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2019-02-13gnu: duperemove: Update to 0.11.1.Tobias Geerinckx-Rice
* gnu/packages/disk.scm (duperemove): Update to 0.11.1.
2019-02-12gnu: netpbm: Fix a hard-coded path.Leo Famulari
Fixes <https://bugs.gnu.org/24735>. * gnu/packages/netpbm.scm (netpbm)[arguments]: Patch a path in the 'configure' phase.
2019-02-12gnu: emacs-biblio: Update to 0.2.Paul Garlick
* gnu/packages/emacs-xyz.scm (emacs-biblio): Update to 0.2. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-13gnu: LXQt: Adjust imports for KDE move.Marius Bakke
This is a follow-up to commit bec2a2e10e199d6ee671ec5713bd103242e91b62. * gnu/packages/lxqt.scm: Import (gnu packages kde-plasma).
2019-02-12gnu: Add font-adobe-source-serif-pro.Jens M
* gnu/packages/fonts.scm (font-adobe-source-serif-pro): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-12gnu: Add font-adobe-source-sans-pro.Jens M
* gnu/packages/fonts.scm (font-adobe-source-sans-pro): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-13gnu: trezor-agent: Update 0.10.0.Vagrant Cascadian
Fixes <https://bugs.gnu.org/34377>. * gnu/packages/finance.scm (trezor-agent): Update to 0.10.0. [arguments]<#:phases>[fixup-agent-py]: New phase. [native-inputs]: Add python-hidapi. [home-page]: Use https url.
2019-02-13gnu: python-trezor-agent: Update to 0.13.0.Vagrant Cascadian
* gnu/packages/finance.scm (python-trezor-agent): Update to 0.13.0. [propagated-inputs]: Add python-configargparse, python-daemon, python-docutils, python-mnemonic, python-pymsgbox, python-wheel. [native-inputs]: Add gnupg. [synopsis]: Generalize description to hardware wallets. [arguments]<#:phases>[remove-requires-backports-shutil-which]: New phase.
2019-02-12gnu: Add kscreenlocker.Hartmut Goebel
* gnu/packages/kde-plasma.scm (kscreenlocker): New public variable. Co-authored-by: Marius Bakke <mbakke@fastmail.com>
2019-02-12gnu: Add kdecoration.Hartmut Goebel
* gnu/packages/kde-plasma.scm (kdecoration): New public variable. Co-authored-by: Marius Bakke <mbakke@fastmail.com>
2019-02-12gnu: KDE Plasma: Update to 5.14.5.Marius Bakke
* gnu/packages/kde-plasma.scm (libkscreen): Update to 5.14.5. (libksysguard): Likewise. [inputs]: Add KGLOBALACCEL and KIO.
2019-02-12gnu: KDE Frameworks: Update to 5.54.0.Marius Bakke
* 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.
2019-02-12gnu: Add copyright line for commit c1144c78ad853dc1bfbd6f32a6.Marius Bakke
* gnu/packages/kde-plasma.scm: Add copyright header.
2019-02-12gnu: Move KDE Plasma components to separate module.Marius Bakke
* 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.
2019-02-12gnu: libjpeg: Use HTTPS URLs.Marius Bakke
* gnu/packages/image.scm (libjpeg, libjpeg-8)[source, home-page]: Use HTTPS.
2019-02-12gnu: Add python-language-server.Brett Gilio
* gnu/packages/python-xyz.scm (python-language-server): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-02-12gnu: Add python-docstyle.Brett Gilio
* gnu/packages/python-xyz.scm (python-docstyle): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-02-12gnu: Add python-jsonrpc-server.Brett Gilio
* gnu/packages/python-xyz.scm (python-jsonrpc-server): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-02-12gnu: Add python-rope.Ludovic Courtès
* gnu/packages/python-xyz.scm (python-rope): New variable. Co-authored-by: Brett Gilio <brettg@posteo.net>
2019-02-12gnu: python2-rope: Change comment to reflect partial python3 supportBrett Gilio
* gnu/packages/python-xyz.scm (python2-rope): Change comment to reflect partial python 3 support Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-02-12pull: Speed up the new/upgraded package computation.Ludovic Courtès
* 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.
2019-02-12pull: Move profile comparison to 'new/upgraded-packages'.Ludovic Courtès
* guix/scripts/pull.scm (new/upgraded-packages): New procedure, with code formerly in 'display-new/upgraded-packages'. (display-new/upgraded-packages): Use it.
2019-02-12inferior: Add 'inferior-available-packages'.Ludovic Courtès
* guix/inferior.scm (inferior-available-packages): New procedure. * tests/inferior.scm ("inferior-available-packages"): New test.
2019-02-12pull: Use 'fold-available-packages' for the current package list.Ludovic Courtès
* 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'.
2019-02-12gnu: Flatpak: Update to 1.2.3 [security fixes].Leo Famulari
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.
2019-02-12gnu: Add frrouting.Gábor Boskovits
* gnu/packages/networking.scm (frrouting): New variable.
2019-02-12gnu: Docker: Update to 18.09.2.Leo Famulari
* 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.
2019-02-12gnu: runc: Update to 1.0.0-rc6 [fixes CVE-2019-5736].Leo Famulari
* 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.
2019-02-12gnu: lzlib: Remove minilzip comment.Tobias Geerinckx-Rice
It lacks lzip's dependency on libstdc++.so and libm.so and may have its uses. * gnu/packages/compression.scm (lzlib): Don't judge.
2019-02-12gnu: lzlib: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lzlib): Update to 1.11.
2019-02-12gnu: lzlib: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME.
2019-02-12gnu: clzip: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (clzip): Update to 1.11.
2019-02-12gnu: clzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME.
2019-02-12gnu: lunzip: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lunzip): Update to 1.11.
2019-02-12gnu: lunzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME.
2019-02-12gnu: plzip: Update to 1.8.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (plzip): Update to 1.8.
2019-02-12gnu: plzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME.
2019-02-12gnu: lziprecover: Update to 1.21.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lziprecover): Update to 1.21.
2019-02-12gnu: lziprecover: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME.
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.
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