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39858 Commits

Author SHA1 Message Date
Marius Bakke 856e3f9cb4
gnu: KDE Plasma: Update to 5.14.5. 
* gnu/packages/kde-plasma.scm (libkscreen): Update to 5.14.5.
(libksysguard): Likewise.
[inputs]: Add KGLOBALACCEL and KIO.
 2019-02-12 23:49:02 +01:00
Marius Bakke fd11c0fd3d
gnu: KDE Frameworks: Update to 5.54.0. 
* gnu/packages/patches/kio-search-smbd-on-PATH.patch: Adjust context.
* gnu/packages/kde-frameworks.scm (kconfig): Update to 5.54.0.
[native-inputs]: Add DBUS.
[arguments]: Run tests with "dbus-launch".
(kio): Update to 5.54.1.
[inputs]: Add KCRASH.
(breeze-icons): Update to 5.54.0.
[arguments]: Remove.
(extra-cmake-modules, attica, bluez-qt, kapidox, karchive,
kcodecs, kcoreaddons, kdbusaddons, kdnssd, kguiaddons, ki18n, kidletime,
kirigami, kitemmodels, kitemviews, kplotting, ksyntaxhighlighting, kwayland,
kwidgetsaddons, kwindowsystem, modemmanager-qt, networkmanager-qt,
oxygen-icons, prison, qqc2-desktop-style, solid, sonnet, threadweaver,
kactivities, kauth, kcompletion, kcrash, kdoctools, kfilemetadata,
kimageformats, kjobwidgets, knotifications, kpackage, kpty, kunitconversion,
baloo, kactivities-stats, kbookmarks, kcmutils, kconfigwidgets, kdeclarative,
kded, kdesignerplugin, kdesu, kdewebkit, kemoticons, kglobalaccel,
kiconthemes, kinit, knewstuff, knotifyconfig, kparts, kpeople, krunner,
kservice, ktexteditor, ktextwidgets, kwallet, kxmlgui, kxmlrpcclient,
plasma-framework, kde-frameworkintegration, kdelibs4support, khtml, kjs,
kjsembed, kmediaplayer, kross): Update to 5.54.0.
 2019-02-12 23:49:02 +01:00
Marius Bakke cdf7fea183
gnu: Add copyright line for commit c1144c78ad. 
* gnu/packages/kde-plasma.scm: Add copyright header.
 2019-02-12 23:49:02 +01:00
Marius Bakke bec2a2e10e
gnu: Move KDE Plasma components to separate module. 
* gnu/packages/kde.scm (libkscreen, libksysguard): Move from here ...
* gnu/packages/kde-plasma.scm: ... to here.  New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
 2019-02-12 23:49:02 +01:00
Marius Bakke 60562ec26b
gnu: libjpeg: Use HTTPS URLs. 
* gnu/packages/image.scm (libjpeg, libjpeg-8)[source, home-page]: Use HTTPS.
 2019-02-12 23:49:02 +01:00
Brett Gilio be4d840cca
gnu: Add python-language-server. 
* gnu/packages/python-xyz.scm (python-language-server): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-02-12 23:30:17 +01:00
Brett Gilio 56f4ad47bd
gnu: Add python-docstyle. 
* gnu/packages/python-xyz.scm (python-docstyle): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-02-12 23:30:16 +01:00
Brett Gilio 346c87522e
gnu: Add python-jsonrpc-server. 
* gnu/packages/python-xyz.scm (python-jsonrpc-server): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-02-12 23:30:16 +01:00
Ludovic Courtès 2c880ef4e5
gnu: Add python-rope. 
* gnu/packages/python-xyz.scm (python-rope): New variable.

Co-authored-by: Brett Gilio <brettg@posteo.net>
 2019-02-12 23:30:16 +01:00
Brett Gilio afb2971506
gnu: python2-rope: Change comment to reflect partial python3 support 
* gnu/packages/python-xyz.scm (python2-rope): Change comment to reflect
  partial python 3 support

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-02-12 23:30:16 +01:00
Ludovic Courtès 201253674b
pull: Speed up the new/upgraded package computation. 
* guix/scripts/pull.scm (new/upgraded-packages): OLD no longer stores
all the versions of each package.  Remove 'vhash-fold*' call and reduce
the number of 'version>?' calls when computing UPGRADED.
 2019-02-12 23:30:16 +01:00
Ludovic Courtès cf0eacceb4
pull: Move profile comparison to 'new/upgraded-packages'. 
* guix/scripts/pull.scm (new/upgraded-packages): New procedure, with
code formerly in 'display-new/upgraded-packages'.
(display-new/upgraded-packages): Use it.
 2019-02-12 23:30:16 +01:00
Ludovic Courtès 739380542d
inferior: Add 'inferior-available-packages'. 
* guix/inferior.scm (inferior-available-packages): New procedure.
* tests/inferior.scm ("inferior-available-packages"): New test.
 2019-02-12 23:30:16 +01:00
Ludovic Courtès 46765f82db
pull: Use 'fold-available-packages' for the current package list. 
* guix/scripts/pull.scm (display-profile-news): Use
'fold-available-packages' instead of 'fold-packages' to compute OLD.
(profile-package-alist): Use 'inferior-available-packages'.
 2019-02-12 23:30:16 +01:00
Leo Famulari e2760d1a8b
gnu: Flatpak: Update to 1.2.3 [security fixes]. 
From 'NEWS' in the source distribution:

The CVE-2019-5736 runc vulnerability is about using /proc/self/exe
to modify the host side binary from the sandbox. This mostly does not
affect flatpak since the flatpak sandbox is not run with root permissions.
However, there is one case (running the apply_extra script for system
installs) where this happens, so this release contains a fix for that.

 * Don't expose /proc in apply_extra script sandbox.

* gnu/packages/package-management.scm (flatpak): Update to 1.2.3.
 2019-02-12 17:14:09 -05:00
Gábor Boskovits dbf87ecb52
gnu: Add frrouting. 
* gnu/packages/networking.scm (frrouting): New variable.
 2019-02-12 22:24:27 +01:00
Leo Famulari ea7cddaac7
gnu: Docker: Update to 18.09.2. 
* gnu/packages/docker.scm (%docker-version, docker, docker-cli): Update to
18.09.2.
(docker)[arguments]: Adjust to the Debian-specific 'iptables-legacy' lookup in
the 'patch-paths' phase.
 2019-02-12 12:53:12 -05:00
Leo Famulari ce4593ec4c
gnu: runc: Update to 1.0.0-rc6 [fixes CVE-2019-5736]. 
* gnu/packages/virtualization.scm (runc): Update to 1.0.0-rc6.
[source]: Use a descriptive file-name. Add 'runc-CVE-2019-5736.patch'
* gnu/packages/patches/runc-CVE-2019-5736.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2019-02-12 12:53:12 -05:00
Tobias Geerinckx-Rice 571a01d8fa
gnu: lzlib: Remove minilzip comment. 
It lacks lzip's dependency on libstdc++.so and libm.so and may have its
uses.

* gnu/packages/compression.scm (lzlib): Don't judge.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 2990422377
gnu: lzlib: Update to 1.11. 
* gnu/packages/compression.scm (lzlib): Update to 1.11.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 76b2f08468
gnu: lzlib: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 11b1c71d2e
gnu: clzip: Update to 1.11. 
* gnu/packages/compression.scm (clzip): Update to 1.11.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 39e5d3b68d
gnu: clzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice 9f4f085f9b
gnu: lunzip: Update to 1.11. 
* gnu/packages/compression.scm (lunzip): Update to 1.11.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice a28cd47702
gnu: lunzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice ff0e1eed32
gnu: plzip: Update to 1.8. 
* gnu/packages/compression.scm (plzip): Update to 1.8.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice 894669a787
gnu: plzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice b099b4a75a
gnu: lziprecover: Update to 1.21. 
* gnu/packages/compression.scm (lziprecover): Update to 1.21.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice f6145bb652
gnu: lziprecover: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice da93d42413
gnu: perl-dbi: Update to 1.642. 
* gnu/packages/databases.scm (perl-dbi): Update to 1.642.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice 245e7a68e7
gnu: kyotocabinet: Update to 1.2.77. 
* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice e9bdef5fb4
gnu: os-prober: Update to 1.77. 
* gnu/packages/bootloaders.scm (os-prober): Update to 1.77.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice 51a8fc8b42
gnu: feh: Update to 3.1.2. 
* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
 2019-02-12 17:38:21 +01:00
Maxim Cournoyer 155194d97d
gnu: python-pybedtools: Update to 0.8.0 and fix build. 
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.
 2019-02-12 17:16:05 +01:00
Efraim Flashner b856a78c94
gnu: efilinux: Set ARCH variable on some architectures. 
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.
 2019-02-12 18:08:19 +02:00
Ricardo Wurmus 385d7546e1
gnu: Add cnvkit. 
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
 2019-02-12 15:41:02 +01:00
Ricardo Wurmus c18dccffa2
gnu: Add r-dnacopy. 
* gnu/packages/bioconductor.scm (r-dnacopy): New variable.
 2019-02-12 15:41:02 +01:00
Ricardo Wurmus ab61ce3730
gnu: python-reportlab: Update to 3.5.13. 
* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13.
[inputs]: Add freetype.
 2019-02-12 15:40:58 +01:00
Efraim Flashner c86b5f1b9b
gnu: glibc@2.27: fix CVE-2018-11236, CVE-2018-11237. 
* 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.
 2019-02-12 09:08:13 +02:00
Tobias Geerinckx-Rice d4c95a237c
gnu: parallel: Update to 20190122. 
* gnu/packages/parallel.scm (parallel): Update to 20190122.
 2019-02-12 02:33:55 +01:00
Tobias Geerinckx-Rice a661af5c9a
gnu: maven-resolver-api: Don't use unstable tarball. 
* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:55 +01:00
Tobias Geerinckx-Rice 57e3f06bbd
gnu: multipath-tools: Update to 0.7.9. 
* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9.
 2019-02-12 02:33:55 +01:00
Tobias Geerinckx-Rice 34920d2adf
gnu: websockify: Don't use unstable tarball. 
* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:55 +01:00
Tobias Geerinckx-Rice 2772debc74
gnu: libyajl: Don't use unstable tarball. 
* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:54 +01:00
Tobias Geerinckx-Rice 3e3414efd4
gnu: rapidjson: Don't use unstable tarball. 
* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:54 +01:00
Tobias Geerinckx-Rice 082504addf
gnu: qjson: Don't use unstable tarball. 
* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:54 +01:00
Tobias Geerinckx-Rice 20ab34c16f
gnu: fcgiwrap: Don't use unstable tarball. 
* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:54 +01:00
Tobias Geerinckx-Rice bff44abb14
gnu: mod-wsgi: Don't use unstable tarball. 
* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2019-02-12 02:33:53 +01:00
Leo Famulari 95c910f499
gnu: Guix: Update snapshot to 0.16.0-10.2637cfd. 
Fixes <https://bugs.gnu.org/34444>.

*  gnu/packages/package-management.scm (guix): Update to 0.16.0-10.2637cfd.
 2019-02-11 18:13:29 -05:00
Ludovic Courtès 2637cfd7a4
Avoid name clash with 'build' from (guix store) and (guix status). 
Since commit 976ef2d978, (guix status)
exports 'build', which clashes with 'build' from (guix store).

* build-aux/run-system-tests.scm: Select 'with-status-verbosity'
from (guix status).
* guix/scripts/archive.scm: Likewise.
* guix/scripts/build.scm: Likewise.
* guix/scripts/copy.scm: Likewise.
* guix/scripts/environment.scm: Likewise.
* guix/scripts/pack.scm: Likewise.
* guix/scripts/package.scm: Likewise.
* guix/scripts/pull.scm: Likewise.
* guix/scripts/system.scm: Likewise.
 2019-02-11 23:23:28 +01:00