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* gnu: libjpeg: Use HTTPS URLs.•••* gnu/packages/image.scm (libjpeg, libjpeg-8)[source, home-page]: Use HTTPS. Marius Bakke2019-02-12
* gnu: Add python-language-server.•••* gnu/packages/python-xyz.scm (python-language-server): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Brett Gilio2019-02-12
* gnu: Add python-docstyle.•••* gnu/packages/python-xyz.scm (python-docstyle): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Brett Gilio2019-02-12
* gnu: Add python-jsonrpc-server.•••* gnu/packages/python-xyz.scm (python-jsonrpc-server): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Brett Gilio2019-02-12
* gnu: Add python-rope.•••* gnu/packages/python-xyz.scm (python-rope): New variable. Co-authored-by: Brett Gilio <brettg@posteo.net> Ludovic Courtès2019-02-12
* gnu: python2-rope: Change comment to reflect partial python3 support•••* gnu/packages/python-xyz.scm (python2-rope): Change comment to reflect partial python 3 support Signed-off-by: Ludovic Courtès <ludo@gnu.org> Brett Gilio2019-02-12
* pull: Speed up the new/upgraded package computation.•••* 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. Ludovic Courtès2019-02-12
* pull: Move profile comparison to 'new/upgraded-packages'.•••* guix/scripts/pull.scm (new/upgraded-packages): New procedure, with code formerly in 'display-new/upgraded-packages'. (display-new/upgraded-packages): Use it. Ludovic Courtès2019-02-12
* inferior: Add 'inferior-available-packages'.•••* guix/inferior.scm (inferior-available-packages): New procedure. * tests/inferior.scm ("inferior-available-packages"): New test. Ludovic Courtès2019-02-12
* 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'. Ludovic Courtès2019-02-12
* 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. Leo Famulari2019-02-12
* gnu: Add frrouting.•••* gnu/packages/networking.scm (frrouting): New variable. Gábor Boskovits2019-02-12
* 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. Leo Famulari2019-02-12
* 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. Leo Famulari2019-02-12
* 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. Tobias Geerinckx-Rice2019-02-12
* gnu: lzlib: Update to 1.11.•••* gnu/packages/compression.scm (lzlib): Update to 1.11. Tobias Geerinckx-Rice2019-02-12
* gnu: lzlib: Don't use NAME in source URI.•••* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: clzip: Update to 1.11.•••* gnu/packages/compression.scm (clzip): Update to 1.11. Tobias Geerinckx-Rice2019-02-12
* gnu: clzip: Don't use NAME in source URI.•••* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: lunzip: Update to 1.11.•••* gnu/packages/compression.scm (lunzip): Update to 1.11. Tobias Geerinckx-Rice2019-02-12
* gnu: lunzip: Don't use NAME in source URI.•••* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: plzip: Update to 1.8.•••* gnu/packages/compression.scm (plzip): Update to 1.8. Tobias Geerinckx-Rice2019-02-12
* gnu: plzip: Don't use NAME in source URI.•••* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: lziprecover: Update to 1.21.•••* gnu/packages/compression.scm (lziprecover): Update to 1.21. Tobias Geerinckx-Rice2019-02-12
* gnu: lziprecover: Don't use NAME in source URI.•••* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: perl-dbi: Update to 1.642.•••* gnu/packages/databases.scm (perl-dbi): Update to 1.642. Tobias Geerinckx-Rice2019-02-12
* gnu: kyotocabinet: Update to 1.2.77.•••* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77. Tobias Geerinckx-Rice2019-02-12
* gnu: os-prober: Update to 1.77.•••* gnu/packages/bootloaders.scm (os-prober): Update to 1.77. Tobias Geerinckx-Rice2019-02-12
* gnu: feh: Update to 3.1.2.•••* gnu/packages/image-viewers.scm (feh): Update to 3.1.2. Tobias Geerinckx-Rice2019-02-12
* 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. Maxim Cournoyer2019-02-12
* 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. Efraim Flashner2019-02-12
* gnu: Add cnvkit.•••* gnu/packages/bioinformatics.scm (cnvkit): New variable. Ricardo Wurmus2019-02-12
* gnu: Add r-dnacopy.•••* gnu/packages/bioconductor.scm (r-dnacopy): New variable. Ricardo Wurmus2019-02-12
* gnu: python-reportlab: Update to 3.5.13.•••* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13. [inputs]: Add freetype. Ricardo Wurmus2019-02-12
* 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. Efraim Flashner2019-02-12
* gnu: parallel: Update to 20190122.•••* gnu/packages/parallel.scm (parallel): Update to 20190122. Tobias Geerinckx-Rice2019-02-12
* gnu: maven-resolver-api: Don't use unstable tarball.•••* gnu/packages/maven.scm (maven-resolver-api)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: multipath-tools: Update to 0.7.9.•••* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9. Tobias Geerinckx-Rice2019-02-12
* gnu: websockify: Don't use unstable tarball.•••* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: libyajl: Don't use unstable tarball.•••* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: rapidjson: Don't use unstable tarball.•••* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: qjson: Don't use unstable tarball.•••* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: fcgiwrap: Don't use unstable tarball.•••* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* gnu: mod-wsgi: Don't use unstable tarball.•••* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice2019-02-12
* 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. Leo Famulari2019-02-11
* Avoid name clash with 'build' from (guix store) and (guix status).•••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. Ludovic Courtès2019-02-11
* 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. Ludovic Courtès2019-02-11
* git: Add an exception printer for 'git-error'.•••* guix/git.scm (print-git-error): New procedure. <top level>: Call 'set-exception-printer!'. Ludovic Courtès2019-02-11
* 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. Ludovic Courtès2019-02-11
* 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. Ludovic Courtès2019-02-11
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