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67318 Commits

Author SHA1 Message Date
Leo Famulari
d72347deec gnu: 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.
 2021-03-18 01:05:48 -04:00
Leo Famulari
1ff0377a52 gnu: 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.
 2021-03-18 01:05:48 -04:00
Leo Famulari
1de35e8036 gnu: 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.
 2021-03-18 01:05:48 -04:00
Leo Famulari
e0dcafc1c2 gnu: 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.
 2021-03-18 01:05:48 -04:00
Leo Famulari
aacfbb8c24 gnu: 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.
 2021-03-18 01:05:48 -04:00
qblade
966e61fb8f gnu: Add libucl. 
* gnu/packages/wm.scm (libucl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-17 23:10:20 +01:00
Maxime Devos
ce10e2b3e9 gnu: 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>
 2021-03-17 23:10:19 +01:00
Tobias Geerinckx-Rice
24f1ce9e71 gnu: scdoc: Cross-compile. 
* gnu/packages/man.scm (scdoc)[arguments]: Use CC-FOR-TARGET.
 2021-03-17 21:22:21 +01:00
Tobias Geerinckx-Rice
841e5fb4dd gnu: 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.
 2021-03-17 21:22:20 +01:00
Christopher Baines
d7b4ccefa9 gnu: libtirpc/hurd: Fix package source. 
Amend the changes in 1a265842e6 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.
 2021-03-17 20:15:15 +00:00
Efraim Flashner
f4f677f223 gnu: lua.scm: Sort package module imports alphabetically. 
* gnu/packages/lua.scm: Sort package module imports alphabetically.
 2021-03-17 21:33:01 +02:00
Léo Le Bouter
2691f57678 gnu: 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.
 2021-03-17 18:36:47 +01:00
Oleg Pykhalov
cb424bad32 gnu: Add emacs-kotlin-mode. 
* gnu/packages/emacs-xyz.scm (emacs-kotlin-mode): New variable.
 2021-03-17 18:48:06 +03:00
Nicolas Goaziou
d79d63e782 gnu: emacs-marginalia: Update to 0.4. 
* gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.4.
 2021-03-17 14:32:45 +01:00
Leo Prikler
284864df91 gnu: komikku: Update to 0.27.0. 
* gnu/packages/gnome.scm (komikku): Update to 0.27.0.
[inputs]: Add python-brotli and webkitgtk.
 2021-03-17 14:21:30 +01:00
Leo Prikler
fef91c0cc8 gnu: 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.
 2021-03-17 14:21:29 +01:00
LibreMiami
d45d779e2a gnu: 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>
 2021-03-17 12:03:25 +01:00
Ludovic Courtès
fe96f64110 gnu: hwloc: Add 'release-monitoring-url' property. 
* gnu/packages/mpi.scm (hwloc-1)[properties]: New field.
 2021-03-17 12:03:25 +01:00
Léo Le Bouter
f194fbf50e gnu: gnome-autoar: Update to 0.3.1 [fixes CVE-2021-28650]. 
* gnu/packages/gnome.scm (gnome-autoar): Update to 0.3.1.
 2021-03-17 11:39:01 +01:00
Léo Le Bouter
b26f958620 gnu: 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.
 2021-03-17 10:58:29 +01:00
Mark H Weaver
1a265842e6 gnu: 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.
 2021-03-17 03:58:10 -04:00
Mark H Weaver
d9f501b619 gnu: 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.
 2021-03-16 22:38:18 -04:00
Mark H Weaver
c3fe23d0de gnu: gnome-shell: Add 'lint-hidden-cve' property. 
* gnu/packages/gnome.scm (gnome-shell)[properties]: New field, marking
CVE-2019-3820 as fixed.
 2021-03-16 22:38:12 -04:00
Maxim Cournoyer
15423d38c5 gnu: 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.
 2021-03-16 16:21:28 -04:00
Maxim Cournoyer
f4259f93ea gnu: Add meson-next. 
* gnu/packages/build-tools.scm (meson-next): New variable.
 2021-03-16 16:21:27 -04:00
Kei Kebreau
109f58444b gnu: 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>
 2021-03-16 19:12:36 +01:00
Léo Le Bouter
82a9538ea0 gnu: varnish-modules: Update to 0.17.1 [fixes CVE-2021-28543]. 
* gnu/packages/web.scm (varnish-modules): Update to 0.17.1.
 2021-03-16 18:41:41 +01:00
Efraim Flashner
09b5cdf80d gnu: tor: Update to 0.4.5.7 [security fixes]. 
* gnu/packages/tor.scm (tor): Update to 0.4.5.7.
 2021-03-16 15:26:33 +02:00
Ricardo Wurmus
4f02c4c4a9 gnu: snakemake: Add missing inputs. 
* gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add
python-nbformat, python-pulp, and python-toposort.
 2021-03-16 14:17:48 +01:00
Ricardo Wurmus
08447ab7cd gnu: Add python-toposort. 
* gnu/packages/python-xyz.scm (python-toposort): New variable.
 2021-03-16 14:17:48 +01:00
Ricardo Wurmus
fa0a18522d gnu: Add python-pulp. 
* gnu/packages/python-xyz.scm (python-pulp): New variable.
 2021-03-16 14:17:47 +01:00
Ricardo Wurmus
c9006a0ee1 gnu: Add python-amply. 
* gnu/packages/python-xyz.scm (python-amply): New variable.
 2021-03-16 14:17:47 +01:00
Nicolas Goaziou
55ef497479 gnu: emacs-easy-kill: Update to 0.9.4. 
* gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.
 2021-03-16 14:11:14 +01:00
Nicolas Goaziou
2724f1b231 gnu: emacs-leaf: Update to 4.4.0. 
* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.
 2021-03-16 14:10:17 +01:00
Nicolas Goaziou
c954f795f9 gnu: python-pikepdf: Update to 2.9.0. 
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.
 2021-03-16 14:09:06 +01:00
Nicolas Goaziou
335af327cd gnu: asymptote: Update to 2.70. 
* gnu/packages/plotutils.scm (asymptote): Update to 2.70.
 2021-03-16 14:06:40 +01:00
Efraim Flashner
451f23df5e gnu: 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>
 2021-03-16 14:28:25 +02:00
Maxim Cournoyer
9bab0950f7 gnu: 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>
 2021-03-16 07:46:20 -04:00
Ricardo Wurmus
fcf8c6c565 gnu: 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.
 2021-03-16 11:12:01 +01:00
Léo Le Bouter
097cf21d1d gnu: 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 feff80cec3 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.
 2021-03-16 11:05:24 +01:00
Léo Le Bouter
0ee5d4f7a8 gnu: git: Fix git-manpages native input's hash. 
This is a follow-up to commit ab9629b7c9.

* gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's
hash.
 2021-03-16 10:58:36 +01:00
Léo Le Bouter
ab9629b7c9 gnu: git: Update to 2.31.0. 
* gnu/packages/version-control.scm (git): Update to 2.31.0.
 2021-03-16 10:52:11 +01:00
Léo Le Bouter
db87d6ddaf gnu: 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.
 2021-03-16 09:25:02 +01:00
Léo Le Bouter
a01bfa7dee gnu: 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.
 2021-03-16 08:59:38 +01:00
Stefan Reichör
e5fcfb82e0 gnu: 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>
 2021-03-16 09:37:16 +02:00
Stefan Reichör
3679286bb4 gnu: 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>
 2021-03-16 09:34:41 +02:00
Leo Famulari
8ec0ca8faf Revert some commits that caused guix pull to fail. 
This reverts commits 821e643921 through
8f9fd9b70c.

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))
 2021-03-15 19:52:34 -04:00
Ricardo Wurmus
8f9fd9b70c gnu: r-biocparallel: Build reproducibly. 
* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase
"make-reproducible".
 2021-03-15 23:31:58 +01:00
zimoun
d99a18252c gnu: r-delayedarray: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
adf45daae9 gnu: r-rsamtools: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
 2021-03-15 23:30:26 +01:00