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
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
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
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
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
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
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
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
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
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
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
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
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
45695cc8a7
Revert "gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363]."
...
In response to commit 1a265842e6https://bugs.gnu.org/47186 >.
This reverts commit db87d6ddaf
2021-03-18 11:26:11 +01:00
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
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
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
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
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
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
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
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
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
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
24f1ce9e71
gnu: scdoc: Cross-compile.
...
* gnu/packages/man.scm (scdoc)[arguments]: Use CC-FOR-TARGET.
2021-03-17 21:22:21 +01:00
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
d7b4ccefa9
gnu: libtirpc/hurd: Fix package source.
...
Amend the changes in 1a265842e6
2021-03-17 20:15:15 +00:00
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
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
cb424bad32
gnu: Add emacs-kotlin-mode.
...
* gnu/packages/emacs-xyz.scm (emacs-kotlin-mode): New variable.
2021-03-17 18:48:06 +03:00
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
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
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
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
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
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
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
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
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
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
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
f4259f93ea
gnu: Add meson-next.
...
* gnu/packages/build-tools.scm (meson-next): New variable.
2021-03-16 16:21:27 -04:00
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
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
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
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
08447ab7cd
gnu: Add python-toposort.
...
* gnu/packages/python-xyz.scm (python-toposort): New variable.
2021-03-16 14:17:48 +01:00
fa0a18522d
gnu: Add python-pulp.
...
* gnu/packages/python-xyz.scm (python-pulp): New variable.
2021-03-16 14:17:47 +01:00
c9006a0ee1
gnu: Add python-amply.
...
* gnu/packages/python-xyz.scm (python-amply): New variable.
2021-03-16 14:17:47 +01:00
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
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
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
335af327cd
gnu: asymptote: Update to 2.70.
...
* gnu/packages/plotutils.scm (asymptote): Update to 2.70.
2021-03-16 14:06:40 +01:00
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
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
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
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
2021-03-16 11:05:24 +01:00
0ee5d4f7a8
gnu: git: Fix git-manpages native input's hash.
...
This is a follow-up to commit ab9629b7c9
2021-03-16 10:58:36 +01:00
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
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
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
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
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
8ec0ca8faf
Revert some commits that caused `guix pull` to fail.
...
This reverts commits 821e6439218f9fd9b70c
2021-03-15 19:52:34 -04:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
ce29866c01
gnu: Add glib-static.
...
* gnu/packages/glib.scm (glib-static): New variable.
2021-03-15 18:00:35 -04:00
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
29e992c030
gnu: r-seurat: Fix build.
...
This is a follow-up to commit e4d4046999
2021-03-15 22:06:57 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
87d3f805b9
gnu: r-utf8: Update to 1.2.1.
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* gnu/packages/cran.scm (r-utf8): Update to 1.2.1.
[native-inputs]: Add r-knitr.
2021-03-15 13:45:30 +01:00
d163c71e0a
gnu: r-xfun: Update to 0.22.
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* gnu/packages/cran.scm (r-xfun): Update to 0.22.
2021-03-15 13:45:30 +01:00
70257ad2c0
gnu: r-ipred: Update to 0.9-11.
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* gnu/packages/cran.scm (r-ipred): Update to 0.9-11.
2021-03-15 13:45:29 +01:00
bfa09fd922
gnu: r-lava: Update to 1.6.9.
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* gnu/packages/cran.scm (r-lava): Update to 1.6.9.
2021-03-15 13:45:29 +01:00
172da782db
gnu: r-rvest: Update to 1.0.0.
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* 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
7bdef3789d
gnu: r-zoo: Update to 1.8-9.
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* gnu/packages/cran.scm (r-zoo): Update to 1.8-9.
2021-03-15 13:45:29 +01:00
e1240e22f5
gnu: Add r-spatstat-linnet.
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* gnu/packages/cran.scm (r-spatstat-linnet): New variable.
2021-03-15 13:45:29 +01:00
3ebae705f9
gnu: Add r-spatstat-core.
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* gnu/packages/cran.scm (r-spatstat-core): New variable.
2021-03-15 13:45:29 +01:00
ddfe3f77a9
gnu: Add r-spatstat-geom.
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* gnu/packages/cran.scm (r-spatstat-geom): New variable.
2021-03-15 13:45:29 +01:00
78373e394d
gnu: Add r-spatstat-sparse.
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* gnu/packages/cran.scm (r-spatstat-sparse): New variable.
2021-03-15 13:45:29 +01:00
1ed435bf39
gnu: python-sphobjinv: Fix build.
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* gnu/packages/sphinx.scm (python-sphobjinv):
[patches]: Remove.
[propagated-inputs]: Add (uncomment) python-certifi.
2021-03-15 12:51:54 +01:00
3096428889
gnu: libcroco/fixed: Make private.
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* gnu/packages/gnome.scm (libcroco/fixed): Use define instead of
define-public.
2021-03-15 12:22:18 +01:00
8a085c1780
gnu: cyrus-sasl/fixed: Make private.
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* gnu/packages/cyrus-sasl.scm (cyrus-sasl/fixed): Use define instead of
define-public.
2021-03-15 12:22:17 +01:00
cddf0b8955
gnu: unzip/fixed: Make private.
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* gnu/packages/compression.scm (unzip/fixed): Use define instead of
define-public.
2021-03-15 12:22:17 +01:00
3e83e99322
gnu: poetry: Update to 1.1.5.
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* 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
014fa5cc6b
gnu: python-poetry-core: Update to 1.0.2.
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* 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
3eeb7dbf04
gnu: r-gkmsvm: Move back to (gnu packages cran).
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* 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
1daedaa864
gnu: libusb-for-axoloti: Revert to 1.0.23.
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* 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
21bc326b9a
gnu: guile-opengl: Fix linking with libGL.so.
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* gnu/packages/gl.scm (guile-opengl)[arguments]: Fix reference to libGL.so.
2021-03-15 11:57:56 +01:00
6e0ed09e68
gnu: Add instrain.
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* gnu/packages/bioinformatics.scm (instrain): New variable.
2021-03-15 11:43:20 +01:00
ad34eb222c
gnu: Add python-drep.
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* gnu/packages/bioinformatics.scm (python-drep): New variable.
2021-03-15 11:43:20 +01:00
c20813bb08
gnu: Add python-lmfit.
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* gnu/packages/python-xyz.scm (python-lmfit): New variable.
2021-03-15 11:43:20 +01:00
0bd166253a
gnu: Add python-asteval.
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* gnu/packages/python-xyz.scm (python-asteval): New variable.
2021-03-15 11:43:19 +01:00
8b85aea49b
gnu: Add python-uncertainties.
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* gnu/packages/python-xyz.scm (python-uncertainties): New variable.
2021-03-15 11:43:19 +01:00
714a8faa04
gnu: guile-email-latest: Update to 0.2.2-1.ca0520a.
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* gnu/packages/guile-xyz.scm (guile-email-latest): Update to 0.2.2-1.ca0520a.
2021-03-15 11:43:19 +01:00
c3163fe6b4
gnu: Add r-textplot.
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* gnu/packages/cran.scm (r-textplot): New variable.
2021-03-15 10:53:22 +01:00
ca3913d1f8
gnu: Add r-btm.
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* gnu/packages/cran.scm (r-btm): New variable.
2021-03-15 10:53:21 +01:00
20fb147c9a
gnu: Add r-eyelinker.
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* gnu/packages/cran.scm (r-eyelinker): New variable.
2021-03-15 10:53:20 +01:00
32603dbba9
gnu: Add r-intervals.
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* gnu/packages/cran.scm (r-intervals): New variable.
2021-03-15 10:53:19 +01:00
181e3c0128
gnu: Add r-rtweet.
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* gnu/packages/cran.scm (r-rtweet): New variable.
2021-03-15 10:53:18 +01:00
83b6d7a33e
gnu: Add r-rworldmap.
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* gnu/packages/cran.scm (r-rworldmap): New variable.
2021-03-15 10:53:16 +01:00
3095255b7b
gnu: Add r-tmaptools.
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* gnu/packages/cran.scm (r-tmaptools): New variable.
2021-03-15 10:53:15 +01:00
82344f5936
gnu: Add r-stars.
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* gnu/packages/cran.scm (r-stars): New variable.
2021-03-15 10:53:15 +01:00
a1dd43e4cd
gnu: Add r-lwgeom.
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* gnu/packages/cran.scm (r-lwgeom): New variable.
2021-03-15 10:53:14 +01:00
5ce5e49c10
gnu: Add r-packcircles.
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* gnu/packages/cran.scm (r-packcircles): New variable.
2021-03-15 10:53:13 +01:00
5d719fe608
gnu: Add r-readtext.
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* gnu/packages/cran.scm (r-readtext): New variable.
2021-03-15 10:53:12 +01:00
6f688733b5
gnu: Add r-antiword.
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* gnu/packages/cran.scm (r-antiword): New variable.
2021-03-15 10:53:11 +01:00
275b7987c0
gnu: Add r-pdftools.
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* gnu/packages/cran.scm (r-pdftools): New variable.
2021-03-15 10:53:10 +01:00
52c70fb66e
gnu: Add r-qpdf.
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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
03af89bd9e
gnu: Add r-readods.
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* gnu/packages/cran.scm (r-readods): New variable.
2021-03-15 10:53:09 +01:00
cb360afd66
gnu: Add r-streamr
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* gnu/packages/cran.scm (r-streamr): New variable.
2021-03-15 10:53:08 +01:00
a64e355ea6
gnu: Add r-ndjson.
...
* gnu/packages/cran.scm (r-ndjson): New variable.
2021-03-15 10:53:07 +01:00
ee4ba54271
gnu: gzstream: Add PIC flag.
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* gnu/packages/compression.scm (gzstream) [arguments]: Add phase 'use-pic.
2021-03-15 10:53:04 +01:00
e415003202
gnu: Add r-striprtf.
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* gnu/packages/cran.scm (r-striprtf): New variable.
2021-03-15 10:53:03 +01:00
804fad34e8
gnu: Add r-textclean.
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* gnu/packages/cran.scm (r-textclean): New variable.
2021-03-15 10:53:02 +01:00
584c868fbd
gnu: Add r-english.
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* gnu/packages/cran.scm (r-english): New variable.
2021-03-15 10:53:01 +01:00
c3a1373c15
gnu: Add r-lexicon.
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* gnu/packages/cran.scm (r-lexicon): New variable.
2021-03-15 10:53:00 +01:00
bc82567b0b
gnu: Add r-syuzhet.
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* gnu/packages/cran.scm (r-syuzhet): New variable.
2021-03-15 10:52:59 +01:00
d332c5c7f2
gnu: Add r-textshape.
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* gnu/packages/cran.scm (r-textshape): New variable.
2021-03-15 10:52:58 +01:00
ed48898931
gnu: Add r-dtt.
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* gnu/packages/algebra.scm (r-dtt): New variable.
2021-03-15 10:52:57 +01:00
4bc1707dba
gnu: Add r-mgsub.
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* gnu/packages/cran.scm (r-mgsub): New variable.
2021-03-15 10:52:56 +01:00
ae807fdb37
gnu: Add r-qdapregex.
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* gnu/packages/cran.scm (r-qdapregex): New variable.
2021-03-15 10:52:55 +01:00
c4e826bbd2
gnu: Add r-esc.
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* gnu/packages/statistics.scm (r-esc): New variable.
2021-03-15 10:52:52 +01:00
d059485257
gnu: unzip: Remove redundant and unused "unzip-symlink.patch".
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This is a followup to commit 31d289a475
2021-03-14 19:16:17 -04:00
b082ea9406
gnu: OpenSSL: Refer to the version number in a more robust way.
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* 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
bb2427fa28
gnu: ImageMagick: Refer to the version number in a more robust way.
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* 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
Marius Bakke
Tobias Geerinckx-Rice
Ryan Prior via Guix-patches via
Morgan Smith
Nicolas Goaziou
Ludovic Courtès
Leo Famulari
Léo Le Bouter
qblade
Maxime Devos
Christopher Baines
Efraim Flashner
Oleg Pykhalov
Leo Prikler
LibreMiami
Mark H Weaver
Maxim Cournoyer
Kei Kebreau
Ricardo Wurmus
Stefan Reichör
zimoun
Tanguy Le Carrour
Lars-Dominik Braun