clipper: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1.
[source]: Add snippet to remove pre-compiled files.
[arguments]: Disable tests, delete 'sanity-check phase, and add
'use-python3-for-cython phase.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
fc797a3e8f
gnu: pbbam: Update to 1.7.0. 
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
 2021-12-07 23:20:30 +01:00
Tobias Geerinckx-Rice
8775efe8f1
gnu: dovecot-pigeonhole: Update to 0.5.17.1. 
* gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.17.1.
 2021-12-07 18:42:48 +01:00
Tobias Geerinckx-Rice
86d8a0460c
gnu: dovecot: Update to 2.3.17.1. 
* gnu/packages/mail.scm (dovecot): Update to 2.3.17.1.
 2021-12-07 18:42:48 +01:00
Ricardo Wurmus
b764d10e91
gnu: bwa-pssm: Fix build. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
 2021-12-07 17:53:14 +01:00
Ricardo Wurmus
4195a877cb
gnu: Add pbcopper. 
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
 2021-12-07 16:00:22 +01:00
Nicolas Goaziou
0a9c946df9
gnu: giac: Update to 1.7.0-43. 
* gnu/packages/algebra.scm (giac): Update to 1.7.0-43.
 2021-12-07 15:39:54 +01:00
Ricardo Wurmus
8dcf062f28
gnu: python-ndg-httpsclient: Add missing input. 
* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add
python-pyasn1.
 2021-12-07 15:39:18 +01:00
Ricardo Wurmus
a98fe1d46e
gnu: fsom: Build with GCC 6. 
* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6.
[arguments]: Remove trailing #T.
 2021-12-07 15:37:16 +01:00
Ricardo Wurmus
cbef1824da
gnu: python-velocyto: Remove generated C files. 
* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all
generated .c files.
 2021-12-07 15:31:33 +01:00
Ricardo Wurmus
6e67cda755
gnu: python-schema-salad: Update to 8.2.20211116214159. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.2.20211116214159.
[arguments]: Remove trailing #T.
[propagated-inputs]: Replace python-cachecontrol-0.11 with
python-cachecontrol.
[native-inputs]: Add python-black.
 2021-12-07 15:28:13 +01:00
Ricardo Wurmus
16474f85cf
gnu: taxtastic: Update to 0.9.2. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases;  adjust
'prepare-directory phase.
 2021-12-07 15:13:06 +01:00
Ricardo Wurmus
00ba04020e
gnu: taxtastic: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
 2021-12-07 15:12:15 +01:00
Ricardo Wurmus
58fecfd18e
gnu: python-dendropy: Update to 4.5.1. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
 2021-12-07 14:53:37 +01:00
Sarah Morgensen
68d15fcf20
gnu: make-gccgo: Override empty GOROOT/GCCGOTOOLDIR 
gnu/packages/gcc.scm (make-gccgo)[arguments]: Set tool paths
(GOROOT and GCCGOTOOLDIR) even if they are already set to "".

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 15:25:54 +02:00
Ricardo Wurmus
2da567d137
gnu: python-cooler: Use python-cytoolz-for-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
 2021-12-07 13:24:58 +01:00
Ricardo Wurmus
92a2f55cf9
gnu: Add python-cytoolz-for-cooler. 
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
 2021-12-07 13:24:49 +01:00
Ricardo Wurmus
c08d6e63a0
gnu: python-sparse: Update to 0.13.0. 
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
 2021-12-07 13:16:47 +01:00
jgart
51bf893e53
gnu: Add diffr. 
* gnu/packages/rust-apps.scm (diffr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:15:28 +02:00
Ricardo Wurmus
224d1c5818
gnu: python-dask: Update to 2021.11.2. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2.
[source]: Fetch from github.
[arguments]: Remove phase 'disable-broken-tests.
 2021-12-07 13:07:46 +01:00
Ricardo Wurmus
ed15986a32
gnu: python-dask: Run tests conditionally. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
 2021-12-07 13:07:23 +01:00
Ricardo Wurmus
ad17046040
gnu: python-dask: Add missing input for tests. 
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add
python-pytest-rerunfailures.
 2021-12-07 13:06:37 +01:00
jgart
f36f58a564
gnu: Add rust-diffr-lib-0.1. 
* gnu/packages/crates-io.scm (rust-diffr-lib-0.1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:05:54 +02:00
Ricardo Wurmus
899121f4d6
gnu: phylip: Update to 3.697. 
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
 2021-12-07 13:05:53 +01:00
Ricardo Wurmus
e86fe9801e
gnu: phylip: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
 2021-12-07 13:05:35 +01:00
Ricardo Wurmus
125fdc3ba4
gnu: phylip: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
 2021-12-07 13:05:15 +01:00
jgart
72dbf04b55
gnu: Add dutree. 
* gnu/packages/rust-apps.scm (dutree): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:01:42 +02:00
Ricardo Wurmus
4561ca7f4e
gnu: subread: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
 2021-12-07 12:59:51 +01:00
Ricardo Wurmus
96b2be833d
gnu: subread: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
 2021-12-07 12:59:36 +01:00
Ricardo Wurmus
9a03587b62
gnu: subread: Update home page.. 
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
 2021-12-07 12:55:08 +01:00
Ricardo Wurmus
aa25c9b1a4
gnu: subread: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
 2021-12-07 12:54:48 +01:00
Ricardo Wurmus
417299f004
gnu: python-pytest-console-scripts: Update to 1.2.1. 
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to
1.2.1.
 2021-12-07 12:41:14 +01:00
Ricardo Wurmus
6874994fa9
gnu: Add python-pytest-rerunfailures. 
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
 2021-12-07 12:35:00 +01:00
Ricardo Wurmus
c25a6d39f3
gnu: mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
 2021-12-07 12:34:34 +01:00
Ricardo Wurmus
b214034109
gnu: python-cytoolz: Update to 0.11.2. 
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2.
[source]: Add snippet.
 2021-12-07 12:34:22 +01:00
Ricardo Wurmus
06fca01968
gnu: hisat: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
 2021-12-07 11:51:10 +01:00
Ricardo Wurmus
2f7287b3a7
gnu: hisat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
9dc727f827
gnu: hisat: Remove invalid characters. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
478e3e714a
gnu: crossmap: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b5c9afb7c5
gnu: Remove python2-bx-python. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12.
[propagated-inputs]: Remove python-six.
[arguments]: Remove.  Tests are still not run, though.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b452d7c2cf
gnu: python-pyfit-sne: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
 2021-12-07 11:51:09 +01:00
Julien Lepiller
05deb26be9
gnu: guile-netlink: Update to 1.1.1. 
* gnu/packages/guile.scm (guile-netlink): Update to 1.1.1.
 2021-12-07 00:09:35 +01:00
Nicolas Goaziou
e21b422f7f
gnu: emacs-csv-mode: Update to 1.17. 
* gnu/packages/emacs-xyz.scm (emacs-csv-mode): Update to 1.17.
 2021-12-06 22:01:31 +01:00
Pierre Langlois
4afacd4546
gnu: helm: Fix build with GCC 9 and later. 
* gnu/packages/music.scm (helm)[origin]: Add patch.
* gnu/packages/patches/helm-fix-gcc-9-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2021-12-06 20:41:18 +00:00
Marius Bakke
757a2eb970
tests: patchwork: Use the default PostgreSQL. 
* gnu/tests/web.scm (patchwork-os)[services]: Change from POSTGRESQL-10 to
POSTGRESQL.
 2021-12-06 21:17:31 +01:00
Marius Bakke
8662057130
gnu: patchwork: Adjust for python-build-system change. 
This is a follow-up to commit db5646d957, et.al.

* gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more
site-packages call.
 2021-12-06 21:15:42 +01:00
Ricardo Wurmus
ca2f851da1
gnu: f-seq: Update name of commons-cli JAR. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
f0763fba5c
gnu: f-seq: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
1310879fb0
gnu: f-seq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
 2021-12-06 18:48:01 +01:00
Leo Famulari
404f695385
gnu: Go 1.17: Update to 1.17.4. 
* gnu/packages/golang.scm (go-1.17): Update to 1.17.4.
 2021-12-06 12:40:38 -05:00
Leo Famulari
e4d8f2fe31
gnu: Go 1.16: Update to 1.16.11. 
* gnu/packages/golang.scm (go-1.16): Update to 1.16.11.
 2021-12-06 12:40:38 -05:00
Leo Famulari
4e282bc934
gnu: Syncthing: Update to 1.18.4. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.18.4.
[arguments]: Build with Go 1.17.
 2021-12-06 12:10:12 -05:00
Mathieu Othacehe
3b6a7693fa
gnu: osinfo-db-next: Fix uri. 
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
 2021-12-06 17:28:22 +01:00
Efraim Flashner
30c776a6a8
gnu: go-gopkg-in-yaml-v2: Update to 2.4.0. 
* gnu/packages/golang.scm (go-gopkg-in-yaml-v2): Update to 2.4.0.
 2021-12-06 14:45:50 +02:00
Efraim Flashner
c569430b6c
gnu: go-gopkg-in-yaml-v2: Fix test suite on 32-bit systems. 
* gnu/packages/golamg.scm (go-gopkg-in-yaml-v2)[source]: Add snippet to
no longer cause integer overflow on 32-bit systems during test suite.
 2021-12-06 14:43:17 +02:00
Efraim Flashner
b6a726222a
gnu: go-github-com-golang-snappy: Adjust test-suite on 32-bit systems. 
* gnu/packages/syncthing.scm (go-github-com-golang-snappy)[source]: Add
patch to skip a test on 32-bit systems.
* gnu/packages/patches/go-github-com-golang-snappy-32bit-test.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2021-12-06 14:04:30 +02:00
Ludovic Courtès
f4d4c40500
gnu: python-kivy: Add missing dependencies. 
* gnu/packages/python-xyz.scm (python-kivy)[arguments]: Add 'set-home'
phase.
[inputs]: Add PYTHON-DOCUTILS, PYTHON-KIVY-GARDEN, and PYTHON-PYGMENTS.
[synopsis, description]: Tweak.
 2021-12-06 11:49:06 +01:00
Ludovic Courtès
7e40d0ee90
gnu: Add python-kivy-garden. 
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
 2021-12-06 11:48:47 +01:00
Ludovic Courtès
9478a25250
gnu: openssh: Remove libfido2 dependency on GNU/Hurd. 
* gnu/packages/ssh.scm (openssh)[inputs]: Remove LIBFIDO2 when
'hurd-target?'.
[arguments]: Likewise for "--with-security-key-builtin".
 2021-12-06 10:56:01 +01:00
Ludovic Courtès
93e9f0bc7f
ci: Cross-build the 'guix' package. 
* gnu/ci.scm (%core-packages): Add GUIX.
 2021-12-06 10:56:01 +01:00
jgart
326e532177
gnu: Add git-absorb. 
* gnu/packages/rust-apps.scm (git-absorb): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-06 10:47:09 +01:00
Efraim Flashner
96416e4256
gnu: poke: Remove generated files. 
* gnu/packages/engineering.scm (poke)[source]: Add snippet to remove
generated files.
 2021-12-06 11:39:08 +02:00
Efraim Flashner
c70df3c467
gnu: poke: Update to 1.4. 
* gnu/packages/engineering.scm (poke): Update to 1.4.
[native-inputs]: Remove clisp, perl, python-2, and python-3.
 2021-12-06 11:39:07 +02:00
Efraim Flashner
e050ddad0b
gnu: poke: Update metadata. 
* gnu/packages/engineering.scm (poke)[home-page]: Use GNU home-page.
[synopsis]: Use upstream synopsis.
[description]: Reflow.
 2021-12-06 11:39:07 +02:00
Ricardo Wurmus
cf32c21ecd
gnu: perl-math-cephes: Build reproducibly. 
* gnu/packages/perl-maths.scm (perl-math-cephes)[source]: Sort result of
readdir.
 2021-12-06 10:12:13 +01:00
Ludovic Courtès
f72db02a6a
gnu: fpm2: Build with '-fcommon'. 
* gnu/packages/password-utils.scm (fpm2)[arguments]: Add #:configure-flags.
 2021-12-06 10:01:32 +01:00
Ludovic Courtès
3686780f31
gnu: xnee: Build with '-fcommon'. 
* gnu/packages/xnee.scm (xnee)[arguments]: New field.
 2021-12-06 10:01:15 +01:00
Leo Famulari
764be13ee6
gnu: isync: Update to 1.4.4 [fixes CVE-2021-{3657,44143}]. 
* gnu/packages/mail.scm (isync): Update to 1.4.4.
 2021-12-05 23:36:42 -05:00
Ludovic Courtès
c162f8582b
gnu: libsoup: Simplify inputs. 
Obtained by running "guix style --input-simplification=always" and by
using 'modify-inputs' instead of list primitives.

* gnu/packages/gnome.scm (libsoup-minimal, libsoup-minimal-2, libsoup):
Simplify inputs.
 2021-12-05 23:53:40 +01:00
Ludovic Courtès
0dc42f5bbf
gnu: librsvg: Simplify inputs. 
Obtained by running "guix style --input-simplification=always".

* gnu/packages/gnome.scm (librsvg, librsvg-2.40): Simplify inputs.
 2021-12-05 23:39:29 +01:00
Ludovic Courtès
dcf308a8bf
gnu: gtk+: Simplify inputs. 
Obtained by running:

  guix style --input-simplification=always gtk+ gtk+@2

* gnu/packages/gtk.scm (gtk+-2, gtk+): Simplify inputs.
 2021-12-05 23:24:48 +01:00
Ludovic Courtès
597119937d
gnu: gtk+@2: Use 'librsvg-for-system'. 
* gnu/packages/gtk.scm (gtk+-2)[propagated-inputs]: Use
'librsvg-for-system' unconditionally.
 2021-12-05 23:15:24 +01:00
Ludovic Courtès
90570b5e9f
gnu: libsoup: Remove unneeded dependency on PHP. 
* gnu/packages/gnome.scm (libsoup-minimal)[native-inputs]: Remove PHP.
 2021-12-05 23:10:44 +01:00
Ludovic Courtès
2561f2720f
gnu: gtk+: Use 'librsvg-for-system'. 
This brings back SVG support on non-x86_64 platforms.

* gnu/packages/gtk.scm (gtk+)[inputs]: Use 'librsvg-for-system'
unconditionally.
[arguments]: In 'disable-failing-tests' phase, remove conditional
substitutions aimed for non-x86_64 targets lacking librsvg support.
* gnu/packages/gnome.scm (libhandy)[arguments]: Likewise, remove
'skip-test-that-requires-svg' phase.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
3bd7ce6053
gnu: emacs: Use 'librsvg-for-system'. 
* gnu/packages/emacs.scm (emacs)[inputs]: Use 'librsvg-for-system'
unconditionally.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
c789d00b5f
gnu: openbox: Use 'librsvg-for-system'. 
* gnu/packages/openbox.scm (openbox)[inputs]: Use 'librsvg-for-system'
unconditionally.
 2021-12-05 22:42:26 +01:00
Ludovic Courtès
efbaa5fcc8
gnu: mate: Depend on 'librsvg-for-system'. 
* gnu/packages/mate.scm (engrampa)[inputs]: Replace LIBRSVG by
LIBRSVG-FOR-SYSTEM.
(libmatekbd)[inputs]: Likewise.
(mate-panel)[inputs]: Likewise.
(mate-screensaver)[inputs]: Likewise.
(mate-utils)[inputs]: Likewise.
(mate-control-center)[inputs]: Likewise.
(eom)[inputs]: Likewise, and remove duplicate
[license]: Remove unnecessary list.
 2021-12-05 22:42:25 +01:00
Ludovic Courtès
c19f968cbd
gnu: librsvg@2.40: Depend on the default Pango version. 
This avoids conflicts where, say, gtk+ would pull pango@1.44 whereas
mate-control-center would additionally pull pango@1.42 via librsvg@2.40
on i686-linux.

* gnu/packages/gnome.scm (librsvg-2.40)[arguments]: In
'remove-failing-tests' phase, remove two additional tests.
[inputs]: Change PANGO-1.42 to PANGO.
 2021-12-05 22:42:25 +01:00
Thiago Jung Bauermann
a9d426c492
gnu: Add texlive-latex-luatex. 
When TeX Live was updated to version 2021 the ‘lualatex’ format started
being generated with the LuaHBTeX engine, but the ‘lualatex’ command still
uses the LuaTeX engine. This causes the command to fail:

  user@popigai:~$ lualatex hello.tex
  This is LuaTeX, Version 1.13.0 (TeX Live 2021/GNU Guix)
  restricted system commands enabled.

  ---! lualatex.fmt was written by luahbtex
  (Fatal format file error; I'm stymied)user@popigai:~$

The correct way to fix this problem would be either to change texlive-bin
to make ‘lualatex’ use the LuaHBTeX engine, or to change texlive-latex-base
to generate ‘lualatex.fmt’ with LuaTeX. Both options would rebuild large
parts of the world.

Ricardo Wurmus suggested creating a new package to provide ‘lualatex.fmt’
for LuaTeX as a workaround. This is what this package does.

Fixes https://issues.guix.gnu.org/51252.

* gnu/packages/tex.scm (texlive-latex-luatex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-12-05 22:42:25 +01:00
Ludovic Courtès
85c07e330c
gnu: gtranslator: Fix URL. 
Reported by Vivien Kraus.

* gnu/packages/gnome.scm (gtranslator)[source]: Change
'version-major+minor' to 'version-major'.
 2021-12-05 22:42:25 +01:00
Ricardo Wurmus
0f2a77e14f
gnu: Add libnftnl/fixed. 
* gnu/packages/linux.scm (libnftnl/fixed): New variable.
 2021-12-05 22:26:26 +01:00
Demis Balbach
d8401fb508
gnu: Add phonesim. 
* gnu/packages/telephony.scm (phonesim): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:56:53 +01:00
jgart
026ac3c010
gnu: Add pounce. 
* gnu/packages/messaging.scm (pounce): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:51:39 +01:00
Luis Felipe
f856c8f1b0
gnu: Add python-django-svg-image-form-field. 
* gnu/packages/django.scm (python-django-svg-image-form-field): New
variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:44:51 +01:00
jgart
648db3ad2b
gnu: Add litterbox. 
* gnu/packages/irc.scm (litterbox): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 21:35:13 +01:00
Nicolas Goaziou
6a8d2499ae
gnu: emacs-telega: Update to 0.7.031. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to 0.7.031.
 2021-12-05 21:32:42 +01:00
Nicolas Goaziou
e0e9aa116e
gnu: emacs-geiser: Update to 0.19. 
* gnu/packages/emacs-xyz.scm (emacs-geiser): Update to 0.19.
 2021-12-05 21:22:43 +01:00
jgart
a3dea002c1
gnu: Add hex. 
* gnu/packages/rust-apps.scm (hex): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:46:10 +01:00
jgart
13f2f2d14d
gnu: Add rust-no-color-0.1. 
* gnu/packages/crates-io.scm (rust-no-color-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:44:26 +01:00
simendsjo
c4699914c9
gnu: font-iosevka: Update to 11.2.0. 
* gnu/packages/fonts.scm (font-iosevka): Update to 11.2.0

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:40:09 +01:00
Aleksandr Vityazev
df4debda05
gnu: sbcl-slynk: Update to 1.0.43-5.0470c02 
* gnu/packages/lisp-xyz.scm (sbcl-slynk): Update to 1.0.43-5.0470c02.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:37:59 +01:00
Aleksandr Vityazev
23e1f3e4f6
gnu: emacs-sly: Update to 1.0.43-5.0470c02 
* gnu/packages/emacs-xyz.scm (emacs-sly): Update to 1.0.43-5.0470c02.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-05 19:37:58 +01:00
Ricardo Wurmus
9bc0f45df5
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-12-05 19:17:41 +01:00
Nicolas Goaziou
b4e97063ba
gnu: trezor-agent: Fix hash. 
* gnu/packages/finance.scm (trezor-agent): Update hash.

Hash was not updated when committing
c7c4f80881.
 2021-12-05 19:17:01 +01:00
Ricardo Wurmus
6db3c536e8
gnu: python-bwapy: Remove sanity-check. 
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.
 2021-12-05 17:38:15 +01:00
Ricardo Wurmus
dd67154e5d
gnu: Remove python2-plastid. 
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
 2021-12-05 17:37:05 +01:00
Ricardo Wurmus
98264531be
gnu: Remove python2-twobitreader. 
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
 2021-12-05 17:36:43 +01:00
Ricardo Wurmus
4202f4d58a
gnu: python-bbknn: Fix sanity-check phase. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
 2021-12-05 17:33:17 +01:00
Ricardo Wurmus
b1bd997d50
gnu: python-bbknn: Add missing input. 
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
 2021-12-05 17:32:50 +01:00
Ricardo Wurmus
19f6b770dc
gnu: velvet: Add missing TeX package. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-05 17:22:11 +01:00
Ricardo Wurmus
fe0f8c627a
gnu: velvet: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
 2021-12-05 17:21:39 +01:00
Ricardo Wurmus
f2b99e3aaf
gnu: python-bwapy: Remove pre-built object files. 
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
57f278ffc4
gnu: metabat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
c13046cb68
gnu: clapack: Pass -fcommon to compiler. 
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
ae0acf6b6d
gnu: clapack: Remove trailing #T. 
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
1d53c697b3
gnu: tla2tools: Remove remaining reference to %output. 
This is a follow-up to commit 7e6ee16d49.

* gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to
%output.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
8ae33d6844
gnu: kraken2: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
c973107a25
gnu: methyldackel: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:04 +01:00