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* gnu: perl-dbi: Update to 1.642.•••* gnu/packages/databases.scm (perl-dbi): Update to 1.642. Tobias Geerinckx-Rice2019-02-121-2/+2
* gnu: kyotocabinet: Update to 1.2.77.•••* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77. Tobias Geerinckx-Rice2019-02-121-3/+3
* gnu: os-prober: Update to 1.77.•••* gnu/packages/bootloaders.scm (os-prober): Update to 1.77. Tobias Geerinckx-Rice2019-02-121-6/+6
* gnu: feh: Update to 3.1.2.•••* gnu/packages/image-viewers.scm (feh): Update to 3.1.2. Tobias Geerinckx-Rice2019-02-121-3/+3
* 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. Maxim Cournoyer2019-02-121-47/+67
* 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. Efraim Flashner2019-02-121-1/+9
* gnu: Add cnvkit.•••* gnu/packages/bioinformatics.scm (cnvkit): New variable. Ricardo Wurmus2019-02-121-0/+36
* gnu: Add r-dnacopy.•••* gnu/packages/bioconductor.scm (r-dnacopy): New variable. Ricardo Wurmus2019-02-121-0/+23
* gnu: python-reportlab: Update to 3.5.13.•••* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13. [inputs]: Add freetype. Ricardo Wurmus2019-02-121-2/+4
* 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. Efraim Flashner2019-02-124-1/+210
* gnu: parallel: Update to 20190122.•••* gnu/packages/parallel.scm (parallel): Update to 20190122. Tobias Geerinckx-Rice2019-02-121-3/+3
* gnu: maven-resolver-api: Don't use unstable tarball.•••* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-4/+8
* gnu: multipath-tools: Update to 0.7.9.•••* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9. Tobias Geerinckx-Rice2019-02-121-5/+5
* gnu: websockify: Don't use unstable tarball.•••* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-5/+6
* gnu: libyajl: Don't use unstable tarball.•••* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-5/+6
* gnu: rapidjson: Don't use unstable tarball.•••* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-6/+6
* gnu: qjson: Don't use unstable tarball.•••* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-7/+7
* gnu: fcgiwrap: Don't use unstable tarball.•••* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-7/+7
* gnu: mod-wsgi: Don't use unstable tarball.•••* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-121-7/+7
* 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. Leo Famulari2019-02-111-3/+3
* Avoid name clash with 'build' from (guix store) and (guix status).•••Since commit 976ef2d97887d16eab8d4eb9dad811786b04d690, (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. Ludovic Courtès2019-02-119-9/+9
* pack, vm: Fix incorrect use of 'package-transitive-propagated-inputs'.•••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. Ludovic Courtès2019-02-112-3/+7
* git: Add an exception printer for 'git-error'.•••* guix/git.scm (print-git-error): New procedure. <top level>: Call 'set-exception-printer!'. Ludovic Courtès2019-02-111-0/+8
* ui: Always print the exception upon load errors.•••Fixes <https://bugs.gnu.org/34402>. Reported by <pkill9@runbox.com>. Previously 'display-error' could be called with the wrong number of arguments (e.g., for 'git-error' exceptions), and thus nothing at all was displayed. * guix/ui.scm (report-load-error): Check whether ARGS matches the parameters for 'display-error' and call 'print-exception' otherwise. Ludovic Courtès2019-02-111-2/+9
* status: Erase the current line upon new builds or downloads.•••* guix/status.scm (print-build-event): Add 'erase-current-line*' call upon 'build-started, 'substituter-started, 'download-started. Ludovic Courtès2019-02-111-0/+3
* HACKING: Update key server.•••* HACKING (Commit Access): Recommend pool.sks-keyservers.net. Ludovic Courtès2019-02-111-3/+4
* gnu: guile-picture-language: Update to 0-2.1ea8b78.•••* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78. Ricardo Wurmus2019-02-111-3/+3
* gnu: disorderfs: Update to 0.5.6.•••* gnu/packages/file-systems (disorderfs): Update to 0.5.6. Signed-off-by: Leo Famulari <leo@famulari.name> Vagrant Cascadian2019-02-111-2/+2
* gnu: diffoscope: Update to 111.•••* gnu/packages/package-management (diffoscope): Update to 111. Signed-off-by: Leo Famulari <leo@famulari.name> Vagrant Cascadian2019-02-111-2/+2
* gnu: python-cython: Update to 0.29.5.•••* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5. Andreas Enge2019-02-111-3/+3
* gnu: pixman: Update source URI.•••* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS. Marius Bakke2019-02-111-1/+1
* gnu: python-django: Update to 1.11.20 [fixes CVE-2019-6975].•••* gnu/packages/django.scm (python-django): Update to 1.11.20. Marius Bakke2019-02-111-2/+2
* gnu: ffmpeg: Update to 4.1.1.•••* gnu/packages/video.scm (ffmpeg): Update to 4.1.1. Marius Bakke2019-02-111-2/+2
* gnu: miniupnpc: Update to 2.1.20190210.•••* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190210. Marius Bakke2019-02-111-2/+2
* gnu: lv2: Update to 1.16.0.•••* 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. Marius Bakke2019-02-112-21/+3
* gnu: vlc: Use libvpx-1.7.•••Fixes <https://bugs.gnu.org/34439>. * gnu/packages/video.scm (vlc)[inputs]: Remove libvpx. Add libvpx-1.7. Danny Milosavljevic2019-02-111-1/+1
* services: docker: Make shepherd service also require "dbus-system",•••"elogind" and "udev". Fixes <https://bugs.gnu.org/34333>. * gnu/services/docker.scm (docker-shepherd-service): Require "dbus-system", "elogind" and "udev". Danny Milosavljevic2019-02-111-1/+4
* gnu: gama: Update to 2.03.•••* gnu/packages/gps.scm (gama): Update to 2.03. Kei Kebreau2019-02-111-2/+2
* services: docker: Make shepherd service require "networking".•••Fixes <https://bugs.gnu.org/34333>. * gnu/services/docker.scm (docker-shepherd-service): Require "networking". Danny Milosavljevic2019-02-111-1/+1
* gnu: gloox: Update to 1.0.22.•••* gnu/packages/messaging.scm (gloox): Update to 1.0.22. Vagrant Cascadian2019-02-111-2/+2
* gnu: python-ecpy: Update to 0.10.0.•••* gnu/packages/python-crypto.scm (python-ecpy): Update to 0.10.0. Vagrant Cascadian2019-02-111-2/+2
* gnu: python-pycryptodome: Update to 3.7.3.•••* gnu/packages/python-crypto (python-cryptodome): Update to 3.7.3. Vagrant Cascadian2019-02-111-2/+2
* gnu: u-boot-novena: Allow booting from raw device offset.•••* gnu/packages/bootloaders.scm (u-boot-novena): Disable loading u-boot.img from a partition. Vagrant Cascadian2019-02-111-1/+19
* gnu: Add python-pymsgbox.•••* gnu/packages/python-xyz.scm (python-pymsgbox): New variable. Vagrant Cascadian2019-02-111-0/+34
* gnu: Add python-daemon.•••* gnu/packages/python-xyz.scm (python-daemon): New variable. Vagrant Cascadian2019-02-111-0/+51
* gnu: dmenu: Update to 4.9.•••* gnu/packages/suckless.scm (dmenu): Update to 4.9. Leo Famulari2019-02-111-2/+2
* gnu: Dropbear: Add a comment about bundled libraries.•••* gnu/packages/ssh.scm (dropbear): Comment. Leo Famulari2019-02-101-0/+3
* gnu: curl: Update to 7.64.0 [fixes CVE-2018-16890 and CVE-2019-{3822,3823}].•••* gnu/packages/curl.scm (curl)[replacement]: New field. (curl-7.64.0): New variable. Leo Famulari2019-02-101-0/+14
* gnu: Dovecot: Update to 2.3.4.1 [fixes CVE-2019-3814].•••* gnu/packages/mail.scm (dovecot): Update to 2.3.4.1. Leo Famulari2019-02-101-3/+4
* gnu: Syncthing: Update to 1.0.1.•••* gnu/packages/syncthing.scm (syncthing): Update to 1.0.1. Leo Famulari2019-02-101-2/+2
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