79f09fa239
gnu: hmmer: Build reproducibly.
...
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
2017-03-10 20:31:30 +10:00
ce79279d34
gnu: python-pandas: Really fix build on 32bit.
...
* gnu/packages/patches/python-pandas-skip-failing-tests.patch: Fix confusion
with same-named test.
2017-03-09 16:39:08 +01:00
7b1866d783
gnu: python-fake-factory: Add back missing patch file.
...
This reverts the removal of "python-fake-factory-fix-build-32bit.patch"
by commit ce7911ddae
2017-03-09 06:08:18 -05:00
b03ee02f0d
gnu: python-pandas: Fix build on 32-bit.
...
* 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.
2017-03-08 18:04:23 +01:00
ce7911ddae
gnu: Add python-faker.
...
* 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(python-fake-factory)[properties]: Superseded by PYTHON-FAKER.
(python2-fake-factory)[properties]: Superseded by PYTHON2-FAKER.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.
2017-03-08 18:00:43 +01:00
9bb766e70d
gnu: pcre2: Update to 10.23.
...
* 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.
2017-03-07 23:21:22 +01:00
f11275c9e5
gnu: gnupg: Update to 2.1.19.
...
* 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.
2017-03-07 16:37:17 -05:00
6cb7477699
gnu: python-statsmodels: Update to 0.8.0.
...
* 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.
2017-03-06 23:24:11 +01:00
4535a93adb
gnu: python-matplotlib: Update to 2.0.0.
...
* 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>
2017-03-06 23:22:22 +01:00
550bd98b41
gnu: Add python2-subprocess32.
...
* 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.
2017-03-06 23:21:34 +01:00
e20784e65e
gnu: texlive: Fix CVE-2016-10243.
...
* 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.
2017-03-06 16:47:37 -05:00
40c611a41d
gnu: wxwidgets: Fix for Filezilla client.
...
* 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>
2017-03-04 23:15:01 -05:00
c35745edc4
gnu: kio: Fix CVE-2017-6410.
...
* 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.
2017-03-04 18:35:17 -05:00
21abf092a4
gnu: arb: Update to 2.10.0.
...
* 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.
2017-03-03 18:33:19 +01:00
3b175eab84
gnu: nss, nss-certs: Update to 3.29.2.
...
* 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.
2017-03-03 17:26:24 +01:00
3f98071ac5
Merge branch 'python-tests'
2017-03-03 16:55:43 +01:00
92ae98e2a0
gnu: mupdf: Fix CVE-2017-{5896,5991}.
...
* 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>
2017-03-03 04:47:52 -05:00
479c4273e6
gnu: Add jacal.
...
* gnu/packages/maths.scm (jacal): New variable.
* gnu/packages/patches/jacal-fix-texinfo.patch: New file.
2017-03-02 18:17:26 +01:00
d8bcf08088
gnu: vdirsyncer: Update to 0.15.0.
...
* 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.
2017-03-01 22:33:11 -05:00
13e4a6c863
gnu: screen: Update to 4.5.1.
...
* 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.
2017-02-28 21:01:26 +02:00
8779987bba
Merge branch 'master' into python-tests
2017-02-27 12:42:22 +01:00
1d8e727357
gnu: gst-plugins-base: Update to 1.10.4.
...
* 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.
2017-02-27 04:04:51 -05:00
b01a89854b
gnu: Remove unused patch.
...
This is a followup to 6f9d5b2e8c
2017-02-26 21:41:21 +01:00
ffa771d2b4
gnu: vim: Use upstream fix for CVE-2017-5953.
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* gnu/packages/patches/vim-CVE-2017-5953.patch: Adjust to match upstream changes.
2017-02-26 12:04:16 -05:00
1885bb0c08
gnu: python-dendropy: Fix failing tests.
...
* 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.
2017-02-24 23:44:31 +01:00
42945fb58c
gnu: python-fake-factory: Fix build on 32bit.
...
* 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.
2017-02-24 18:55:29 +01:00
1d311009fe
gnu: util-linux: Fix CVE-2017-2616.
...
* 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.
2017-02-23 15:01:54 -05:00
1c851cbe0c
gnu: shadow: Fix CVE-2017-2616.
...
* 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.
2017-02-23 14:59:50 -05:00
bd1450f1e4
gnu: ntfs-3g: Fix patch for CVE-2017-0358.
...
This is a followup to commit 1a82ba660e
2017-02-18 14:20:38 -05:00
a1e3ed6e8b
gnu: python-pbr: Support python-sphinx>=1.2.1.
...
* gnu/packages/patches/python-pbr-fix-man-page-support.patch: New file.
* gnu/packages/python.scm (python-pbr-minimal): Use the new patch file.
2017-02-18 16:43:37 +01:00
945b6721eb
gnu: vdirsyncer: Don't fail the test suite when the build machine is slow.
...
* 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.
2017-02-18 10:24:03 -05:00
1ae04e3511
gnu: vim: Fix CVE-2017-5953.
...
* 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.
2017-02-14 14:24:04 -05:00
4fc282b32a
gnu: netsurf: Enable tests.
...
* 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.
2017-02-13 22:28:33 -06:00
710806b57b
gnu: netsurf: Use unbundled source.
...
* 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.
2017-02-13 22:28:33 -06:00
43bfbf1370
gnu: Add hubbub.
...
* gnu/packages/web.scm (hubbub): New variable.
2017-02-13 22:28:25 -06:00
57c211cd71
gnu: netsurf: Upgrade to 3.6.
...
* 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.
2017-02-13 20:59:19 -06:00
bb6043fe9f
gnu: python-pygit2: Skip tests requiring network access.
...
* 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.
2017-02-14 00:04:59 +01:00
424b1ae769
Merge branch 'master' into python-tests
2017-02-13 22:35:05 +01:00
d6065945ff
gnu: screen: Fix CVE-2017-5618.
...
* 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.
2017-02-12 10:26:02 -05:00
37acc8a07b
gnu: qemu: Fix CVE-2017-{5667,5898,5931}.
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* 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.
2017-02-12 10:25:53 -05:00
ae953ead0f
gnu: spice: Fix CVE-2016-9577 and CVE-2016-9578.
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* 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.
2017-02-11 20:12:41 +01:00
dcb550e599
gnu: slurm: Update to 16.05.9.1.
...
* 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>
2017-02-11 20:12:41 +01:00
4153ef23f5
gnu: shadow: Update to 4.4.
...
* 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>
2017-02-11 13:43:42 -05:00
1a82ba660e
gnu: ntfs-3g: Fix CVE-2017-0358.
...
* 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.
2017-02-09 22:27:51 -05:00
65064909ed
gnu: libvpx: Update to 1.6.1.
...
* gnu/packages/video.scm (libvpx): Update to 1.6.1.
* gnu/packages/patches/libvpx-CVE-2016-2818.patch: Adjust to indentation changes.
2017-02-09 14:58:54 +01:00
206af46fe1
gnu: vsearch: Update to 2.4.0.
...
* 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.
2017-02-09 21:21:29 +10:00
1ac675a583
gnu: p7zip: Fix CVE-2016-9256.
...
* 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.
2017-02-03 22:17:41 +02:00
b352b57655
gnu: qemu: Patch CVE-2017-{2615, 5578, 5579, 5856}.
...
* 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.
2017-02-03 21:56:35 +02:00
feeeee2418
gnu: gst-plugins-base: Fix build on 32bit.
...
* 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.
2017-02-02 16:55:35 +01:00
a3df7e9f86
gnu: httpd: Update to 2.4.25 [fixes CVE-2016-{0736,2161,5387,8743}].
...
* 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.
2017-02-01 18:14:55 -05:00
Ben J. Woodcroft