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Author SHA1 Message Date
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 1a265842e634656411bc7304c4648273f174f65e 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 feff80cec3c97a3df2c20d300be12d67f79d4f22 was right since while
the main license file wasnt altered to SSPL, some files in the tree contain
SSPL headers.

* gnu/packages/databases.scm (go-gopkg.in-mgo.v2): Remove.
* gnu/packages/databases.scm (mongo-tools): Remove.
* doc/guix.texi (mongodb-service-type): Remove.
* gnu/tests/databases.scm (%test-mongodb, %mongodb-os, run-mongodb-test):
Remove.
* gnu/services/databases.scm (mongodb-configuration, mongodb-configuration?,
mongodb-configuration-mongodb, mongodb-configuration-config-file,
mongodb-configuration-data-directory, mongodb-service-type,
%default-mongodb-configuration-file, %mongodb-accounts, mongodb-activation,
mongodb-shepherd-service): Remove.
* gnu/packages/databases.scm (mongodb): Remove.
 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 ab9629b7c91ff7d6392a03512cfe442823267777.

* 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 821e6439212f8e94580674eaaff2ce6752cd3b18 through
8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
 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