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2021-03-18gnu: imagemagick/fixed: Redirect old sonames to new sonames....* gnu/packages/imagemagick.scm (imagemagick/fixed)[arguments]: Add 'fix-compat-cheat-rename-so phase to redirect old soname paths (expected without grafting) to new sonames introduced by ImageMagick 6.9.12-0 and later. These sonames are probably not forward compatible but most probably backwards compatible so it should suffice until we remove the graft. Léo Le Bouter
2021-03-18gnu: linux-libre 4.4: Update to 4.4.262....* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.262. (linux-libre-4.4-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre 4.9: Update to 4.9.262....* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.262. (linux-libre-4.9-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre 4.14: Update to 4.14.226....* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.226. (linux-libre-4.14-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre 4.19: Update to 4.19.181....* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.181. (linux-libre-4.19-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre 5.4: Update to 5.4.106....* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.106. (linux-libre-5.4-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre 5.10: Update to 5.10.24....* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.24. (linux-libre-5.10-pristine-source): Update hash. Leo Famulari
2021-03-18gnu: linux-libre: Update to 5.11.7....* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.7. (linux-libre-5.11-pristine-source): Update hash. Leo Famulari
2021-03-17gnu: Add libucl....* gnu/packages/wm.scm (libucl): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> qblade
2021-03-17gnu: Use autoconf instead of autoconf-wrapper when possible....This should reduce confusion on when to use the "autoconf" package and when to use "autoconf-wrapper" instead in package definitions. Fixes <https://bugs.gnu.org/46564>. * gnu/packages/autotools.scm (autoconf-wrapper): advise to use the "autoconf" package instead where possible. * gnu/packages/game-development.scm (tsukundere)[native-inputs]: use "autoconf" instead of "autoconf-wrapper". * gnu/packages/gimp.scm (glimpse)[native-inputs]: likewise. (gimp-resynthesizer)[native-inputs]: add comment on why "autoconf-wrapper" is used. * gnu/packages/gnunet.scm (gnunet)[native-inputs]: use "autoconf" instead of "autoconf-wrapper". * gnu/packages/gnupg.scm (signing-party)[native-inputs]: add comment on why "autoconf-wrapper" is used. * gnu/packages/guile-xyz.scm (guile-bash,guile-filesystem,guile-ics,guile-udev)[native-inputs]: use "autoconf" instead of "autoconf-wrapper". * gnu/packages/libevent.scm (libuv)[native-inputs]: indicates "autoconf-wrapper" needs to be replaced with "autoconf" on core-updates. * gnu/packages/logging.scm (glog)[native-inputs]: use "autoconf" instead of "autoconf-wrapper". * gnu/packages/mail.scm (libetpan)[native-inputs]: likewise. * gnu/packages/mate.scm (mate-icon-theme-faenza)[native-inputs]: add comment on why "autoconf-wrapper" is used. (mate-screensaver)[native-inputs]: use "autoconf" instead of "autoconf-wrapper". * gnu/packages/package-management.scm (guix)[native-inputs]: likewise. * gnu/packages/sawfish.scm (librep)[native-inputs]: likewise. * gnu/packages/video.scm (motion)[native-inputs]: likewise. * gnu/packages/zile.scm (zile)[native-inputs]: likewise. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Maxime Devos
2021-03-17gnu: scdoc: Cross-compile....* gnu/packages/man.scm (scdoc)[arguments]: Use CC-FOR-TARGET. Tobias Geerinckx-Rice
2021-03-17gnu: scdoc: Don't use unstable tarball....The autogenerated tarball was modified upstream. * gnu/packages/man.scm (scdoc)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2021-03-17gnu: libtirpc/hurd: Fix package source....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. Christopher Baines
2021-03-17gnu: lua.scm: Sort package module imports alphabetically....* gnu/packages/lua.scm: Sort package module imports alphabetically. Efraim Flashner
2021-03-17gnu: python-pygments: Update to 2.7.4 [fixes CVE-2021-27291]....* gnu/packages/python-xyz.scm (python-pygments/fixed): New variable. (python-pygments)[replacement]: Graft. Léo Le Bouter
2021-03-17gnu: Add emacs-kotlin-mode....* gnu/packages/emacs-xyz.scm (emacs-kotlin-mode): New variable. Oleg Pykhalov
2021-03-17gnu: emacs-marginalia: Update to 0.4....* gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.4. Nicolas Goaziou
2021-03-17gnu: komikku: Update to 0.27.0....* gnu/packages/gnome.scm (komikku): Update to 0.27.0. [inputs]: Add python-brotli and webkitgtk. Leo Prikler
2021-03-17gnu: Move lolcode to esolangs....* 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. Leo Prikler
2021-03-17gnu: tig: Update to 2.5.3....* 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> LibreMiami
2021-03-17gnu: hwloc: Add 'release-monitoring-url' property....* gnu/packages/mpi.scm (hwloc-1)[properties]: New field. Ludovic Courtès
2021-03-17gnu: gnome-autoar: Update to 0.3.1 [fixes CVE-2021-28650]....* gnu/packages/gnome.scm (gnome-autoar): Update to 0.3.1. Léo Le Bouter
2021-03-17gnu: pzstd: Update to 1.4.9 [fixes CVE-2021-24032]....* 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. Léo Le Bouter
2021-03-17gnu: Use PACKAGE/INHERIT in more places....* 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. Mark H Weaver
2021-03-16gnu: gvfs: Add 'lint-hidden-cve' property....* gnu/packages/gnome.scm (gvfs)[properties]: New field, marking CVE-2019-12447, CVE-2019-12448, and CVE-2019-12449 as fixed. Mark H Weaver
2021-03-16gnu: gnome-shell: Add 'lint-hidden-cve' property....* gnu/packages/gnome.scm (gnome-shell)[properties]: New field, marking CVE-2019-3820 as fixed. Mark H Weaver
2021-03-16gnu: qemu: Enable reproducible builds....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. Maxim Cournoyer
2021-03-16gnu: Add meson-next....* gnu/packages/build-tools.scm (meson-next): New variable. Maxim Cournoyer
2021-03-16gnu: mpg321: Fix CVE-2019-14247....* 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> Kei Kebreau
2021-03-16gnu: varnish-modules: Update to 0.17.1 [fixes CVE-2021-28543]....* gnu/packages/web.scm (varnish-modules): Update to 0.17.1. Léo Le Bouter
2021-03-16gnu: tor: Update to 0.4.5.7 [security fixes]....* gnu/packages/tor.scm (tor): Update to 0.4.5.7. Efraim Flashner
2021-03-16gnu: snakemake: Add missing inputs....* gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add python-nbformat, python-pulp, and python-toposort. Ricardo Wurmus
2021-03-16gnu: Add python-toposort....* gnu/packages/python-xyz.scm (python-toposort): New variable. Ricardo Wurmus
2021-03-16gnu: Add python-pulp....* gnu/packages/python-xyz.scm (python-pulp): New variable. Ricardo Wurmus
2021-03-16gnu: Add python-amply....* gnu/packages/python-xyz.scm (python-amply): New variable. Ricardo Wurmus
2021-03-16gnu: emacs-easy-kill: Update to 0.9.4....* gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4. Nicolas Goaziou
2021-03-16gnu: emacs-leaf: Update to 4.4.0....* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0. Nicolas Goaziou
2021-03-16gnu: python-pikepdf: Update to 2.9.0....* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0. Nicolas Goaziou
2021-03-16gnu: asymptote: Update to 2.70....* gnu/packages/plotutils.scm (asymptote): Update to 2.70. Nicolas Goaziou
2021-03-16gnu: b4: Fix setup.py version incompatibility....* gnu/packages/version-control.scm (b4)[source]: Add snippet to not require too specific of a version. Reported-by: Kyle Meyer <kyle@kyleam.com> Efraim Flashner
2021-03-16gnu: libmemcached: Disable test suite....* 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> Maxim Cournoyer
2021-03-16gnu: hisat2: Update to 2.2.1....* 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. Ricardo Wurmus
2021-03-16gnu: Remove MongoDB....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. Léo Le Bouter
2021-03-16gnu: git: Fix git-manpages native input's hash....This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777. * gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's hash. Léo Le Bouter
2021-03-16gnu: git: Update to 2.31.0....* gnu/packages/version-control.scm (git): Update to 2.31.0. Léo Le Bouter
2021-03-16gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363]....* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of python-urllib3/fixed. Léo Le Bouter
2021-03-16gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363]....* gnu/packages/python-web.scm (python-urllib3/fixed): New variable. (python-urllib3)[replacement]: Graft. Léo Le Bouter
2021-03-16gnu: tmsu: Improve installation....* 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> Stefan Reichör
2021-03-16gnu: glances: Update to 3.1.6....* gnu/packages/python-xyz.scm (glances): Update to 3.1.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Stefan Reichör
2021-03-15Revert some commits that caused `guix pull` to fail....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)) Leo Famulari