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2019-02-12pull: 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 Courtès
2019-02-12pull: 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 Courtès
2019-02-12inferior: Add 'inferior-available-packages'....* guix/inferior.scm (inferior-available-packages): New procedure. * tests/inferior.scm ("inferior-available-packages"): New test. Ludovic Courtès
2019-02-12pull: 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 Courtès
2019-02-12gnu: 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 Famulari
2019-02-12gnu: Add frrouting....* gnu/packages/networking.scm (frrouting): New variable. Gábor Boskovits
2019-02-12gnu: 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 Famulari
2019-02-12gnu: 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 Famulari
2019-02-12gnu: 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-Rice
2019-02-12gnu: lzlib: Update to 1.11....* gnu/packages/compression.scm (lzlib): Update to 1.11. Tobias Geerinckx-Rice
2019-02-12gnu: lzlib: Don't use NAME in source URI....* gnu/packages/compression.scm (lzlib)[source]: Hard-code NAME. Tobias Geerinckx-Rice
2019-02-12gnu: clzip: Update to 1.11....* gnu/packages/compression.scm (clzip): Update to 1.11. Tobias Geerinckx-Rice
2019-02-12gnu: clzip: Don't use NAME in source URI....* gnu/packages/compression.scm (clzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice
2019-02-12gnu: lunzip: Update to 1.11....* gnu/packages/compression.scm (lunzip): Update to 1.11. Tobias Geerinckx-Rice
2019-02-12gnu: lunzip: Don't use NAME in source URI....* gnu/packages/compression.scm (lunzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice
2019-02-12gnu: plzip: Update to 1.8....* gnu/packages/compression.scm (plzip): Update to 1.8. Tobias Geerinckx-Rice
2019-02-12gnu: plzip: Don't use NAME in source URI....* gnu/packages/compression.scm (plzip)[source]: Hard-code NAME. Tobias Geerinckx-Rice
2019-02-12gnu: lziprecover: Update to 1.21....* gnu/packages/compression.scm (lziprecover): Update to 1.21. Tobias Geerinckx-Rice
2019-02-12gnu: lziprecover: Don't use NAME in source URI....* gnu/packages/compression.scm (lziprecover)[source]: Hard-code NAME. Tobias Geerinckx-Rice
2019-02-12gnu: perl-dbi: Update to 1.642....* gnu/packages/databases.scm (perl-dbi): Update to 1.642. Tobias Geerinckx-Rice
2019-02-12gnu: kyotocabinet: Update to 1.2.77....* gnu/packages/databases.scm (kyotocabinet): Update to 1.2.77. Tobias Geerinckx-Rice
2019-02-12gnu: os-prober: Update to 1.77....* gnu/packages/bootloaders.scm (os-prober): Update to 1.77. Tobias Geerinckx-Rice
2019-02-12gnu: feh: Update to 3.1.2....* gnu/packages/image-viewers.scm (feh): Update to 3.1.2. Tobias Geerinckx-Rice
2019-02-12gnu: 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 Cournoyer
2019-02-12gnu: 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 Flashner
2019-02-12gnu: Add cnvkit....* gnu/packages/bioinformatics.scm (cnvkit): New variable. Ricardo Wurmus
2019-02-12gnu: Add r-dnacopy....* gnu/packages/bioconductor.scm (r-dnacopy): New variable. Ricardo Wurmus
2019-02-12gnu: python-reportlab: Update to 3.5.13....* gnu/packages/pdf.scm (python-reportlab): Update to 3.5.13. [inputs]: Add freetype. Ricardo Wurmus
2019-02-12gnu: 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 Flashner
2019-02-12gnu: parallel: Update to 20190122....* gnu/packages/parallel.scm (parallel): Update to 20190122. Tobias Geerinckx-Rice
2019-02-12gnu: 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-Rice
2019-02-12gnu: multipath-tools: Update to 0.7.9....* gnu/packages/linux.scm (multipath-tools): Update to 0.7.9. Tobias Geerinckx-Rice
2019-02-12gnu: websockify: Don't use unstable tarball....* gnu/packages/web.scm (websockify)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-12gnu: libyajl: Don't use unstable tarball....* gnu/packages/web.scm (libyajl)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-12gnu: rapidjson: Don't use unstable tarball....* gnu/packages/web.scm (rapidjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-12gnu: qjson: Don't use unstable tarball....* gnu/packages/web.scm (qjson)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-12gnu: fcgiwrap: Don't use unstable tarball....* gnu/packages/web.scm (fcgiwrap)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-12gnu: mod-wsgi: Don't use unstable tarball....* gnu/packages/web.scm (mod-wsgi)[source]: Use GIT-FETCH and GIT-FILE-NAME. Tobias Geerinckx-Rice
2019-02-11gnu: 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 Famulari
2019-02-11Avoid 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 Courtès
2019-02-11pack, 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 Courtès
2019-02-11git: Add an exception printer for 'git-error'....* guix/git.scm (print-git-error): New procedure. <top level>: Call 'set-exception-printer!'. Ludovic Courtès
2019-02-11ui: 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 Courtès
2019-02-11status: 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 Courtès
2019-02-11HACKING: Update key server....* HACKING (Commit Access): Recommend pool.sks-keyservers.net. Ludovic Courtès
2019-02-11gnu: guile-picture-language: Update to 0-2.1ea8b78....* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0-2.1ea8b78. Ricardo Wurmus
2019-02-11gnu: disorderfs: Update to 0.5.6....* gnu/packages/file-systems (disorderfs): Update to 0.5.6. Signed-off-by: Leo Famulari <leo@famulari.name> Vagrant Cascadian
2019-02-11gnu: diffoscope: Update to 111....* gnu/packages/package-management (diffoscope): Update to 111. Signed-off-by: Leo Famulari <leo@famulari.name> Vagrant Cascadian
2019-02-11gnu: python-cython: Update to 0.29.5....* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.5. Andreas Enge
2019-02-11gnu: pixman: Update source URI....* gnu/packages/xdisorg.scm (pixman)[source](uri): Use HTTPS. Marius Bakke
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