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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
Julien Lepiller ed27614660
nls: Update 'es' translation. 2021-12-08 01:19:45 +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