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* gnu-maintenance: 'latest-html-release' better computes version number.Ludovic Courtès2021-03-17
| | | | | | | | * guix/gnu-maintenance.scm (latest-html-release): Use 'tarball->version' rather than 'package-name->name+version' to extract the version number. This fixes problems with packages like 'netsurf' and 'libdom' that have "-src" in their tarball name, where "src" would be taken as the new version number.
* gnu-maintenance: 'latest-html-release' can determine signature file name.Ludovic Courtès2021-03-17
| | | | | | | | | | | * guix/gnu-maintenance.scm (latest-html-release): #:file->signature defaults to #f. [file->signature/guess]: New procedure. [url->release]: Use it when FILE->SIGNATURE is #f. Introduce 'links' variable. (url-prefix-rewrite): Check whether URL is true before calling 'string-prefix?'. (latest-savannah-release): Adjust comment about detached signatures.
* gnu-maintenance: 'release-file?' rejects checksum files.Ludovic Courtès2021-03-17
| | | | | * guix/gnu-maintenance.scm (release-file?): Reject ".md5sum", ".sha1sum", and ".sha256sum".
* gnu-maintenance: 'latest-html-release' considers non-relative URLs.Ludovic Courtès2021-03-17
| | | | | * guix/gnu-maintenance.scm (latest-html-release): Allow for URL to be an arbitrary URL rather than a relative URL reference.
* gnu-maintenance: Use (htmlprag) for 'latest-html-release'.Ludovic Courtès2021-03-17
| | | | | | | * guix/gnu-maintenance.scm (html->sxml): Remove. Autoload (htmlprag) instead. * doc/guix.texi (Requirements): Mention 'guix refresh' for the Guile-Lib dependency.
* maint: Check whether Guile-zlib is recent enough.Ludovic Courtès2021-03-17
| | | | | | | This is a followup to a04aef2430645357d7796969d4b6453478ff8a3f. * m4/guix.m4 (GUIX_CHECK_GUILE_ZLIB): New macro. * configure.ac: Use it when checking for Guile-zlib.
* doc: Define the term "profile".Ludovic Courtès2021-03-17
| | | | | | | | Fixes <https://bugs.gnu.org/46803>. Reported by Luis Felipe <luis.felipe.la@protonmail.com>. * doc/guix.texi (Getting Started): Introduce the term "profile". (Invoking guix package): Likewise.
* daemon: Correctly handle '--discover' with no value.Ludovic Courtès2021-03-17
| | | | | | | | | | Previously, we'd get: $ guix-daemon --discover error: basic_string::_M_construct null not valid * nix/nix-daemon/guix-daemon.cc (parse_opt): Change second argument to 'settings.set' to properly handle case where ARG is NULL.
* gnu: gnome-autoar: Update to 0.3.1 [fixes CVE-2021-28650].Léo Le Bouter2021-03-17
| | | | * gnu/packages/gnome.scm (gnome-autoar): Update to 0.3.1.
* gnu: pzstd: Update to 1.4.9 [fixes CVE-2021-24032].Léo Le Bouter2021-03-17
| | | | | | * 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.
* gnu: Use PACKAGE/INHERIT in more places.Mark H Weaver2021-03-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: gvfs: Add 'lint-hidden-cve' property.Mark H Weaver2021-03-16
| | | | | * gnu/packages/gnome.scm (gvfs)[properties]: New field, marking CVE-2019-12447, CVE-2019-12448, and CVE-2019-12449 as fixed.
* gnu: gnome-shell: Add 'lint-hidden-cve' property.Mark H Weaver2021-03-16
| | | | | * gnu/packages/gnome.scm (gnome-shell)[properties]: New field, marking CVE-2019-3820 as fixed.
* gnu: qemu: Enable reproducible builds.Maxim Cournoyer2021-03-16
| | | | | | | | 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.
* gnu: Add meson-next.Maxim Cournoyer2021-03-16
| | | | * gnu/packages/build-tools.scm (meson-next): New variable.
* gnu: mpg321: Fix CVE-2019-14247.Kei Kebreau2021-03-16
| | | | | | | | | * 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>
* gnu: varnish-modules: Update to 0.17.1 [fixes CVE-2021-28543].Léo Le Bouter2021-03-16
| | | | * gnu/packages/web.scm (varnish-modules): Update to 0.17.1.
* news: Add ‘de’ translation.Florian Pelz2021-03-16
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* gnu: tor: Update to 0.4.5.7 [security fixes].Efraim Flashner2021-03-16
| | | | * gnu/packages/tor.scm (tor): Update to 0.4.5.7.
* gnu: snakemake: Add missing inputs.Ricardo Wurmus2021-03-16
| | | | | * gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add python-nbformat, python-pulp, and python-toposort.
* gnu: Add python-toposort.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-toposort): New variable.
* gnu: Add python-pulp.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-pulp): New variable.
* gnu: Add python-amply.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-amply): New variable.
* gnu: emacs-easy-kill: Update to 0.9.4.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.
* gnu: emacs-leaf: Update to 4.4.0.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.
* gnu: python-pikepdf: Update to 2.9.0.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.
* gnu: asymptote: Update to 2.70.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/plotutils.scm (asymptote): Update to 2.70.
* gnu: b4: Fix setup.py version incompatibility.Efraim Flashner2021-03-16
| | | | | | | * gnu/packages/version-control.scm (b4)[source]: Add snippet to not require too specific of a version. Reported-by: Kyle Meyer <kyle@kyleam.com>
* gnu: libmemcached: Disable test suite.Maxim Cournoyer2021-03-16
| | | | | | | | | | | * 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>
* gnu: hisat2: Update to 2.2.1.Ricardo Wurmus2021-03-16
| | | | | | | | | * 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.
* gnu: Remove MongoDB.Léo Le Bouter2021-03-16
| | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: git: Fix git-manpages native input's hash.Léo Le Bouter2021-03-16
| | | | | | | This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777. * gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's hash.
* gnu: git: Update to 2.31.0.Léo Le Bouter2021-03-16
| | | | * gnu/packages/version-control.scm (git): Update to 2.31.0.
* gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter2021-03-16
| | | | | * gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of python-urllib3/fixed.
* gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter2021-03-16
| | | | | * gnu/packages/python-web.scm (python-urllib3/fixed): New variable. (python-urllib3)[replacement]: Graft.
* gnu: tmsu: Improve installation.Stefan Reichör2021-03-16
| | | | | | | * 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>
* gnu: glances: Update to 3.1.6.Stefan Reichör2021-03-16
| | | | | | * gnu/packages/python-xyz.scm (glances): Update to 3.1.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* syscalls: mounts: Fix a matching bug.Chris Marusich2021-03-15
| | | | | | | | | | | | | | | | | | On some systems, the columns in /proc/self/mountinfo look like this: 23 28 0:21 / /proc rw,nosuid,nodev,noexec,relatime shared:11 - proc proc rw Before this change, the mounts procedure was written with the assumption that the type and source could always be found in columns 8 and 9, respectively. However, the proc(5) man page explains that there can be zero or more optional fields starting at column 7 (e.g., "shared:11" above), so this assumption is false in some situations. * guix/build/syscalls.scm (mounts): Update the match pattern to use ellipsis to match zero or more optional fields followed by a single hyphen. Remove the trailing ellipsis, since multiple ellipses are not allowed in the same level. The proc(5) man page indicates that there are no additional columns, so it is probably OK to match an exact number of columns at the end like this.
* Revert some commits that caused `guix pull` to fail.Leo Famulari2021-03-15
| | | | | | | | | | | | | 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))
* gnu: r-biocparallel: Build reproducibly.Ricardo Wurmus2021-03-15
| | | | | * gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible".
* gnu: r-delayedarray: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
* gnu: r-rsamtools: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
* gnu: r-biostrings: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here.
* gnu: r-biocparallel: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
* gnu: r-biomart: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here.
* gnu: r-annotationdbi: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
* gnu: r-biobase: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here.
* gnu: r-genomicranges: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
* gnu: r-xvector: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here.
* gnu: r-limma: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here.
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-11 05:11:37 +0000