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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
2021-03-15gnu: r-biocparallel: Build reproducibly....* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible". Ricardo Wurmus
2021-03-15gnu: r-delayedarray: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here. zimoun
2021-03-15gnu: r-rsamtools: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here. zimoun
2021-03-15gnu: r-biostrings: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here. zimoun
2021-03-15gnu: r-biocparallel: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here. zimoun
2021-03-15gnu: r-biomart: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. zimoun
2021-03-15gnu: r-annotationdbi: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here. zimoun
2021-03-15gnu: r-biobase: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here. zimoun
2021-03-15gnu: r-genomicranges: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here. zimoun
2021-03-15gnu: r-xvector: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here. zimoun
2021-03-15gnu: r-limma: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here. zimoun
2021-03-15gnu: dbus-c++: Fix command name in description....* gnu/packages/glib.scm (dbus-c++)[description]: Fix command prefix in description, and mention the second command installed as well. Maxim Cournoyer
2021-03-15gnu: qemu: Update to 5.2.0....* gnu/packages/virtualization.scm (qemu): Update to 5.2.0. [source]: Re-indent and break long lines, to appease 'guix lint'. [arguments]{disable-unusable-tests}: Adjust for the new Meson build system. Remove patching for a test workaround that has been resolved in 5.2.0. {patch-test-shebangs, patch-/bin/sh-references}: Combine into... {patch-embedded-shebangs}: ... this new phase. Patch the SHELL variable in the Makefile. {fix-optionrom-makefile}: New phase. {install-user-static}: Adjust as the binaries are now symbolic links pointing to their actual build path. [native-inputs]: Add ninja. * gnu/packages/patches/qemu-build-info-manual.patch: Update patch. Co-authored-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Leo Famulari
2021-03-15gnu: qemu: Add a static output....The static output is equivalent to what other distributions commonly package as 'qemu-user-static'. * gnu/packages/virtualization.scm (qemu)[outputs]: Add a static output. [phases]{configure}: Configure the main build as an out-of-source build. Move all configure flags to ... [configure-flags]: ... here. The options explicitly enabling optional features are removed; the configure script does a good job at enabling all the features available based on the inputs present and this allows reusing the flags in variant packages such as qemu-minimal. {configure-user-static, build-user-static, install-user-static}: New phases. {patch-test-shebangs}: New phase, extracted from the configure phase. [native-inputs]: Add glib-static, pcre:static and zlib:static. (qemu-minimal)[arguments]: Reuse the configure-flags argument. Rewrite to use match instead of cond. Maxim Cournoyer
2021-03-15gnu: Add glib-static....* gnu/packages/glib.scm (glib-static): New variable. Maxim Cournoyer
2021-03-15gnu: qemu: Fix indentation and remove trailing #t....* gnu/packages/virtualization.scm (qemu): Fix indentation and remove trailing #t, appeasing 'guix lint'. Maxim Cournoyer
2021-03-15gnu: r-seurat: Fix build....This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7 * gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file. Ricardo Wurmus
2021-03-15gnu: xterm: Fix uxterm in pure environments....* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names phase. Tobias Geerinckx-Rice
2021-03-15gnu: sudo: Update to 1.9.6p1....* gnu/packages/admin.scm (sudo): Update to 1.9.6p1. Tobias Geerinckx-Rice
2021-03-15gnu: ibus-libpinyin: Update to 1.12.0....* gnu/packages/ibus.scm (ibus-libpinyin): Update to 1.12.0. [arguments]: Enable opencc; include setup files on PYTHONPATH; override PYTHONPATH instead of prefixing. [inputs]: Add opencc; remove python-pyxdg. [license]: Change to GPLv3+. Ricardo Wurmus
2021-03-15gnu: libpinyin: Update to 2.6.0....* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0. Ricardo Wurmus
2021-03-15gnu: r-genomicfeatures: Update to 1.42.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2. Ricardo Wurmus
2021-03-15gnu: r-delayedarray: Update to 0.16.2....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2. Ricardo Wurmus
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