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* Merge branch 'master' into core-updatesMarius Bakke2018-11-20
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| * gnu: Add missing patch to local.mk.Marius Bakke2018-11-20
| | | | | | | | | | | | This line was removed by accident in 0a41123f01d5d2466d6f533be3644ac8c9a2bdf9. * gnu/local.mk (dist_patch_DATA): Add "clang-3.5-libc-search-path.patch".
| * gnu: Add ClamAV.Eric Bavier2018-11-17
| | | | | | | | | | | | | | | | | | | | * 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>
| * gnu: Add TomsFastMath.Eric Bavier2018-11-17
| | | | | | | | | | | | * gnu/packages/multiprecision.scm (tomsfastmath): New variable. * gnu/packages/patches/tomsfastmath-constness.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it.
| * gnu: emacs-realgud: Patch configure.ac to repair the build.Maxim Cournoyer2018-11-15
| | | | | | | | | | | | | | | | | | 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.
* | gnu: qt@5: Fix build failure on glibc 2.28.Ludovic Courtès2018-11-18
| | | | | | | | | | | | * gnu/packages/patches/qt-5-renameat2.patch: New file. * gnu/packages/qt.scm (qt)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* | Merge branch 'master' into core-updatesMarius Bakke2018-11-14
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| * gnu: Poppler: Fix CVE-2018-19149.Leo Famulari2018-11-13
| | | | | | | | | | | | | | | | * 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.
| * gnu: icecat: Update to 60.3.0-gnu1.Mark H Weaver2018-11-10
| | | | | | | | | | | | | | | | * 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 Remove patches that are no longer applicable.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.
* | gnu: python-cffi: Fix test failure on i686.Marius Bakke2018-11-11
| | | | | | | | | | | | * gnu/packages/patches/python-cffi-x87-stack-clean.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/libffi.scm (python-cffi)[source](patches): Add it.
* | gnu: python-paste: Update to 3.0.4.Efraim Flashner2018-11-11
| | | | | | | | | | | | | | | | | | * gnu/packages/python-web.scm (python-paste): Update to 3.0.4. [source]: Remove patch, add snippet to remove one test. [native-inputs]: Add python-pytest, python-pytest-runner. * gnu/packages/patches/python-paste-remove-website-test.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* | gnu: python-networkx2: Remove variable.Efraim Flashner2018-11-11
| | | | | | | | | | | | | | * gnu/packages/python.scm (python-networkx2): Remove variable. * gnu/packages/patches/python-networkx2-reproducible-build.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* | Merge branch 'master' into core-updatesMarius Bakke2018-11-09
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| * gnu: wxmaxima: Update to 18.10.1.Kei Kebreau2018-11-09
| | | | | | | | | | | | | | | | * 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.
| * gnu: hplip: Remove bundled non-free blobs.Efraim Flashner2018-11-07
| | | | | | | | | | | | | | | | | | 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.
* | Merge branch 'master' into core-updatesMarius Bakke2018-11-07
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| * gnu: gemma: Update to 0.98.Ricardo Wurmus2018-11-07
| | | | | | | | | | | | | | | | | | * 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".
| * gnu: libgit2: Work around test failures on 32-bit platforms.Ludovic Courtès2018-11-06
| | | | | | | | | | | | * 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.
| * gnu: jq: Update to 1.6.Tobias Geerinckx-Rice2018-11-06
| | | | | | | | | | | | | | * 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.
* | gnu: ceph: Update to 13.2.2.Marius Bakke2018-11-07
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/ceph-skip-unittest_blockdev.patch: Adjust for 13.2.2. * gnu/packages/patches/ceph-rocksdb-compat.patch: Delete file. * gnu/packages/patches/ceph-detect-rocksdb.patch, gnu/packages/patches/ceph-volume-respect-PATH.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/storage.scm (ceph): Update to 13.2.2. [source]: Don't remove src/dpdk, which has been moved to src/spdk/dpdk and is purged elsewhere. Drop bundled rapidjson. Adjust patch list. [arguments]: Add "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" and "-DWITH_SPDK=OFF" to #:configure-flags. Drop obsolete "-DWITH_EMBEDDED". Add workaround for <https://bugs.gnu.org/30756>. Remove obsolete test substitution. Rework 'wrap-python-script' to be less verbose and wrap more scripts. [native-inputs]: Add GCC-7. [inputs]: Add OATH-TOOLKIT, RAPIDJSON and PYTHON2-SIX.
* | gnu: qtbase: Remove obsolete patch.Marius Bakke2018-11-06
| | | | | | | | | | | | | | | | | | This patch is no longer needed since 7930cfc98923eda64ec4a37d56b19f96f86f5f59 was merged to core-updates. * gnu/packages/patches/qtbase-glibc-compat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/qt.scm (qtbase)[source](patches): Drop it.
* | Merge branch 'master' into core-updatesMarius Bakke2018-11-05
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| * gnu: xapian: Update to 1.4.9.Marius Bakke2018-11-05
| | | | | | | | | | | | | | | | * 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.
| * gnu: myrepos: Update to 1.20180726.Efraim Flashner2018-10-31
| | | | | | | | | | | | | | * 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.
| * gnu: meandmyshadow: Update to 0.5.Tobias Geerinckx-Rice2018-10-31
| | | | | | | | | | | | | | | | | | * 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.
| * gnu: zathura-pdf-mupdf: Update to 0.3.4.Efraim Flashner2018-10-30
| | | | | | | | | | | | | | | | * 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.
| * gnu: mailutils: Update to 3.5.Efraim Flashner2018-10-28
| | | | | | | | | | | | | | | | | | * 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.
| * gnu: Add telegram-purple.Tomáš Čech2018-10-27
| | | | | | | | | | | | | | | | * 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>
| * gnu: rust: Work around rust 1.25...1.27 reproducibility issues.Nikolai Merinov2018-10-26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * gnu: Add go-github-com-ipfs-go-ipfs-cmdkit-files.Pierre Neidhardt2018-10-24
| | | | | | | | * gnu/packages/ipfs.scm (go-github-com-ipfs-go-ipfs-cmdkit-files): New variable.
* | Merge branch 'master' into core-updatesMarius Bakke2018-10-22
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| * gnu: liblxqt: Update to 0.13.0.Meiyo Peng2018-10-22
| | | | | | | | | | | | | | | | | | | | * 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>
| * gnu: delly: Update to 0.7.9.Ricardo Wurmus2018-10-21
| | | | | | | | | | | | | | | | | | | | * 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.
| * gnu: crossmap: Update to 0.2.9.Ricardo Wurmus2018-10-21
| | | | | | | | | | | | * 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.
| * gnu: tophat: Update to 2.1.1.Ricardo Wurmus2018-10-21
| | | | | | | | | | | | * 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.
* | Merge branch 'master' into core-updatesMarius Bakke2018-10-21
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| * gnu: libgxps: Update to 0.3.0.Marius Bakke2018-10-21
| | | | | | | | | | | | | | | | | | * 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.
| * gnu: Add soundconverter.Christopher Baines2018-10-20
| | | | | | | | | | | | * 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.
* | gnu: swig: Fix build on i686.Marius Bakke2018-10-18
| | | | | | | | | | | | * gnu/packages/patches/swig-guile-gc.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/swig.scm (swig)[source](patches): Use it.
* | gnu: Python: Adjust grafts for core-updates merge.Marius Bakke2018-10-17
| | | | | | | | | | | | | | | | | | | | | | | | This adjust the grafts from a55ebe2e3a7b438b4eec06c594440d3a0fb06a25 and 90aeaee861845142843a0f988fa4ff016c723cdb to apply to Python 2.7.15 and 3.7.0. * gnu/packages/patches/python2-CVE-2018-1060.patch, gnu/packages/patches/python2-CVE-2018-1061.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. * gnu/packages/python.scm (python-2/fixed): Remove patches that are already present in 2.7.15. (python-3/fixed): Remove obsolete phase.
* | Merge branch 'master' into core-updatesMarius Bakke2018-10-17
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| * gnu: python2: Add upstream security fixes.Marius Bakke2018-10-17
| | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * gnu: python: Fix CVE-2018-14647.Marius Bakke2018-10-17
| | | | | | | | | | | | | | | | | | * 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.
| * gnu: emacs-exwm: Update to 0.20.Clément Lassieur2018-10-16
| | | | | | | | | | | | | | * 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.
| * gnu: x265: Fix building on armhf-linux and aarch64-linux.Efraim Flashner2018-10-15
| | | | | | | | | | | | | | | | * 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.
| * gnu: x265: Update to 2.9.Tobias Geerinckx-Rice2018-10-15
| | | | | | | | | | | | | | * 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.
| * gnu: clisp: Update to 2.49.92.Efraim Flashner2018-10-10
| | | | | | | | | | | | | | | | | | | | | | * 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.
| * gnu: zstd: Update to 1.3.6.Tobias Geerinckx-Rice2018-10-09
| | | | | | | | | | | | | | | | * 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.
* | gnu: clang-runtime: Adapt for glibc@2.28.Efraim Flashner2018-10-15
| | | | | | | | | | | | | | * gnu/packages/llvm.scm (clang-runtime@3.7, clang-runtime@3.8, clang-runtime@3.9)[patches]: Add patch to work around removed ustat.h. * gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
* | gnu: python-testtools: Fix regression in test suite.Efraim Flashner2018-10-11
| | | | | | | | | | | | * gnu/packages/check.scm (python-testtools)[source]: Add patch. * gnu/packages/patches/python-testtools.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
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