939882f734
gnu: python-pysam: Update to 0.15.1.
...
* 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.
2018-10-05 09:21:54 +02:00
1a28b9ab55
gnu: python-plotly: Add python-pandas to inputs.
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* gnu/packages/graph.scm (python-plotly)[propagated-inputs]: Add
python-pandas.
2018-10-05 09:21:54 +02:00
f79b59e311
gnu: bcftools: Update to 1.9.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
2018-10-05 09:21:54 +02:00
4ae4a15232
gnu: samtools: Update to 1.9.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
2018-10-05 09:21:54 +02:00
bd5f5eece9
gnu: htslib: Update to 1.9.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
2018-10-05 09:21:50 +02:00
4a5e2a90d8
gnu: icecat: Add fixes from mozilla-esr60 [security fixes].
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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.
2018-10-04 21:35:01 -04:00
2e073dc23c
gnu: linux-libre: Update to 4.18.12.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.12.
(%linux-libre-hash): Update hash.
2018-10-04 20:36:32 -04:00
2195636cc1
gnu: linux-libre@4.14: Update to 4.14.74.
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* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.74.
(%linux-libre-4.14-hash): Update hash.
2018-10-04 20:36:30 -04:00
45f4ddd7c0
gnu: linux-libre@4.9: Update to 4.9.131.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.131.
2018-10-04 20:36:28 -04:00
9e2aa70bad
gnu: petsc-openmpi: Configure with support for MUMPS solver.
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* 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>
2018-10-04 18:21:17 -04:00
d8b042326d
gnu: hiawatha: Set sane run-time directory defaults.
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* gnu/packages/web.scm (hiawatha)[arguments]: Set sane default
directories. Replace the 'remove-empty-dirs' phase with a
'install-no-empty-directories' one.
2018-10-04 21:28:24 +02:00
b9b53fb4ff
gnu: hwloc: Update to 2.0.2.
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* gnu/packages/mpi.scm (hwloc): Update to 2.0.2.
2018-10-04 21:28:24 +02:00
7382ecd818
gnu: Add nsd.
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* gnu/packages/dns.scm (nsd): New public variable.
2018-10-04 21:10:34 +02:00
55b616fd15
gnu: guile-next: Update to commit 6f3357b0df64c4be17e72079864c09a542f1c779.
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* gnu/packages/guile.scm (guile-next): Update to commit
6f3357b0df64c4be17e72079864c09a542f1c779.
2018-10-04 13:22:02 -04:00
e14b3067e3
gnu: guile-next: Add the correct native search paths.
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* gnu/packages/guile.scm (guile-next): Add native search paths for version 3.0.
2018-10-04 13:21:50 -04:00
aff91b0d0b
gnu: hiawatha: Support HTTP/2.
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* gnu/packages/web.sck (hiawatha)[arguments]: USE_SYSTEM_NGHTTP2
to ENABLE_HTTP2.
[inputs]: Add nghttp2:lib.
2018-10-04 19:06:06 +02:00
8e87aa0497
gnu: hiawatha: Update to 10.8.3.
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* 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.
2018-10-04 18:34:29 +02:00
38a9bf805d
gnu: mbedtls-apache: Update to 2.13.0 [security fixes].
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* gnu/packages/tls.scm (mbedtls-apache): Update to 2.13.0.
[native-inputs]: Add python.
2018-10-04 17:42:30 +02:00
68c0a6260f
gnu: geos: Update to 3.7.0.
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* gnu/packages/geo.scm (geos): Update to 3.7.0.
2018-10-04 20:01:06 +05:30
0136fbd167
gnu: hexedit: Update to 1.4.2.
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* 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.
2018-10-04 15:59:08 +02:00
4fab0da096
gnu: html-xml-utils: Update to 7.7.
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* gnu/packages/xml.scm (html-xml-utils): Update to 7.7.
2018-10-04 15:59:08 +02:00
ddf72f5059
gnu: perl-xml-feed: Update to 0.54.
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* gnu/packages/xml.scm (perl-xml-feed): Update to 0.54.
2018-10-04 15:59:07 +02:00
ca91d35225
gnu: guix: Update to 1d0be47.
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* gnu/packages/package-management.scm (guix): Update to 1d0be47
2018-10-04 11:21:37 +02:00
1d0be47ab6
progress: Generate valid 'download-progress' traces when the size is unknown.
...
Fixes <https://bugs.gnu.org/32895 >.
Reported by Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>.
* guix/progress.scm (progress-reporter/trace): In 'stop', make sure SIZE
is an integer. Previously we'd generate a "@ download-progress" trace
with #f for the 'transferred' number when downloading files whose size
is not known in advance.
2018-10-04 10:24:34 +02:00
ff30bb010b
gnu: escpr: Update to 1.6.30.
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* gnu/packages/cups.scm (escpr): Update to 1.6.30.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-10-04 09:51:47 +02:00
63856931db
gnu: opencv: Update to 3.4.3.
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[[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>
2018-10-04 09:48:45 +02:00
666fb2884a
gnu: r-acclma: Fix uses of @acronym in description.
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* gnu/packages/cran.scm (r-acclma)[description]: Fix order of arguments
to @acronym. The wrong order was causing 'stexi->shtml' to fail (match
error).
2018-10-04 09:46:43 +02:00
89fdd9ee0c
services: rottlog: Use command strings in the mcron jobs.
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* 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").
2018-10-04 09:32:51 +02:00
cd81c9e2a7
gnu: mpv: Update to 0.29.1.
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* gnu/packages/video.scm (mpv): Update to 0.29.1.
2018-10-04 08:13:57 +02:00
689ca9ba23
gnu: retroarch: Update to 1.7.5.
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* gnu/packages/emulators.scm (retroarch): Update to 1.7.5.
2018-10-04 06:28:27 +02:00
1fc346de4e
gnu: retroarch: Don't use unstable tarball.
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* gnu/packages/emulators.scm (retroarch)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2018-10-04 06:28:27 +02:00
fe30eb6d24
gnu: ephoto: Fix typos in description.
...
* gnu/packages/enlightenment.scm (ephoto)[description]: Fix typos.
Wrap at 80 columns.
2018-10-04 06:28:27 +02:00
104f475f9b
gnu: perl-string-copyright: Update to 0.003006.
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* gnu/packages/license.scm (perl-string-copyright): Update to 0.003006.
2018-10-04 06:28:26 +02:00
91a3c8005d
gnu: rpm: Update to 4.14.2.
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* 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.
2018-10-04 06:28:26 +02:00
88abd73eeb
gnu: imapfilter: Update to 2.6.12.
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* gnu/packages/mail.scm (imapfilter): Update to 2.6.12.
2018-10-04 06:28:26 +02:00
b1d30f46c1
gnu: imapfilter: Don't use unstable tarball.
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* gnu/packages/mail.scm (imapfilter)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2018-10-04 06:28:26 +02:00
1f2cf5d9db
gnu: nickle: Update to 2.82.
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* gnu/packages/nickle.scm (nickle): Update to 2.82.
2018-10-04 06:28:25 +02:00
9e783d0bf2
gnu: ddcutil: Update to 0.9.2.
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* gnu/packages/hardware.scm (ddcutil): Update to 0.9.2.
2018-10-04 04:20:06 +02:00
a926109d62
gnu: ndctl: Return #t from phases.
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* gnu/packages/disk (ndctl)[arguments]: Rename inaccurately named
'autogen' phase to 'patch-FHS-file-names'. Explicitly return #t.
2018-10-04 04:20:06 +02:00
7f12d8134e
gnu: disorderfs: Update to 0.5.4.
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* gnu/packages/file-systems.scm (disorderfs): Update to 0.5.4.
2018-10-04 04:20:06 +02:00
99f97a7752
gnu: packagekit: Update to 1.1.11.
...
* gnu/packages/freedesktop.scm (packagekit): Update to 1.1.11.
2018-10-04 04:20:05 +02:00
18995af2cd
gnu: Add freedroidrpg.
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* gnu/packages/games.scm (freedroidrpg): New public variable.
2018-10-04 04:20:05 +02:00
8d54e7ff22
gnu: wpa-supplicant-gui: Remove redundant code.
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* gnu/packages/admin.scm (wpa-supplicant-gui)[arguments]: Remove
substitution already handled by the build system.
2018-10-04 04:20:05 +02:00
20377e4a99
gnu: rubberband: Use HTTPS home page.
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* gnu/packages/audio.scm (rubberband)[home-page]: Use HTTPS.
2018-10-04 04:20:05 +02:00
fb54125114
gnu: Add memtester.
...
* gnu/packages/hardware.scm (memtester): New public variable.
2018-10-04 04:20:04 +02:00
5eff43804e
gnu: Add memtest86+.
...
* gnu/packages/hardware.scm (memtest86+): New public variable.
2018-10-04 04:20:04 +02:00
84ae0e29fd
gnu: rtags: Don't use unstable tarball.
...
* gnu/packages/code.scm (rtags)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2018-10-04 04:20:04 +02:00
5165fb40f4
gnu: Add java-fasterxml-jackson-modules-base-mrbean.
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* gnu/packages/java.scm (java-fasterxml-jackson-modules-base-mrbean): New
variable.
2018-10-04 03:05:10 +02:00
615a7eec56
gnu: Add stlink.
...
* gnu/packages/embedded.scm (stlink): New variable.
2018-10-04 00:18:05 +02:00
46f9022c99
gnu: Add java-commons-exec.
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* gnu/packages/java.scm (java-commons-exec-1.1): New variable.
(java-commons-exec): New variable.
2018-10-04 00:06:42 +02:00
Ricardo Wurmus