51a8fc8b42
gnu: feh: Update to 3.1.2.
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* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
2019-02-12 17:38:21 +01:00
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
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
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
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
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
44a06c942c
gnu: gnome: Remove '--disable-acceleration-check' flag from 'gnome.desktop'.
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With this change the GNOME session is now listed in the log-in screen of
GDM.
* gnu/packages/gnome.scm (gnome-session)[arguments]: Remove
'disable-hardware-acceleration-check' phase. That phase was apparently
no longer needed. Furthermore, GDM expects 'TryExec' to be a file name,
not a file name followed by arguments; thus, the option led GDM to
discard 'gnome.desktop' with "GdmSession: Command not found: TryExec".
2019-02-10 23:25:01 +01:00
b717d0f90e
gnu: qtwebkit: Build sequentially.
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Fixes <https://bugs.gnu.org/34062 >.
* gnu/packages/qt.scm (qtwebkit)[arguments]: Add #:parallel-build? #f.
2019-02-10 23:25:01 +01:00
2356b7ab6d
gnu: Add ghc-stylish-haskell.
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* gnu/packages/haskell.scm (ghc-stylish-haskell): New variable.
2019-02-10 21:47:24 +01:00
d4ce1c5029
gnu: Add ghc-base-unicode-symbols.
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* gnu/packages/haskell.scm (ghc-base-unicode-symbols): New variable.
2019-02-10 21:45:04 +01:00
3fc88ff0f3
gnu: Add ghc-alsa-core.
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* gnu/packages/haskell.scm (ghc-alsa-core): New variable.
2019-02-10 21:30:32 +01:00
8c16b8a40c
gnu: python-trezor: Update to 0.11.1.
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* gnu/packages/finance.scm (python-trezor): Update to 0.11.1.
[arguments]: Remove obsolete "slow_cosi" test.
Delete "test_tx_api" test, which requires network access.
[propagated-inputs]: Add python-construct and python-typing-extensions,
Remove python-hidapi, python-protobuf and python-typing.
[native-inputs]: Remove python-mock, Add protobuf, python-black,
python-protobuf and python-isort.
2019-02-10 20:41:59 +01:00
f98232a39e
gnu: Add python-construct.
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* gnu/packages/python-xyz.scm (python-construct): New variable.
2019-02-10 20:40:25 +01:00
f89d443be1
gnu: Add python-typing-extensions.
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* gnu/packages/python-xyz.scm (python-typing-extensions): New variable.
2019-02-10 20:37:10 +01:00
02d9e5d285
gnu: python-keepkey: Update to 6.0.2.
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* gnu/packages/finance.scm (python-keepkey): Update to 6.0.2.
[propagated-inputs]: Add python-libusb1.
2019-02-10 20:30:52 +01:00
Tobias Geerinckx-Rice