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Author SHA1 Message Date
Tobias Geerinckx-Rice 000e27b3d7
gnu: bind: Update to 9.16.13. 
* gnu/packages/dns.scm (isc-bind): Update to 9.16.13.
 2021-03-18 17:08:10 +01:00
Ludovic Courtès 94f0312546
gnu: guix: Update to ec7fb66 [security]. 
This updates the 'guix' package so that it provides the fix
for <https://bugs.gnu.org/47229>.

* gnu/packages/package-management.scm (guix): Update to ec7fb66.
 2021-03-18 12:32:03 +01:00
Leo Famulari 898489f48e
services: Enable "protected hardlinks" and "protected symlinks" by default. 
References:

https://sysctl-explorer.net/fs/protected_hardlinks/
https://sysctl-explorer.net/fs/protected_symlinks/

* gnu/services/sysctl.scm (%default-sysctl-settings): New public variable.
(<sysctl-configuration>): Use %default-sysctl-settings as the default value.
* gnu/services/base.scm (%base-services): Add sysctl-service-type.
* doc/guix.texi (Miscellaneous Services): Document the new defaults.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-18 12:17:33 +01:00
Léo Le Bouter 45695cc8a7
Revert "gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363]." 
In response to commit 1a265842e6 we should no
longer need this. Also see <https://bugs.gnu.org/47186>.

This reverts commit db87d6ddaf.
 2021-03-18 11:26:11 +01:00
Léo Le Bouter 2e0ff59f0c
gnu: 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.
 2021-03-18 11:13:18 +01:00
Leo Famulari 334c6850c6
gnu: 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.
 2021-03-18 01:05:49 -04:00
Leo Famulari c3504337cc
gnu: 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.
 2021-03-18 01:05:48 -04:00
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
Efraim Flashner 61877a51c5
gnu: mesa: Update to 20.2.6. 
* gnu/packages/gl.scm (mesa): Update to 20.2.6.
 2021-03-17 15:21:36 +02:00
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
Efraim Flashner 29eee5f631
gnu: mesa: Update configure flags. 
* gnu/packages/gl.scm (mesa)[arguments]: Adjust flags to silence
warnings during configure phase.
 2021-03-17 15:15:06 +02:00
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
zimoun b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 821e643921
gnu: r-limma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
 2021-03-15 23:30:26 +01:00
Maxim Cournoyer 74fdd0fea0
gnu: 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.
 2021-03-15 18:03:17 -04:00
Leo Famulari d15fdb66f3
gnu: 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>
 2021-03-15 18:00:35 -04:00
Maxim Cournoyer 77c2f4e206
services/qemu-binfmt: Use the F flag and the static output of QEMU. 
Fixes <https://issues.guix.gnu.org/36117>.

Before this change, the 'binfmt_misc' entries registered for QEMU would not be
usable in container contexts outside of guix-daemon (without manually bind
mounting file names).

For example:

$ docker run --rm arm32v7/debian true
standard_init_linux.go:207: exec user process caused "no such file or directory"

After this change, any container can make use of the QEMU binfmt_misc
registrations, as their corresponding QEMU static binaries are fully
pre-loaded by the kernel.

* gnu/services/virtualization.scm (<qemu-platform>): Define using
'define-record-type*'.
[flags]: New field, which defaults to "F" (fix binary).
(%i386, %i486, %alpha, %arm, %armeb, %sparc, %sparc32plus, %ppc, %ppc64)
(%ppc64le, %m68k, %mips, %mipsel, %mipsn32, %mipsn32el, %mips64, %mips64el)
(%riscv32, %riscv64, %sh4, %sh4eb, %s390x, %aarch64, %hppa): Adjust.
(qemu-binfmt-guix-chroot): Remove variable.
(qemu-binfmt-service-type): Remove the qemu-binfmt-guix-chroot extension.
* gnu/services/qemu-binfmt (qemu-platform->binfmt):  Use the static output of
QEMU.
* doc/contributing.texi (Submitting Patches): Update doc.
* doc/guix.texi (Virtualization Services): Update doc.
 2021-03-15 18:00:35 -04:00
Maxim Cournoyer d184fd4216
gnu: 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.
 2021-03-15 18:00:35 -04:00
Maxim Cournoyer ce29866c01
gnu: Add glib-static. 
* gnu/packages/glib.scm (glib-static): New variable.
 2021-03-15 18:00:35 -04:00
Maxim Cournoyer 3fe46eef57
gnu: qemu: Fix indentation and remove trailing #t. 
* gnu/packages/virtualization.scm (qemu): Fix indentation and remove
trailing #t, appeasing 'guix lint'.
 2021-03-15 18:00:34 -04:00
Ricardo Wurmus 29e992c030
gnu: r-seurat: Fix build. 
This is a follow-up to commit e4d4046999

* gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.
 2021-03-15 22:06:57 +01:00
Tobias Geerinckx-Rice fcb122b4ed
gnu: xterm: Fix uxterm in pure environments. 
* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names
phase.
 2021-03-15 20:31:24 +01:00
Tobias Geerinckx-Rice 20d090f435
gnu: sudo: Update to 1.9.6p1. 
* gnu/packages/admin.scm (sudo): Update to 1.9.6p1.
 2021-03-15 20:31:24 +01:00
Ricardo Wurmus 266d55dc30
gnu: 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+.
 2021-03-15 15:24:01 +01:00
Ricardo Wurmus f9e016baec
gnu: libpinyin: Update to 2.6.0. 
* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.
 2021-03-15 15:23:50 +01:00
Ricardo Wurmus 14204d696c
gnu: r-genomicfeatures: Update to 1.42.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus f10f2745eb
gnu: r-delayedarray: Update to 0.16.2. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus 1ada8ea96c
gnu: r-scater: Update to 1.18.6. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus fa6bb614c8
gnu: r-cytoml: Update to 2.2.2. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus 11dc49afc2
gnu: r-diffbind: Update to 3.0.14. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus ee61edb621
gnu: r-reportingtools: Update to 2.30.2. 
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus fa227c9640
gnu: r-genomeinfodb: Update to 1.26.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus b45c625f10
gnu: r-deseq2: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
 2021-03-15 15:03:07 +01:00
Efraim Flashner 4ce712aca4
gnu: alacritty: Use more packaged rust libraries. 
* gnu/packages/terminals.scm (alacritty)[arguments]: Move
rust-bitflags-1, rust-dirs-2, rust-libc-0.2, rust-unicode-width-0.1,
rust-winapi-0.3 from cargo-inputs ...
[inputs]: ... to here.
 2021-03-15 15:53:17 +02:00
Efraim Flashner ca3b97baaa
gnu: rust-dirs-2: Adapt for new build system. 
* gnu/packages/crates-io.scm (rust-dirs-2)[inputs]: Add rust-cfg-if-0.1,
rust-dirs-sys-0.3.
 2021-03-15 15:53:17 +02:00
Efraim Flashner a4bbebb2b3
gnu: rust-dirs-sys-0.3: Adapt for new build system. 
* gnu/packages/crates-io.scm (rust-dirs-sys-0.3)[inputs]: Add
rust-cfg-if-0.1, rust-libc-0.2, rust-redox-users-0.3, rust-winapi-0.3.
 2021-03-15 15:53:17 +02:00
Efraim Flashner 647dfa788e
gnu: rust-lazy-static-1: Adapt for new build system. 
* gnu/packages/crates-io.scm (rust-lazy-static-1)[inputs]: Add
rust-spin-0.5.
 2021-03-15 15:53:16 +02:00
Efraim Flashner f69a3fe28c
gnu: alacritty: Use packaged rust-wayland-client. 
* gnu/packages/terminals.scm (alacritty)[arguments]: Remove
rust-wayland-client-0.28 from cargo-inputs. In custom
'add-absolute-library-references remove substitutions for
rust-wayland-client.
[inputs]: Add rust-wayland-client-0.28.
 2021-03-15 15:53:16 +02:00
Efraim Flashner 190e94b278
gnu: rust-glutin-0.26: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-glutin-0.26)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-egl-0.28.
 2021-03-15 15:53:16 +02:00
Efraim Flashner 87d747860d
gnu: rust-winit-0.24: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-winit-0.24)[arguments]: Move
rust-wayland-client-0.28 from cargo-inputs ...
[inputs]: ... to here.
 2021-03-15 15:53:16 +02:00
Efraim Flashner 6f655caf42
gnu: rust-wayland-server-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-server-0.28)
[arguments]: Don't skip build. Remove rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28 from cargo-inputs.
[inputs]: Add rust-bitflags-1, rust-downcast-rs-1, rust-lazy-static-1,
rust-libc-0.2, rust-nix-0.18, rust-parking-lot-0.18, rust-scoped-tls-1,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-sys-0.28.
(rust-wayland-server-0.23): Adjust accordingly.
 2021-03-15 15:53:16 +02:00
Efraim Flashner fb6f926193
gnu: rust-wayland-scanner-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-scanner-0.28):
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-proc-macro2-1, rust-quote-1, rust-xml-rs-0.8.
(rust-wayland-scanner-0.23): Adjust accordingly.
 2021-03-15 15:53:16 +02:00
Efraim Flashner facf27e08b
gnu: rust-wayland-protocols-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-protocols-0.28)
[arguments]: Don't skip build. Remove everything from cargo-inputs
except rust-bitflags-1.
[inputs]: Add rust-bitflags-1, rust-wayland-client-0.28,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-server-0.28.
(rust-wayland-protocols-0.23): Adjust accordingly.
 2021-03-15 15:53:16 +02:00
Efraim Flashner bb06a747b2
gnu: rust-wayland-egl-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-egl-0.28)
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-sys-0.28.
[native-inputs]: Add pkg-config.
 2021-03-15 15:53:15 +02:00
Efraim Flashner 3b6ec859c2
gnu: rust-wayland-cursor-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-cursor-0.28)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-wayland-client-0.28, rust-xcursor-0.3.
 2021-03-15 15:53:15 +02:00
Efraim Flashner 770e326fdb
gnu: rust-wayland-client-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-client-0.28)
[arguments]: Don't skip build. Remove rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28 from cargo-inputs.
[inputs]: Add rust-bitflags-1, rust-downcast-rs-1, rust-libc-0.2,
rust-nix-0.18, rust-scoped-tls-1, rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28.
(rust-wayland-client-0.23): Adjust accordingly.
 2021-03-15 15:53:15 +02:00
Efraim Flashner f35ab79e03
gnu: rust-wayland-commons-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-commons-0.28)
[arguments]: Don't skip build. Remove rust-wayland-sys-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-once-cell-1, rust-smallvec-1,
rust-wayland-sys-0.28.
(rust-wayland-commons-0.23): Adjust accordingly.
 2021-03-15 15:53:15 +02:00
Efraim Flashner b10c637e48
gnu: rust-libloading-0.6: Update to 0.6.7. 
* gnu/packages/crates-io.scm (rust-libloading-0.6): Update to 0.6.
[arguments]: Replace rust-cfg-if-0.1 with 1.
[inputs]: Add rust-cfg-if-1, rust-winapi-0.3.
 2021-03-15 15:53:15 +02:00
Efraim Flashner bafeee4f6d
gnu: dlib-0.4: Update to 0.4.2. 
* gnu/packages/crates-io.scm (rust-dlib-0.4): Update to 0.4.2.
[arguments]: Replace rust-libloading-0.5 with 0.6.
[inputs]: Add rust-libloading-0.6.
 2021-03-15 15:53:15 +02:00
Efraim Flashner 358f5d9b1b
gnu: rust-proc-macro2-1: Adapt for new build system. 
* gnu/packages/crates-io.scm (rust-proc-macro2-1)[inputs]: Add
rust-unicode-xid-0.2.
 2021-03-15 15:53:15 +02:00
Efraim Flashner c805bdd550
gnu: rust-winapi-0.3: Adjust for new build system. 
* gnu/packages/crates-io.scm (rust-winapi-0.3)[inputs]: Add
rust-winapi-i686-pc-windows-gnu, rust-winapi-x86-64-pc-windows-gnu.
 2021-03-15 15:53:14 +02:00
Efraim Flashner 12c699572c
gnu: rust-pkg-config-0.3: Hardcode location of pkg-config. 
* gnu/packages/crates-io.scm (rust-pkg-config-0.3)[arguments]: Add phase
to hardcode location of pkg-config binary.
 2021-03-15 15:53:14 +02:00
Efraim Flashner d499911432
gnu: rust-pkg-config-0.3: Update to 0.3.19. 
* gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.19.
 2021-03-15 15:53:14 +02:00
Efraim Flashner 4363b542f2
gnu: rust-wayland-sys-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-sys-0.28)[arguments]:
Don't skip build. Add phase to refer explicitly to wayland libraries.
[inputs]: Add rust-dlib-0.4, rust-lazy-static-1, rust-libc-0.2,
rust-pkg-config-0.3.
[propagated-inputs]: Add wayland.
(rust-wayland-sys-0.23): Adjust accordingly.
 2021-03-15 15:53:14 +02:00
Efraim Flashner 69c757c45a
gnu: rust-quote-1: Update to 1.0.9. 
* gnu/packages/crates-io.scm (rust-quote-1): Update to 1.0.9.
 2021-03-15 15:53:14 +02:00
zimoun bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun 082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun 35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun 8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00
zimoun 9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
 2021-03-15 14:05:37 +01:00
zimoun d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
 2021-03-15 14:05:27 +01:00
zimoun 852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
 2021-03-15 14:05:22 +01:00
zimoun d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
 2021-03-15 14:04:26 +01:00
zimoun 5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
 2021-03-15 14:03:21 +01:00
zimoun 134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
 2021-03-15 14:03:18 +01:00
Ricardo Wurmus 53dff6ac8f
gnu: r-rsqlite: Update to 2.2.4. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.2.4.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus 2e2cc58681
gnu: r-rcpparmadillo: Update to 0.10.2.2.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.2.2.0.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus 2fc2983e59
gnu: r-formatr: Update to 1.8. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.8.
[native-inputs]: Add r-knitr.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus fe903cb89d
gnu: r-survival: Update to 3.2-9. 
* gnu/packages/statistics.scm (r-survival): Update to 3.2-9.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus bbc542b53c
gnu: r-textshaping: Update to 0.3.2. 
* gnu/packages/cran.scm (r-textshaping): Update to 0.3.2.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus ea23f17ece
gnu: r-mlr3tuning: Update to 0.8.0. 
* gnu/packages/cran.scm (r-mlr3tuning): Update to 0.8.0.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus 921ecdba7c
gnu: r-bbotk: Update to 0.3.1. 
* gnu/packages/cran.scm (r-bbotk): Update to 0.3.1.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus ee92bb9004
gnu: r-workflows: Update to 0.2.2. 
* gnu/packages/cran.scm (r-workflows): Update to 0.2.2.
[propagated-inputs]: Add r-vctrs.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus e4d4046999
gnu: r-spatstat: Update to 2.0-1. 
* gnu/packages/cran.scm (r-spatstat): Update to 2.0-1.
[propagated-inputs]: Remove r-abind, r-deldir, r-goftest, r-matrix, r-mgcv,
r-nlme, r-polyclip, r-rpart, and r-tensor; add r-spatstat-core,
r-spatstat-geom, and r-spatstat-linnet.
 2021-03-15 13:45:31 +01:00
Ricardo Wurmus b0036b407c
gnu: r-brms: Update to 2.15.0. 
* gnu/packages/cran.scm (r-brms): Update to 2.15.0.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 7bd5a64303
gnu: r-forecast: Update to 8.14. 
* gnu/packages/cran.scm (r-forecast): Update to 8.14.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 58a2c438d3
gnu: r-lavaan: Update to 0.6-8. 
* gnu/packages/cran.scm (r-lavaan): Update to 0.6-8.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus dae999bc48
gnu: r-parallelly: Update to 1.24.0. 
* gnu/packages/cran.scm (r-parallelly): Update to 1.24.0.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus ecd03401c6
gnu: r-effectsize: Update to 0.4.4. 
* gnu/packages/cran.scm (r-effectsize): Update to 0.4.4.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus b5aa552e63
gnu: r-magick: Update to 2.7.0. 
* gnu/packages/cran.scm (r-magick): Update to 2.7.0.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus dfa052bbc9
gnu: r-blockfest: Update to 2.0. 
* gnu/packages/cran.scm (r-blockfest): Update to 2.0.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 796a2241e3
gnu: r-flextable: Update to 0.6.4. 
* gnu/packages/cran.scm (r-flextable): Update to 0.6.4.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 77e5a20c43
gnu: r-maptools: Update to 1.1-1. 
* gnu/packages/cran.scm (r-maptools): Update to 1.1-1.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 87d3f805b9
gnu: r-utf8: Update to 1.2.1. 
* gnu/packages/cran.scm (r-utf8): Update to 1.2.1.
[native-inputs]: Add r-knitr.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus d163c71e0a
gnu: r-xfun: Update to 0.22. 
* gnu/packages/cran.scm (r-xfun): Update to 0.22.
 2021-03-15 13:45:30 +01:00
Ricardo Wurmus 70257ad2c0
gnu: r-ipred: Update to 0.9-11. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-11.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus bfa09fd922
gnu: r-lava: Update to 1.6.9. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.9.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus 172da782db
gnu: r-rvest: Update to 1.0.0. 
* gnu/packages/cran.scm (r-rvest): Update to 1.0.0.
[propagated-inputs]: Add r-lifecycle, r-rlang, and r-tibble.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus 7bdef3789d
gnu: r-zoo: Update to 1.8-9. 
* gnu/packages/cran.scm (r-zoo): Update to 1.8-9.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus e1240e22f5
gnu: Add r-spatstat-linnet. 
* gnu/packages/cran.scm (r-spatstat-linnet): New variable.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus 3ebae705f9
gnu: Add r-spatstat-core. 
* gnu/packages/cran.scm (r-spatstat-core): New variable.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus ddfe3f77a9
gnu: Add r-spatstat-geom. 
* gnu/packages/cran.scm (r-spatstat-geom): New variable.
 2021-03-15 13:45:29 +01:00
Ricardo Wurmus 78373e394d
gnu: Add r-spatstat-sparse. 
* gnu/packages/cran.scm (r-spatstat-sparse): New variable.
 2021-03-15 13:45:29 +01:00
Léo Le Bouter 1ed435bf39
gnu: python-sphobjinv: Fix build. 
* gnu/packages/sphinx.scm (python-sphobjinv):
[patches]: Remove.
[propagated-inputs]: Add (uncomment) python-certifi.
 2021-03-15 12:51:54 +01:00
Léo Le Bouter 3096428889
gnu: libcroco/fixed: Make private. 
* gnu/packages/gnome.scm (libcroco/fixed): Use define instead of
define-public.
 2021-03-15 12:22:18 +01:00
Léo Le Bouter 8a085c1780
gnu: cyrus-sasl/fixed: Make private. 
* gnu/packages/cyrus-sasl.scm (cyrus-sasl/fixed): Use define instead of
define-public.
 2021-03-15 12:22:17 +01:00
Léo Le Bouter cddf0b8955
gnu: unzip/fixed: Make private. 
* gnu/packages/compression.scm (unzip/fixed): Use define instead of
define-public.
 2021-03-15 12:22:17 +01:00
Tanguy Le Carrour 3e83e99322
gnu: poetry: Update to 1.1.5. 
* gnu/packages/python-xyz.scm (poetry): Update to 1.1.5.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2021-03-15 11:19:37 +00:00
Tanguy Le Carrour 014fa5cc6b
gnu: python-poetry-core: Update to 1.0.2. 
* gnu/packages/python-build.scm (python-poetry-core): Update to 1.0.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2021-03-15 11:19:35 +00:00
Ricardo Wurmus 3eeb7dbf04
gnu: r-gkmsvm: Move back to (gnu packages cran). 
* gnu/packages/bioconductor.scm (r-gkmsvm): Move this variable from here...
* gnu/packages/cran.scm (r-gkmsvm): ...to here.
 2021-03-15 12:15:18 +01:00
Ricardo Wurmus 1daedaa864
gnu: libusb-for-axoloti: Revert to 1.0.23. 
* gnu/packages/axoloti.scm (libusb-for-axoloti): Revert to 1.0.23, because the
patch does not apply to the latest version.
 2021-03-15 12:05:50 +01:00
Ricardo Wurmus 21bc326b9a
gnu: guile-opengl: Fix linking with libGL.so. 
* gnu/packages/gl.scm (guile-opengl)[arguments]: Fix reference to libGL.so.
 2021-03-15 11:57:56 +01:00
Ricardo Wurmus 6e0ed09e68
gnu: Add instrain. 
* gnu/packages/bioinformatics.scm (instrain): New variable.
 2021-03-15 11:43:20 +01:00
Ricardo Wurmus ad34eb222c
gnu: Add python-drep. 
* gnu/packages/bioinformatics.scm (python-drep): New variable.
 2021-03-15 11:43:20 +01:00
Ricardo Wurmus c20813bb08
gnu: Add python-lmfit. 
* gnu/packages/python-xyz.scm (python-lmfit): New variable.
 2021-03-15 11:43:20 +01:00
Ricardo Wurmus 0bd166253a
gnu: Add python-asteval. 
* gnu/packages/python-xyz.scm (python-asteval): New variable.
 2021-03-15 11:43:19 +01:00
Ricardo Wurmus 8b85aea49b
gnu: Add python-uncertainties. 
* gnu/packages/python-xyz.scm (python-uncertainties): New variable.
 2021-03-15 11:43:19 +01:00
Ricardo Wurmus 714a8faa04
gnu: guile-email-latest: Update to 0.2.2-1.ca0520a. 
* gnu/packages/guile-xyz.scm (guile-email-latest): Update to 0.2.2-1.ca0520a.
 2021-03-15 11:43:19 +01:00
Lars-Dominik Braun c3163fe6b4
gnu: Add r-textplot. 
* gnu/packages/cran.scm (r-textplot): New variable.
 2021-03-15 10:53:22 +01:00
Lars-Dominik Braun ca3913d1f8
gnu: Add r-btm. 
* gnu/packages/cran.scm (r-btm): New variable.
 2021-03-15 10:53:21 +01:00
Lars-Dominik Braun 20fb147c9a
gnu: Add r-eyelinker. 
* gnu/packages/cran.scm (r-eyelinker): New variable.
 2021-03-15 10:53:20 +01:00
Lars-Dominik Braun 32603dbba9
gnu: Add r-intervals. 
* gnu/packages/cran.scm (r-intervals): New variable.
 2021-03-15 10:53:19 +01:00
Lars-Dominik Braun 181e3c0128
gnu: Add r-rtweet. 
* gnu/packages/cran.scm (r-rtweet): New variable.
 2021-03-15 10:53:18 +01:00
Lars-Dominik Braun 83b6d7a33e
gnu: Add r-rworldmap. 
* gnu/packages/cran.scm (r-rworldmap): New variable.
 2021-03-15 10:53:16 +01:00
Lars-Dominik Braun 3095255b7b
gnu: Add r-tmaptools. 
* gnu/packages/cran.scm (r-tmaptools): New variable.
 2021-03-15 10:53:15 +01:00
Lars-Dominik Braun 82344f5936
gnu: Add r-stars. 
* gnu/packages/cran.scm (r-stars): New variable.
 2021-03-15 10:53:15 +01:00
Lars-Dominik Braun a1dd43e4cd
gnu: Add r-lwgeom. 
* gnu/packages/cran.scm (r-lwgeom): New variable.
 2021-03-15 10:53:14 +01:00
Lars-Dominik Braun 5ce5e49c10
gnu: Add r-packcircles. 
* gnu/packages/cran.scm (r-packcircles): New variable.
 2021-03-15 10:53:13 +01:00
Lars-Dominik Braun 5d719fe608
gnu: Add r-readtext. 
* gnu/packages/cran.scm (r-readtext): New variable.
 2021-03-15 10:53:12 +01:00
Lars-Dominik Braun 6f688733b5
gnu: Add r-antiword. 
* gnu/packages/cran.scm (r-antiword): New variable.
 2021-03-15 10:53:11 +01:00
Lars-Dominik Braun 275b7987c0
gnu: Add r-pdftools. 
* gnu/packages/cran.scm (r-pdftools): New variable.
 2021-03-15 10:53:10 +01:00
Lars-Dominik Braun 52c70fb66e
gnu: Add r-qpdf. 
Cannot add to (gnu packages pdf) due to circular module dependency.

* gnu/packages/cran.scm (r-qpdf): New variable.
 2021-03-15 10:53:10 +01:00
Lars-Dominik Braun 03af89bd9e
gnu: Add r-readods. 
* gnu/packages/cran.scm (r-readods): New variable.
 2021-03-15 10:53:09 +01:00
Lars-Dominik Braun cb360afd66
gnu: Add r-streamr 
* gnu/packages/cran.scm (r-streamr): New variable.
 2021-03-15 10:53:08 +01:00
Lars-Dominik Braun a64e355ea6
gnu: Add r-ndjson. 
* gnu/packages/cran.scm (r-ndjson): New variable.
 2021-03-15 10:53:07 +01:00
Lars-Dominik Braun ee4ba54271
gnu: gzstream: Add PIC flag. 
* gnu/packages/compression.scm (gzstream) [arguments]: Add phase 'use-pic.
 2021-03-15 10:53:04 +01:00
Lars-Dominik Braun e415003202
gnu: Add r-striprtf. 
* gnu/packages/cran.scm (r-striprtf): New variable.
 2021-03-15 10:53:03 +01:00
Lars-Dominik Braun 804fad34e8
gnu: Add r-textclean. 
* gnu/packages/cran.scm (r-textclean): New variable.
 2021-03-15 10:53:02 +01:00
Lars-Dominik Braun 584c868fbd
gnu: Add r-english. 
* gnu/packages/cran.scm (r-english): New variable.
 2021-03-15 10:53:01 +01:00
Lars-Dominik Braun c3a1373c15
gnu: Add r-lexicon. 
* gnu/packages/cran.scm (r-lexicon): New variable.
 2021-03-15 10:53:00 +01:00
Lars-Dominik Braun bc82567b0b
gnu: Add r-syuzhet. 
* gnu/packages/cran.scm (r-syuzhet): New variable.
 2021-03-15 10:52:59 +01:00
Lars-Dominik Braun d332c5c7f2
gnu: Add r-textshape. 
* gnu/packages/cran.scm (r-textshape): New variable.
 2021-03-15 10:52:58 +01:00
Lars-Dominik Braun ed48898931
gnu: Add r-dtt. 
* gnu/packages/algebra.scm (r-dtt): New variable.
 2021-03-15 10:52:57 +01:00
Lars-Dominik Braun 4bc1707dba
gnu: Add r-mgsub. 
* gnu/packages/cran.scm (r-mgsub): New variable.
 2021-03-15 10:52:56 +01:00
Lars-Dominik Braun ae807fdb37
gnu: Add r-qdapregex. 
* gnu/packages/cran.scm (r-qdapregex): New variable.
 2021-03-15 10:52:55 +01:00
Lars-Dominik Braun c4e826bbd2
gnu: Add r-esc. 
* gnu/packages/statistics.scm (r-esc): New variable.
 2021-03-15 10:52:52 +01:00
Efraim Flashner 9562d50d8e
gnu: libffi: Inline all patches. 
* gnu/packages/libffi.scm (libffi)[source]: Add patch.
[arguments]: Remove custom patch phases.
[inputs]: Remove field.
 2021-03-15 11:41:16 +02:00
Efraim Flashner 0ca7e19093
gnu: gd: Update to 2.3.2. 
* gnu/packages/gd.scm (gd): Update to 2.3.2.
[arguments]: Adjust comment on custom 'disable-failing-test phase.
 2021-03-15 11:26:50 +02:00
Mark H Weaver d059485257
gnu: unzip: Remove redundant and unused "unzip-symlink.patch". 
This is a followup to commit 31d289a475,
which added, but did not use, "unzip-symlink.patch", which is
redundant with the pre-existing "unzip-initialize-symlink-flag.patch".

* gnu/packages/patches/unzip-symlink.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-03-14 19:16:17 -04:00
Leo Famulari b082ea9406
gnu: OpenSSL: Refer to the version number in a more robust way. 
* gnu/packages/tls.scm (openssl)[arguments]: Replace use of VERSION with
(PACKAGE-VERSION THIS-PACKAGE).
(openssl/fixed): Adjust accordingly.
 2021-03-14 16:33:12 -04:00
Leo Famulari bb2427fa28
gnu: ImageMagick: Refer to the version number in a more robust way. 
* gnu/packages/imagemagick.scm (imagemagick)[arguments]: Replace use of VERSION
with (PACKAGE-VERSION THIS-PACKAGE).
(imagemagick/fixed): Adjust accordingly.
 2021-03-14 16:33:12 -04:00
Leo Famulari 43cbb05f4b
gnu: libtiff: Refer to the version number in a more robust way. 
* gnu/packages/image.scm (libtiff)[arguments]: Replace use of VERSION
with (PACKAGE-VERSION THIS-PACKAGE).
(libtiff/fixed): Adjust accordingly.
 2021-03-14 16:33:08 -04:00
Leo Prikler d4e29f3628
gnu: libhandy: Update to 1.2.0. 
* gnu/packages/gnome.scm (libhandy): Update to 1.2.0.
 2021-03-14 19:47:08 +01:00
Mathieu Othacehe cbfcbb79df
ci: Support packages with multiple channels. 
This is a follow-up of 61a1165340. For packages
provided by external channels, package-channels procedure will return at least
two channels. Take it into account.

* gnu/ci.scm (cuirass-jobs): Fix channels subset argument.
 2021-03-14 19:43:35 +01:00
Eric Bavier b76762a9b7
gnu: Update OnionShare to 2.3.1. 
* gnu/packages/tor.scm (onionshare-cli): New variable.
(onionshare): Inherit from onionshare-cli.
[arguments]: Add patch-tests and install-data phases.  Adjust check phase for
new tests.
[inputs]: Remove python-pycryptodome, python-nautilus, python-sip,
python-stem, and python-pyqt.  Add onionshare-cli, python-shiboken-2,
python-pyside-2, python-qrcode.
[description]: Use new upstream description.
 2021-03-14 13:24:22 -05:00
Eric Bavier 620206b680
gnu: python-eventlet: Add missing dependencies. 
* gnu/packages/python-xyz.scm (python-eventlet)[propagated-inputs]: Add
python-dnspython and python-monotonic.
 2021-03-14 13:24:22 -05:00
Eric Bavier 5a31eb7d35
gnu: Add python-flask-socketio. 
* gnu/packages/python-web.scm (python-flask-socketio): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier 078f3288e2
gnu: Add python-socketio. 
* gnu/packages/python-web.scm (python-socketio): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier 7164d2105a
gnu: Add python-engineio 
* gnu/packages/python-web.scm (python-engineio): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier af25357b7d
gnu: Add python-bidict. 
* gnu/packages/python-xyz.scm (python-bidict): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier 30f5381487
gnu: Add python-sortedcollections. 
* gnu/packages/python-xyz.scm (python-sortedcollections): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier 207aa62e6b
gnu: Add python-sphinx-autodoc-typehints. 
* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints): New variable.
 2021-03-14 13:24:21 -05:00
Eric Bavier b15720182e
gnu: Add python-sphobjinv. 
* gnu/packages/sphinx.scm (python-sphobjinv): New variable.
 2021-03-14 13:24:21 -05:00
Nicolas Goaziou 2babf7d831
gnu: pdfarranger: Update to 1.7.1. 
* gnu/packages/pdf.scm (pdfarranger): Update to 1.7.1.
 2021-03-14 19:16:55 +01:00
Efraim Flashner e598556ee5
gnu: alacritty: Adjust to changes in the cargo-build-system. 
* gnu/packages/terminals.scm (alacritty)[arguments]: Add flag to not
install source.
 2021-03-14 19:52:44 +02:00
Efraim Flashner 21ead0fc5b
gnu: newsboat: Adjust to changes in cargo-build-system. 
* gnu/packages/syndication.scm (newsboat)[arguments]: Add flag to not
install source.
 2021-03-14 19:52:44 +02:00
Efraim Flashner 7af3daa757
gnu: librsvg-next: Adjust to changes in cargo-build-system. 
* gnu/packages/gnome.scm (librsvg-next)[arguments]: Add flag to not
install source.
 2021-03-14 19:52:44 +02:00
Mathieu Othacehe 61a1165340
ci: Add channel subset support. 
* gnu/ci.scm (cuirass-jobs): Add channel subset support.
 2021-03-14 18:19:41 +01:00
Jan (janneke) Nieuwenhuizen 7327295462
gnu: mes: Remove aarch64-linux from supported-systems. 
* gnu/packages/mes.scm (mes)[supported-systems]: Remove aarch64-linux.
Thinko: mes only builds on aarch64-linux using --system=armhf-linux.
 2021-03-14 17:32:01 +01:00
Jan (janneke) Nieuwenhuizen 7982adb40a
gnu: mescc-tools: Build for armhf-linux and aarch64-linux too. 
* gnu/packages/mes.scm (mescc-tools)[supported-systems]: New field, overriding
the v0.5.2 version.
 2021-03-14 16:49:49 +01:00
Jan (janneke) Nieuwenhuizen a9d537594d
bootstrap: mescc-tools-static: Base arguments on version 0.5.2. 
* gnu/packages/make-bootstrap.scm (%mescc-tools-static)[arguments]: Use
fixed package-arguments of mescc-tools-0.5.2.
 2021-03-14 16:43:46 +01:00
Jan (janneke) Nieuwenhuizen 1d684aedf8
gnu: mes: Update to 0.23. 
* gnu/packages/mes.scm (mes)[source]: Update to 0.23.
[supported-systems]: Add aarch64-linux, armhf-linux.
(mes-rb5)[version,source,supported-systems]: Revert to v0.22.
 2021-03-14 12:10:07 +01:00
Jan (janneke) Nieuwenhuizen ba485217b8
gnu: mes: Update to nyacc-1.00.2. 
* gnu/packages/mes.scm (mes)[propagated-inputs]: Use nyacc-1.00.2.
 2021-03-14 11:50:55 +01:00
Jan (janneke) Nieuwenhuizen 8b05461cab
gnu: Add nyacc-1.00.2. 
* gnu/packages/mes.scm (nyacc-1.00.2): New variable.
 2021-03-14 11:50:51 +01:00
Jan (janneke) Nieuwenhuizen 87a8eaf671
gnu: mescc-tools: Update to 0.7.0. 
* gnu/packages/mes.scm (mescc-tools)[source]: Update to 0.7.0.
[arguments]: Add patch-prefix phase to remove hardcoded "/usr/bin".
 2021-03-14 11:50:43 +01:00
Lars-Dominik Braun 930d22883d
gnu: font-libertinus: Update to 7.040. 
* gnu/packages/fonts.scm (font-libertinus): Update to 7.040.
 2021-03-14 10:45:58 +01:00
Lars-Dominik Braun cd3b4c85f9
gnu: font-abattis-cantarell: Update to 0.301. 
* gnu/packages/fonts.scm (font-abattis-cantarell): Update to 0.301.
 2021-03-14 10:39:43 +01:00
Lars-Dominik Braun dc1e643601
gnu: font-ibm-plex: Update to 5.1.3. 
* gnu/packages/fonts.scm (font-ibm-plex): Update to 5.1.3.
 2021-03-14 10:30:35 +01:00
Léo Le Bouter 703843922a
gun: unzip/fixed: Fix tests on 32-bit systems. 
* gnu/packages/patches/unzip-32bit-zipbomb-fix.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/compression.scm (unzip/fixed): Apply patch.
 2021-03-14 09:09:45 +01:00
Efraim Flashner 699a56e3a3
gnu: unzip: Fix patch name. 
This is what happens when you push without testing your changes :/

* gnu/packages/compression.scm (unzip)[source]: Adjust patch name.
 2021-03-14 09:27:43 +02:00
Efraim Flashner cd73a812a3
gnu: unzip: Rename patch. 
* gnu/packages/patches/unzip-case-insensitive.patch: Rename from
unzip-caseinsensitive.patch.
 2021-03-14 09:25:21 +02:00
Léo Le Bouter 31d289a475
gnu: unzip: Add patches from Fedora [security fixes]. 
Non-exhaustively fixes CVE-2016-9844, CVE-2018-1000035, CVE-2018-18384, and
CVE-2019-13232.

* gnu/packages/patches/unzip-COVSCAN-fix-unterminated-string.patch,
gnu/packages/patches/unzip-CVE-2016-9844.patch,
gnu/packages/patches/unzip-CVE-2018-1000035.patch,
gnu/packages/patches/unzip-CVE-2018-18384.patch,
gnu/packages/patches/unzip-case-insensitive.patch,
gnu/packages/patches/unzip-alt-iconv-utf8-print.patch,
gnu/packages/patches/unzip-alt-iconv-utf8.patch,
gnu/packages/patches/unzip-close.patch,
gnu/packages/patches/unzip-exec-shield.patch,
gnu/packages/patches/unzip-fix-recmatch.patch,
gnu/packages/patches/unzip-manpage-fix.patch,
gnu/packages/patches/unzip-overflow.patch,
gnu/packages/patches/unzip-symlink.patch,
gnu/packages/patches/unzip-timestamp.patch,
gnu/packages/patches/unzip-valgrind.patch,
gnu/packages/patches/unzip-x-option.patch,
gnu/packages/patches/unzip-zipbomb-manpage.patch,
gnu/packages/patches/unzip-zipbomb-part1.patch,
gnu/packages/patches/unzip-zipbomb-part2.patch,
gnu/packages/patches/unzip-zipbomb-part3.patch: New patches.
* gnu/local.mk (dist_patch_DATA): Register them.
* gnu/packages/compression.scm (unzip/fixed): New variable. Apply patches.
(unzip)[replacement]: Graft.
 2021-03-14 06:11:20 +01:00
Léo Le Bouter 92d0949a26
gnu: webkitgtk: Enable WOFF2 support. 
* gnu/packages/webkit.scm (webkitgtk):
[arguments]<#:configure-flags>: Remove "-DUSE_WOFF2=OFF".
[inputs]: Add woff2.
 2021-03-14 06:07:10 +01:00
Léo Le Bouter 37b5e79154
gnu: wpewebkit: Update to 2.30.5 [security fixes]. 
* gnu/packages/webkit.scm (wpewebkit): Update to 2.30.5.
[arguments]<#:configure-flags>: Add "-DUSE_SYSTEMD=OFF" and
"-DUSE_GSTREAMER_GL=OFF". Change "-DENABLE_ENCRYPTED_MEDIA=ON" to
"-DENABLE_ENCRYPTED_MEDIA=OFF" (DRM).
 2021-03-14 06:04:33 +01:00
Ludovic Courtès 8154beffd8
gnu: guix: Update to c8887a5. 
* gnu/packages/package-management.scm (guix): Update to c8887a5.
 2021-03-13 23:59:03 +01:00
Ludovic Courtès c8887a5c6e
gnu: emacs-elfeed-score: Fix description Texinfo syntax. 
* gnu/packages/emacs-xyz.scm (emacs-elfeed-score)[description]:
Remove extra "@".
 2021-03-13 23:22:37 +01:00
Tobias Geerinckx-Rice faf271e96e
gnu: sudo: Update to 1.9.6. 
* gnu/packages/admin.scm (sudo): Update to 1.9.6.
 2021-03-13 22:16:56 +01:00
Tobias Geerinckx-Rice 15b39826ff
gnu: quagga: Use archived source tarball. 
* gnu/packages/networking.scm (quagga)[source]: Download from Fossies archive.
 2021-03-13 17:06:50 +01:00
Tobias Geerinckx-Rice ca8c2d1750
gnu: console-setup: Update to 1.201. 
* gnu/packages/xorg.scm (console-setup): Update to 1.201.
 2021-03-13 15:36:53 +01:00
Tobias Geerinckx-Rice 8698829587
gnu: qjackctl: Update to 0.9.1. 
* gnu/packages/audio.scm (qjackctl): Update to 0.9.1.
 2021-03-13 15:36:53 +01:00
Gerd Heber cb70485201
gnu: Add syscall-intercept. 
* gnu/packages/engineering.scm (syscall-intercept): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 15:11:46 +01:00
Xinglu Chen aa0598974b
gnu: Add guile-f-scm. 
* gnu/packages/guile-xyz.scm (guile-f-scm): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 14:58:28 +01:00
Xinglu Chen e06b1ebcaa
gnu: Add l2md. 
* gnu/packages/mail.scm (l2md): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 14:52:37 +01:00
Andy Tai 80a4b150fc
gnu: terminator: Update to 2.1.0. 
* gnu/packages/gnome.scm (terminator): Update to 2.1.0.
[inputs]: Add python, python-dbus, python-notify2.
[arguments]: Add a phase to handle Python DBus. Disable tests.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 14:43:49 +01:00
Milkey Mouse de84dfbed5
gnu: opencl-headers: Update to 2020.12.18 
* gnu/packages/opencl.scm (opencl-headers): Update to 2020.12.18.
[version]: Use the latest tagged version, now that they exist.
[arguments]: Replace all phases with trivial header copy.
[license]: Change license to Apache 2.0 (happened in March 2020).

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 14:31:51 +01:00
Zhu Zihao 2ee7524c76
gnu: opencc: Update to 1.1.1. 
* gnu/packages/textutils.scm(opencc): Update to 1.1.1
[arguments]<#:out-of-source?>: Build in source tree.
<#:parallel-build?>: Disable.
<#:phases>: In "patch-3rd-party-references", fix the version of dependency.
Add phases "patch-python-binding-installation", "install-python-binding"
and "enable-bytecode-determinism".
[native-inputs]: Add python-setuptools and python-wheel.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 14:26:02 +01:00
Nicolas Goaziou 5e753287c8
gnu: cagebreak: Update to 1.6.0. 
* gnu/packages/wm.scm (cagebreak): Update to 1.6.0.
 2021-03-13 14:17:32 +01:00
Vinicius Monego 0455c19fa5
gnu: python-scikit-image: Enable tests. 
* gnu/packages/python-science.scm (python-scikit-image)[arguments]: Add phases
related to tests.
[native-inputs]: Add python-codecov, python-flake8, python-pytest,
python-pytest-cov, python-pytest-localserver, python-wheel.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:56:07 +01:00
Vinicius Monego 36062f16b6
gnu: python-scikit-image: Update to 0.18.1. 
* gnu/packages/python-science.scm (python-scikit-image): Update to 0.18.1.
[propagated-inputs]: Remove python-six.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:55:15 +01:00
Vinicius Monego 211c933077
gnu: Add python-pooch. 
* gnu/packages/python-xyz.scm (python-pooch): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:54:58 +01:00
Xinglu Chen c0641c0965
gnu: Add emacs-org-msg. 
* gnu/packages/emacs-xyz.scm (emacs-org-msg): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:53:49 +01:00
Xinglu Chen fe53300263
gnu: Add emacs-elfeed-score. 
* gnu/packages/emacs-xyz.scm (emacs-elfeed-score): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:50:54 +01:00
Stefan Reichör 71c97c89b0
gnu: Add xe. 
* gnu/packages/parallel.scm (xe): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 13:46:26 +01:00
LibreMiami 8dc25b4bb3
gnu: Add clikan. 
* gnu/packages/task-management.scm (clikan): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 12:22:56 +01:00
LibreMiami e5d526d758
gnu: Add python-click-default-group. 
* /gnu/packages/python-xyz.scm (python-click-default-group): New
variable.

Co-authored-by: Raghav Gururajan <rg@raghavgururajan.name>
Co-authored-by: jgart <jgart@dismail.de>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 12:16:22 +01:00
Xinglu Chen 339200699f
gnu: Add emacs-ox-haunt. 
* gnu/packages/emacs-xyz.scm (emacs-ox-haunt): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 12:13:03 +01:00
Nicolas Goaziou aa59697509
gnu: emacs-ox-gemini: Fix version number. 
* gnu/packages/emacs-xyz.scm (emacs-ox-gemini)[version]: Set version number to
0 as set in the main library.
 2021-03-13 12:09:08 +01:00
Xinglu Chen 9693868579
gnu: Add emacs-ox-gemini. 
* gnu/packages/emacs-xyz.scm (emacs-ox-gemini): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-13 12:07:03 +01:00
Pierre Langlois d091371c59
gnu: emacs-ivy-rich: Update to 0.1.6-1.7b9b7b2. 
* gnu/packages/emacs-xyz.scm (emacs-ivy-rich): Update to git snapshot
0.1.6-1.7b9b7b2.
 2021-03-13 10:52:51 +00:00
Mark H Weaver 74e2c0e00f
gnu: gnutls: Fix CVE-2021-20231 and CVE-2021-20232. 
* gnu/packages/patches/gnutls-CVE-2021-20231.patch,
gnu/packages/patches/gnutls-CVE-2021-20232.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/tls.scm (gnutls)[replacement]: New field.
(gnutls/fixed): New variable.
(guile2.2-gnutls): Use package/inherit.
 2021-03-13 04:58:12 -05:00
Lars-Dominik Braun ca8fa11754
gnu: mergerfs: Update to 2.32.4. 
* gnu/packages/file-systems.scm (mergerfs): Update to 2.32.4.
 2021-03-13 09:43:09 +01:00
Nicolas Goaziou a61bdc5887
gnu: rust-resolv-conf-0.7: Use HTTPS home page URI. 
* gnu/packages/crates-io.scm (rust-resolv-conf-0.7)[home-page]: Use HTTPS URI.
 2021-03-13 09:13:23 +01:00
Kei Kebreau b7c19f2850
gnu: wxmaxima: Update to 21.02.0. 
* gnu/packages/maths.scm (wxmaxima): Update to 21.02.0.
 2021-03-13 00:19:00 -05:00
Léo Le Bouter 373c7b5791
gnu: Remove bsdiff. 
As discussed in
<https://lists.gnu.org/archive/html/guix-devel/2021-03/msg00154.html>, remove
because of unpatched CVE-2020-14315 with no non-FreeBSD patch in sight.

* gnu/packages/compression.scm (bsdiff): Remove.
 2021-03-13 02:31:53 +01:00
Léo Le Bouter 77f1bd9dea
gnu: rust-diesel: Update to 1.4.6 [fixes CVE-2021-28305]. 
* gnu/packages/crates-io.scm (rust-diesel): Update to 1.4.6.
[native-inputs]: Add sqlite for tests.
[arguments]<#:cargo-inputs>: Remove rust-bigdecimal-0.2 (incompatible),
rust-libsqlite3-sys-0.15, rust-num-bigint-0.3 and rust-uuid-0.7. Add
rust-bigdecimal-0.1, rust-libsqlite3-sys-0.20, rust-num-bigint-0.2,
rust-uuid-0.5 and rust-uuid-0.8.
[arguments]<#:phases>: Replace 'check phase to provide required feature
arguments and  exclude failing 'expression::count::count' test.
[synopsis]: Solve lint error by removing article at the beginning.
 2021-03-13 02:07:28 +01:00
Léo Le Bouter 372a16e5c7
gnu: rust-dotenv-0.10: Fix build by adding missing cargo input. 
* gnu/packages/crates-io.scm (rust-dotenv-0.10)[arguments]<#:cargo-inputs>:
Add rust-syn-0.11.
 2021-03-13 02:04:29 +01:00
Léo Le Bouter 62b1ae7444
gnu: Add rust-bigdecimal-0.1. 
* gnu/packages/crates-io.scm (rust-bigdecimal-0.1): New variable.
 2021-03-13 02:04:28 +01:00
Tobias Geerinckx-Rice cad4aa667c
gnu: nginx-documentation: Update to 1.19.8-2673-4398fd0f0341. 
* gnu/packages/web.scm (nginx-documentation): Update to 1.19.8-2673-4398fd0f0341.
 2021-03-13 01:00:31 +01:00
Tobias Geerinckx-Rice c325099535
gnu: nginx: Update to 1.19.8. 
* gnu/packages/web.scm (nginx): Update to 1.19.8.
 2021-03-13 01:00:31 +01:00
Tobias Geerinckx-Rice 347cc54200
gnu: apache-thrift: Update to 0.14.1. 
* gnu/packages/rpc.scm (apache-thrift): Update to 0.14.1.
 2021-03-13 01:00:31 +01:00
Tobias Geerinckx-Rice fab02edde0
gnu: wireguard-tools: Update to 1.0.20210223. 
* gnu/packages/vpn.scm (wireguard-tools): Update to 1.0.20210223.
 2021-03-13 01:00:30 +01:00
Tobias Geerinckx-Rice deb8853243
gnu: eid-mw: Update to 5.0.14. 
* gnu/packages/security-token.scm (eid-mw): Update to 5.0.14.
 2021-03-13 01:00:30 +01:00
Tobias Geerinckx-Rice 1e71578c4a
gnu: micropython: Update to 1.14. 
* gnu/packages/python.scm (micropython): Update to 1.14.
 2021-03-13 01:00:30 +01:00
Tobias Geerinckx-Rice 4ddf56c136
gnu: libfreenect: Update to 0.6.2. 
* gnu/packages/openkinect.scm (libfreenect): Update to 0.6.2.
 2021-03-13 01:00:30 +01:00
Tobias Geerinckx-Rice 6862ae1a61
gnu: photoflare: Update to 1.6.7. 
* gnu/packages/photo.scm (photoflare): Update to 1.6.7.
 2021-03-13 01:00:30 +01:00
Greg Hogan bd0808f131
gnu: aws-sdk-cpp: Update to 1.8.159. 
* gnu/packages/cpp.scm (aws-sdk-cpp): Update to 1.8.159.
[arguments]: Build as shared library

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:55 +01:00
Greg Hogan 9719084535
gnu: aws-c-event-stream: Update to 0.2.7. 
* gnu/packages/c.scm (aws-c-event-stream): Update to 0.2.7.
[arguments]: Build as shared library.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:55 +01:00
Greg Hogan 8ea7b6f91e
gnu: Add aws-c-io. 
* gnu/packages/c.scm (aws-c-io): New variable.
* gnu/packages/patches/aws-c-io-cmake-prefix.patch,
gnu/packages/patches/aws-c-io-disable-networking-tests.patch:
New files.
* gnu/local.mk (dist_patch_DATA): Add them.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:54 +01:00
Greg Hogan 1b51888863
gnu: Add s2n. 
* gnu/packages/tls.scm (s2n): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:54 +01:00
Greg Hogan 748e2ec07a
gnu: Add aws-c-cal. 
* gnu/packages/c.scm (aws-c-cal): New variable.
* gnu/packages/patches/aws-c-cal-cmake-prefix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:54 +01:00
Greg Hogan cc95d03ec7
gnu: aws-checksums: Build as shared library. 
* gnu/packages/c.scm (aws-checksums)[arguments]: Build as shared library.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:54 +01:00
Greg Hogan 9d541e97e9
gnu: aws-c-common: Update to 0.5.2. 
* gnu/packages/c.scm (aws-c-common): Update to 0.5.2.
[arguments]: Build as shared library.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-12 23:58:54 +01:00
Leo Famulari bb5d84a048
gnu: ImageMagick: Fix version number in build configuration of grafted replacement. 
Fixes <https://bugs.gnu.org/47110>.

This is a followup to commits 852ba914a4 and
82e887ba48.

* gnu/packages/imagemagick.scm (imagemagick/fixed)[name, arguments]: New
fields.
 2021-03-12 14:41:17 -05:00
Leo Famulari a39faf1abd
gnu: OpenSSL: Fix version number in build configuration. 
Fixes <https://bugs.gnu.org/47108>.

This is a followup to commit 4a8b529ce1.

* gnu/packages/tls.scm (openssl/fixed)[arguments]: New field.
 2021-03-12 14:22:21 -05:00
Leo Famulari 35b3ab8e57
gnu: libtiff: Fix documentation directory name in grafted replacement. 
Fixes <https://bugs.gnu.org/47107>.

This is a followup to commit 6320700b11.

* gnu/packages/image.scm (libtiff/fixed)[name, arguments]: New fields.
 2021-03-12 14:10:31 -05:00
Nicolas Goaziou a5a5ec5603
gnu: nushell: Update to 0.28.0. 
* gnu/packages/shells.scm (nushell):
(rust-nu-cli-0.28):
(rust-nu-command-0.28):
(rust-nu-data-0.28):
(rust-nu-engine-0.28):
(rust-nu-errors-0.28):
(rust-nu-json-0.28):
(rust-nu-plugin-0.28):
(rust-nu-plugin-binaryview-0.28):
(rust-nu-plugin-chart-0.28):
(rust-nu-plugin-fetch-0.28):
(rust-nu-plugin-from-sqlite-0.28):
(rust-nu-plugin-inc-0.28):
(rust-nu-plugin-match-0.28):
(rust-nu-plugin-post-0.28):
(rust-nu-plugin-ps-0.28):
(rust-nu-plugin-s3-0.28):
(rust-nu-plugin-sys-0.28):
(rust-nu-plugin-textview-0.28):
(rust-nu-plugin-to-bson-0.28):
(rust-nu-plugin-to-sqlite-0.28):
(rust-nu-plugin-tree-0.28):
(rust-nu-plugin-xpath-0.28):
(rust-nu-protocol-0.28):
(rust-nu-source-0.28):
(rust-nu-stream-0.28):
(rust-nu-test-support-0.28):
(rust-nu-value-ext-0.28): Update to 0.28.0.
(rust-nu-ansi-term-0.28): New variable.
 2021-03-12 16:09:37 +01:00
Nicolas Goaziou 56613cc619
gnu: Add rust-minus-3. 
* gnu/packages/crates-io.scm (rust-minus-3): New variable.
 2021-03-12 16:09:37 +01:00
Nicolas Goaziou 1fcaac7941
gnu: rust-surf-2: Update to 2.2.0. 
* gnu/packages/crates-io.scm (rust-surf-2): Update to 2.2.0.
 2021-03-12 16:09:37 +01:00
Nicolas Goaziou 7d29bfd567
gnu: rust-http-client-6: Update to 6.3.4. 
* gnu/packages/crates-io.scm (rust-http-client-6): Update to 6.3.4.
 2021-03-12 16:09:36 +01:00
Nicolas Goaziou 10a1ab0d26
gnu: Add rust-async-tls-0.10. 
* gnu/packages/crates-io.scm (rust-async-tls-0.10): New variable.
 2021-03-12 16:09:36 +01:00
Nicolas Goaziou 6fe6ab50bd
gnu: rust-webpki-0.21: Update to 0.21.4. 
* gnu/packages/crates-io.scm (rust-webpki-0.21): Update to 0.21.4.
 2021-03-12 16:09:36 +01:00
Nicolas Goaziou a7c8060360
gnu: rust-ring-0.16: Update to 0.16.20. 
* gnu/packages/crates-io.scm (rust-ring-0.16): Update to 0.16.20.
[arguments]: Skip tests.
 2021-03-12 16:09:35 +01:00
Nicolas Goaziou 0f0589b8cd
gnu: Add rust-deadpool-0.7. 
* gnu/packages/crates-io.scm (rust-deadpool-0.7): New variable.
 2021-03-12 16:09:35 +01:00
Nicolas Goaziou b89714b40a
gnu: rust-url-2: Update to 2.2.1. 
* gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.1.
 2021-03-12 16:09:09 +01:00
Ludovic Courtès 97b45977f4
gnu: guile-zlib: Update to 0.1.0. 
* gnu/packages/guile.scm (guile-zlib): Update to 0.1.0.
 2021-03-12 15:59:45 +01:00
Sharlatan Hellseher 2e5ac371e7
gnu: Add sbcl-stumpwm-disk. 
* gnu/packages/wm.scm: (sbcl-stumpwm-disk): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-03-12 15:06:51 +01:00
Sharlatan Hellseher 77ee8af58c
gnu: stumpwm-contrib: Update to 0.0.1-3.a7dc1c. 
* gnu/packages/wm.scm (stumpwm-contrib): Update to 0.0.1-3.a7dc1c.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-03-12 15:06:51 +01:00
Guillaume Le Vaillant a56b331e07
gnu: Add gnuais. 
* gnu/packages/radio.scm (gnuais): New variable.
 2021-03-12 15:06:50 +01:00
zimoun df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
 2021-03-12 14:45:55 +01:00
zimoun 8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun 373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
 2021-03-12 14:45:53 +01:00
Ricardo Wurmus 323aec6ad9
gnu: r-bioassayr: Update home page. 
* gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent
redirect.
 2021-03-12 14:41:15 +01:00
zimoun 2528cad451
gnu: r-bioassayr: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
 2021-03-12 14:41:14 +01:00
zimoun 8c8d365ca3
gnu: r-chemminer: Update to 3.42.2. 
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
 2021-03-12 14:41:14 +01:00
zimoun 4f617bfb8e
gnu: r-circrnaprofiler: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
 2021-03-12 14:41:14 +01:00
Lars-Dominik Braun 8a8e8198ec
gnu: Add r-puniform. 
* gnu/packages/statistics.scm (r-puniform): New variable.
 2021-03-12 14:34:22 +01:00
Lars-Dominik Braun 28df54d776
gnu: Add r-clubsandwich. 
* gnu/packages/statistics.scm (r-clubsandwich): New variable.
 2021-03-12 14:34:20 +01:00
Lars-Dominik Braun 3a82f1fba2
gnu: Add r-quantpsyc. 
* gnu/packages/statistics.scm (r-quantpsyc): New variable.
 2021-03-12 14:34:19 +01:00
Lars-Dominik Braun 23bfd152c2
gnu: Add r-ez. 
* gnu/packages/cran.scm (r-ez): New variable.
 2021-03-12 14:34:18 +01:00
Lars-Dominik Braun 8a51be3cdd
gnu: Add r-prereg. 
* gnu/packages/cran.scm (r-prereg): New variable.
 2021-03-12 14:34:14 +01:00
Ricardo Wurmus 456355c253
gnu: Add python-upsetplot. 
* gnu/packages/python-science.scm (python-upsetplot): New variable.
 2021-03-12 13:56:12 +01:00
Ricardo Wurmus 4d0fdde344
gnu: Add python-statannot. 
* gnu/packages/python-science.scm (python-statannot): New variable.
 2021-03-12 13:35:02 +01:00
Pierre Neidhardt 5fa4814b4f
gnu: lisp-repl-core-dumper: Update to 0.7.0. 
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Update to 0.7.0.
 2021-03-12 13:09:36 +01:00
Ricardo Wurmus ddc1cddded
gnu: snakemake: Update to 5.32.2. 
* gnu/packages/python-xyz.scm (snakemake): Update to 5.32.2.
[arguments]: Adjust patch in call-wrapper-not-wrapped-snakemake.
 2021-03-12 13:03:33 +01:00
Mark H Weaver 825cc7e0d4
gnu: gnome-shell: Fix CVE-2020-17489. 
* gnu/packages/patches/gnome-shell-CVE-2020-17489.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnome.scm (gnome-shell)[source]: Add patch.
 2021-03-12 06:08:33 -05:00
Mark H Weaver db7c3410d5
gnu: gnome-shell: Update to 3.34.5. 
* gnu/packages/gnome.scm (gnome-shell): Update to 3.34.5.
 2021-03-12 06:08:33 -05:00
Mark H Weaver f5e1909d9f
gnu: gvfs: Update to 1.40.2 [security fixes]. 
Includes fixes for CVE-2019-12447, CVE-2019-12448, CVE-2019-12449,
and CVE-2019-12795.

* gnu/packages/gnome.scm (gvfs): Update to 1.40.2.
 2021-03-12 06:08:33 -05:00
Mark H Weaver bc16eacc99
gnu: cairo: Fix CVE-2018-19876 and CVE-2020-35492. 
* gnu/packages/patches/cairo-CVE-2018-19876.patch,
gnu/packages/patches/cairo-CVE-2020-35492.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/gtk.scm (cairo)[replacement]: New field.
(cairo/fixed): New variable.
(cairo-xcb): Use package/inherit.
 2021-03-12 06:08:33 -05:00
Mark H Weaver 453e101fc3
gnu: gdk-pixbuf: Fix CVE-2020-29385. 
* gnu/packages/patches/gdk-pixbuf-CVE-2020-29385.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gdk-pixbuf)[replacement]: New field.
(gdk-pixbuf/fixed): New variable.
(gdk-pixbuf+svg): Use package/inherit.
 2021-03-12 06:08:32 -05:00
Ricardo Wurmus 57853d69fe
gnu: java-openjfx-graphics: Install native libraries. 
* gnu/packages/java.scm (java-openjfx-graphics)[arguments]: Add phase
copy-missing-file and build-native.
[native-inputs]: Add missing source file.
 2021-03-12 10:32:13 +01:00
Mark H Weaver 5a06b83fc9
gnu: glib: Fix CVE-2021-28153. 
* gnu/packages/patches/glib-CVE-2021-28153.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/glib.scm (glib/fixed): Add the new patch.
 2021-03-12 01:44:26 -05:00
Leo Famulari c3a7537396
gnu: certbot, python-acme: Update to 1.13.0. 
* gnu/packages/tls.scm (python-acme): Update to 1.13.0.
[native-inputs]: Remove python-mock.
[propagated-inputs]: Remove python-six.
(certbot): Update to 1.13.0.
[propagated-inputs]: Remove python-six.
[arguments]: Remove 'build-documentation' phase.
 2021-03-11 21:41:47 -05:00
Kyle Meyer 09c05fde52
gnu: git-annex: Update to 8.20210310. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210310.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-03-11 18:06:39 -05:00
Leo Famulari df632e3225
gnu: linux-libre 4.4: Update to 4.4.261. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.261.
(linux-libre-4.4-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 2c5aff6160
gnu: linux-libre 4.9: Update to 4.9.261. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.261.
(linux-libre-4.9-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 0988cbaeab
gnu: linux-libre 4.14: Update to 4.14.225. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.225.
(linux-libre-4.14-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 129db4f104
gnu: linux-libre 4.19: Update to 4.19.180. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.180.
(linux-libre-4.19-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari a4905b424e
gnu: linux-libre 5.4: Update to 5.4.105. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.105.
(linux-libre-5.4-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Leo Famulari 234aa6c964
gnu: linux-libre 5.10: Update to 5.10.23. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.23.
(linux-libre-5.10-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Leo Famulari c39d8a11c0
gnu: linux-libre: Update to 5.11.6. 
* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.6.
(linux-libre-5.11-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Xinglu Chen 42d5efc001
gnu: guile-curl: Update to 0.9. 
* gnu/packages/curl.scm (guile-curl): Update to 0.9.
[#:phases]: Update path to module.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-11 23:22:04 +01:00
Tobias Geerinckx-Rice ebd5000263
gnu: wireshark: Update to 3.4.4. 
* gnu/packages/networking.scm (wireshark): Update to 3.4.4.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice d3e2ad740f
gnu: hangups: Update to 0.4.13. 
* gnu/packages/messaging.scm (hangups): Update to 0.4.13.
 2021-03-11 23:11:58 +01:00
Greg Hogan 47093ca4cd
gnu: fmt: Update to 7.1.3. 
* gnu/packages/pretty-print.scm (fmt): Update to 7.1.3.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice c518925391
gnu: btrfs-progs: Update to 5.11. 
* gnu/packages/linux.scm (btrfs-progs): Update to 5.11.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice 8a9d3e9420
gnu: libdatrie: Update to 0.2.13. 
* gnu/packages/gtk.scm (libdatrie): Update to 0.2.13.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice ed6900f974
gnu: libinih: Update to 53. 
* gnu/packages/linux.scm (libinih): Update to 53.
 2021-03-11 23:11:57 +01:00
Léo Le Bouter 0aaac779d4
gnu: flatpak: Update to 1.10.2 [fixes CVE-2021-21381]. 
* gnu/packages/package-management.scm (flatpak): Update to 1.10.2.
 2021-03-11 22:58:05 +01:00
Efraim Flashner aa983626a2
gnu: mongodb: Update comment about package license. 
* gnu/packages/databases.scm (mongodb): Adjust the comment about the
licensing status of the package, there are still older branches
receiving updates under the AGPL license.
 2021-03-11 23:26:01 +02:00
Efraim Flashner 2f9132e2e0
Revert "Revert "gnu: mongodb: Update to 3.4.24 [security fixes]."" 
This reverts commit feff80cec3.

I was mistaken, there are still branches of mongodb which are still
licensed under the AGPL3
 2021-03-11 23:23:00 +02:00
Pierre Neidhardt 6dda223631
gnu: Add computable-reals. 
* gnu/packages/lisp-xyz.scm (cl-computable-reals, ecl-computable-reals,
sbcl-computable-reals): New variables.
 2021-03-11 21:11:51 +01:00
Raghav Gururajan 340e6dd51b
gnu: Add python-praw. 
* gnu/packages/python-web.scm (python-raw): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:05 +02:00
Raghav Gururajan 532fc2fbaf
gnu: Add python-prawcore. 
* gnu/packages/python-web.scm (python-prawcore): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:03 +02:00
Raghav Gururajan cfa564bcef
gnu: Add python-testfixtures. 
* gnu/packages/python-check.scm (python-testfixtures): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:01 +02:00
Raghav Gururajan ce2637c003
gnu: Add python-betamax-serializers. 
* gnu/packages/python-web.scm (python-betamax-serializers): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:47:55 +02:00
Tobias Geerinckx-Rice c47f0dea8c
gnu: jasper: Update to 2.0.26. 
* gnu/packages/image.scm (jasper): Update to 2.0.26.
 2021-03-11 18:06:56 +01:00
Tobias Geerinckx-Rice 2e2a3b248b
gnu: thermald: Update to 2.4.3. 
* gnu/packages/admin.scm (thermald): Update to 2.4.3.
 2021-03-11 18:06:56 +01:00
Tobias Geerinckx-Rice b8f0d11f76
gnu: doctest: Update to 2.4.5. 
* gnu/packages/check.scm (doctest): Update to 2.4.5.
 2021-03-11 18:06:56 +01:00
Tobias Geerinckx-Rice affeb3def7
gnu: jetring: Update to 0.30. 
* gnu/packages/gnupg.scm (jetring): Update to 0.30.
 2021-03-11 18:06:56 +01:00
Tobias Geerinckx-Rice 444a38b991
gnu: memkind: Remove duplicate COPYING file. 
* gnu/packages/disk.scm (memkind)[arguments]: Add the standard
"--docdir=" location to #:configure-flags.
 2021-03-11 18:06:56 +01:00