155194d97d
gnu: python-pybedtools: Update to 0.8.0 and fix build.
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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
b856a78c94
gnu: efilinux: Set ARCH variable on some architectures.
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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
385d7546e1
gnu: Add cnvkit.
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* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12 15:41:02 +01:00
c18dccffa2
gnu: Add r-dnacopy.
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* gnu/packages/bioconductor.scm (r-dnacopy): New variable.
2019-02-12 15:41:02 +01:00
ab61ce3730
gnu: python-reportlab: Update to 3.5.13.
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* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13.
[inputs]: Add freetype.
2019-02-12 15:40:58 +01:00
c86b5f1b9b
gnu: glibc@2.27: fix CVE-2018-11236, CVE-2018-11237.
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* 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
d4c95a237c
gnu: parallel: Update to 20190122.
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* gnu/packages/parallel.scm (parallel): Update to 20190122.
2019-02-12 02:33:55 +01:00
a661af5c9a
gnu: maven-resolver-api: Don't use unstable tarball.
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* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:55 +01:00
57e3f06bbd
gnu: multipath-tools: Update to 0.7.9.
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* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9.
2019-02-12 02:33:55 +01:00
34920d2adf
gnu: websockify: Don't use unstable tarball.
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* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:55 +01:00
2772debc74
gnu: libyajl: Don't use unstable tarball.
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* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:54 +01:00
3e3414efd4
gnu: rapidjson: Don't use unstable tarball.
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* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:54 +01:00
082504addf
gnu: qjson: Don't use unstable tarball.
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* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:54 +01:00
20ab34c16f
gnu: fcgiwrap: Don't use unstable tarball.
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* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:54 +01:00
bff44abb14
gnu: mod-wsgi: Don't use unstable tarball.
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* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2019-02-12 02:33:53 +01:00
95c910f499
gnu: Guix: Update snapshot to 0.16.0-10.2637cfd.
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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
2637cfd7a4
Avoid name clash with 'build' from (guix store) and (guix status).
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Since commit 976ef2d978
2019-02-11 23:23:28 +01:00
910d0121a8
pack, vm: Fix incorrect use of 'package-transitive-propagated-inputs'.
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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
1d8b10d00f
git: Add an exception printer for 'git-error'.
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* guix/git.scm (print-git-error): New procedure.
<top level>: Call 'set-exception-printer!'.
2019-02-11 23:23:28 +01:00
70a50305c4
ui: Always print the exception upon load errors.
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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
5ea206a8a9
status: Erase the current line upon new builds or downloads.
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* 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
6701edbfad
HACKING: Update key server.
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* HACKING (Commit Access): Recommend pool.sks-keyservers.net.
2019-02-11 23:23:27 +01:00
8d11b6ddb8
gnu: guile-picture-language: Update to 0-2.1ea8b78.
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* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78.
2019-02-11 23:03:35 +01:00
75d12c40f7
gnu: disorderfs: Update to 0.5.6.
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* 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
295de8cc1a
gnu: diffoscope: Update to 111.
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* gnu/packages/package-management (diffoscope): Update to 111.
Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-11 16:54:37 -05:00
fa8ffaa0df
gnu: python-cython: Update to 0.29.5.
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* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5.
2019-02-11 21:20:41 +01:00
c8b69863eb
gnu: pixman: Update source URI.
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* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS.
2019-02-11 19:20:55 +01:00
93617188d9
gnu: python-django: Update to 1.11.20 [fixes CVE-2019-6975].
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* gnu/packages/django.scm (python-django): Update to 1.11.20.
2019-02-11 19:20:55 +01:00
c508c06573
gnu: ffmpeg: Update to 4.1.1.
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* gnu/packages/video.scm (ffmpeg): Update to 4.1.1.
2019-02-11 19:20:55 +01:00
b861fc157c
gnu: miniupnpc: Update to 2.1.20190210.
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* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190210.
2019-02-11 19:20:55 +01:00
a2467954b8
gnu: lv2: Update to 1.16.0.
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* 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
86b2ab8f5b
gnu: vlc: Use libvpx-1.7.
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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
1c84e68bde
services: docker: Make shepherd service also require "dbus-system",
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"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
df56098220
gnu: gama: Update to 2.03.
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* gnu/packages/gps.scm (gama): Update to 2.03.
2019-02-11 05:49:19 -05:00
268e12a894
services: docker: Make shepherd service require "networking".
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Fixes <https://bugs.gnu.org/34333 >.
* gnu/services/docker.scm (docker-shepherd-service): Require "networking".
2019-02-11 11:45:12 +01:00
4a14ee9127
gnu: gloox: Update to 1.0.22.
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* gnu/packages/messaging.scm (gloox): Update to 1.0.22.
2019-02-11 11:12:27 +01:00
37da5813e9
gnu: python-ecpy: Update to 0.10.0.
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* gnu/packages/python-crypto.scm (python-ecpy): Update to 0.10.0.
2019-02-11 11:08:40 +01:00
a62887d30d
gnu: python-pycryptodome: Update to 3.7.3.
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* gnu/packages/python-crypto (python-cryptodome): Update to 3.7.3.
2019-02-11 11:04:44 +01:00
6e2bad000f
gnu: u-boot-novena: Allow booting from raw device offset.
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* gnu/packages/bootloaders.scm (u-boot-novena): Disable loading u-boot.img
from a partition.
2019-02-11 10:59:23 +01:00
8d22f7e31f
gnu: Add python-pymsgbox.
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* gnu/packages/python-xyz.scm (python-pymsgbox): New variable.
2019-02-11 10:51:11 +01:00
a336334196
gnu: Add python-daemon.
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* gnu/packages/python-xyz.scm (python-daemon): New variable.
2019-02-11 10:37:54 +01:00
f5c46fa0d0
gnu: dmenu: Update to 4.9.
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* gnu/packages/suckless.scm (dmenu): Update to 4.9.
2019-02-11 02:41:26 -05:00
d561243917
gnu: Dropbear: Add a comment about bundled libraries.
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* gnu/packages/ssh.scm (dropbear): Comment.
2019-02-10 23:03:57 -05:00
8f9c5aa3ba
gnu: curl: Update to 7.64.0 [fixes CVE-2018-16890 and CVE-2019-{3822,3823}].
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* gnu/packages/curl.scm (curl)[replacement]: New field.
(curl-7.64.0): New variable.
2019-02-10 22:03:50 -05:00
c03b355fa7
gnu: Dovecot: Update to 2.3.4.1 [fixes CVE-2019-3814].
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* gnu/packages/mail.scm (dovecot): Update to 2.3.4.1.
2019-02-10 22:03:50 -05:00
f6e64282b4
gnu: Syncthing: Update to 1.0.1.
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* gnu/packages/syncthing.scm (syncthing): Update to 1.0.1.
2019-02-10 21:38:07 -05:00
f52bd828ed
gnu: MPD: Update to 0.21.4.
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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.
2019-02-10 20:21:53 -05:00
30d77f45eb
services: gdm: Disable debugging output.
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* gnu/services/xorg.scm (gdm-etc-service)[gdm-configuration-file]:
Comment out debugging setting.
2019-02-10 23:25:01 +01:00
a76d0f032b
gnu: gnome-shell: Customize the GDM log-in screen.
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* 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.
2019-02-10 23:25:01 +01:00
5e6a5aeebd
artwork: Update snapshot to e951905.
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* gnu/artwork.scm (%artwork-repository): Update to e951905.
2019-02-10 23:25:01 +01:00
Maxim Cournoyer