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2021-12-08gnu: tadbit: Update to 1.0.1-1.5c4c1dd.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd. [arguments]: Remove trailing #T from build phases; pass -fcommon to test binaries; run tests conditionally.
2021-12-08gnu: python2-sphinx: Remove websupport test.Ricardo Wurmus
* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test file.
2021-12-08gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2.Ricardo Wurmus
* 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.
2021-12-08gnu: python2-jinja2: Downgrade to 2.11.3Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version supporting Python 2. (python-jinja2)[properties]: Record python2-variant.
2021-12-08gnu: fastboot: Fix ‘--version’ output.Tobias Geerinckx-Rice
* gnu/packages/android.scm (fastboot)[arguments]: Replace broken ‘git rev-parse’ shell command with the actual package VERSION. Reported by kwjc on #guix.
2021-12-08gnu: rtl8821ce-linux-module: Update to 0.0.0-4-ca204c6.Zhu Zihao
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>
2021-12-08gnu: python2-markupsafe: Downgrade to 1.1.1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1, because that's the last version to support Python 2.
2021-12-08gnu: ocaml-mcl: Add -fcommon to compiler flags.Ricardo Wurmus
* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
2021-12-08gnu: paml: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
2021-12-08gnu: paml: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from build phases.
2021-12-08gnu: sambamba: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T from build phases.
2021-12-08gnu: discrover: Add texlive-fonts-ec to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-fonts-ec.
2021-12-08gnu: discrover: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T from build phases.
2021-12-08gnu: tbsp: Update to 1.0.0-2.dc30c03.Ricardo Wurmus
* 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.
2021-12-08gnu: mantis: Update to 0.1-2.b6979a2.Ricardo Wurmus
* 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.
2021-12-08gnu: imp: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite.
2021-12-08gnu: snap-aligner: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
2021-12-08gnu: snap-aligner: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase.
2021-12-08gnu: snap-aligner: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option.
2021-12-08gnu: khmer: Cythonize source files.Ricardo Wurmus
* 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.
2021-12-08gnu: cwltool: Update to 3.1.20211107152837.Ricardo Wurmus
* 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.
2021-12-08gnu: monero: Improve check phase.Guillaume Le Vaillant
* gnu/packages/finance.scm (monero)[arguments]: Take 'tests?' parameter into consideration in 'check' phase.
2021-12-08gnu: monero-gui: Update to 0.17.3.0.Guillaume Le Vaillant
* gnu/packages/finance.scm (monero-gui): Update to 0.17.3.0.
2021-12-08gnu: monero: Update to 0.17.3.0.Guillaume Le Vaillant
* gnu/packages/finance.scm (monero): Update to 0.17.3.0. * gnu/packages/patches/monero-use-system-miniupnpc.patch: Update patch.
2021-12-08gnu: python-userspacefs: Update to 2.0.4.Efraim Flashner
* gnu/packages/python-xyz.scm (python-userspacefs): Update to 2.0.4.
2021-12-08gnu: python-dropbox: Update to 11.25.0.Efraim Flashner
* gnu/packages/file-systems.scm (python-dropbox): Update to 11.25.0. [propagated-inputs]: Remove python-certifi, python-chardet, and python-urllib3.
2021-12-08gnu: lollypop: Update to 1.4.24.Marius Bakke
* gnu/packages/gnome.scm (lollypop): Update to 1.4.24. [native-inputs]: Remove INTLTOOL and ITSTOOL. Add GETTEXT-MINIMAL.
2021-12-08gnu: python-toolz: Update to 0.11.2.Marius Bakke
* gnu/packages/python-xyz.scm (python-toolz): Update to 0.11.2.
2021-12-08gnu: python-django: Update to 3.2.10 [fixes CVE-2021-4442].Marius Bakke
* gnu/packages/django.scm (python-django): Update to 3.2.10.
2021-12-08gnu: python-django@2.2: Update to 2.2.25 [fixes CVE-2021-4442].Marius Bakke
* gnu/packages/django.scm (python-django-2.2): Update to 2.2.25.
2021-12-08gnu: hitch: Update to 1.7.2.Marius Bakke
* gnu/packages/web.scm (hitch): Update to 1.7.2.
2021-12-08gnu: lollypop: Build with libsoup@2.Marius Bakke
* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2.
2021-12-08gnu: rhythmbox: Adjust inputs.Marius Bakke
* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
2021-12-08gnu: labelme: Loosen Python requirements.Marius Bakke
* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib.
2021-12-07gnu: icecat: Update to 91.4.0-guix0-preview1 [security fixes].Mark H Weaver
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.
2021-12-07gnu: Add kiwix-tools.Denis 'GNUtoo' Carikli
* gnu/packages/web.scm (kiwix-tools): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-07gnu: newick-utils: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
2021-12-07gnu: blasr: Update to 5.3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
2021-12-07gnu: blasr: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase.
2021-12-07gnu: blasr-libcpp: Update to 5.3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib.
2021-12-07gnu: htseq: Update to 0.12.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
2021-12-07gnu: clipper: Update to 2.0.1.Ricardo Wurmus
* 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.
2021-12-07gnu: pbbam: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper.
2021-12-07gnu: dovecot-pigeonhole: Update to 0.5.17.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.17.1.
2021-12-07gnu: dovecot: Update to 2.3.17.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot): Update to 2.3.17.1.
2021-12-07gnu: bwa-pssm: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error.
2021-12-07gnu: Add pbcopper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
2021-12-07gnu: giac: Update to 1.7.0-43.Nicolas Goaziou
* gnu/packages/algebra.scm (giac): Update to 1.7.0-43.
2021-12-07gnu: python-ndg-httpsclient: Add missing input.Ricardo Wurmus
* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1.
2021-12-07gnu: fsom: Build with GCC 6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T.
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