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2022-01-10gnu: binutils: Fix CVE-2021-45078.Leo Famulari
This is for the release branch. Should we also use a graft for the master branch? It would be even better if we could add a binutils-next package that users could install, in my opinion. * gnu/packages/patches/binutils-CVE-2021-45078.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (binutils)[source]: Use it. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: glib: Update to 2.70.2.Maxim Cournoyer
* gnu/packages/glib.scm (glib): Update to 2.70.2.
2022-01-10gnu: meson: Update to 0.60.3.Maxim Cournoyer
* gnu/packages/build-tools.scm (gn): Update to 0.60.3.
2022-01-10gnu: glibmm: Update to 2.70.0 and apply guix style.Maxim Cournoyer
* gnu/packages/glib.scm (glibmm): Update to 2.70.0. [native-inputs]: Use new style.
2022-01-10gnu: cpuid: Remove obsolete file permissions change.Sarah Morgensen
* gnu/packages/linux.scm (cpuid)[arguments]<#:phases>{fix-makefile}: Remove Makefile gzip permissions patch. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: pre-commit: Remove obsolete phase.Sarah Morgensen
* gnu/packages/version-control.scm (pre-commit)[arguments]<#:phases>: Remove 'make-gz-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-prometheus-common: Remove obsolete phase.Sarah Morgensen
* gnu/packages/syncthing.scm (go-github-com-prometheus-common) [arguments]<#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-pdfminer-six: Remove obsolete phase.Sarah Morgensen
* gnu/packages/python-xyz.scm (python-pdfminer-six)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: arcanist: Remove obsolete phase.Sarah Morgensen
* gnu/packages/phabricator.scm (arcanist)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: helm: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (helm)[arguments]<#:phases>: Remove 'make-gz-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: lmms: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (lmms)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: jalv-select: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (jalv-select)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-scikit-learn: Remove obsolete phase.Sarah Morgensen
* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-ipfs: Remove obsolete phase.Sarah Morgensen
* gnu/packages/ipfs.scm (go-ipfs)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-plotly: Remove obsolete phase.Sarah Morgensen
* gnu/packages/graph.scm (python-plotly)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-gdamore-tcell: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-github-com-gdamore-tcell)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-docker-distribution: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-github-com-docker-distribution)[arguments] <#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-golang-org-x-crypto: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-golang-org-x-crypto)[arguments]<#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: po4a: Remove obsolete phase.Sarah Morgensen
* gnu/packages/gettext.scm (po4a)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: emacs: Remove obsolete phase.Sarah Morgensen
* gnu/packages/emacs.scm (emacs)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: cups-minimal: Remove obsolete phase.Sarah Morgensen
* gnu/packages/cups.scm (cups-minimal)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: clipper: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-biom-format: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10build-system/gnu: Make gzip files writable before resetting timestamps.Sarah Morgensen
guix/build/gnu-build-system.scm (reset-gzip-timestamps): Ensure gzip files are writable before resetting their timestamps. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: tbb-2020: Use ld.gold to work around segfaults in check phase.Maxim Cournoyer
* gnu/packages/tbb.scm (tbb-2020) [configure-flags]: Use -fuse-ld=gold in CFLAGS. [native-inputs]: Add ld-gold-wrapper.
2022-01-10gnu: python-igraph: Update to 0.9.8.Maxim Cournoyer
* gnu/packages/graph.scm (python-igraph): Update to 0.9.8. [origin]: Fetch from git. [configure-flags]: Delete argument. [phases]{build}: No longer override phase. {check}: Preserve ordering and streamline. {specify-libigraph-location}: New phase. [native-inputs]: Remove pkg-config. [home-page]: Update.
2022-01-10gnu: igraph: Update to 0.9.5.Maxim Cournoyer
* gnu/packages/graph.scm (igraph): Update to 0.9.5. [source]: Add snippet to fully unbundle. [build-system]: Use cmake-build-system. [configure-flags]: Replace all by just '-DBUILD_SHARED_LIBS=ON'. [native-inputs]: Add pkg-config. [inputs]{zlib}: Delete input. {arpack-ng, plfit, suitesparse}: New inputs.
2022-01-10gnu: Add plfit.Maxim Cournoyer
* gnu/packages/graph.scm (plfit): New variable.
2022-01-10gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
2022-01-10gnu: bcftools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
2022-01-10gnu: samtools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable.
2022-01-10gnu: htslib: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
2022-01-10gnu: python-beautifulsoup4: Update to 4.10.0.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-beautifulsoup4): Update to 4.10.0. [propagated-inputs]{python-html5lib, python-lxml}: New inputs. [arguments]: Delete field. (python2-beautifulsoup4): Peg at version 4.9.3.
2022-01-10gnu: poetry: Update to 1.1.12.Maxim Cournoyer
* gnu/packages/python-xyz.scm (poetry): Update to 1.1.12. [phases]{patch-setup-py}: Relax packaging version requirement. [propagated-inputs]{python-msgpack-transitional}: Replace with... {python-msgpack}: ... this. {python-requests-toolbelt-0.9.1}: Replace with... {python-requests-toolbelt}: ... this. {python-msgpack-transitional}: Delete variable.
2022-01-10gnu: python-requests-toolbelt: Update to 0.9.1 and enable tests.Maxim Cournoyer
* gnu/packages/python-web.scm (pyhton-requests-toolbelt): Update to 0.9.1. [phases]{delete-problematic-tests}: New phase. (python-requests-toolbelt-0.9.1): Delete variable. (python2-requests-toolbelt): Likewise. (python-cloudscraper): Adjust accordingly.
2022-01-10gnu: python-cachecontrol: Update to 0.12.10.Maxim Cournoyer
* gnu/packages/python-web.scm (python-cachecontrol): Update to 0.12.10.
2022-01-10gnu: python-os-testr: Propagate python-testtools and python-babel.Maxim Cournoyer
Lack of python-testtools was causing the sanity-check phase to fail. * gnu/packages/openstack.scm (python-os-testr) [native-inputs]{python-testtools, python-babel}: Move to... [propagated-inputs]: ... here.
2022-01-10gnu: webkitgtk: Enable GStreamer GL support.Maxim Cournoyer
* gnu/packages/webkit.scm (webkitgtk)[configure-flags]: Remove the '-DUSE_GSTREAMER_GL=OFF' build option.
2022-01-10gnu: webkitgtk: Add a note about plugins in description.Maxim Cournoyer
This is in response to <https://issues.guix.gnu.org/52375>. * gnu/packages/webkit.scm (webkitgtk): Add a note about GStreamer plugins. Reported-by: Jack Hill <jackhill@jackhill.us>
2022-01-10gnu: python2-matplotlib: Update to 2.2.5.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python2-matplotlib): Update to 2.2.5. [phases]: Use G-exp. {install-jquery-ui}: Delete phase. JQuery is bundled in this release. [native-inputs]: Remove all exception pkg-config. [propagated-inputs]: Sort and explicitly specify all inputs to ease maintenance.
2022-01-10gnu: python-matplotlib: Update to 3.5.1 and run tests in parallel.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.5.1. [propagated-inputs]: Add python-fonttools, python-wxpython and python-packaging. [native-inputs]: Remove python-mock, python-wheel, unzip and jquery-ui. Add python-pytest-timeout, python-pytest-xdist, python-setuptools-scm and python-setuptools-scm-git-archive. [phases]: Delete trailing #t. {pretend-version}: New phase. {install-jquery-ui}: Delete phase. {check}: Honor TESTS?. Do not skip webagg tests anymore. Invoke using '-n' argument to run tests in parallel via pytest-xdist. {configure-environment}: Do not set LD_LIBRARY_PATH nor HOME. Rename setup.cfg to mplsetup.cfg. Set the backend to Agg.
2022-01-10gnu: python-fonttools: Update to 4.28.5.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-fonttools): Update to 4.28.5 and hide the package. [properties]: New field. (python-fonttools-with-tests): New variable.
2022-01-10gnu: Add python-zopfli.Maxim Cournoyer
* gnu/packages/python-compression.scm (python-zopfli): New variable.
2022-01-10gnu: Add zopfli.Maxim Cournoyer
* gnu/packages/compression.scm (zopfli): New variable.
2022-01-10gnu: Add python-fs.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-fs): New variable.
2022-01-10gnu: Add python-pyftpdlib.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-pyftpdlib): New variable.
2022-01-10gnu: Add python-pysendfile.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-pysendfile): New variable.
2022-01-10gnu: python-pylint: Update to 2.12.2.Maxim Cournoyer
* gnu/packages/check.scm (python-pylint): Update to 2.12.2. [phases]{check}: Override phase. [native-inputs]: Remove python-pytest-benchmark, python-pytest-runner. [propagated-inputs]: Add python-platformdirs, python-typing-extensions. [synopsis]: Streamline.
2022-01-10gnu: python-platformdirs: Update to 2.4.0, run tests and fix metadata.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-platformdirs): Update to 2.4.0. [phases]{pretend-version}: New phase. {check}: Override to run tests. [native-inputs]{python-setuptools-scm}: New input.
2022-01-10gnu: python-flit: Update to 3.5.1, enable tests and apply guix style.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-flit)[origin]: Fetch from pypi-uri, to ease updating the package. [phases]{bootstrap}: Delete phase. {build, install}: Do a PEP 517 build using pypa-build. {check}: New phase. [tests?]: Enable. [propagated-inputs]{python-pytoml, python-toml}: Remove. {python-pypa-build, python-tomli-w, python-flit-core, python-requests}: New inputs. {python-docutils}: New input, moved from... [native-inputs]: ... here. Apply guix style. {python-testpath}: Use the regular python-testpath package. [synopsis, description]: Re-indent.
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