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2018-11-17gnu: Add ClamAV....* gnu/packages/antivirus.scm: New file. * gnu/packages/patches/clamav-system-tomsfastmath.patch, gnu/packages/patches/clamav-config-llvm-libs.patch: New files. * gnu/local.mk (GNU_SYSTEM_MODULES): Add new module. (dist_patch_DATA): Add patches. Co-authored-by: Christopher Baines <mail@cbaines.net> Eric Bavier
2018-11-17gnu: Add TomsFastMath....* gnu/packages/multiprecision.scm (tomsfastmath): New variable. * gnu/packages/patches/tomsfastmath-constness.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it. Eric Bavier
2018-11-15gnu: emacs-realgud: Patch configure.ac to repair the build....This fixes https://bugs.gnu.org/33196, a build problem caused by a defective Elisp snippet in a check in configure.ac. * gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/emacs.scm (emacs-realgud)[source]: Use it. Maxim Cournoyer
2018-11-13gnu: Poppler: Fix CVE-2018-19149....* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (poppler)[replacement]: New field. (poppler/fixed): New variable. (poppler-qt4, poppler-qt5): Use package/inherit. Leo Famulari
2018-11-10gnu: icecat: Update to 60.3.0-gnu1....* gnu/packages/gnuzilla.scm (icecat): Update to 60.3.0-gnu1. [source]: Switch back to the normal source URI. Remove patches that are no longer applicable. * gnu/packages/patches/icecat-CVE-2018-12383.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Mark H Weaver
2018-11-09gnu: wxmaxima: Update to 18.10.1....* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1. [source]: Update URL and remove patch. * gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch. Kei Kebreau
2018-11-07gnu: hplip: Remove bundled non-free blobs....This fixes <https://bugs.gnu.org/32184>. * gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to remove non-free code and binary blobs. * gnu/packages/patches/hplip-remove-imageprocessor.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2018-11-07gnu: gemma: Update to 0.98....* gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/gemma-intel-compat.patch: Remove file. * gnu/packages/bioinformatics.scm (gemma): Update to 0.98. [source]: Remove patch. [inputs]: Add eigen, gfortran:lib, and openblas. [arguments]: Add phase "find-eigen". Ricardo Wurmus
2018-11-06gnu: libgit2: Work around test failures on 32-bit platforms....* gnu/packages/patches/libgit2-oom-test.patch: New file. * gnu/packages/version-control.scm (libgit2)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Ludovic Courtès
2018-11-06gnu: jq: Update to 1.6....* gnu/packages/web.scm (jq): Update to 1.6. [source]: Remove upstreamed patch. * gnu/packages/patches/jq-CVE-2015-8863.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-11-05gnu: xapian: Update to 1.4.9....* gnu/packages/patches/xapian-revert-5489fb2f8.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/search.scm (xapian): Update to 1.4.9. [source](patches): Remove. (python-xapian-bindings): Update to 1.4.9. Marius Bakke
2018-10-31gnu: myrepos: Update to 1.20180726....* gnu/packages/version-control.scm (myrepos): Update to 1.20180726. [source]: Remove patch. * gnu/packages/patches/myrepos-CVE-2018-7032.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner
2018-10-31gnu: meandmyshadow: Update to 0.5....* gnu/packages/games.scm (meandmyshadow): Update to 0.5. [source]: Add unreleased bugfix patch. [arguments]: Remove obsolete ‘set-sdl'paths’ phase. [inputs]: Switch to SDL 2. Add lua. Remove libx11, mesa, and glu. * gnu/packages/patches/meandmyshadow-define-paths-earlier.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Tobias Geerinckx-Rice
2018-10-30gnu: zathura-pdf-mupdf: Update to 0.3.4....* gnu/packages/pdf.scm (zathura-pdf-mupdf): Update to 0.3.4. [source]: Remove patch. * gnu/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner
2018-10-28gnu: mailutils: Update to 3.5....* gnu/packages/mail.scm (mailutils): Update to 3.5. [source]: Remove patch, remove snippet. [native-inputs]: Remove flex, bison. [inputs]: Remove guile-2.0, add guile-2.2. * gnu/packages/patches/mailutils-uninitialized-memory.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Efraim Flashner
2018-10-27gnu: Add telegram-purple....* gnu/packages/messaging.scm (telegram-purple): New variable. * gnu/packages/patches/telegram-purple-adjust-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Tomáš Čech
2018-10-26gnu: rust: Work around rust 1.25...1.27 reproducibility issues....* gnu/packages/patches/rust-mdbook-support-reproducible-builds-by-forcing-window.search.patch: New file. * gnu/local.mk (dist_patch_DATA): Add new patch file. * gnu/packages/rust.scm (rust-1.19): Use system libssh2 library. during cargo build. Note: libgit2 still bundled, because cargo tests assume specific libgit2 minor release. (rust-1.23): Inherit native-inputs from previous package. (rust-1.25): Switch back to llvm 3.9.1 as workaround for https://github.com/rust-lang/rust/issues/50556 issue. (rust-1.27): Apply changes from https://github.com/rust-lang-nursery/mdBook/pull/692 to make generation of "searchindex.js" files reproducible. Disable cargo test that required llvm 6. Nikolai Merinov
2018-10-24gnu: Add go-github-com-ipfs-go-ipfs-cmdkit-files....* gnu/packages/ipfs.scm (go-github-com-ipfs-go-ipfs-cmdkit-files): New variable. Pierre Neidhardt
2018-10-22gnu: 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 Peng
2018-10-21gnu: 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 Wurmus
2018-10-21gnu: 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 Wurmus
2018-10-21gnu: 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 Wurmus
2018-10-21gnu: 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 Bakke
2018-10-20gnu: 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 Baines
2018-10-17gnu: 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 Bakke
2018-10-17gnu: 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 Bakke
2018-10-16gnu: 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 Lassieur
2018-10-15gnu: 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 Flashner
2018-10-15gnu: 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-Rice
2018-10-10gnu: 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 Flashner
2018-10-09gnu: 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-Rice
2018-10-07gnu: 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 Famulari
2018-10-07gnu: 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 Nieuwenhuizen
2018-10-07gnu: Add java-w3c-smil....* gnu/packages/batik.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Danny Milosavljevic
2018-10-05gnu: 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 Kebreau
2018-10-05gnu: 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-Rice
2018-10-03quilt: 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 Bavier
2018-10-02quilt: 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 Bavier
2018-09-25gnu: 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 Weaver
2018-09-25gnu: 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 Weaver
2018-09-22gnu: 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 Weaver
2018-09-22gnu: 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 Woodcroft
2018-09-21gnu: 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 Weaver
2018-09-21gnu: 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 Weaver
2018-09-20gnu: 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 Wurmus
2018-09-19gnu: 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 Bakke
2018-09-14gnu: 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 Famulari
2018-09-13gnu: 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 Milosavljevic
2018-09-11netsurf: Register patch....Follow-up to f9e140a243b6d6b5d28bd0813b69604562a39653. * gnu/local.mk (dist_patch_DATA): Add netsurf-message-timestamp.patch. Eric Bavier
2018-09-10gnu: 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-Rice
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