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2019-12-27gnu: r-multiassayexperiment: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.1.
2019-12-27gnu: r-rgadem: Update to 2.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.34.1. [propagated-inputs]: Add r-genomicranges.
2019-12-27gnu: r-clusterprofiler: Update to 3.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.2.
2019-12-27gnu: r-enrichplot: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.1.
2019-12-27gnu: r-biocsingular: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.2.1.
2019-12-27gnu: r-affycoretools: Update to 1.58.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.58.3.
2019-12-27gnu: r-car: Update to 3.0-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 3.0-6.
2019-12-27gnu: r-robust: Update to 0.4-18.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robust): Update to 0.4-18.2.
2019-12-27gnu: r-bigmemory: Update to 4.5.36.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.36.
2019-12-27gnu: r-foreign: Update to 0.8-74.Ricardo Wurmus
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-74.
2019-12-27gnu: r-slam: Update to 0.1-47.Ricardo Wurmus
* gnu/packages/cran.scm (r-slam): Update to 0.1-47.
2019-12-27gnu: r-bibtex: Update to 0.4.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-bibtex): Update to 0.4.2.1.
2019-12-27gnu: r-topgo: Update to 2.38.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27gnu: r-summarizedexperiment: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27gnu: r-delayedarray: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27gnu: r-biocparallel: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27gnu: r-shortread: Update to 1.44.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
2019-12-27gnu: guix-data-service: Update to 0.0.1-12.f56935a.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-12.f56935a.
2019-12-27doc: Mention "make authenticate".Ludovic Courtès
* doc/contributing.texi (Building from Git): Add instructions to run 'git verify-commit' and 'make authenticate'.
2019-12-27git-authenticate: Keep a local cache of previously-authenticated commits.Ludovic Courtès
A list of already-authenticated commits is kept in ~/.cache/guix/authentication. This speeds up subsequent "make authenticate" invocations. * build-aux/git-authenticate.scm (authenticated-commit-cache-file) (previously-authenticated-commits, cache-authenticated-commit): New procedures. (git-authenticate): Define 'authenticated-commits' and pass it as a third argument to 'commit-difference'. Add call to 'cache-authenticated-commit'. Don't display signing stats when STATS is null.
2019-12-27git: 'commit-difference' takes a list of excluded commits.Ludovic Courtès
* guix/git.scm (commit-closure): Add 'visited' optional parameter. (commit-difference): Add 'excluded' optional parameter; pass second argument to 'commit-closure'. * tests/git.scm ("commit-difference, excluded commits"): New test.
2019-12-27Add 'build-aux/git-authenticate.scm'.Ludovic Courtès
* build-aux/git-authenticate.scm: New file. * Makefile.am (EXTRA_DIST): Add it. (commit_v1_0_1): New variable. (authenticate): New target.
2019-12-27gnu: emacs-org-contrib: Update to 20191226.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20191226.
2019-12-27gnu: emacs-org: Update to 9.3.1.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.1.
2019-12-26gnu: emacs-telega: Update to 0.5.4.Brett Gilio
* 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.
2019-12-26gnu: Add ffmpegthumbs.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (ffmpegthumbs): New variable.
2019-12-26gnu: Add audiocd-kio.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (audiocd-kio): New variable.
2019-12-26gnu: Add libkcompactdisc.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (libkcompactdisc): New variable.
2019-12-26gnu: Add kamoso.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kamoso): New variable.
2019-12-26gnu: Add elisa.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (elisa): New variable.
2019-12-26gnu: Add kwave.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kwave): New variable.
2019-12-26gnu: Add kmplayer.Hartmut Goebel
`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.
2019-12-26gnu: Add kmix.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kmix): New variable.
2019-12-26gnu: Add kaffeine.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kaffeine): New variable.
2019-12-26gnu: Add libkcddb.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (libkcddb): New variable.
2019-12-26gnu: Add k3b.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (k3b): New variable.
2019-12-26gnu: Add juk.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (juk): New variable.
2019-12-26gnu: Add dragon.Hartmut Goebel
* gnu/packages/kde-multimedia.scm: New file. * gnu/lokal.mk (MODULES): Add it.
2019-12-26gnu: Add audiofile.Hartmut Goebel
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.
2019-12-26gnu: python-fonttools: Update home-page.Riku Viitanen
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>
2019-12-26gnu: i3-gaps: Update source checksum.Marius Bakke
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.
2019-12-26download: Enable TLS 1.3.Marius Bakke
This reverts commit e4ee84202633636b4c8cef4a332f0c74912a3b23. * guix/build/download.scm (tls-wrap): Dot not disable TLS 1.3.
2019-12-26gnu: gdal: Use HTTPS home page URI.Arun Isaac
* gnu/packages/geo.scm (gdal)[home-page]: Use HTTPS URI.
2019-12-26gnu: gdal: Enable netCDF format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Add netcdf.
2019-12-26gnu: gdal: Enable GPKG format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Enable sqlite. [arguments]: Add --with-sqlite3 to #:configure-flags.
2019-12-26gnu: gdal: Enable ODS format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Add expat. [arguments]: Add --with-expat to #:configure-flags.
2019-12-26gnu: libspatialindex: Update to 1.9.3.Arun Isaac
* gnu/packages/geo.scm (libspatialindex): Update to 1.9.3. [build-system]: Switch to cmake-build-system. [source]: Update URI.
2019-12-26gnu: postgis: Update to 3.0.0.Arun Isaac
* gnu/packages/geo.scm (postgis): Update to 3.0.0. [inputs]: Add json-c and libjpeg-turbo. Replace proj.4 with proj.
2019-12-26gnu: gdal: Update to 3.0.2.Arun Isaac
* gnu/packages/geo.scm (gdal): Update to 3.0.2. [inputs]: Add proj.
2019-12-26gnu: libgeotiff: Update to 1.5.1.Arun Isaac
* 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.
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