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2019-02-12gnu: python2-rope: Change comment to reflect partial python3 supportBrett Gilio
* gnu/packages/python-xyz.scm (python2-rope): Change comment to reflect partial python 3 support Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-02-12pull: Speed up the new/upgraded package computation.Ludovic Courtès
* guix/scripts/pull.scm (new/upgraded-packages): OLD no longer stores all the versions of each package. Remove 'vhash-fold*' call and reduce the number of 'version>?' calls when computing UPGRADED.
2019-02-12pull: Move profile comparison to 'new/upgraded-packages'.Ludovic Courtès
* guix/scripts/pull.scm (new/upgraded-packages): New procedure, with code formerly in 'display-new/upgraded-packages'. (display-new/upgraded-packages): Use it.
2019-02-12inferior: Add 'inferior-available-packages'.Ludovic Courtès
* guix/inferior.scm (inferior-available-packages): New procedure. * tests/inferior.scm ("inferior-available-packages"): New test.
2019-02-12pull: Use 'fold-available-packages' for the current package list.Ludovic Courtès
* 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'.
2019-02-12gnu: Flatpak: Update to 1.2.3 [security fixes].Leo Famulari
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.
2019-02-12gnu: Add frrouting.Gábor Boskovits
* gnu/packages/networking.scm (frrouting): New variable.
2019-02-12gnu: Docker: Update to 18.09.2.Leo Famulari
* 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.
2019-02-12gnu: runc: Update to 1.0.0-rc6 [fixes CVE-2019-5736].Leo Famulari
* 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.
2019-02-12gnu: lzlib: Remove minilzip comment.Tobias Geerinckx-Rice
It lacks lzip's dependency on libstdc++.so and libm.so and may have its uses. * gnu/packages/compression.scm (lzlib): Don't judge.
2019-02-12gnu: lzlib: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lzlib): Update to 1.11.
2019-02-12gnu: lzlib: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME.
2019-02-12gnu: clzip: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (clzip): Update to 1.11.
2019-02-12gnu: clzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME.
2019-02-12gnu: lunzip: Update to 1.11.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lunzip): Update to 1.11.
2019-02-12gnu: lunzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME.
2019-02-12gnu: plzip: Update to 1.8.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (plzip): Update to 1.8.
2019-02-12gnu: plzip: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME.
2019-02-12gnu: lziprecover: Update to 1.21.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lziprecover): Update to 1.21.
2019-02-12gnu: lziprecover: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME.
2019-02-12gnu: perl-dbi: Update to 1.642.Tobias Geerinckx-Rice
* gnu/packages/databases.scm (perl-dbi): Update to 1.642.
2019-02-12gnu: kyotocabinet: Update to 1.2.77.Tobias Geerinckx-Rice
* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77.
2019-02-12gnu: os-prober: Update to 1.77.Tobias Geerinckx-Rice
* gnu/packages/bootloaders.scm (os-prober): Update to 1.77.
2019-02-12gnu: feh: Update to 3.1.2.Tobias Geerinckx-Rice
* gnu/packages/image-viewers.scm (feh): Update to 3.1.2.
2019-02-12gnu: python-pybedtools: Update to 0.8.0 and fix build.Maxim Cournoyer
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.
2019-02-12gnu: efilinux: Set ARCH variable on some architectures.Efraim Flashner
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.
2019-02-12gnu: Add cnvkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12gnu: Add r-dnacopy.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dnacopy): New variable.
2019-02-12gnu: python-reportlab: Update to 3.5.13.Ricardo Wurmus
* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13. [inputs]: Add freetype.
2019-02-12gnu: glibc@2.27: fix CVE-2018-11236, CVE-2018-11237.Efraim Flashner
* 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.
2019-02-12gnu: parallel: Update to 20190122.Tobias Geerinckx-Rice
* gnu/packages/parallel.scm (parallel): Update to 20190122.
2019-02-12gnu: maven-resolver-api: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: multipath-tools: Update to 0.7.9.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9.
2019-02-12gnu: websockify: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: libyajl: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: rapidjson: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: qjson: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: fcgiwrap: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-12gnu: mod-wsgi: Don't use unstable tarball.Tobias Geerinckx-Rice
* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2019-02-11gnu: Guix: Update snapshot to 0.16.0-10.2637cfd.Leo Famulari
Fixes <https://bugs.gnu.org/34444>. * gnu/packages/package-management.scm (guix): Update to 0.16.0-10.2637cfd.
2019-02-11Avoid name clash with 'build' from (guix store) and (guix status).Ludovic Courtès
Since commit 976ef2d97887d16eab8d4eb9dad811786b04d690, (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.
2019-02-11pack, vm: Fix incorrect use of 'package-transitive-propagated-inputs'.Ludovic Courtès
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.
2019-02-11git: Add an exception printer for 'git-error'.Ludovic Courtès
* guix/git.scm (print-git-error): New procedure. <top level>: Call 'set-exception-printer!'.
2019-02-11ui: Always print the exception upon load errors.Ludovic Courtès
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.
2019-02-11status: Erase the current line upon new builds or downloads.Ludovic Courtès
* guix/status.scm (print-build-event): Add 'erase-current-line*' call upon 'build-started, 'substituter-started, 'download-started.
2019-02-11HACKING: Update key server.Ludovic Courtès
* HACKING (Commit Access): Recommend pool.sks-keyservers.net.
2019-02-11gnu: guile-picture-language: Update to 0-2.1ea8b78.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78.
2019-02-11gnu: disorderfs: Update to 0.5.6.Vagrant Cascadian
* gnu/packages/file-systems (disorderfs): Update to 0.5.6. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-11gnu: diffoscope: Update to 111.Vagrant Cascadian
* gnu/packages/package-management (diffoscope): Update to 111. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-02-11gnu: python-cython: Update to 0.29.5.Andreas Enge
* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5.
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