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2017-03-10gnu: hmmer: Build reproducibly.Ben J. Woodcroft
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file. * gnu/packages/bioinformatics.scm (hmmer): Use it.
2017-03-09gnu: python-pandas: Really fix build on 32bit.Marius Bakke
* gnu/packages/patches/python-pandas-skip-failing-tests.patch: Fix confusion with same-named test.
2017-03-09gnu: python-fake-factory: Add back missing patch file.Mark H Weaver
This reverts the removal of "python-fake-factory-fix-build-32bit.patch" by commit ce7911ddae5d30ba73c8c9552b7d4e71268e5db3. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-03-08gnu: python-pandas: Fix build on 32-bit.Marius Bakke
* gnu/packages/patches/python-pandas-skip-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pandas, python2-pandas): Use it.
2017-03-08gnu: Add python-faker.Marius Bakke
* gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Adjust paths. Also rename to ... * gnu/packages/patches/python-faker-fix-build-32bit.patch: ... this. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python.scm (python-faker, python2-faker): New variables. (python-fake-factory)[properties]: Superseded by PYTHON-FAKER. (python2-fake-factory)[properties]: Superseded by PYTHON2-FAKER. (python-orator, python2-orator)[propagated-inputs]: Replace PYTHON-FAKE-FACTORY with PYTHON-FAKER.
2017-03-07gnu: pcre2: Update to 10.23.Marius Bakke
* gnu/packages/pcre.scm (pcre2): Update to 10.23. [source]: Remove patch. [arguments]: Add phase to substitute /bin/echo reference. * gnu/packages/patches/pcre2-CVE-2016-3191.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-03-07gnu: gnupg: Update to 2.1.19.Leo Famulari
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.19. [arguments]: Add 'patch-test-paths' phase and remove 'set-gnupg-home' phase. Add '--enable-gnupg-builddir-envvar' to #:configure-flags. [source]: Add 'gnupg-2.1-fix-Y2038-test-failure.patch'. * gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-03-06gnu: python-statsmodels: Update to 0.8.0.Marius Bakke
* gnu/packages/statistics.scm (python-statsmodels, python2-statsmodels): Update to 0.8.0. [source]: Use 'pypi-uri'. [arguments]: Add more files to matplotlib backend substitution. * gnu/packages/patches/python-statsmodels-fix-tests.patch: Drop test that fails with numpy 1.12. Remove previous contents.
2017-03-06gnu: python-matplotlib: Update to 2.0.0.Thomas Danckaert
* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Update to 2.0.0. [source]: Remove Tk backend patch, use Github instead of Sourceforge. [outputs]: Remove "doc" output. [inputs]: Add python-pyqt. [propagated-inputs]: Add python-cycler. [native-inputs]: Remove python-sphinx, python-numpydoc, texlive and texinfo. (python2-matplotlib)[native-inputs]: Add python2-functools32 and python2-subprocess32. (python-matplotlib-documentation, python2-matplotlib-documentation): New variables. * gnu/packages/patches/matplotlib-setupext-tk.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-03-06gnu: Add python2-subprocess32.Marius Bakke
* gnu/packages/python.scm (python2-subprocess32): New variable. * gnu/packages/patches/python2-subprocess32-disable-input-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-03-06gnu: texlive: Fix CVE-2016-10243.Leo Famulari
* gnu/packages/patches/texlive-texmf-CVE-2016-10243.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/tex.scm (texlive-texmf-src): Use it.
2017-03-04gnu: wxwidgets: Fix for Filezilla client.rennes
* gnu/packages/patches/wxwidgets-fix-windowGTK.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-04gnu: kio: Fix CVE-2017-6410.Leo Famulari
* gnu/packages/patches/kio-CVE-2017-6410.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/kde-frameworks.scm (kio)[source]: Use it.
2017-03-03gnu: arb: Update to 2.10.0.Andreas Enge
* gnu/packages/algebra.scm (arb): Update to 2.10.0. * gnu/packages/patches/arb-ldconfig.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
2017-03-03gnu: nss, nss-certs: Update to 3.29.2.Marius Bakke
* gnu/packages/certs.scm (nss-certs): Update to 3.29.2. * gnu/packages/gnuzilla.scm (nss): Update to 3.29.2. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to context changes.
2017-03-03Merge branch 'python-tests'Marius Bakke
2017-03-03gnu: mupdf: Fix CVE-2017-{5896,5991}.Alex Vong
* gnu/packages/patches/mupdf-CVE-2017-5896.patch, gnu/packages/patches/mupdf-CVE-2017-5991.patch: New files. * gnu/packages/pdf.scm (mupdf/fixed)[source]: Add patches. * gnu/local.mk (dist_patch_DATA): Add them. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-03-02gnu: Add jacal.John Darrington
* gnu/packages/maths.scm (jacal): New variable. * gnu/packages/patches/jacal-fix-texinfo.patch: New file.
2017-03-01gnu: vdirsyncer: Update to 0.15.0.Leo Famulari
* gnu/packages/dav.scm (vdirsyncer): Update to 0.15.0. [source]: Remove obsolete patch 'vdirsyncer-test-suite-slow-machines.patch'. * gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-02-28gnu: screen: Update to 4.5.1.Efraim Flashner
* gnu/packages/screen.scm (screen): Update to 4.5.1. [source]: Remove patch. * gnu/packages/patches/screen-CVE-2017-5618.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-02-27Merge branch 'master' into python-testsMarius Bakke
2017-02-27gnu: gst-plugins-base: Update to 1.10.4.Leo Famulari
* gnu/packages/gstreamer.scm (gst-plugins-base): Update to 1.10.4. [source]: Remove obsolete patch 'gst-plugins-base-fix-test-on-32bit.patch' * gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-02-26gnu: Remove unused patch.Marius Bakke
This is a followup to 6f9d5b2e8c861c3a1243937a26400f8394946346. * gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-02-26gnu: vim: Use upstream fix for CVE-2017-5953.Leo Famulari
* gnu/packages/patches/vim-CVE-2017-5953.patch: Adjust to match upstream changes.
2017-02-24gnu: python-dendropy: Fix failing tests.Ricardo Wurmus
* gnu/packages/patches/python-dendropy-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch.
2017-02-24gnu: python-fake-factory: Fix build on 32bit.Marius Bakke
* gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory)[source]: Use it.
2017-02-23gnu: util-linux: Fix CVE-2017-2616.Leo Famulari
* gnu/packages/patches/util-linux-CVE-2017-2616.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.
2017-02-23gnu: shadow: Fix CVE-2017-2616.Leo Famulari
* gnu/packages/patches/shadow-CVE-2017-2616.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (shadow): Use it.
2017-02-18gnu: ntfs-3g: Fix patch for CVE-2017-0358.Leo Famulari
This is a followup to commit 1a82ba660e88e731841882523084e5d878267b53. * gnu/packages/patches/ntfs-3g-CVE-2017-0358.patch: Make patch apply.
2017-02-18gnu: python-pbr: Support python-sphinx>=1.2.1.Danny Milosavljevic
* gnu/packages/patches/python-pbr-fix-man-page-support.patch: New file. * gnu/packages/python.scm (python-pbr-minimal): Use the new patch file.
2017-02-18gnu: vdirsyncer: Don't fail the test suite when the build machine is slow.Leo Famulari
* gnu/packages/patches/vdirsyncer-test-suite-slow-machines.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/dav.scm (vdirsyncer)[source]: Use it.
2017-02-14gnu: vim: Fix CVE-2017-5953.Leo Famulari
* gnu/packages/patches/vim-CVE-2017-5953.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/vim.scm (vim)[source]: Use it.
2017-02-13gnu: netsurf: Enable tests.Eric Bavier
* gnu/packages/patches/netsurf-longer-test-timeout.patch, gnu/packages/patches/netsurf-y2038-tests.patch: New patches. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/web.scm (netsurf)[source]: Use them. [native-inputs]: Add libidn, check. [inputs]: Add miscfiles. [arguments]: Remove #:tests?, add #:test-target. Add 'patch-check phase.
2017-02-13gnu: netsurf: Use unbundled source.Eric Bavier
* gnu/packages/patches/netsurf-system-utf8proc.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/web.scm (netsurf)[source]: Use it. Change to unbundled source tarball. [native-inputs]: Add netsurf-buildsystem, nsgenbind. Remove flex, bison. [inputs]: Add utf8proc, libcss, libdom, libnsbmp, libnsgif, libnspsl, libnsutils, libsvgtiny. Remove expat, gperf. [arguments]: Adjust #:make-flags for netsurf-buildsystem. Delete configure phase. Adjust source directories.
2017-02-13gnu: Add hubbub.Eric Bavier
* gnu/packages/web.scm (hubbub): New variable.
2017-02-13gnu: netsurf: Upgrade to 3.6.Eric Bavier
* gnu/packages/web.scm (netsurf): Upgrade to 3.6. [source]: 'https' -> 'http'. Remove modules, snippet, and patches. [home-page]: 'https' -> 'http'. [arguments]: Adjust source directories. * gnu/packages/patches/netsurf-about.patch: Delete patch. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-02-14gnu: python-pygit2: Skip tests requiring network access.Marius Bakke
* gnu/packages/python.scm (python-pygit2, python2-pygit2)[source](patches): New field. * gnu/packages/patches/python-pygit2-disable-network-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-02-13Merge branch 'master' into python-testsMarius Bakke
2017-02-12gnu: screen: Fix CVE-2017-5618.Leo Famulari
* gnu/packages/patches/screen-CVE-2017-5618.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/screen.scm (screen)[source]: Use it.
2017-02-12gnu: qemu: Fix CVE-2017-{5667,5898,5931}.Leo Famulari
* gnu/packages/patches/qemu-CVE-2017-5667.patch, gnu/packages/patches/qemu-CVE-2017-5898.patch, gnu/packages/patches/qemu-CVE-2017-5931.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. gnu/packages/qemu.scm (qemu)[source]: Use them.
2017-02-11gnu: spice: Fix CVE-2016-9577 and CVE-2016-9578.Marius Bakke
* gnu/packages/patches/spice-CVE-2016-9577.patch, gnu/packages/patches/spice-CVE-2016-9578-1.patch, gnu/packages/patches/spice-CVE-2016-9578-2.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them. * gnu/packages/spice.scm (spice)[source]: Use them.
2017-02-11gnu: slurm: Update to 16.05.9.1.Carolili
* gnu/packages/parallel.scm (slurm): Update to 16.05.9.1. * gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch: Removing two contribs which are added in the new version. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-02-11gnu: shadow: Update to 4.4.ng0
* gnu/packages/admin.scm (shadow): Update to 4.4. [source]: Adjust URL. * gnu/packages/patches/shadow-4.4-su-snprintf-fix.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patch. Signed-off-by: Leo Famulari <leo@famulari.name>
2017-02-09gnu: ntfs-3g: Fix CVE-2017-0358.Kei Kebreau
* gnu/packages/linux.scm (ntfs-3g)[source]: Add patch. * gnu/packages/patches/ntfs-3g-CVE-2017-0358.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2017-02-09gnu: libvpx: Update to 1.6.1.Marius Bakke
* gnu/packages/video.scm (libvpx): Update to 1.6.1. * gnu/packages/patches/libvpx-CVE-2016-2818.patch: Adjust to indentation changes.
2017-02-09gnu: vsearch: Update to 2.4.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0. [source]: Convert most operations in the snippet to patch form and adjust for 2.4.0. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-02-03gnu: p7zip: Fix CVE-2016-9256.Efraim Flashner
* gnu/packages/compression.scm (p7zip)[source]: Add patch. * gnu/packages/patches/p7zip-CVE-2016-9296.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2017-02-03gnu: qemu: Patch CVE-2017-{2615, 5578, 5579, 5856}.Efraim Flashner
* gnu/packages/qemu.scm (qemu)[source]: Add patches. * gnu/packages/patches/qemu-CVE-2017-2615, gnu/packages/patches/qemu-CVE-2017-5578, gnu/packages/patches/qemu-CVE-2017-5579, gnu/packages/patches/qemu-CVE-2017-5856: New files. * gnu/local.mk (dist_patch_DATA): Register them.
2017-02-02gnu: gst-plugins-base: Fix build on 32bit.Marius Bakke
* gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gstreamer.scm (gst-plugins-base)[source]: Use it.
2017-02-01gnu: httpd: Update to 2.4.25 [fixes CVE-2016-{0736,2161,5387,8743}].Leo Famulari
* gnu/packages/web.scm (httpd): Update to 2.4.25. [source]: Remove obsolete patch 'httpd-CVE-2016-8740.patch'. * gnu/packages/patches/httpd-CVE-2016-8740.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
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