| Commit message (Collapse) | Author | Age |
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* gnu/packages/compression.scm (lunzip): Update to 1.11.
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* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME.
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* gnu/packages/compression.scm (plzip): Update to 1.8.
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* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME.
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* gnu/packages/compression.scm (lziprecover): Update to 1.21.
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* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME.
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* gnu/packages/databases.scm (perl-dbi): Update to 1.642.
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* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77.
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* gnu/packages/bootloaders.scm (os-prober): Update to 1.77.
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* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
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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.
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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.
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* gnu/packages/bioinformatics.scm (cnvkit): New variable.
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* gnu/packages/bioconductor.scm (r-dnacopy): New variable.
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* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13.
[inputs]: Add freetype.
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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.
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* gnu/packages/parallel.scm (parallel): Update to 20190122.
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* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9.
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* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
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Fixes <https://bugs.gnu.org/34444>.
* gnu/packages/package-management.scm (guix): Update to 0.16.0-10.2637cfd.
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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.
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* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78.
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* gnu/packages/file-systems (disorderfs): Update to 0.5.6.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/package-management (diffoscope): Update to 111.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5.
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* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS.
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* gnu/packages/django.scm (python-django): Update to 1.11.20.
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* gnu/packages/video.scm (ffmpeg): Update to 4.1.1.
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* gnu/packages/upnp.scm (miniupnpc): Update to 2.1.20190210.
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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.
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Fixes <https://bugs.gnu.org/34439>.
* gnu/packages/video.scm (vlc)[inputs]: Remove libvpx. Add libvpx-1.7.
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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".
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* gnu/packages/gps.scm (gama): Update to 2.03.
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Fixes <https://bugs.gnu.org/34333>.
* gnu/services/docker.scm (docker-shepherd-service): Require "networking".
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* gnu/packages/messaging.scm (gloox): Update to 1.0.22.
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* gnu/packages/python-crypto.scm (python-ecpy): Update to 0.10.0.
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* gnu/packages/python-crypto (python-cryptodome): Update to 3.7.3.
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* gnu/packages/bootloaders.scm (u-boot-novena): Disable loading u-boot.img
from a partition.
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* gnu/packages/python-xyz.scm (python-pymsgbox): New variable.
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* gnu/packages/python-xyz.scm (python-daemon): New variable.
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* gnu/packages/suckless.scm (dmenu): Update to 4.9.
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* gnu/packages/ssh.scm (dropbear): Comment.
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* gnu/packages/curl.scm (curl)[replacement]: New field.
(curl-7.64.0): New variable.
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* gnu/packages/mail.scm (dovecot): Update to 2.3.4.1.
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