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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
2018-03-29Merge branch 'master' into core-updatesMarius Bakke
2018-03-29gnu: libusb-for-axoloti: Update patch.•••* gnu/packages/patches/libusb-for-axoloti.patch: Update context for libusb 1.0.22. Ricardo Wurmus
2018-03-29gnu: util-linux: Update to 2.32.•••* gnu/packages/patches/util-linux-tests.patch: Adjust context. * gnu/packages/patches/util-linux-CVE-2018-7738.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/linux.scm (util-linux): Update to 2.32. [source](patches): Remove 'util-linux-CVE-2018-7738.patch'. Marius Bakke
2018-03-28gnu: elogind: Fix build with glibc-2.27.•••* gnu/packages/patches/elogind-glibc-2.27.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/freedesktop.scm (elogind)[source]: Add patch. [arguments]: Replace the bootstrap phase with what was previously the autogen phase. Mark H Weaver
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: make-bootstrap: Adapt glibc-bootstrap-system.patch for glibc-2.27.•••* gnu/packages/patches/glibc-bootstrap-system.patch: Adapt for glibc-2.27. Mark H Weaver
2018-03-25gnu: pulseaudio: Fix build with glibc-2.27.•••* gnu/packages/patches/pulseaudio-glibc-2.27.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pulseaudio.scm (pulseaudio)[source]: Add the patch. [arguments]: Replace 'bootstrap' phase. [native-inputs]: Add autoconf, automake, and libtool. Mark H Weaver
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
2018-03-23gnu: cmake: Update to 3.10.2.•••* gnu/packages/cmake.scm (cmake): Update to 3.10.2. [source]: Remove cmake-fix-tests patch. Do not remove bundled cmlibuv. [arguments]: Replace system* with invoke. [inputs]: Add rhash. Sort. [home-page]: Update URL. * gnu/packages/patches/cmake-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Unregister it. Arun Isaac
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: make: Fix compatibility with glibc 2.27.•••* gnu/packages/patches/make-glibc-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/base.scm (gnu-make)[source](patches): Use it. Marius Bakke
2018-03-22gnu: glibc: Update to 2.27.•••* gnu/packages/base.scm (glibc/linux): Update to 2.27. [source](patches): Add 'glibc-hidden-visibility-ldconfig.patch' and 'glibc-2.27-git-fixes.patch'. [native-inputs]: Add BISON. [arguments]: Remove deprecated "--enable-add-ons" from #:configure-flags. Also remove unneeded "libc_cv_ssp=no" and "libcv_ssp_strong=no". (glibc-2.26): New public variable. * gnu/packages/commencement.scm (glibc-final-with-bootstrap-bash)[native-inputs]: Add BISON-BOOT0. * gnu/packages/patches/glibc-2.27-git-fixes.patch, gnu/packages/patches/glibc-hidden-visibility-ldconfig.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them. Marius Bakke
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
2018-03-20gnu: gcc: Adjust 'strmov' patch for string constants in variables.•••Fixes <https://bugs.gnu.org/30395>. * gnu/packages/patches/gcc-strmov-store-file-names.patch: Update patch to deal with string constants stored in 'static' variables. Ludovic Courtès
2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-20Merge branch 'staging'Marius Bakke
2018-03-20gnu: fontconfig: Update to 2.13.0.•••* gnu/packages/patches/fontconfig-remove-debug-printf.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/fontutils.scm (fontconfig): Update to 2.13.0. [source](patches): Remove. [propagated-inputs]: Add UTIL-LINUX. Marius Bakke
2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-19gnu: bash-completion: Update to 2.8.•••* gnu/packages/bash.scm (bash-completion): Update to 2.8. * gnu/packages/patches/bash-completion-directories.patch: Update context. Tobias Geerinckx-Rice
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
2018-03-18gnu: guile-gdbm-ffi: Add support for gdbm-1.14.•••* gnu/packages/patches/guile-gdbm-ffi-support-gdbm-1.14.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/guile.scm (guile-gdbm-ffi)[inputs]: Move above arguments. Add the patch, and the 'patch' program. [propagated-inputs]: Move above arguments. [arguments]: In the builder, add code to apply the patch. Mark H Weaver
2018-03-18Merge branch 'master' into stagingMarius Bakke
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
2018-03-17gnu: libvorbis: Ungraft.•••* gnu/packages/xiph.scm (libvorbis): Update to 1.3.6. [replacement]: Remove field. [source]: Remove patches. (libvorbis-1.3.6): Remove variable. Mark H Weaver
2018-03-17Merge branch 'master' into core-updatesMark H Weaver
2018-03-16gnu: binutils: Update to 2.30.•••* gnu/packages/patches/binutils-ld-new-dtags.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/base.scm (binutils): Update to 2.30. [source](patches): Remove obsolete patch. [arguments]: Add "--enable-new-dtags" in #:configure-flags. Marius Bakke
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
2018-03-16gnu: tar: Fix sparse file detection on Btrfs file systems.•••* gnu/packages/patches/tar-remove-wholesparse-check.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (tar)[source]: Add patch. Mark H Weaver
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
2018-03-15gnu: python: Update to 3.6.4.•••* gnu/packages/patches/python-3-search-paths.patch: Adjust context. * gnu/packages/python.scm (python): Update to 3.6.4. [source]: Re-enable test_socket.py. Marius Bakke
2018-03-15gnu: glib: Update to 2.56.0.•••* gnu/packages/glib.scm (glib): Update to 2.56.0. [source](patches): Remove obsolete patch. [arguments]: Disable new MIME test. * gnu/packages/patches/glib-respect-datadir.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Marius Bakke
2018-03-14gnu: patch: Update to 2.7.6.•••* gnu/packages/base.scm (patch): Update to 2.7.6. * gnu/packages/patches/patch-hurd-path-max.patch: Adjust to upstream changes. Marius Bakke
2018-03-14Merge branch 'master' into core-updatesRicardo Wurmus
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: libxcb: Update to 1.13.•••* gnu/packages/xorg.scm (libxcb): Update to 1.13. [source](patches): Remove. * gnu/packages/patches/libxcb-python-3.5-compat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Marius Bakke
2018-03-08gnu: xcb-proto: Update to 1.13.•••* gnu/packages/xorg.scm (xcb-proto): Update to 1.13. [source](patches): Remove. * gnu/packages/patches/xcb-proto-python3-print.patch, gnu/packages/patches/xcb-proto-python3-whitespace.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Marius Bakke
2018-03-08gnu: graphite2: Update to 1.3.11.•••* gnu/packages/patches/graphite2-ffloat-store.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/fontutils.scm (graphite2): Update to 1.3.11. [source](patches): Remove. Marius 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: glibc: Add a comment in the patch.•••* gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: Add a comment. Ludovic Courtès
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: thefuck: Update to 3.25.•••* gnu/packages/admin.scm (thefuck): Update to 3.25 [inputs]: Add python-pyte. [native-inputs]: Remove python-setuptools. * gnu/packages/patches/thefuck-test-environ.patch: Adjust to latest source. Eric Bavier
2018-03-06Merge branch 'master' into stagingLeo Famulari
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