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* gnu: liblxqt: Update to 0.13.0.•••* gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0. [source]: Remove patches. [home-page]: Use HTTPS. * gnu/packages/patches/liblxqt-include.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: 宋文武 <iyzsong@member.fsf.org> Meiyo Peng2018-10-221-14/+0
* gnu: delly: Update to 0.7.9.•••* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus2018-10-211-56/+0
* gnu: crossmap: Update to 0.2.9.•••* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus2018-10-211-121/+0
* gnu: tophat: Update to 2.1.1.•••* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus2018-10-211-24/+0
* gnu: libgxps: Update to 0.3.0.•••* gnu/packages/gnome.scm (libgxps): Update to 0.3.0. [source](patches): Remove. [build-system]: Switch to MESON-BUILD-SYSTEM. [inputs]: Change LIBJPEG to LIBJPEG-TURBO. * gnu/packages/patches/libgxps-CVE-2017-11590.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Marius Bakke2018-10-211-48/+0
* gnu: Add soundconverter.•••* gnu/packages/gnome.scm (soundconverter): New variable. * gnu/packages/patches/soundconverter-remove-gconf-dependency.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Christopher Baines2018-10-201-0/+83
* gnu: libssh: Update to 0.7.6 [fixes CVE-2018-10933].•••* gnu/packages/ssh.scm (libssh): Update to 0.7.6. * gnu/packages/patches/libssh-hostname-parser-bug.patch: Adjust patch. Leo Famulari2018-10-181-18/+4
* gnu: grub-efi: Fix an uninitialized variable issue.•••* gnu/packages/patches/grub-check-error-efibootmgr.patch: Add hunk to correct uninitialized variable. Ludovic Courtès2018-10-191-1/+22
* gnu: python2: Add upstream security fixes.•••This addresses CVE-2018-{1060,1061,14647,1000802}. * gnu/packages/patches/python2-CVE-2018-1000802.patch, gnu/packages/patches/python2-CVE-2018-1060.patch, gnu/packages/patches/python2-CVE-2018-1061.patch, gnu/packages/patches/python2-CVE-2018-14647.patch: New files. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/python.scm (python-2/fixed): New variable. (python-2.7)[replacement]: New field. (python2-minimal): Use PACKAGE/INHERIT. Marius Bakke2018-10-174-0/+148
* gnu: python: Fix CVE-2018-14647.•••* gnu/packages/patches/python-CVE-2018-14647.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/python.scm (python-3/fixed): New variable. (python-3.6)[replacement]: New field. (python-minimal, python-debug, wrap-python3): Use PACKAGE/INHERIT instead of standard inheritance. Marius Bakke2018-10-171-0/+61
* gnu: emacs-exwm: Update to 0.20.•••* gnu/packages/emacs.scm (emacs-exwm): Update to 0.20. [source]: Remove emacs-exwm-fix-fullscreen-issue.patch. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch: Remove patch. Clément Lassieur2018-10-161-27/+0
* gnu: x265: Fix building on armhf-linux and aarch64-linux.•••* gnu/packages/video.scm (x265)[source]: Update list of patches. [arguments]: Change configure flag to ensure PIC for all architectures. * gnu/packages/patches/x265-arm-asm-primitives.patch: Remove file. * gnu/packages/patches/x265-detect512-all-arches.patch: New file. * gnu/local.mk (dist_patch_DATA): Update patch registry. Efraim Flashner2018-10-152-360/+37
* gnu: x265: Update to 2.9.•••* gnu/packages/video.scm (x265): Update to 2.9. [source]: Remove x265-fix-ppc64le-build.patch. * gnu/packages/patches/x265-fix-ppc64le-build.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice2018-10-151-25/+0
* gnu: clisp: Update to 2.49.92.•••* gnu/packages/lisp.scm (clisp): Update to 2.49.92. [source]: Switch to git-fetch. Remove unneeded patch. [arguments]: Remove '--enable-portability' flag, add CFLAGS for armhf-linux. Update list of files needing substitutions in custom 'patch-sh-and-pwd phase. [home-page]: Update to new home-page. * gnu/packages/patches/clisp-glibc-2.26.patch: Remove file. & gnu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner2018-10-101-20/+0
* gnu: zstd: Update to 1.3.6.•••* gnu/packages/compression.scm (zstd): Update to 1.3.6. [source]: Remove merged patches. * gnu/packages/patches/zstd-fix-stdin-list-test.patch, gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. Tobias Geerinckx-Rice2018-10-092-97/+0
* gnu: crawl, crawl-tiles: Update to 0.22.1.•••* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.22.1. * gnu/packages/patches/crawl-upgrade-saves.patch: Update accordingly. Kei Kebreau2018-10-071-12/+13
* gnu: borg: The backup client cannot override the server-side storage quota.•••* gnu/packages/patches/borg-respect-storage-quota.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/backup.scm (borg)[source]: Use it. Leo Famulari2018-10-071-0/+32
* gnu: mes: Update to 0.18.•••* gnu/packages/patches/mes-nyacc-0.86.0.patch: Removef file. * gnu/local.mk (dist_patch_DATA): Remove entry. * gnu/packages/mes.scm (mes): Update to 0.18. Jan Nieuwenhuizen2018-10-071-197/+0
* gnu: gnucash: Update to 3.3.•••* gnu/packages/patches/gnucash-disable-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/gnucash.scm (gnucash): Update to 3.3. [source]: Add patch. [arguments]: Add 'set-env-vars', 'glib-or-gtk-compile-schemas', and 'glib-or-gtk-wrap' phases. Kei Kebreau2018-10-052-2/+42
* gnu: Add bastet.•••* gnu/packages/games.scm (bastet): New public variable. * gnu/packages/patches/bastet-change-source-of-unordered_set.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Tobias Geerinckx-Rice2018-10-051-0/+40
* quilt: Remove test workarounds.•••* gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch, gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/patchutils.scm (quilt)[source]: Use them. [arguments]: Remove workarounds in 'patch-tests' phase. Eric Bavier2018-10-032-0/+103
* quilt: Upgrade to 0.65.•••* gnu/packages/patches/quilt-test-fix-regex.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/patchutils.scm (quilt)[version]: Upgrade to 0.65. [source]: Use patch. [arguments]: Adjust 'patch-tests' phase for new tests. Re-enable "mail" test. Eric Bavier2018-10-021-0/+41
* gnu: ghc-haddock-library: Update to 1.5.0.1.•••* gnu/packages/patches/ghc-haddock-library-unbundle.patch: New file. * gnu/packages/haskell.scm (ghc-haddock-library): Update to 1.5.0.1. [source]: Add the patch; add a snippet to remove the bundled library. [arguments]: Add a phase to relax test suite dependency constraints and another to add a missing directory required for tests. [native-inputs]: Add ghc-base-compat, ghc-optparse-applicative, and ghc-tree-diff. Timothy Sample2018-10-011-0/+86
* gnu: icecat: Unbundle libevent, libogg, and libvorbis.•••* gnu/packages/patches/icecat-use-system-media-libs.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Add another hunk to enable removal of libevent. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch. In the snippet, add libevent, libogg, libvorbis, and libtremor to the list of bundled libraries to remove. Add a comment regarding theora. Remove comments regarding unbundling cairo, which is no longer supported. [inputs]: Add libevent, libogg, and libvorbis. [arguments]: Add --with-system-{libevent,ogg,vorbis} to configure flags. Add custom bootstrap phase. Add comments. Mark H Weaver2018-09-252-0/+395
* gnu: icecat: Unbundle graphite2 and harfbuzz.•••* gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch: New file. * gnu/packages/patches/icecat-use-system-graphite2.patch, gnu/packages/patches/icecat-use-system-harfbuzz.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Update accordingly. * gnu/packages/gnuzilla.scm (icecat)[source]: Add new patch. Delete bundled graphite2 and harfbuzz in snippet. [inputs]: Add graphite2 and harfbuzz. [arguments]: Add --with-system-{graphite2,harfbuzz} to configure flags. Mark H Weaver2018-09-253-527/+226
* gnu: icecat: Add fixes from upstream mozilla-esr60 [security fixes].•••Includes fixes for CVE-2018-12383 and CVE-2018-12385. * gnu/packages/patches/icecat-CVE-2018-12383.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Adapt to apply cleanly to IceCat 60. * gnu/packages/gnuzilla.scm (mozilla-patch): Update to fetch from mozilla-esr60. (icecat): Add selected changesets from upstream mozilla-esr60. Mark H Weaver2018-09-222-10/+113
* gnu: hmmer: Update to 3.2.1.•••* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1. [origin]: Remove patch. [license]: Change to BSD-3. [supported-systems]: New field. * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Ben Woodcroft2018-09-221-22/+0
* gnu: icecat: Update to 60.2.0-gnu1 (pre-release).•••* gnu/packages/gnuzilla.scm (icecat): Update to 60.2.0-gnu1. [source]: Download pre-release from alpha.gnu.org. Remove obsolete patches. Comment out the code to delete the bundled copies of libevent, cairo, harfbuzz, and graphite2. [inputs]: Use the latest ffmpeg. Comment out libevent, cairo, harfbuzz, and graphite2. [native-inputs]: Add rust and cargo. [arguments]: Remove --enable-gio and --disable-gnomeui. Add --disable-stylo. Comment out --with-system-{libevent,harfbuzz,graphite2}, --enable-system-cairo. Import %cargo-build-system-modules. Add 'patch-cargo-checksums' phase. * gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch, gnu/packages/patches/icecat-bug-1413868-pt1.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. Mark H Weaver2018-09-212-1104/+0
* gnu: libvpx: Add upstream security fix.•••* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/video.scm (libvpx)[source]: Add patch. Mark H Weaver2018-09-211-0/+34
* gnu: rsem: Update to 1.3.1.•••* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1. [source]: Fetch from git; remove patch; delete bundled samtools. [arguments]: Pass make flags; adjust phases. [inputs]: Remove ncurses and samtools-0.1; add htslib-1.3. * gnu/packages/patches/rsem-makefile.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus2018-09-201-682/+0
* gnu: Reinstate xf86-video-ast.•••* gnu/packages/patches/xf86-video-ast-remove-mibstore.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/xorg.scm (xf86-video-ast): New public variable. Marius Bakke2018-09-191-90/+0
* gnu: OpenSSL 1.1: Update to 1.1.1.•••* gnu/packages/tls.scm (openssl-next): Update to 1.1.1. [arguments]: Patch a `/usr/bin/env` invocation in the 'config' script. Adjust the documentation output. * gnu/packages/patches/openssl-1.1.0-c-rehash-in.patch: Rename and ... * gnu/packages/patches/openssl-1.1-c-rehash-in.patch: ... adjust patch. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Leo Famulari2018-09-141-3/+3
* gnu: rust: Accept more detailed gdb responses.•••* gnu/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/rust.scm (rust-1.25): Use it. (rust-1.26): Use it. (rust): Use it. Danny Milosavljevic2018-09-131-0/+94
* gnu: python-genshi: Update to 0.7.1.•••* gnu/packages/python-web.scm (python-genshi): Update to 0.7.1. [source]: Use GIT-FETCH and GIT-FILE-NAME. Remove patches. * gnu/packages/patches/python-genshi-add-support-for-python-3.4-AST.patch, gnu/packages/patches/python-genshi-buildable-on-python-2.7.patch, gnu/packages/patches/python-genshi-disable-speedups-on-python-3.3.patch, gnu/packages/patches/python-genshi-fix-tests-on-python-3.5.patch, gnu/packages/patches/python-genshi-isstring-helper.patch, gnu/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. Tobias Geerinckx-Rice2018-09-106-408/+0
* gnu: ldc: Update to 1.10.0.•••* gnu/packages/ldc.scm (ldc): Update to 1.10.0. [native-inputs]: Switch to LLVM and CLANG. (ldc-bootstrap)[synopsis, description]: Tweak. * gnu/packages/patches/ldc-disable-phobos-tests.patch: New file. * gnu/packages/patches/ldc-1.7.0-disable-phobos-tests.patch: Remove. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pjotr Prins2018-09-102-88/+22
* gnu: libgd: Fix CVE-2018-{5711,1000222}.•••* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd/fixed): New variable. * gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'. Leo Famulari2018-09-091-0/+87
* gnu: ghostscript: Update replacement to 9.24 [security fixes].•••The following CVEs are fixed with this release: CVE-2018-15908, CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509, CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539, CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543. * gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file. * gnu/packages/patches/ghostscript-CVE-2018-16509.patch, gnu/packages/patches/ghostscript-bug-699708.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24. [source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and 'ghostscript-runpath.patch'. Add 'ghostscript-CVE-2018-16509.patch' and 'ghostscript-bug-699708.patch'. [arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output directory. Marius Bakke2018-09-093-52/+353
* gnu: mes: Update to 0.17.1.•••* gnu/packages/patches/mes-nyacc-0.86.0.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0. (nyacc-for-mes): Remove. Jan Nieuwenhuizen2018-09-081-0/+197
* gnu: nyacc: Update to 0.86.0.•••* gnu/packages/patches/nyacc-binary-literals.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch. Jan Nieuwenhuizen2018-09-081-0/+29
* gnu: openexr: Update to 2.3.0.•••* gnu/packages/graphics.scm (openexr): Update to 2.3.0. [source](uri): Change to new download location. [source](snippet): Remove workaround. [source](patches): Remove. * gnu/packages/patches/openexr-missing-samples.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Marius Bakke2018-09-031-23/+0
* gnu: haskell-mode: Fix test failure.•••Fixes <https://bugs.gnu.org/31726>. Thanks to Jack Hill <jackhill@jackhill.us> for exploring different solutions at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31726>. * gnu/packages/patches/haskell-mode-unused-variables.patch, gnu/packages/patches/haskell-mode-make-check.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/emacs.scm (haskell-mode)[source]: Use them. [arguments]: Adjust 'pre-build' phase to embed file name. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Alex Vong2018-09-022-0/+79
* gnu: rust: Bootstrap (only) Rust 1.19.0 by mrustc.•••* gnu/packages/patches/rust-1.19-mrustc.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/rust.scm (rust-1.19)[source]: Add patch "rust-1.19-mrustc.patch". [arguments]<#:modules>: New field. <#:phases>[patch-cargo-tomls]: New phase. <#:phases>[build]: Modify. <#:phases>[install]: Modify. [native-inputs]: Replace rust-bootstrap by mrustc. (rust-1.23)[native-inputs]: New field. [arguments]<#:phases>: Delete phase "patch-cargo-tomls". Danny Milosavljevic2018-09-021-0/+28
* netsurf: Upgrade to 3.8.•••* gnu/packages/patches/netsurf-message-timestamp.patch: New patch. * gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source. * gnu/packages/web.scm (netsurf): Upgrade to 3.8. [source]: Add the new patch. Eric Bavier2018-08-302-12/+24
* Revert "gnu: snappy: Optimise."•••This causes too many rebuilds for the master branch. This reverts commit f96ed06805db934ff735e80596f1373dc1c2b5a8. Marius Bakke2018-08-291-36/+0
* gnu: snappy: Optimise.•••* gnu/packages/compression.scm (snappy)[source]: Build with ‘-O2’. * gnu/package/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Tobias Geerinckx-Rice2018-08-281-0/+36
* gnu: dropbear: Fix CVE-2018-15599.•••* gnu/packages/patches/dropbear-CVE-2018-15599.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ssh.scm (dropbear)[source]: Use it. Leo Famulari2018-08-281-0/+240
* gnu: GRUB: Check for errors from efibootmgr.•••* gnu/packages/patches/grub-check-error-efibootmgr.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/bootloaders.scm (grub)[source](patches): New field. Marius Bakke2018-08-281-0/+176
* gnu: python-pygit2: Update to 0.26.4.•••* gnu/packages/python.scm (python-pygit2, python2-pygit2): Update to 0.26.4. [source]: Remove 'python-pygit2-disable-network-tests.patch'. * gnu/packages/patches/python-pygit2-disable-network-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Leo Famulari2018-08-271-43/+0
* gnu: Add avogadro.•••* gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. Kei Kebreau2018-08-253-0/+833
* gnu: OpenSSH: Update to 7.8p1.•••* gnu/packages/ssh.scm (openssh): Update to 7.8p1. [source]: Remove 'openssh-CVE-2018-15473.patch'. * gnu/packages/patches/openssh-CVE-2018-15473.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Leo Famulari2018-08-241-165/+0
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