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75716 Commits (b09967bc587dd61c638da3d6fb5bbda7e87ed85c)

Author SHA1 Message Date
Ludovic Courtès 71f6acd28d
gnu-maintenance: Use (htmlprag) for 'latest-html-release'.
* guix/gnu-maintenance.scm (html->sxml): Remove.  Autoload (htmlprag)
instead.
* doc/guix.texi (Requirements): Mention 'guix refresh' for the Guile-Lib
dependency.
2021-03-17 12:03:24 +01:00
Ludovic Courtès 62a091368d
maint: Check whether Guile-zlib is recent enough.
This is a followup to a04aef2430.

* m4/guix.m4 (GUIX_CHECK_GUILE_ZLIB): New macro.
* configure.ac: Use it when checking for Guile-zlib.
2021-03-17 12:03:23 +01:00
Ludovic Courtès 0571aa7abf
doc: Define the term "profile".
Fixes <https://bugs.gnu.org/46803>.
Reported by Luis Felipe <luis.felipe.la@protonmail.com>.

* doc/guix.texi (Getting Started): Introduce the term "profile".
(Invoking guix package): Likewise.
2021-03-17 12:03:23 +01:00
Ludovic Courtès bc3896db25
daemon: Correctly handle '--discover' with no value.
Previously, we'd get:

  $ guix-daemon --discover
  error: basic_string::_M_construct null not valid

* nix/nix-daemon/guix-daemon.cc (parse_opt): Change second argument to
'settings.set' to properly handle case where ARG is NULL.
2021-03-17 12:03:23 +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
Florian Pelz 9ed2a26d04
news: Add ‘de’ translation. 2021-03-16 13:43:32 +00:00
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
Chris Marusich 341dfe7eda
syscalls: mounts: Fix a matching bug.
On some systems, the columns in /proc/self/mountinfo look like this:

23 28 0:21 / /proc rw,nosuid,nodev,noexec,relatime shared:11 - proc proc rw

Before this change, the mounts procedure was written with the assumption that
the type and source could always be found in columns 8 and 9, respectively.
However, the proc(5) man page explains that there can be zero or more optional
fields starting at column 7 (e.g., "shared:11" above), so this assumption is
false in some situations.

* guix/build/syscalls.scm (mounts): Update the match pattern to use ellipsis
to match zero or more optional fields followed by a single hyphen.  Remove the
trailing ellipsis, since multiple ellipses are not allowed in the same level.
The proc(5) man page indicates that there are no additional columns, so it is
probably OK to match an exact number of columns at the end like this.
2021-03-15 21:22:43 -07:00
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
Maxim Cournoyer 1ea2c82355
news: Add news entry about changes to the QEMU binfmt service.
* etc/news.scm: Add entry.
2021-03-15 18:03:16 -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