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2019-02-12gnu: perl-dbi: Update to 1.642.Tobias Geerinckx-Rice
* gnu/packages/databases.scm (perl-dbi): Update to 1.642.
2019-02-12gnu: kyotocabinet: Update to 1.2.77.Tobias Geerinckx-Rice
* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77.
2019-02-12gnu: os-prober: Update to 1.77.Tobias Geerinckx-Rice
* gnu/packages/bootloaders.scm (os-prober): Update to 1.77.
2019-02-12gnu: feh: Update to 3.1.2.Tobias Geerinckx-Rice
* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
2019-02-12gnu: python-pybedtools: Update to 0.8.0 and fix build.Maxim Cournoyer
From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer <maxim.cournoyer@gmail.com> Date: Sun, 10 Feb 2019 23:39:25 -0500 Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0. [phases]{disable-broken-tests}: Do not disable "test_issue_157" and "test_to_dataframe" tests. Disable the "test_getting_example_beds". {remove-cython-generated-files}: Add phase. {generate-cython-extensions}: Add phase. {check}: Move from python2-pybedtools to here. Add a scripts subdirectory of the build directory to the PATH, so that the tests can call them. Invoke pytest rather than nosetests. [modules]: Move from python2-pybedtools to here. [propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26. [native-inputs]: Replace python-nose by python-pytest and add python-psutil.
2019-02-12gnu: efilinux: Set ARCH variable on some architectures.Efraim Flashner
Even with this patch efilinux does not build for arm*. * gnu/packages/efi.scm (efilinux)[arguments]: On armhf-linux and aarch64-linux set the ARCH variable apropriately.
2019-02-12gnu: Add cnvkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12gnu: Add r-dnacopy.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dnacopy): New variable.
2019-02-12gnu: python-reportlab: Update to 3.5.13.Ricardo Wurmus
* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13. [inputs]: Add freetype.
2019-02-12gnu: glibc@2.27: fix CVE-2018-11236, CVE-2018-11237.Efraim Flashner
* gnu/packages/base.scm (glibc@2.27)[sources]: Add patches. [properties]: New field, mark CVE-2017-18269 fixed. * gnu/packages/patches/glibc-CVE-2018-11236.patch, gnu/packages/patches/glibc-CVE-2018-11237.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them.
2019-02-12gnu: parallel: Update to 20190122.Tobias Geerinckx-Rice
* gnu/packages/parallel.scm (parallel): Update to 20190122.
2019-02-12gnu: maven-resolver-api: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: multipath-tools: Update to 0.7.9.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9.
2019-02-12gnu: websockify: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: libyajl: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: rapidjson: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: qjson: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: fcgiwrap: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: mod-wsgi: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-11gnu: Guix: Update snapshot to 0.16.0-10.2637cfd.Leo Famulari
Fixes <https://bugs.gnu.org/34444>. * gnu/packages/package-management.scm (guix): Update to 0.16.0-10.2637cfd.
2019-02-11pack, vm: Fix incorrect use of 'package-transitive-propagated-inputs'.Ludovic Courtès
In practice the error was not triggered because 'package-transitive-propagated-inputs' currently returns the empty list for these two packages. * guix/scripts/pack.scm (gcrypt-sqlite3&co): Remove labels from the result. * gnu/system/vm.scm (gcrypt-sqlite3&co): Likewise.
2019-02-11gnu: guile-picture-language: Update to 0-2.1ea8b78.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78.
2019-02-11gnu: disorderfs: Update to 0.5.6.Vagrant Cascadian
* gnu/packages/file-systems (disorderfs): Update to 0.5.6. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-11gnu: diffoscope: Update to 111.Vagrant Cascadian
* gnu/packages/package-management (diffoscope): Update to 111. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-11gnu: python-cython: Update to 0.29.5.Andreas Enge
* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5.
2019-02-11gnu: pixman: Update source URI.Marius Bakke
* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS.
2019-02-11gnu: python-django: Update to 1.11.20 [fixes CVE-2019-6975].Marius Bakke
* gnu/packages/django.scm (python-django): Update to 1.11.20.
2019-02-11gnu: ffmpeg: Update to 4.1.1.Marius Bakke
* gnu/packages/video.scm (ffmpeg): Update to 4.1.1.
2019-02-11gnu: miniupnpc: Update to 2.1.20190210.Marius Bakke
* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190210.
2019-02-11gnu: lv2: Update to 1.16.0.Marius Bakke
* gnu/packages/audio.scm (lv2): Update to 1.16.0. [arguments]: Remove #:python. (lv2-devel): Remove variable. * gnu/packages/music.scm (ingen)[inputs]: Change LV2-DEVEL to LV2.
2019-02-11gnu: vlc: Use libvpx-1.7.Danny Milosavljevic
Fixes <https://bugs.gnu.org/34439>. * gnu/packages/video.scm (vlc)[inputs]: Remove libvpx. Add libvpx-1.7.
2019-02-11services: docker: Make shepherd service also require "dbus-system",Danny Milosavljevic
"elogind" and "udev". Fixes <https://bugs.gnu.org/34333>. * gnu/services/docker.scm (docker-shepherd-service): Require "dbus-system", "elogind" and "udev".
2019-02-11gnu: gama: Update to 2.03.Kei Kebreau
* gnu/packages/gps.scm (gama): Update to 2.03.
2019-02-11services: docker: Make shepherd service require "networking".Danny Milosavljevic
Fixes <https://bugs.gnu.org/34333>. * gnu/services/docker.scm (docker-shepherd-service): Require "networking".
2019-02-11gnu: gloox: Update to 1.0.22.Vagrant Cascadian
* gnu/packages/messaging.scm (gloox): Update to 1.0.22.
2019-02-11gnu: python-ecpy: Update to 0.10.0.Vagrant Cascadian
* gnu/packages/python-crypto.scm (python-ecpy): Update to 0.10.0.
2019-02-11gnu: python-pycryptodome: Update to 3.7.3.Vagrant Cascadian
* gnu/packages/python-crypto (python-cryptodome): Update to 3.7.3.
2019-02-11gnu: u-boot-novena: Allow booting from raw device offset.Vagrant Cascadian
* gnu/packages/bootloaders.scm (u-boot-novena): Disable loading u-boot.img from a partition.
2019-02-11gnu: Add python-pymsgbox.Vagrant Cascadian
* gnu/packages/python-xyz.scm (python-pymsgbox): New variable.
2019-02-11gnu: Add python-daemon.Vagrant Cascadian
* gnu/packages/python-xyz.scm (python-daemon): New variable.
2019-02-11gnu: dmenu: Update to 4.9.Leo Famulari
* gnu/packages/suckless.scm (dmenu): Update to 4.9.
2019-02-10gnu: Dropbear: Add a comment about bundled libraries.Leo Famulari
* gnu/packages/ssh.scm (dropbear): Comment.
2019-02-10gnu: curl: Update to 7.64.0 [fixes CVE-2018-16890 and CVE-2019-{3822,3823}].Leo Famulari
* gnu/packages/curl.scm (curl)[replacement]: New field. (curl-7.64.0): New variable.
2019-02-10gnu: Dovecot: Update to 2.3.4.1 [fixes CVE-2019-3814].Leo Famulari
* gnu/packages/mail.scm (dovecot): Update to 2.3.4.1.
2019-02-10gnu: Syncthing: Update to 1.0.1.Leo Famulari
* gnu/packages/syncthing.scm (syncthing): Update to 1.0.1.
2019-02-10gnu: MPD: Update to 0.21.4.Leo Famulari
We no longer install any systemd unit files for MPD because this is no longer supported upstream as a matter of policy or via MPD's build system. [0] Specifically, they don't support using MPD with systemd unless MPD was linked with libsystemd. The unit files are only built when this is the case. [0] <https://github.com/MusicPlayerDaemon/MPD/issues/124#issuecomment-334930456> * gnu/packages/mpd.scm (mpd): Update to 0.21.4. [build-system]: Use meson-build-system. [native-inputs]: Add gcc-8, gcc-8:lib, and python-sphinx. [arguments]: Add a 'expand-C++-include-path' phase. Remove the 'install-service-files' phase. Make sure to build the documentation.
2019-02-10services: gdm: Disable debugging output.Ludovic Courtès
* gnu/services/xorg.scm (gdm-etc-service)[gdm-configuration-file]: Comment out debugging setting.
2019-02-10gnu: gnome-shell: Customize the GDM log-in screen.Ludovic Courtès
* gnu/packages/patches/gnome-shell-theme.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnome.scm (gnome-shell)[source](patches, modules) (snippet): New fields. [arguments]: Add 'rebuild-css' phase. [native-inputs]: Add RUBY-SASS.
2019-02-10artwork: Update snapshot to e951905.Ludovic Courtès
* gnu/artwork.scm (%artwork-repository): Update to e951905.
2019-02-10gnu: gnome: Remove '--disable-acceleration-check' flag from 'gnome.desktop'.Ludovic Courtès
With this change the GNOME session is now listed in the log-in screen of GDM. * gnu/packages/gnome.scm (gnome-session)[arguments]: Remove 'disable-hardware-acceleration-check' phase. That phase was apparently no longer needed. Furthermore, GDM expects 'TryExec' to be a file name, not a file name followed by arguments; thus, the option led GDM to discard 'gnome.desktop' with "GdmSession: Command not found: TryExec".
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