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* gnu: r-clusterprofiler: Update to 3.14.2.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.2.
* gnu: r-enrichplot: Update to 1.6.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.1.
* gnu: r-biocsingular: Update to 1.2.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.2.1.
* gnu: r-affycoretools: Update to 1.58.3.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.58.3.
* gnu: r-car: Update to 3.0-6.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/statistics.scm (r-car): Update to 3.0-6.
* gnu: r-robust: Update to 0.4-18.2.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/statistics.scm (r-robust): Update to 0.4-18.2.
* gnu: r-bigmemory: Update to 4.5.36.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.36.
* gnu: r-foreign: Update to 0.8-74.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/statistics.scm (r-foreign): Update to 0.8-74.
* gnu: r-slam: Update to 0.1-47.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/cran.scm (r-slam): Update to 0.1-47.
* gnu: r-bibtex: Update to 0.4.2.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/cran.scm (r-bibtex): Update to 0.4.2.1.
* gnu: r-topgo: Update to 2.38.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
* gnu: r-summarizedexperiment: Update to 1.16.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
* gnu: r-delayedarray: Update to 0.12.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
* gnu: r-biocparallel: Update to 1.20.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
* gnu: r-shortread: Update to 1.44.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
* gnu: guix-data-service: Update to 0.0.1-12.f56935a.Christopher Baines2019-12-27
| | | | * gnu/packages/web.scm (guix-data-service): Update to 0.0.1-12.f56935a.
* gnu: emacs-org-contrib: Update to 20191226.Nicolas Goaziou2019-12-27
| | | | * gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20191226.
* gnu: emacs-org: Update to 9.3.1.Nicolas Goaziou2019-12-27
| | | | * gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.1.
* gnu: emacs-telega: Update to 0.5.4.Brett Gilio2019-12-26
| | | | | | | * 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.
* gnu: Add ffmpegthumbs.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (ffmpegthumbs): New variable.
* gnu: Add audiocd-kio.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (audiocd-kio): New variable.
* gnu: Add libkcompactdisc.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (libkcompactdisc): New variable.
* gnu: Add kamoso.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (kamoso): New variable.
* gnu: Add elisa.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (elisa): New variable.
* gnu: Add kwave.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (kwave): New variable.
* gnu: Add kmplayer.Hartmut Goebel2019-12-26
| | | | | | | | | | | | | | `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.
* gnu: Add kmix.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (kmix): New variable.
* gnu: Add kaffeine.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (kaffeine): New variable.
* gnu: Add libkcddb.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (libkcddb): New variable.
* gnu: Add k3b.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (k3b): New variable.
* gnu: Add juk.Hartmut Goebel2019-12-26
| | | | * gnu/packages/kde-multimedia.scm (juk): New variable.
* gnu: Add dragon.Hartmut Goebel2019-12-26
| | | | | * gnu/packages/kde-multimedia.scm: New file. * gnu/lokal.mk (MODULES): Add it.
* gnu: Add audiofile.Hartmut Goebel2019-12-26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: python-fonttools: Update home-page.Riku Viitanen2019-12-26
| | | | | | | | | 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>
* gnu: i3-gaps: Update source checksum.Marius Bakke2019-12-26
| | | | | | | | Fixes <https://bugs.gnu.org/38739>. This is a follow-up to commit 88c9408070280db51d1a0e604b9ec77f1611ab3c. * gnu/packages/wm.scm (i3-gaps)[source](sha256): Change to the correct hash. [build-system]: Remove field, because it is superfluous.
* gnu: gdal: Use HTTPS home page URI.Arun Isaac2019-12-26
| | | | * gnu/packages/geo.scm (gdal)[home-page]: Use HTTPS URI.
* gnu: gdal: Enable netCDF format driver.Arun Isaac2019-12-26
| | | | * gnu/packages/geo.scm (gdal)[inputs]: Add netcdf.
* gnu: gdal: Enable GPKG format driver.Arun Isaac2019-12-26
| | | | | * gnu/packages/geo.scm (gdal)[inputs]: Enable sqlite. [arguments]: Add --with-sqlite3 to #:configure-flags.
* gnu: gdal: Enable ODS format driver.Arun Isaac2019-12-26
| | | | | * gnu/packages/geo.scm (gdal)[inputs]: Add expat. [arguments]: Add --with-expat to #:configure-flags.
* gnu: libspatialindex: Update to 1.9.3.Arun Isaac2019-12-26
| | | | | | * gnu/packages/geo.scm (libspatialindex): Update to 1.9.3. [build-system]: Switch to cmake-build-system. [source]: Update URI.
* gnu: postgis: Update to 3.0.0.Arun Isaac2019-12-26
| | | | | * gnu/packages/geo.scm (postgis): Update to 3.0.0. [inputs]: Add json-c and libjpeg-turbo. Replace proj.4 with proj.
* gnu: gdal: Update to 3.0.2.Arun Isaac2019-12-26
| | | | | * gnu/packages/geo.scm (gdal): Update to 3.0.2. [inputs]: Add proj.
* gnu: libgeotiff: Update to 1.5.1.Arun Isaac2019-12-26
| | | | | | | | | | * 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.
* gnu: Add proj.Arun Isaac2019-12-26
| | | | * gnu/packages/geo.scm (proj): New variable.
* gnu: geos: Update to 3.8.0.Arun Isaac2019-12-26
| | | | * gnu/packages/geo.scm (geos): Update to 3.8.0.
* gnu: python-pyserial: Update to 3.4.Björn Höfling2019-12-26
| | | | * gnu/packages/python-xyz.scm (python-pyserial): Update to 3.4.
* gnu: Remove squashfs-tools-next.Ricardo Wurmus2019-12-26
| | | | | | * 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.
* gnu: axoloti-patcher-next: Remove commented expression.Ricardo Wurmus2019-12-26
| | | | | * gnu/packages/axoloti.scm (axoloti-patcher-next)[arguments]: Remove commented substitute* expression.
* gnu: guix-data-service: Update to 0.0.1-11.7342280.Christopher Baines2019-12-26
| | | | * gnu/packages/web.scm (guix-data-service): Update to 0.0.1-11.7342280.
* gnu: mumimu: Remove reference to guile-email.Christopher Baines2019-12-26
| | | | | | | | | | | | | 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: c7b2b539802eaa3f969e212c98eb671a1a75e9f3 * gnu/packages/mail.scm (mumimu)[version]: Inline the current value of (package-version guile-email) as a string.
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