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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
728c90862e
gnu-maintenance: Add a timeout on FTP connection establishment. 
* guix/gnu-maintenance.scm (latest-ftp-release): Pass #:timeout to
'ftp-open'.
 2021-03-17 12:03:25 +01:00
Ludovic Courtès
29330b57e2
gnu-maintenance: Remove unused parameters of 'latest-ftp-release'. 
* guix/gnu-maintenance.scm (latest-ftp-release): Remove #:ftp-open, #:ftp-close,
and #:keep-file?.
 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
Ludovic Courtès
af9af2180e
gnu-maintenance: Add 'generic-html' updater. 
This brings total updater coverage, as reported by 'guix refresh
--list-updaters', from 78% to 88.3%.  Among many other things, it covers
freedesktop.org packages.

* guix/gnu-maintenance.scm (html-updatable-package?)
(latest-html-updatable-release): New procedures.
(%generic-html-updater): New variable.
* doc/guix.texi (Invoking guix refresh): Document it.
 2021-03-17 12:03:24 +01:00
Ludovic Courtès
1d5a946ce5
gnu-maintenance: 'latest-html-release' better computes version number. 
* guix/gnu-maintenance.scm (latest-html-release): Use 'tarball->version'
rather than 'package-name->name+version' to extract the version number.
This fixes problems with packages like 'netsurf' and 'libdom' that have
"-src" in their tarball name, where "src" would be taken as the new
version number.
 2021-03-17 12:03:24 +01:00
Ludovic Courtès
99f42e14d4
gnu-maintenance: 'latest-html-release' can determine signature file name. 
* guix/gnu-maintenance.scm (latest-html-release): #:file->signature
defaults to #f.
[file->signature/guess]: New procedure.
[url->release]: Use it when FILE->SIGNATURE is #f.
Introduce 'links' variable.
(url-prefix-rewrite): Check whether URL is true before calling
'string-prefix?'.
(latest-savannah-release): Adjust comment about detached signatures.
 2021-03-17 12:03:24 +01:00
Ludovic Courtès
9e75b31b39
gnu-maintenance: 'release-file?' rejects checksum files. 
* guix/gnu-maintenance.scm (release-file?): Reject ".md5sum",
".sha1sum", and ".sha256sum".
 2021-03-17 12:03:24 +01:00
Ludovic Courtès
db69ebb9de
gnu-maintenance: 'latest-html-release' considers non-relative URLs. 
* guix/gnu-maintenance.scm (latest-html-release): Allow for URL to be an
arbitrary URL rather than a relative URL reference.
 2021-03-17 12:03:24 +01:00
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