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* Merge branch 'master' into core-updatesMarius Bakke2018-10-05
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| * gnu: samtools-0.1: Adjust to match changes in samtools.Ricardo Wurmus2018-10-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make flags.
| * gnu: deeptools: Update to 3.1.2.Ricardo Wurmus2018-10-05
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2. [source]: Fetch from git. [arguments]: Delete reset-gzip-timestamps phase. [inputs]: Add python-plotly.
| * gnu: python-pysam: Update to 0.15.1.Ricardo Wurmus2018-10-05
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1. [source]: Fetch from git. [arguments]: Delete tests requiring internet access; use "invoke". [inputs]: Add curl.
| * gnu: python-plotly: Add python-pandas to inputs.Ricardo Wurmus2018-10-05
| | | | | | | | | | * gnu/packages/graph.scm (python-plotly)[propagated-inputs]: Add python-pandas.
| * gnu: bcftools: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.9. [arguments]: Remove obsolete make flags.
| * gnu: samtools: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.9. [origin]: Remove bundled htslib sources. [arguments]: Remove obsolete make-flags.
| * gnu: htslib: Update to 1.9.Ricardo Wurmus2018-10-05
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
| * gnu: icecat: Add fixes from mozilla-esr60 [security fixes].Mark H Weaver2018-10-04
| | | | | | | | | | | | | | Includes fixes for CVE-2018-12386 and CVE-2018-12387. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr60 repository.
| * gnu: linux-libre: Update to 4.18.12.Mark H Weaver2018-10-04
| | | | | | | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.12. (%linux-libre-hash): Update hash.
| * gnu: linux-libre@4.14: Update to 4.14.74.Mark H Weaver2018-10-04
| | | | | | | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.74. (%linux-libre-4.14-hash): Update hash.
| * gnu: linux-libre@4.9: Update to 4.9.131.Mark H Weaver2018-10-04
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.131.
| * gnu: petsc-openmpi: Configure with support for MUMPS solver.Paul Garlick2018-10-04
| | | | | | | | | | | | | | | | | | * gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add metis, mumps-openmpi, scalapack and pt-scotch. [arguments]: Add "--with-PACKAGENAME=1" flags. Move 'mpi-setup' phase ahead of 'configure' phase. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: hiawatha: Set sane run-time directory defaults.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | | | * gnu/packages/web.scm (hiawatha)[arguments]: Set sane default directories. Replace the 'remove-empty-dirs' phase with a 'install-no-empty-directories' one.
| * gnu: hwloc: Update to 2.0.2.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/mpi.scm (hwloc): Update to 2.0.2.
| * gnu: Add nsd.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/dns.scm (nsd): New public variable.
| * gnu: guile-next: Update to commit 6f3357b0df64c4be17e72079864c09a542f1c779.David Thompson2018-10-04
| | | | | | | | | | * gnu/packages/guile.scm (guile-next): Update to commit 6f3357b0df64c4be17e72079864c09a542f1c779.
| * gnu: guile-next: Add the correct native search paths.David Thompson2018-10-04
| | | | | | | | * gnu/packages/guile.scm (guile-next): Add native search paths for version 3.0.
| * gnu: hiawatha: Support HTTP/2.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | | | * gnu/packages/web.sck (hiawatha)[arguments]: USE_SYSTEM_NGHTTP2 to ENABLE_HTTP2. [inputs]: Add nghttp2:lib.
| * gnu: hiawatha: Update to 10.8.3.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | | | | | * gnu/packages/web.scm (hiawatha): Update to 10.8.3. [source]: Also delete bundled copy of nghttp2. [inputs]: Use mbedtls-for-hiawatha instead of vanilla mbedtls-apache. * gnu/packages/tls.scm (mbedtls-for-hiawatha): New public variable.
| * gnu: mbedtls-apache: Update to 2.13.0 [security fixes].Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | * gnu/packages/tls.scm (mbedtls-apache): Update to 2.13.0. [native-inputs]: Add python.
| * gnu: geos: Update to 3.7.0.Arun Isaac2018-10-04
| | | | | | | | * gnu/packages/geo.scm (geos): Update to 3.7.0.
| * gnu: hexedit: Update to 1.4.2.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | | | * gnu/packages/hexedit.scm (hexedit): Update to 1.4.2. [source]: Use the author's more up-to-date git repository. [native-inputs]: Add autoconf and automake.
| * gnu: html-xml-utils: Update to 7.7.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/xml.scm (html-xml-utils): Update to 7.7.
| * gnu: perl-xml-feed: Update to 0.54.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/xml.scm (perl-xml-feed): Update to 0.54.
| * gnu: guix: Update to 1d0be47.Ludovic Courtès2018-10-04
| | | | | | | | * gnu/packages/package-management.scm (guix): Update to 1d0be47.
| * gnu: escpr: Update to 1.6.30.Diego Nicola Barbato2018-10-04
| | | | | | | | | | | | * gnu/packages/cups.scm (escpr): Update to 1.6.30. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: opencv: Update to 3.4.3.Björn Höfling2018-10-04
| | | | | | | | | | | | | | | | [[PGP Signed Part:Good signature from BF286CB6593E5FFD Björn Höfling <bjoern.hoefling@bjoernhoefling.de> (trust undefined) created at 2018-10-03T22:28:20+0200 using DSA]] * gnu/packages/image-processing.scm (opencv): Update to 3.4.3. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: r-acclma: Fix uses of @acronym in description.Ludovic Courtès2018-10-04
| | | | | | | | | | | | * gnu/packages/cran.scm (r-acclma)[description]: Fix order of arguments to @acronym. The wrong order was causing 'stexi->shtml' to fail (match error).
| * services: rottlog: Use command strings in the mcron jobs.Ludovic Courtès2018-10-04
| | | | | | | | | | | | * gnu/services/admin.scm (default-jobs): Remove the lambda around "/…/bin/rottlog" to make "herd schedule mcron" more transparent (otherwise it just says "Lambda function").
| * gnu: mpv: Update to 0.29.1.Rutger Helling2018-10-04
| | | | | | | | * gnu/packages/video.scm (mpv): Update to 0.29.1.
| * gnu: retroarch: Update to 1.7.5.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/emulators.scm (retroarch): Update to 1.7.5.
| * gnu: retroarch: Don't use unstable tarball.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/emulators.scm (retroarch)[source]: Use GIT-FETCH and GIT-FILE-NAME.
| * gnu: ephoto: Fix typos in description.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | * gnu/packages/enlightenment.scm (ephoto)[description]: Fix typos. Wrap at 80 columns.
| * gnu: perl-string-copyright: Update to 0.003006.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/license.scm (perl-string-copyright): Update to 0.003006.
| * gnu: rpm: Update to 4.14.2.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | | | | | | | * gnu/packages/package-management.scm (rpm): Update to 4.14.2. [arguments]: Rename 'set-nspr-search-path' phase to 'set-nss-library-path' and remove CPATH work-around. Remove obsolete 'fix-rpm-symlinks' phase. [home-page]: Drop www.
| * gnu: imapfilter: Update to 2.6.12.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/mail.scm (imapfilter): Update to 2.6.12.
| * gnu: imapfilter: Don't use unstable tarball.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/mail.scm (imapfilter)[source]: Use GIT-FETCH and GIT-FILE-NAME.
| * gnu: nickle: Update to 2.82.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/nickle.scm (nickle): Update to 2.82.
| * gnu: ddcutil: Update to 0.9.2.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/hardware.scm (ddcutil): Update to 0.9.2.
| * gnu: ndctl: Return #t from phases.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | * gnu/packages/disk (ndctl)[arguments]: Rename inaccurately named 'autogen' phase to 'patch-FHS-file-names'. Explicitly return #t.
| * gnu: disorderfs: Update to 0.5.4.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/file-systems.scm (disorderfs): Update to 0.5.4.
| * gnu: packagekit: Update to 1.1.11.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/freedesktop.scm (packagekit): Update to 1.1.11.
| * gnu: Add freedroidrpg.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/games.scm (freedroidrpg): New public variable.
| * gnu: wpa-supplicant-gui: Remove redundant code.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | | | * gnu/packages/admin.scm (wpa-supplicant-gui)[arguments]: Remove substitution already handled by the build system.
| * gnu: rubberband: Use HTTPS home page.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/audio.scm (rubberband)[home-page]: Use HTTPS.
| * gnu: Add memtester.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/hardware.scm (memtester): New public variable.
| * gnu: Add memtest86+.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/hardware.scm (memtest86+): New public variable.
| * gnu: rtags: Don't use unstable tarball.Tobias Geerinckx-Rice2018-10-04
| | | | | | | | * gnu/packages/code.scm (rtags)[source]: Use GIT-FETCH and GIT-FILE-NAME.
| * gnu: Add java-fasterxml-jackson-modules-base-mrbean.Danny Milosavljevic2018-10-04
| | | | | | | | | | * gnu/packages/java.scm (java-fasterxml-jackson-modules-base-mrbean): New variable.
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