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Commit Graph

45859 Commits

Author SHA1 Message Date
Ricardo Wurmus
c314ff7cd4 gnu: r-multiassayexperiment: Update to 1.12.1.
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.1.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
0718948912 gnu: r-rgadem: Update to 2.34.1.
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.34.1.
[propagated-inputs]: Add r-genomicranges.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
0be4d7de9c gnu: r-clusterprofiler: Update to 3.14.2.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.2.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
7621bf2d19 gnu: r-enrichplot: Update to 1.6.1.
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.1.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
eb6d1adf15 gnu: r-biocsingular: Update to 1.2.1.
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.2.1.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
be94400cd4 gnu: r-affycoretools: Update to 1.58.3.
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.58.3.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
366cb041e1 gnu: r-car: Update to 3.0-6.
* gnu/packages/statistics.scm (r-car): Update to 3.0-6.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
e2eb77598a gnu: r-robust: Update to 0.4-18.2.
* gnu/packages/statistics.scm (r-robust): Update to 0.4-18.2.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
96211e3f33 gnu: r-bigmemory: Update to 4.5.36.
* gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.36.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
adc1f22332 gnu: r-foreign: Update to 0.8-74.
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-74.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
976ef4cd52 gnu: r-slam: Update to 0.1-47.
* gnu/packages/cran.scm (r-slam): Update to 0.1-47.
2019-12-27 21:30:26 +01:00
Ricardo Wurmus
1d3c31a23c gnu: r-bibtex: Update to 0.4.2.1.
* gnu/packages/cran.scm (r-bibtex): Update to 0.4.2.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
04b181cb15 gnu: r-topgo: Update to 2.38.1.
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
4997ff5c1b gnu: r-summarizedexperiment: Update to 1.16.1.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
ba17429d67 gnu: r-delayedarray: Update to 0.12.1.
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
152a408051 gnu: r-biocparallel: Update to 1.20.1.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
827d0fa846 gnu: r-shortread: Update to 1.44.1.
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
2019-12-27 21:30:21 +01:00
Christopher Baines
abfe3c5aa2 gnu: guix-data-service: Update to 0.0.1-12.f56935a.
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-12.f56935a.
2019-12-27 14:47:29 +00:00
Nicolas Goaziou
6ab59cfd27 gnu: emacs-org-contrib: Update to 20191226.
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20191226.
2019-12-27 09:44:26 +01:00
Nicolas Goaziou
50257d2764 gnu: emacs-org: Update to 9.3.1.
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.1.
2019-12-27 09:42:02 +01:00
Brett Gilio
a9650f1135 gnu: emacs-telega: Update to 0.5.4.
* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.5.4.
[arguments]: Working around imagemagick and svg is no longer needed.
[native-inputs]: Replace emacs-minimal with emacs. This is needed because
bytecompilation requires fringe-bitmap support.
2019-12-26 13:10:37 -06:00
Hartmut Goebel
b291c9570d gnu: Add ffmpegthumbs.
* gnu/packages/kde-multimedia.scm (ffmpegthumbs): New variable.
2019-12-26 16:44:54 +01:00
Hartmut Goebel
2d11fbcf10 gnu: Add audiocd-kio.
* gnu/packages/kde-multimedia.scm (audiocd-kio): New variable.
2019-12-26 16:44:54 +01:00
Hartmut Goebel
6f936d8740 gnu: Add libkcompactdisc.
* gnu/packages/kde-multimedia.scm (libkcompactdisc): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
ca632dc175 gnu: Add kamoso.
* gnu/packages/kde-multimedia.scm (kamoso): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
abd4d57851 gnu: Add elisa.
* gnu/packages/kde-multimedia.scm (elisa): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
f66c7a5c0b gnu: Add kwave.
* gnu/packages/kde-multimedia.scm (kwave): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
49d40e60b8 gnu: Add kmplayer.
`guix lint` reports two CVEs, both are unrelated:
- CVE-2018-5200: for vendor "pandora" and some 4.2.2.x version
- CVE-2019-9133: windows only (I assume it it alsow relates to the "pandora"
  vendor, since the version the CVE refers to as "solving the issue" does not
  exist at KDE.)

* gnu/packages/kde-multimedia.scm (kmplayer): New variable.
* gnu/packages/patches/kmplayer-aarch64.patch,
  gnu/packages/patches/kmplayer-upstream_Fix-build-with-Qt-5.9.patch: New
  files.
* gnu/local.mk: Add them.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
d695c51dad gnu: Add kmix.
* gnu/packages/kde-multimedia.scm (kmix): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
d720ecb613 gnu: Add kaffeine.
* gnu/packages/kde-multimedia.scm (kaffeine): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
d1a6a94650 gnu: Add libkcddb.
* gnu/packages/kde-multimedia.scm (libkcddb): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
a5eddcd00f gnu: Add k3b.
* gnu/packages/kde-multimedia.scm (k3b): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
2f9bb949cb gnu: Add juk.
* gnu/packages/kde-multimedia.scm (juk): New variable.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
22b26dd257 gnu: Add dragon.
* gnu/packages/kde-multimedia.scm: New file.
* gnu/lokal.mk (MODULES): Add it.
2019-12-26 16:44:53 +01:00
Hartmut Goebel
a8e149434e gnu: Add audiofile.
Patches should fix all CVEs reported by `guix lint`:
CVE-2015-7747; CVE-2017-6827, CVE-2017-6828, CVE-2017-6829,
CVE-2017-6830, CVE-2017-6831, CVE-2017-6832, CVE-2017-6833,
CVE-2017-6834, CVE-2017-6835, CVE-2017-6836, CVE-2017-6837,
CVE-2017-6838, CVE-2017-6839; CVE-2018-13440; CVE-2018-17095

Since the patches do not reference to CVEs, it's a bit hard to tell which
patch actually closes which CVE.  Debian reports all these to be closed by
the patches below and NixPkgs provides references.

* gnu/packages/audio.scm (audiofile): New variable.
* gnu/packages/patches/audiofile-fix-datatypes-in-tests.patch,
  gnu/packages/patches/audiofile-fix-sign-conversion.patch,
  gnu/packages/patches/audiofile-CVE-2015-7747.patch,
  gnu/packages/patches/audiofile-CVE-2018-13440.patch,
  gnu/packages/patches/audiofile-CVE-2018-17095.patch,
  gnu/packages/patches/audiofile-Check-the-number-of-coefficients.patch,
  gnu/packages/patches/audiofile-Fail-on-error-in-parseFormat.patch,
  gnu/packages/patches/audiofile-Fix-index-overflow-in-IMA.cpp.patch,
  gnu/packages/patches/audiofile-Fix-multiply-overflow-sfconvert.patch,
  gnu/packages/patches/audiofile-Fix-overflow-in-MSADPCM-decodeSam.patch,
  gnu/packages/patches/audiofile-division-by-zero-BlockCodec-runPull.patch,
  gnu/packages/patches/audiofile-hurd.patch,
  gnu/packages/patches/audiofile-signature-of-multiplyCheckOverflow.patch:
  New files.
* gnu/local.mk: Add them.
2019-12-26 16:44:53 +01:00
Riku Viitanen
9d25a4548c gnu: python-fonttools: Update home-page.
https://github.com/behdad/fonttools permanently redirects to
https://github.com/fonttools/fonttools.

* gnu/packages/python-xyz.scm (python-fonttools)[home-page]: Change to current.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-12-26 15:58:21 +01:00
Marius Bakke
3ebaa635f7 gnu: i3-gaps: Update source checksum.
Fixes <https://bugs.gnu.org/38739>.  This is a follow-up to commit
88c9408070.

* gnu/packages/wm.scm (i3-gaps)[source](sha256): Change to the correct hash.
[build-system]: Remove field, because it is superfluous.
2019-12-26 15:45:13 +01:00
Arun Isaac
e7453b3cb5 gnu: gdal: Use HTTPS home page URI.
* gnu/packages/geo.scm (gdal)[home-page]: Use HTTPS URI.
2019-12-26 18:54:43 +05:30
Arun Isaac
6cde07379f gnu: gdal: Enable netCDF format driver.
* gnu/packages/geo.scm (gdal)[inputs]: Add netcdf.
2019-12-26 18:54:43 +05:30
Arun Isaac
838db4fcc7 gnu: gdal: Enable GPKG format driver.
* gnu/packages/geo.scm (gdal)[inputs]: Enable sqlite.
[arguments]: Add --with-sqlite3 to #:configure-flags.
2019-12-26 18:54:43 +05:30
Arun Isaac
0f05435682 gnu: gdal: Enable ODS format driver.
* gnu/packages/geo.scm (gdal)[inputs]: Add expat.
[arguments]: Add --with-expat to #:configure-flags.
2019-12-26 18:54:42 +05:30
Arun Isaac
1cbe7a3ed6 gnu: libspatialindex: Update to 1.9.3.
* gnu/packages/geo.scm (libspatialindex): Update to 1.9.3.
[build-system]: Switch to cmake-build-system.
[source]: Update URI.
2019-12-26 18:54:42 +05:30
Arun Isaac
75e2c05496 gnu: postgis: Update to 3.0.0.
* gnu/packages/geo.scm (postgis): Update to 3.0.0.
[inputs]: Add json-c and libjpeg-turbo. Replace proj.4 with proj.
2019-12-26 18:54:42 +05:30
Arun Isaac
e72557c08f gnu: gdal: Update to 3.0.2.
* gnu/packages/geo.scm (gdal): Update to 3.0.2.
[inputs]: Add proj.
2019-12-26 18:54:42 +05:30
Arun Isaac
f9d328833f gnu: libgeotiff: Update to 1.5.1.
* gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/geo.scm (libgeotiff): Update to 1.5.1.
[inputs]: Replace proj.4 with proj.
[sources]: Add libgeotiff-adapt-test-script-for-proj-6.2.patch
to patches.
2019-12-26 18:54:42 +05:30
Arun Isaac
3500d7addc gnu: Add proj.
* gnu/packages/geo.scm (proj): New variable.
2019-12-26 18:54:42 +05:30
Arun Isaac
d33afa26b4 gnu: geos: Update to 3.8.0.
* gnu/packages/geo.scm (geos): Update to 3.8.0.
2019-12-26 18:54:34 +05:30
Björn Höfling
00d81f9866 gnu: python-pyserial: Update to 3.4.
* gnu/packages/python-xyz.scm (python-pyserial): Update to 3.4.
2019-12-26 12:38:06 +01:00
Ricardo Wurmus
3c45b53ec9 gnu: Remove squashfs-tools-next.
* gnu/packages/compression.scm (squashfs-tools-next): Remove variable.
* guix/scripts/pack.scm (squashfs-image, guix-pack): Use squashfs-tools.
* tests/pack.scm: Use squashfs-tools.
2019-12-26 12:29:44 +01:00
Ricardo Wurmus
dedc66ef8e gnu: axoloti-patcher-next: Remove commented expression.
* gnu/packages/axoloti.scm (axoloti-patcher-next)[arguments]: Remove commented
substitute* expression.
2019-12-26 12:00:01 +01:00