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45852 Commits

Author SHA1 Message Date
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
Christopher Baines 450a51b335 gnu: guix-data-service: Update to 0.0.1-11.7342280.
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-11.7342280.
2019-12-26 10:53:44 +00:00
Christopher Baines 03460d2bd3 gnu: mumimu: Remove reference to guile-email.
The use of guile-email in this package definition seems to cause errors when
working with other packages, errors like: error: guile-email: unbound variable

I'm not sure why the version of the Guile email package is appropriate here
either, but for now just to avoid the problems, inline the current version of
the package (and add a comment so this is more obvious). This issue was
probably introduced in: c7b2b53980

* gnu/packages/mail.scm (mumimu)[version]: Inline the current value
of (package-version guile-email) as a string.
2019-12-26 10:35:37 +00:00
Ricardo Wurmus 8f2e2120c7 gnu: bluez-alsa: Place dbus configuration in canonical location.
* gnu/packages/audio.scm (bluez-alsa)[arguments]: Install dbus configuration
files to /etc/dbus-1/system.d.
2019-12-26 11:22:28 +01:00
Ricardo Wurmus 1a37fd1e72 gnu: artanis: Update to 0.4.1.
* gnu/packages/guile-xyz.scm (artanis): Update to 0.4.1.
[inputs]: Add nss; move guile-json-1 and guile-redis from here...
[propagated-inputs]: ...to here; add guile-readline.
[arguments]: Add phase "patch-references-to-libnss".
2019-12-26 11:19:15 +01:00
Efraim Flashner fe338d7f00 gnu: Add zfs.
* gnu/packages/file-systems.scm (zfs): New variable.
2019-12-26 10:41:25 +02:00
Nicolas Goaziou 11140cf194 gnu: python-funcparserlib: Fix typo.
* gnu/packages/python-xyz.scm (python-funcparserlib): Fix typo in description.
2019-12-26 09:17:50 +01:00
Efraim Flashner 8f82e7e3dc gnu: python-pathos: Run test suite.
* gnu/packages/python-xyz.scm (python-pathos)[arguments]: Use custom
'check phase.
[native-inputs]: Add python-pytest.
2019-12-26 09:38:37 +02:00