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2018-03-30gnu: Add delly....* gnu/packages/bioinformatics.scm (delly): New variable. * gnu/packages/patches/delly-use-system-libraries.patch: New file. * gnu/local.mk: Include delly-use-system-libraries.patch. Signed-off-by: Leo Famulari <leo@famulari.name> Roel Janssen
2018-03-27gnu: mupdf: Fix CVE-2018-{6544,1000051}....* gnu/packages/patches/mupdf-CVE-2018-1000051.patch, gnu/packages/patches/mupdf-CVE-2018-6544.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/pdf.scm (mupdf)[source]: Use them. Leo Famulari
2018-03-26gnu: translate-shell: Update to 0.9.6.7....* gnu/packages/patches/translate-shell-fix-curl-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/dictionaries.scm (translate-shell): Update to 0.9.6.7. [source](patches): Add it. [home-page]: Append slash. Oleg Pykhalov
2018-03-26gnu: hwloc@2: Update to 2.0.1....* gnu/packages/mpi.scm (hwloc-2.0): Update to 2.0.1. [source]: Remove 'patches'. * gnu/packages/patches/hwloc-tests-without-sysfs.patch: Remove. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Ludovic Courtès
2018-03-26gnu: classpath: Add aarch64-linux support....* gnu/packages/java.scm (classpath-bootstrap, classpath-0.99)[source]: Add patch. * gnu/packages/patches/classpath-aarch64-support.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2018-03-25gnu: Add pure....* gnu/packages/pure.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Danny Milosavljevic
2018-03-25gnu: links: Update to 2.15....* gnu/packages/web-browsers.scm (links): Update to 2.15. [source]: Remove patch for fixed CVE. * gnu/packages/patches/links-CVE-2017-11114.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-03-22gnu: Add lyx....* gnu/packages/patches/lyx-2.2.3-fix-test.patch: New file. * gnu/local.mk: Add it. * gnu/packages/tex.scm (lyx): New variable. Danny Milosavljevic
2018-03-22gnu: shepherd: Update to 0.4.0....* gnu/packages/admin.scm (shepherd): Update to 0.4.0. Remove patches. * gnu/packages/patches/shepherd-close-fds.patch, gnu/packages/patches/shepherd-herd-status-sorted.patch: Remove. * gnu/local.mk (dist_patch_DATA): Remove them. * gnu/services/admin.scm (%default-rotations): Remove /var/log/shepherd.log. Ludovic Courtès
2018-03-20Merge branch 'staging'Marius Bakke
2018-03-19gnu: libtirpc: Update to 1.0.3....* gnu/packages/onc-rpc.scm (libtirpc): Update to 1.0.3. [source]: Remove patch. * gnu/packages/patches/libtirpc-missing-headers.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-03-18Merge branch 'master' into stagingMarius Bakke
2018-03-17gnu: Add terraform-docs....* gnu/packages/terraform.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Christopher Baines
2018-03-18gnu: java-simple-xml: Fix java8 test failures....* gnu/packages/patches/javas-simple-xml-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/java.scm (java-simple-xml)[source](patches): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Gábor Boskovits
2018-03-16gnu: util-linux: Fix CVE-2018-7738....* gnu/packages/patches/util-linux-CVE-2018-7738.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/linux.scm (util-linux)[replacement]: New field. (util-linux/fixed): New variable. Leo Famulari
2018-03-15gnu: shadow: Fix CVE-2018-7169....* gnu/packages/patches/shadow-CVE-2018-7169.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (shadow)[source]: Use it. Leo Famulari
2018-03-14gnu: Add ada.scm to GNU_SYSTEM_MODULES....This is a follow-up to commit ebd43a2a45f9ac0ce702ef5810eddafd0830db5f. * gnu/local.mk (GNU_SYSTEM_MODULES): Add ada.scm. Ricardo Wurmus
2018-03-12gnu: Add debian-archive-keyring....* gnu/packages/debian.scm (debian-archive-keyring): New variable. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Efraim Flashner
2018-03-12Merge branch 'staging-next' into stagingMarius Bakke
2018-03-12gnu: lrzip: Fix CVE-2017-8842....* gnu/packages/compression.scm (lrzip)[source]: Add patch. * gnu/packages/patches/lrzip-CVE-2017-8842.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Tobias Geerinckx-Rice
2018-03-11gnu: java-jeromq: Fix tests....* gnu/packages/patches/java-jeromq-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/java.scm (java-jeromq)[source](patches): Add it. [arguments](#test-exclude): Disable more failing tests. Gábor Boskovits
2018-03-10gnu: zsh: Fix CVE-2018-{7548,7549}....* gnu/packages/patches/zsh-CVE-2018-7548.patch, gnu/packages/patches/zsh-CVE-2018-7549.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/shells.scm (zsh)[source]: Use them. Leo Famulari
2018-03-08Merge branch 'master' into stagingMarius Bakke
2018-03-08gnu: giflib: Make "reallocarray" private, solve glibc@2.26 conflict....Rename the function and move the declaration from gif_lib.h to gif_lib_private.h to solve conflicts when some .c-file #includes both stdlib.h and gif_lib.h. See also https://sourceforge.net/p/giflib/bugs/110/ * gnu/packages/patches/giflib-make-reallocarray-private.patch: New file * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image.scm(giflib)[source](patches): New field. Hartmut Goebel
2018-03-07gnu: gnome-todo: Fix compatibility with libical >= 3.0....* gnu/packages/patches/gnome-todo-libical-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/gnome.scm (gnome-todo)[source](patches): Use it. Marius Bakke
2018-03-06gnu: Add maven-resolver-api....* gnu/packages/maven.scm: New file. (maven-resolver-api): New variable. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Julien Lepiller
2018-03-06Merge branch 'master' into stagingLeo Famulari
2018-03-04gnu: ceph: Update to 12.2.4....* gnu/packages/patches/ceph-disable-cpu-optimizations.patch: Adjust to upstream changes. * gnu/packages/patches/ceph-disable-unittest-throttle.patch: Delete file. * gnu/packages/patches/ceph-rocksdb-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/storage.scm (ceph): Update to 12.2.4. [source](patches): Adjust. [arguments]: Add "-DWITH_BABELTRACE=OFF" in #:configure-flags. Build with CMAKE-3.11. Adjust file substitutions. Wrap 'ceph' executable. [native-inputs]: Add GPERF. [inputs]: Replace BOOST with BOOST-1.66. Add PYTHON2-PRETTYTABLE. Marius Bakke
2018-03-04gnu: antlr3-3.3: Fix java8 issue....* gnu/packages/java.scm (antlr3-3.3)[source]: Add patch. * gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Gábor Boskovits
2018-03-04gnu: antlr3-3.1: Fix java8 issue....* gnu/packages/java.scm (antlr3-3.1)[source]: Add patch. * gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Gábor Boskovits
2018-03-02gnu: Add r-hpar....* gnu/packages/bioconductor.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Ricardo Wurmus
2018-03-02gnu: icecat: Update to 52.6.0-gnu1....* gnu/packages/gnuzilla.scm (icecat): Update to 52.6.0-gnu1. [source]: Remove patches that are no longer needed. * gnu/packages/patches/icecat-bug-1348660-pt5.patch, gnu/packages/patches/icecat-bug-1414945.patch, gnu/packages/patches/icecat-bug-1415133.patch, gnu/packages/patches/icecat-bug-1424373-pt2.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. Mark H Weaver
2018-03-01gnu: php: Fix test failure....* gnu/packages/php.scm (php)[inputs]: Use gd-for-php. (gd-for-php): New private variable. * gnu/packages/patches/gd-CVE-2018-5711.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Julien Lepiller
2018-03-01gnu: Graft glibc to allow execution on Linux 2.6.32....* gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (glibc/linux)[replacement]: New field. (glibc-2.26-patched): New variable. Ricardo Wurmus
2018-03-01Merge branch 'master' into stagingMarius Bakke
2018-02-28gnu: dovecot: Update to 2.3.0.1 [fixes CVE-2017-14461]....* gnu/packages/mail.scm (dovecot): Update to 2.3.0.1. [source]: Remove upstreamed patch. * gnu/packages/patches/dovecot-CVE-2017-15132.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-02-28gnu: wavpack: Fix CVE-2018-6767....* gnu/packages/patches/wavpack-CVE-2018-6767.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/audio.scm (wavpack)[source](patches): Add it. Marius Bakke
2018-02-28gnu: python-mox3: Update to 0.24.0....* gnu/packages/openstack.scm (python-mox3): Update to 0.24.0. [source](patches): New field. [arguments]: Remove. [native-inputs]: Add PYTHON-OPENSTACKDOCSTHEME and PYTHON-SUBUNIT. Replace PYTHON-SPHINX with PYTHON-SPHINX-1.6. Move PYTHON-PBR and PYTHON-FIXTURES ... [propagated-inputs]: ... here. New field. [description]: Don't mention explicit Python versions. * gnu/packages/patches/python-mox3-python3.6-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Marius Bakke
2018-02-28gnu: dblatex: Update to 0.3.10....* gnu/packages/docbook.scm (dblatex): Update to 0.3.10. [source]: Remove patch. * gnu/packages/patches/dblatex-remove-multirow.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-02-28services: cgit: Add more configuration fields....* gnu/services/version-control.scm (cgit-service-type): Move to separate file. * gnu/services/cgit.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add this. * gnu/tests/version-control.scm: Add this. * doc/guix.texi (Cgit Service): Document this. Oleg Pykhalov
2018-02-27gnu: perl-gd: Update to 2.68....* gnu/packages/gd.scm (perl-gd): Update to 2.68. [source]: Remove obsolete patch. [native-inputs]: Remove perl-module-build. [inputs]: Use canonical package names and order alphabetically. [arguments]: Replace #:module-build-flags with fewer #:make-maker-flags, enable #:tests?, and remove ‘clear-autogenerated-files’ phase. * gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-02-26gnu: python-parse: Update to 1.8.2....* gnu/packages/patches/python-parse-too-many-fields.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/python.scm (python-parse): Update to 1.8.2. [source](patches): Remove. [arguments]: Use INVOKE instead of SYSTEM*. Marius Bakke
2018-02-26gnu: Add agda....* gnu/packages/agda.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add adga.scm. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Alex ter Weele
2018-02-25gnu: json-glib: Fix 32-bit test failures....* gnu/packages/patches/json-glib-fix-tests-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/gnome.scm (json-glib)[source](patches): New field. Marius Bakke
2018-02-24gnu: wxmaxima: Update to 18.02.0....* gnu/packages/maths.scm (wxmaxima): Update to 18.02.0. [source]: Add patch. [build-system]: Use the cmake-build-system. [native-inputs]: Remove autoconf and automake. [arguments]: Disable tests, remove 'autoconf' phase. * gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Kei Kebreau
2018-02-24Merge branch 'master' into stagingMarius Bakke
2018-02-24gnu: Add perl-regexp-pattern-license....* gnu/packages/license.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add this. Oleg Pykhalov
2018-02-24gnu: password-store: Fix compatibility with GnuPG 2.2.5....* gnu/packages/patches/password-store-gnupg-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/password-utils.scm (password-store)[source]: Use it. Clément Lassieur
2018-02-23gnu: wavpack: Fix CVE-2018-7253 and CVE-2018-7254....* gnu/packages/patches/wavpack-CVE-2018-7253.patch, gnu/packages/patches/wavpack-CVE-2018-7254.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them. * gnu/packages/audio.scm (wavpack)[source](patches): Use them. Marius Bakke
2018-02-23gnu: optipng: Update to 0.7.7 [security fixes]....This release claims to fix 2 vulnerabilities: - ‘an integer overflow vulnerability in the TIFF decoder’ (CVE-2017-1000229, previously patched in Guix), and - ‘a buffer overflow vulnerability in the GIF decoder’. * gnu/packages/image.scm (optipng): Update to 0.7.7. [source]: Remove patch. [arguments]: Substitute INVOKE for SYSTEM* and end phase with #t. * gnu/packages/patches/optipng-CVE-2017-1000229.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
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