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39846 Commits

Author SHA1 Message Date
Ludovic Courtès 739380542d
inferior: Add 'inferior-available-packages'. 
* guix/inferior.scm (inferior-available-packages): New procedure.
* tests/inferior.scm ("inferior-available-packages"): New test.
 2019-02-12 23:30:16 +01:00
Ludovic Courtès 46765f82db
pull: Use 'fold-available-packages' for the current package list. 
* guix/scripts/pull.scm (display-profile-news): Use
'fold-available-packages' instead of 'fold-packages' to compute OLD.
(profile-package-alist): Use 'inferior-available-packages'.
 2019-02-12 23:30:16 +01:00
Leo Famulari e2760d1a8b
gnu: Flatpak: Update to 1.2.3 [security fixes]. 
From 'NEWS' in the source distribution:

The CVE-2019-5736 runc vulnerability is about using /proc/self/exe
to modify the host side binary from the sandbox. This mostly does not
affect flatpak since the flatpak sandbox is not run with root permissions.
However, there is one case (running the apply_extra script for system
installs) where this happens, so this release contains a fix for that.

 * Don't expose /proc in apply_extra script sandbox.

* gnu/packages/package-management.scm (flatpak): Update to 1.2.3.
 2019-02-12 17:14:09 -05:00
Gábor Boskovits dbf87ecb52
gnu: Add frrouting. 
* gnu/packages/networking.scm (frrouting): New variable.
 2019-02-12 22:24:27 +01:00
Leo Famulari ea7cddaac7
gnu: Docker: Update to 18.09.2. 
* gnu/packages/docker.scm (%docker-version, docker, docker-cli): Update to
18.09.2.
(docker)[arguments]: Adjust to the Debian-specific 'iptables-legacy' lookup in
the 'patch-paths' phase.
 2019-02-12 12:53:12 -05:00
Leo Famulari ce4593ec4c
gnu: runc: Update to 1.0.0-rc6 [fixes CVE-2019-5736]. 
* gnu/packages/virtualization.scm (runc): Update to 1.0.0-rc6.
[source]: Use a descriptive file-name. Add 'runc-CVE-2019-5736.patch'
* gnu/packages/patches/runc-CVE-2019-5736.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2019-02-12 12:53:12 -05:00
Tobias Geerinckx-Rice 571a01d8fa
gnu: lzlib: Remove minilzip comment. 
It lacks lzip's dependency on libstdc++.so and libm.so and may have its
uses.

* gnu/packages/compression.scm (lzlib): Don't judge.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 2990422377
gnu: lzlib: Update to 1.11. 
* gnu/packages/compression.scm (lzlib): Update to 1.11.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 76b2f08468
gnu: lzlib: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 11b1c71d2e
gnu: clzip: Update to 1.11. 
* gnu/packages/compression.scm (clzip): Update to 1.11.
 2019-02-12 17:38:24 +01:00
Tobias Geerinckx-Rice 39e5d3b68d
gnu: clzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice 9f4f085f9b
gnu: lunzip: Update to 1.11. 
* gnu/packages/compression.scm (lunzip): Update to 1.11.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice a28cd47702
gnu: lunzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME.
 2019-02-12 17:38:23 +01:00
Tobias Geerinckx-Rice ff0e1eed32
gnu: plzip: Update to 1.8. 
* gnu/packages/compression.scm (plzip): Update to 1.8.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice 894669a787
gnu: plzip: Don't use NAME in source URI. 
* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice b099b4a75a
gnu: lziprecover: Update to 1.21. 
* gnu/packages/compression.scm (lziprecover): Update to 1.21.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice f6145bb652
gnu: lziprecover: Don't use NAME in source URI. 
* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME.
 2019-02-12 17:38:22 +01:00
Tobias Geerinckx-Rice da93d42413
gnu: perl-dbi: Update to 1.642. 
* gnu/packages/databases.scm (perl-dbi): Update to 1.642.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice 245e7a68e7
gnu: kyotocabinet: Update to 1.2.77. 
* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice e9bdef5fb4
gnu: os-prober: Update to 1.77. 
* gnu/packages/bootloaders.scm (os-prober): Update to 1.77.
 2019-02-12 17:38:21 +01:00
Tobias Geerinckx-Rice 51a8fc8b42
gnu: feh: Update to 3.1.2. 
* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
 2019-02-12 17:38:21 +01:00
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 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