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Commit Graph

67303 Commits

Author SHA1 Message Date
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