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2021-03-17gnu: scdoc: Cross-compile.Tobias Geerinckx-Rice
* gnu/packages/man.scm (scdoc)[arguments]: Use CC-FOR-TARGET.
2021-03-17gnu: scdoc: Don't use unstable tarball.Tobias Geerinckx-Rice
The autogenerated tarball was modified upstream. * gnu/packages/man.scm (scdoc)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2021-03-17gnu: libtirpc/hurd: Fix package source.Christopher Baines
Amend the changes in 1a265842e634656411bc7304c4648273f174f65e to properly access the origin patches from libtirpc. I noticed this as guix weather didn't work for this package. * gnu/packages/onc-rpc.scm (libtirpc/hurd)[source]: Call origin-patches on (package-source libtirpc) rather than the libtirpc package.
2021-03-17gnu: lua.scm: Sort package module imports alphabetically.Efraim Flashner
* gnu/packages/lua.scm: Sort package module imports alphabetically.
2021-03-17gnu: python-pygments: Update to 2.7.4 [fixes CVE-2021-27291].Léo Le Bouter
* gnu/packages/python-xyz.scm (python-pygments/fixed): New variable. (python-pygments)[replacement]: Graft.
2021-03-17gnu: Add emacs-kotlin-mode.Oleg Pykhalov
* gnu/packages/emacs-xyz.scm (emacs-kotlin-mode): New variable.
2021-03-17gnu: emacs-marginalia: Update to 0.4.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.4.
2021-03-17gnu: komikku: Update to 0.27.0.Leo Prikler
* gnu/packages/gnome.scm (komikku): Update to 0.27.0. [inputs]: Add python-brotli and webkitgtk.
2021-03-17gnu: Move lolcode to esolangs.Leo Prikler
* gnu/packages/lolcode.scm (lci): Move from here... * gnu/packages/esolangs.scm (lolcode-lci): ... to here. * gnu/packages/lolcode.scm: Delete file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
2021-03-17gnu: tig: Update to 2.5.3.LibreMiami
* gnu/packages/version-control.scm (tig): Update to 2.5.3. Co-authored-by: jgart <jgart@dismail.de> Co-authored-by: donotshake <donotshake:matrix.org> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-03-17gnu: hwloc: Add 'release-monitoring-url' property.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-1)[properties]: New field.
2021-03-17gnu: gnome-autoar: Update to 0.3.1 [fixes CVE-2021-28650].Léo Le Bouter
* gnu/packages/gnome.scm (gnome-autoar): Update to 0.3.1.
2021-03-17gnu: pzstd: Update to 1.4.9 [fixes CVE-2021-24032].Léo Le Bouter
* gnu/packages/compression.scm (pzstd): Use 'package/inherit' over zstd so any graft applied to zstd cascades onto pzstd which is built from the same source.
2021-03-17gnu: Use PACKAGE/INHERIT in more places.Mark H Weaver
* gnu/packages/algebra.scm (fftwf, fftw-openmpi), gnu/packages/audio.scm (ztoolkit-rsvg), gnu/packages/bioinformatics.scm (python2-dendropy), gnu/packages/boost.scm (boost-with-python2), gnu/packages/check.scm (python2-mock, python2-pytest-mock), gnu/packages/cups.scm (hplip-minimal), gnu/packages/freedesktop.scm (libinput-minimal), gnu/packages/gettext.scm (gnu-gettext), gnu/packages/glib.scm (python2-pygobject), gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi), gnu/packages/groff.scm (groff-minimal), gnu/packages/jami.scm (ffmpeg-jami), gnu/packages/libcanberra.scm (libcanberra/gtk+-2), gnu/packages/lirc.scm (python2-lirc), gnu/packages/llvm.scm (clang-runtime-3.5), gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple), gnu/packages/node.scm (libnode), gnu/packages/onc-rpc.scm (libtirpc/hurd), gnu/packages/python-compression.scm (bitshuffle-for-snappy), gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography) (python2-cryptography, python2-m2crypto), gnu/packages/python-web.scm (python2-html2text, python2-tornado) (python2-terminado, python2-ndg-httpsclient, python2-websocket-client) (python2-rauth, python2-url, python2-s3transfer), gnu/packages/python-xyz.scm (python2-psutil, python2-serpent) (python2-humanfriendly, python2-empy, python2-parse-type, python2-polib) (python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc) (python2-ipyparallel, python2-traitlets, python2-dbus) (python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse) (python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal) (python2-contextlib2, python2-promise, python2-anyjson, python2-amqp) (python2-kombu, python2-billiard, python2-celery, python2-whoosh) (python2-jellyfish, python-rope, ptpython-2, python2-binaryornot) (python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort) (python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash) (python2-cloudpickle, python2-reparser), gnu/packages/python.scm (python2-called-python), gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt) (python-qscintilla, python-pyqt+qscintilla), gnu/packages/scanner.scm (sane-backends), gnu/packages/sdl.scm (guile3.0-sdl2), gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc) (python-sepolgen, policycoreutils), gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack), gnu/packages/simulation.scm (fenics), gnu/packages/statistics.scm (python2-statsmodels), gnu/packages/texinfo.scm (info-reader), gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1), gnu/packages/xml.scm (xmlsec-nss), gnu/packages/xorg.scm (uim-gtk, uim-qt), guix/build-system/python.scm (package-with-explicit-python) (strip-python2-variant): Use PACKAGE/INHERIT.
2021-03-16gnu: gvfs: Add 'lint-hidden-cve' property.Mark H Weaver
* gnu/packages/gnome.scm (gvfs)[properties]: New field, marking CVE-2019-12447, CVE-2019-12448, and CVE-2019-12449 as fixed.
2021-03-16gnu: gnome-shell: Add 'lint-hidden-cve' property.Mark H Weaver
* gnu/packages/gnome.scm (gnome-shell)[properties]: New field, marking CVE-2019-3820 as fixed.
2021-03-16gnu: qemu: Enable reproducible builds.Maxim Cournoyer
Fixes <https://issues.guix.gnu.org/47176>. The solution was suggested by bonzini on OFTC's #qemu channel. * gnu/packages/virtualization.scm (qemu)[snippet]: Delete bundled meson copy. [native-inputs]: Add meson-next.
2021-03-16gnu: Add meson-next.Maxim Cournoyer
* gnu/packages/build-tools.scm (meson-next): New variable.
2021-03-16gnu: mpg321: Fix CVE-2019-14247.Kei Kebreau
* gnu/packages/patches/mpg321-CVE-2019-14247.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/mp3.scm (mpg321)[source]: Apply it. Signed-off-by: Léo Le Bouter <lle-bout@zaclys.net> Signed-off-by: Leo Famulari <leo@famulari.name>
2021-03-16gnu: varnish-modules: Update to 0.17.1 [fixes CVE-2021-28543].Léo Le Bouter
* gnu/packages/web.scm (varnish-modules): Update to 0.17.1.
2021-03-16gnu: tor: Update to 0.4.5.7 [security fixes].Efraim Flashner
* gnu/packages/tor.scm (tor): Update to 0.4.5.7.
2021-03-16gnu: snakemake: Add missing inputs.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add python-nbformat, python-pulp, and python-toposort.
2021-03-16gnu: Add python-toposort.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-toposort): New variable.
2021-03-16gnu: Add python-pulp.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pulp): New variable.
2021-03-16gnu: Add python-amply.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-amply): New variable.
2021-03-16gnu: emacs-easy-kill: Update to 0.9.4.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.
2021-03-16gnu: emacs-leaf: Update to 4.4.0.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.
2021-03-16gnu: python-pikepdf: Update to 2.9.0.Nicolas Goaziou
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.
2021-03-16gnu: asymptote: Update to 2.70.Nicolas Goaziou
* gnu/packages/plotutils.scm (asymptote): Update to 2.70.
2021-03-16gnu: b4: Fix setup.py version incompatibility.Efraim Flashner
* gnu/packages/version-control.scm (b4)[source]: Add snippet to not require too specific of a version. Reported-by: Kyle Meyer <kyle@kyleam.com>
2021-03-16gnu: libmemcached: Disable test suite.Maxim Cournoyer
* gnu/packages/databases.scm (libmemcached): Disable test suite. Removing trailing #t. [phases]{fix-configure}: Remove useless group in pattern. {disable-failing-tests}: Remove phase. {build-and-install-html-doc}: Order after the build phase. [home-page]: Please 'guix lint'. Reported-by: Simon Tournier <zimon.toutoune@gmail.com>
2021-03-16gnu: hisat2: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1. [source]: Fetch from git repository on Github. [arguments]: Add phase to build manual; remove trailing #t from other phases. [native-inputs]: Remove unzip. [home-page]: Update. [inputs]: Add python-wrapper.
2021-03-16gnu: Remove MongoDB.Léo Le Bouter
mongodb 3.4.10 has unpatched CVEs and mongodb 3.4.24 has some files in the release tarball under the SSPL, therefore we cannot provide mongodb while upholding to good security standards. It turns out feff80cec3c97a3df2c20d300be12d67f79d4f22 was right since while the main license file wasnt altered to SSPL, some files in the tree contain SSPL headers. * gnu/packages/databases.scm (go-gopkg.in-mgo.v2): Remove. * gnu/packages/databases.scm (mongo-tools): Remove. * doc/guix.texi (mongodb-service-type): Remove. * gnu/tests/databases.scm (%test-mongodb, %mongodb-os, run-mongodb-test): Remove. * gnu/services/databases.scm (mongodb-configuration, mongodb-configuration?, mongodb-configuration-mongodb, mongodb-configuration-config-file, mongodb-configuration-data-directory, mongodb-service-type, %default-mongodb-configuration-file, %mongodb-accounts, mongodb-activation, mongodb-shepherd-service): Remove. * gnu/packages/databases.scm (mongodb): Remove.
2021-03-16gnu: git: Fix git-manpages native input's hash.Léo Le Bouter
This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777. * gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's hash.
2021-03-16gnu: git: Update to 2.31.0.Léo Le Bouter
* gnu/packages/version-control.scm (git): Update to 2.31.0.
2021-03-16gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter
* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of python-urllib3/fixed.
2021-03-16gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter
* gnu/packages/python-web.scm (python-urllib3/fixed): New variable. (python-urllib3)[replacement]: Graft.
2021-03-16gnu: tmsu: Improve installation.Stefan Reichör
* gnu/packages/file-systems.scm (tmsu)[arguments]: Don't install go source files. Install binary as tmsu instead of TMSU. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-16gnu: glances: Update to 3.1.6.Stefan Reichör
* gnu/packages/python-xyz.scm (glances): Update to 3.1.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-15Revert some commits that caused `guix pull` to fail.Leo Famulari
This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through 8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5. Specifically, these commits caused the build failure of guix-package-cache.drv like this: ------ (repl-version 0 1 1) Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'... (exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
2021-03-15gnu: r-biocparallel: Build reproducibly.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible".
2021-03-15gnu: r-delayedarray: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
2021-03-15gnu: r-rsamtools: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
2021-03-15gnu: r-biostrings: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here.
2021-03-15gnu: r-biocparallel: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
2021-03-15gnu: r-biomart: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here.
2021-03-15gnu: r-annotationdbi: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
2021-03-15gnu: r-biobase: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here.
2021-03-15gnu: r-genomicranges: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
2021-03-15gnu: r-xvector: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here.
generated by cgit v1.2.3 (git 2.44.0) at 2024-07-04 23:29:11 +0000