futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
75,797 Commits 3 Branches 0 Tags 412 MiB
75a95ed95f
Commit Graph

67438 Commits

Author SHA1 Message Date
Léo Le Bouter
60d629d777
gnu: busybox: Update to 1.33.0. 
* gnu/packages/busybox.scm (busybox): Update to 1.33.0.
 2021-03-19 12:00:13 +01:00
Léo Le Bouter
572528e7dd
gnu: busybox: Fix CVE-2021-28831. 
* gnu/packages/patches/busybox-CVE-2021-28831.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/busybox.scm (busybox): Apply it.
 2021-03-19 11:56:38 +01:00
Léo Le Bouter
c1245f01ef
gnu: ruby-kramdown: Update to 2.3.1 [fixes CVE-2021-28834]. 
* gnu/packages/ruby.scm (ruby-kramdown): Update to 2.3.1.
 2021-03-19 11:44:41 +01:00
Marius Bakke
1155a88308
gnu: ungoogled-chromium: Update to 89.0.4389.90-1. 
* gnu/packages/patches/ungoogled-chromium-system-opus.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 89.
(%chromium-version): Remove variable.
(%ungoogled-revision): Set to 89.0.4389.90-1.
(%ungoogled-origin): Conditionally set file name based on commit/tag.
(%guix-patches): Add the new file.
(libvpx/chromium): Update to 1.9.0-104-gb5d77a48d.
(ungoogled-chromium)[version]: Use %UNGOOGLED-REVISION.
[source]: Update hash.
[arguments]: Adjust #:configure-flags for build system changes.  Don't build
with external WebRTC SSL library.  Remove obsolete substitution.
[inputs]: Remove OPENSSL.  Change from PIPEWIRE to PIPEWIRE-0.3.
 2021-03-19 00:14:11 +01:00
Tobias Geerinckx-Rice
bb8a0d8057
gnu: emacsy-minimal: Fix build. 
* gnu/packages/guile-xyz.scm (emacsy-minimal)[native-inputs]:
Add autoconf, automake, gettext-minimal, libtool, pkg-config,
and texinfo.
 2021-03-18 21:07:46 +01:00
Ryan Prior via Guix-patches via
efe7a17406
gnu: Add countdown. 
* gnu/packages/time.scm (countdown): New variable.

Also adds copyright, adds necessary module dependencies, and sorts them alphabetically.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-18 19:41:32 +01:00
Morgan Smith
a398e06cad
gnu: emacs-flymake-shellcheck: Update to 0.1-1.ac534e9 
* gnu/packages/emacs-xyz.scm (emacs-flymake-shellcheck): Update to 0.1-1.ac534e9

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-03-18 19:37:35 +01:00
Nicolas Goaziou
bfaeee5675
gnu: emacs-leaf: Update to 4.4.4. 
* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.4.
 2021-03-18 17:35:22 +01:00
Tobias Geerinckx-Rice
b6df89efb0
gnu: dhewm3: Update to 1.5.1. 
* gnu/packages/game-development.scm (dhewm3): Update to 1.5.1.
 2021-03-18 17:08:11 +01:00
Tobias Geerinckx-Rice
c2265e0285
gnu: elixir: Update to 1.11.4. 
* gnu/packages/elixir.scm (elixir): Update to 1.11.4.
 2021-03-18 17:08:10 +01:00
Tobias Geerinckx-Rice
d9bdd6fa92
gnu: goffice: Update to 0.10.49. 
* gnu/packages/gnome.scm (goffice): Update to 0.10.49.
 2021-03-18 17:08:10 +01:00
Tobias Geerinckx-Rice
e999ea12ea
gnu: di: Update to 4.49. 
* gnu/packages/admin.scm (di): Update to 4.49.
[source]: Update URL.
 2021-03-18 17:08:10 +01:00
Tobias Geerinckx-Rice
2baae75e82
gnu: isc-dhcp: Update bundled bind to 9.11.29. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled bind to
9.11.29.
 2021-03-18 17:08:10 +01:00
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
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
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