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Author SHA1 Message Date
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
Ludovic Courtès 910d0121a8
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.
 2019-02-11 23:23:28 +01:00
Ludovic Courtès 1d8b10d00f
git: Add an exception printer for 'git-error'. 
* guix/git.scm (print-git-error): New procedure.
<top level>: Call 'set-exception-printer!'.
 2019-02-11 23:23:28 +01:00
Ludovic Courtès 70a50305c4
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.
 2019-02-11 23:23:28 +01:00
Ludovic Courtès 5ea206a8a9
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.
 2019-02-11 23:23:27 +01:00
Ludovic Courtès 6701edbfad
HACKING: Update key server. 
* HACKING (Commit Access): Recommend pool.sks-keyservers.net.
 2019-02-11 23:23:27 +01:00
Ricardo Wurmus 8d11b6ddb8
gnu: guile-picture-language: Update to 0-2.1ea8b78. 
* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78.
 2019-02-11 23:03:35 +01:00
Vagrant Cascadian 75d12c40f7
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>
 2019-02-11 16:54:37 -05:00
Vagrant Cascadian 295de8cc1a
gnu: diffoscope: Update to 111. 
* gnu/packages/package-management (diffoscope): Update to 111.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-02-11 16:54:37 -05:00
Andreas Enge fa8ffaa0df
gnu: python-cython: Update to 0.29.5. 
* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5.
 2019-02-11 21:20:41 +01:00
Marius Bakke 63d4ef52eb
gnu: Remove GCC < 7 workarounds. 
* gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Remove GCC-7.
[arguments]: Adjust accordingly.
* gnu/packages/games.scm (openrct2): Likewise.
* gnu/packages/linux.scm (make-linux-libre): Likewise.
* gnu/packages/mpd.scm (mpd): Likewise.
* gnu/packages/storage.scm (ceph): Likewise.
 2019-02-11 19:49:27 +01:00
Marius Bakke f85ca6eda0
gnu: Remove WebKitGTK@2.20. 
* gnu/packages/gnome.scm (eolie, epiphany)[native-inputs]: Remove GCC-7.
[inputs]: Change WEBKITGTK-2.22 to WEBKITGTK.
[arguments]: Adjust accordingly.
* gnu/packages/web-browsers.scm (next-gtk-webkit): Likewise.
* gnu/packages/webkit.scm (webkitgtk): Update to 2.22.6.
(webkitgtk-2.22): Remove variable.
 2019-02-11 19:48:32 +01:00
Marius Bakke 66679ab978
gnu: libreoffice.scm: Fix build failures with GCC7. 
* gnu/packages/libreoffice.scm (libwpd, libcmis, libpagemaker)[arguments]: Add
"--disable-werror" to #:configure-flags.
 2019-02-11 19:48:32 +01:00
Marius Bakke 4e546e546d
gnu: libxau: Update to 1.0.9. 
* gnu/packages/xorg.scm (libxau): Update to 1.0.9.
 2019-02-11 19:48:32 +01:00
Marius Bakke 709fdfc21e
gnu: libsm: Update to 1.2.3. 2019-02-11 19:48:32 +01:00
Marius Bakke 0b7c0b699d
gnu: libx11: Update to 1.6.7. 
* gnu/packages/xorg.scm (libx11): Update to 1.6.7.
 2019-02-11 19:48:32 +01:00
Marius Bakke 9df397508d
gnu: poppler: Update to 0.74.0. 
* gnu/packages/patches/scribus-poppler-0.73.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/scribus.scm (scribus)[source](patches): Add it.
* gnu/packages/pdf.scm (poppler): Update to 0.74.0.
[arguments]: Adjust renamed configure flag.
* gnu/packages/tex.scm (texlive-bin)[arguments]: Add phase 'use-code-for-even-newer-poppler'.
 2019-02-11 19:48:31 +01:00
Marius Bakke 35b259eed0
gnu: pixman: Update to 0.38.0. 
* gnu/packages/xdisorg.scm (pixman): Update to 0.38.0.
 2019-02-11 19:48:31 +01:00
Marius Bakke fe82194394
gnu: gdbm: Update to 1.18.1. 
* gnu/packages/dbm.scm (gdbm): Update to 1.18.1.
 2019-02-11 19:48:31 +01:00
Marius Bakke 7d9ca5c4b5
gnu: curl: Remove graft for 7.64.0. 
* gnu/packages/curl.scm (curl): Update to 7.64.0.
(curl-7.64.0): Remove variable.
 2019-02-11 19:48:31 +01:00
Marius Bakke c3f47e44cd
Merge branch 'master' into core-updates 2019-02-11 19:25:16 +01:00
Marius Bakke c8b69863eb
gnu: pixman: Update source URI. 
* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS.
 2019-02-11 19:20:55 +01:00
Marius Bakke 93617188d9
gnu: python-django: Update to 1.11.20 [fixes CVE-2019-6975]. 
* gnu/packages/django.scm (python-django): Update to 1.11.20.
 2019-02-11 19:20:55 +01:00
Marius Bakke c508c06573
gnu: ffmpeg: Update to 4.1.1. 
* gnu/packages/video.scm (ffmpeg): Update to 4.1.1.
 2019-02-11 19:20:55 +01:00
Marius Bakke b861fc157c
gnu: miniupnpc: Update to 2.1.20190210. 
* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190210.
 2019-02-11 19:20:55 +01:00
Marius Bakke a2467954b8
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.
 2019-02-11 19:20:55 +01:00
Danny Milosavljevic 86b2ab8f5b
gnu: vlc: Use libvpx-1.7. 
Fixes <https://bugs.gnu.org/34439>.

* gnu/packages/video.scm (vlc)[inputs]: Remove libvpx.  Add libvpx-1.7.
 2019-02-11 18:48:42 +01:00
Danny Milosavljevic 1c84e68bde
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".
 2019-02-11 18:29:01 +01:00
Kei Kebreau df56098220
gnu: gama: Update to 2.03. 
* gnu/packages/gps.scm (gama): Update to 2.03.
 2019-02-11 05:49:19 -05:00
Danny Milosavljevic 268e12a894
services: docker: Make shepherd service require "networking". 
Fixes <https://bugs.gnu.org/34333>.

* gnu/services/docker.scm (docker-shepherd-service): Require "networking".
 2019-02-11 11:45:12 +01:00
Vagrant Cascadian 4a14ee9127
gnu: gloox: Update to 1.0.22. 
* gnu/packages/messaging.scm (gloox): Update to 1.0.22.
 2019-02-11 11:12:27 +01:00
Vagrant Cascadian 37da5813e9
gnu: python-ecpy: Update to 0.10.0. 
* gnu/packages/python-crypto.scm (python-ecpy): Update to 0.10.0.
 2019-02-11 11:08:40 +01:00
Vagrant Cascadian a62887d30d
gnu: python-pycryptodome: Update to 3.7.3. 
* gnu/packages/python-crypto (python-cryptodome): Update to 3.7.3.
 2019-02-11 11:04:44 +01:00
Vagrant Cascadian 6e2bad000f
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.
 2019-02-11 10:59:23 +01:00