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* gnu: metabat: Fix boost-related compilation issue.Ben Woodcroft2017-07-23
| | | | | | | | Reported by Leo Famulari. * gnu/packages/patches/metabat-fix-boost-issue.patch: New file. * gnu/packages/bioinformatics.scm (metabat): Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* Merge branch 'master' into core-updatesLeo Famulari2017-07-23
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| * gnu: metabat: Update to 2.11.1.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
| * gnu: bcftools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: bcftools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
| * gnu: quassel: Enable TLS.Ryan Moe2017-07-22
| | | | | | | | | | | | | | | | * gnu/packages/patches/quassel-fix-tls-check.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/irc.scm (quassel)[source]: Use it. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: Add openmolar.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | | | * gnu/packages/medical.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Co-authored-by: Quiliro <quiliro@fsfla.org>
| * gnu: Add cran module.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | * gnu/packages/cran.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/statistics.scm (r-colorspace): Move to cran.scm.
| * gnu: Remove python-fake-factory leftovers.Marius Bakke2017-07-22
| | | | | | | | | | | | | | This is a followup to c799eb2eb8b1a820147af96988eddaa9f752994b. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: python-pyopenssl: Update to 17.2.0.Marius Bakke2017-07-22
| | | | | | | | | | | | | | | | * gnu/packages/patches/python-pyopenssl-17.1.0-test-overflow.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update to 17.2.0. [native-inputs]: Add PYTHON-FLAKY. [source](patches): Remove.
| * gnu: heimdal: Fix CVE-2017-{6594,11103}.Alex Vong2017-07-20
| | | | | | | | | | | | | | * gnu/packages/patches/heimdal-CVE-2017-6594.patch, gnu/packages/patches/heimdal-CVE-2017-11103.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/kerberos.scm (heimdal)[source]: Use them.
| * gnu: Remove a left-over patch.Leo Famulari2017-07-20
| | | | | | | | | | | | | | This is a followup to commit 426b0b898f70a58133d80779980f163a5761686e. * gnu/packages/patches/pcre-CVE-2017-7186.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: Add libusb@0.1.Jonathan Brielmaier2017-07-20
| | | | | | | | | | | | | | | | * gnu/packages/libusb.scm (libusb-0.1): New variable. * gnu/packages/patches/libusb-0.1-disable-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
| * gnu: Add patches missing from dist_patch_DATA.Ben Woodcroft2017-07-20
| | | | | | | | | | | | | | | | | | | | Reported by Eric Bavier. * gnu/local.mk (dist_patch_DATA): Add gnu/packages/patches/hmmer-remove-cpu-specificity.patch, gnu/packages/patches/jacal-fix-texinfo.patch, gnu/packages/patches/python-pbr-fix-man-page-support.patch and gnu/packages/patches/vsearch-unbundle-cityhash.patch.
| * gnu: Rename (gnu packages gforth) to (gnu packages forth).ng02017-07-18
| | | | | | | | | | | | * gnu/local.mk (GNU_SYSTEM_MODULES): Rename gforth.scm to forth.scm. * gnu/packages/gforth.scm: Rename file to forth.scm. * gnu/packages/forth.scm: Renamed from gforth.scm.
| * gnu: qemu: Fix CVE-2017-11334.Leo Famulari2017-07-17
| | | | | | | | | | | | * gnu/packages/patches/qemu-CVE-2017-11334.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/virtualization.scm (qemu)[source]: Use it.
| * gnu: chicken: Fix CVE-2017-11343.Leo Famulari2017-07-17
| | | | | | | | | | | | * gnu/packages/patches/chicken-CVE-2017-11343.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/scheme.scm (chicken)[source]: Use it.
| * gnu: Add Poly/ML.Andy Patterson2017-07-17
| | | | | | | | | | | | | | * gnu/packages/sml.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: supertuxkart: Fix build on aarch64.Efraim Flashner2017-07-17
| | | | | | | | | | | | * gnu/packages/games.scm (supertuxkart)[source]: Add patch. * gnu/packages/patches/supertuxkart-angelscript-ftbfs.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
| * gnu: Add sooperlooper.Ricardo Wurmus2017-07-17
| | | | | | | | | | | | * gnu/packages/patches/sooperlooper-build-with-wx-30.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/music.scm (sooperlooper): New variable.
| * gnu: Rename (gnu packages qemu) to (gnu packages virtualization).宋文武2017-07-15
| | | | | | | | | | | | | | | | | | * gnu/packages/qemu.scm: Rename this ... * gnu/packages/virtualization.scm: ... to this. * gnu/local.mk (GNU_SYSTEM_MODULES), gnu/packages/bootloaders.scm, gnu/packages/debug.scm, gnu/packages/gnome.scm, gnu/system/vm.scm, gnu/tests/install.scm: Adjust accordingly.
| * bootloader: Add u-boot.Danny Milosavljevic2017-07-15
| | | | | | | | | | | | * gnu/bootloader/u-boot.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * doc/guix.texi: Document it.
| * gnu: evince: Fix CVE-2017-1000083.Marius Bakke2017-07-13
| | | | | | | | | | | | * gnu/packages/patches/evince-CVE-2017-1000083.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnome.scm (evince)[source]: Use it.
| * gnu: spice: Fix CVE-2017-7506.Leo Famulari2017-07-12
| | | | | | | | | | | | * gnu/packages/patches/spice-CVE-2017-7506.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/spice.scm (spice)[source]: Use it.
| * gnu: hop: Update to 3.1.0-pre2.Kei Kebreau2017-07-10
| | | | | | | | | | | | | | | | | | | | * gnu/packages/scheme.scm (hop): Update to 3.1.0-pre2. [source]: Remove unnecessary patch. [arguments]: Enable tests; disable parallel building; specify BIGLOO in make-flags. [inputs]: Add libgc, libunistring, libuv, pcre and sqlite. * gnu/local.mk (dist_patch_DATA): Remove unnecessary patch. * gnu/packages/patches/hop-linker-flags.patch: Delete file.
| * gnu: bigloo: Update to 4.3a.Kei Kebreau2017-07-10
| | | | | | | | | | | | | | * gnu/packages/scheme.scm (bigloo): Update to 4.3a. [source]: Remove old patch. Add snippet. [arguments]: Adjust the build phases accordingly. [inputs]: Add libgc, libunistring, libuv, openssl, pcre and sqlite.
* | gnu: guile-static-stripped: Update to 2.2.Ludovic Courtès2017-07-18
| | | | | | | | | | | | | | | | * gnu/packages/make-bootstrap.scm (%guile-static): Replace GUILE-2.0 with GUILE-2.2. Use "guile-2.2-default-utf8.patch" instead of "guile-default-utf8.patch". * gnu/packages/patches/guile-2.2-default-utf8.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* | Merge branch 'master' into core-updatesLeo Famulari2017-07-10
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| * gnu: libtiff: Fix two integer overflows.Leo Famulari2017-07-10
| | | | | | | | | | | | | | | | * gnu/packages/patches/libtiff-tiffycbcrtorgb-integer-overflow.patch, gnu/packages/patches/libtiff-tiffycbcrtorgbinit-integer-overflow.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/image.scm (libtiff-4.0.8)[source]: Use them.
| * gnu: ncurses: Fix CVE-2017-10684 and CVE-2017-10685.Leo Famulari2017-07-10
| | | | | | | | | | | | | | * gnu/packages/patches/ncurses-CVE-2017-10684-10685.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ncurses.scm (ncurses)[replacement]: New field. (ncurses/fixed): New variable.
| * gnu: poppler: Fix null pointer dereferences.Mark H Weaver2017-07-10
| | | | | | | | | | | | | | * gnu/packages/patches/poppler-fix-crash-with-broken-documents.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (poppler/fixed)[source]: Add the patch.
| * gnu: dblatex: Use texlive-union.Ricardo Wurmus2017-07-09
| | | | | | | | | | | | | | * gnu/packages/patches/dblatex-remove-multirow.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/docbook.scm (dblatex)[source]: Use patch. [inputs]: Replace "texlive" with a texlive-union.
| * gnu: poppler: Use an ABI-compatible replacement to fix CVE-2017-9776.Leo Famulari2017-07-09
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is a followup to commit 95bbaa02aa63bc5eae36f686f1ed9915663aa4cf. See <https://bugs.gnu.org/27621> for more information. Poppler 0.56.0's ABI is not compatible with Poppler 0.52.0, so it's not possible to graft the newer version in place of the older one. This change leaves CVE-2017-9775 unfixed for now. * gnu/packages/patches/poppler-CVE-2017-9776.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (poppler-0.56.0): Replace with ... (poppler/fixed): ... new variable. (poppler)[replacement]: Replaced with poppler/fixed.
| * gnu: blast+: Update to 2.6.0.Ben Woodcroft2017-07-08
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. Add patch. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. * gnu/packages/patches/blast+-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
| * gnu: python-pyopenssl: Fix test failure on 32-bit platforms.Marius Bakke2017-07-07
| | | | | | | | | | | | * gnu/packages/patches/python-pyopenssl-17.1.0-test-overflow.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pyopenssl)[source]: Use it.
| * gnu: libtiff: Fix CVE-2017-{9936,10688}.Alex Vong2017-07-07
| | | | | | | | | | | | | | | | | | * gnu/packages/patches/libtiff-CVE-2017-9936.patch, gnu/packages/patches/libtiff-CVE-2017-10688.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/image.scm (libtiff-4.0.8)[source]: Use them. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: xorg-server: Fix CVE-2017-{10971,10972}.Kei Kebreau2017-07-06
| | | | | | | | | | | | | | | | | | * gnu/packages/patches/xorg-server-CVE-2017-10971.patch, gnu/packages/patches/xorg-server-CVE-2017-10972.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xorg.scm (xorg-server)[source]: Use them. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: gemma: Fix building on non-Intel architectures.Efraim Flashner2017-07-04
| | | | | | | | | | | | | | * gnu/packages/patches/gemma-intel-compat.patch: New file. * gnu/packages/bioinformatics.scm (gemma)[source]: Add patch. [arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures. * gnu/local.mk (dist_patch_DATA): Register patch.
| * gnu: gajim: Update to 0.16.8.Arun Isaac2017-07-04
| | | | | | | | | | | | | | * gnu/packages/messaging.scm (gajim): Update to 0.16.8. [source]: Remove patch. * gnu/packages/patches/gajim-CVE-2016-10376.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * services: Add 'sysctl-service-type'.宋文武2017-07-04
| | | | | | | | | | | | * gnu/services/sysctl.scm: New file. * doc/guix.texi (Miscellaneous Services): Document it. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
| * gnu: python-pyopenssl: Update to 17.1.0.Marius Bakke2017-07-04
| | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update to 17.1.0. [source]: Remove patch. [native-inputs]: Add PYTHON-PRETEND. [arguments]<#:phases>: Disable the network test here instead of via a patch. Also disable one new test. * gnu/packages/patches/python-pyopenssl-skip-network-test.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: gcr: Enable working tests.Kei Kebreau2017-07-03
| | | | | | | | | | | | | | | | | | * gnu/packages/patches/gcr-disable-failing-tests.patch, gnu/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch: New files. * gnu/local.mk (dist_patch_DATA): Add patches. * gnu/packages/gnome.scm (gcr)[source]: Use patches. [arguments]: Enable tests.
* | gnu: ghostscript: Make "/CreationDate", "/ModDate" optional, depending on ↵Danny Milosavljevic2017-07-10
| | | | | | | | | | | | | | | | environment variable. * gnu/packages/patches/ghostscript-no-header-creationdate.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ghostscript.scm (ghostscript): Use it.
* | gnu: ghostscript: Make XMP UUID headers optional, depending on environment ↵Danny Milosavljevic2017-07-10
| | | | | | | | | | | | | | | | variable. * gnu/packages/patches/ghostscript-no-header-uuid.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ghostscript.scm (ghostscript): Use it.
* | gnu: ghostscript: Make "/ID" optional, depending on environment variable.Danny Milosavljevic2017-07-10
| | | | | | | | | | | | * gnu/packages/patches/ghostscript-no-header-id.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it * gnu/packages/ghostscript.scm (ghostscript): Use it.
* | gnu: groff: Remove timestamps.Danny Milosavljevic2017-07-10
| | | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/27593>. * gnu/packages/patches/groff-source-date-epoch.patch: New file. * gnu/local.mk: Add it. * gnu/packages/groff.scm (groff)[source]: Add it.
* | gnu: wget: Fix compilation with Perl 5.26; skip faulty tests.Ludovic Courtès2017-07-07
| | | | | | | | | | | | | | * gnu/packages/wget.scm (wget)[arguments]: New field. [source](patches): Add "wget-perl-5.26.patch". * gnu/packages/patches/wget-perl-5.26.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* | gnu: shishi: Build with latest libgcrypt.Leo Famulari2017-06-30
| | | | | | | | | | | | | | | | | | * gnu/packages/patches/shishi-fix-libgcrypt-detection.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/kerberos.scm (shishi)[source]: Use it. [inputs]: Use libgcrypt instead of libgcrypt-1.5. [arguments]: Set 'ac_cv_libgcrypt=yes' in #:configure-flags. * gnu/packages/gnupg.scm (libgcrypt-1.5): Remove variable.
* | Merge branch 'master' into core-updatesLeo Famulari2017-06-29
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| * gnu: ansible: Apply experimental patch to deal with wrapping of ansible script.Jelle Licht2017-06-29
| | | | | | | | | | | | | | | | | | | | | | See <http://lists.gnu.org/archive/html/bug-guix/2017-05/msg00015.html> for the rationale. * gnu/packages/patches/ansible-wrap-program-hack.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (ansible)[source]: Use it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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