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36300 Commits

Author SHA1 Message Date
Ricardo Wurmus a45c64701b
gnu: ghc-http-conduit: Remove ghc-http-client from native-inputs. 
* gnu/packages/haskell-web.scm (ghc-http-conduit)[native-inputs]: Remove
ghc-http-client.
 2018-10-05 23:59:25 +02:00
Ludovic Courtès 42384b517e
progress: Fix total size in "@ download-succeeded" traces. 
Fixes a regression introduced in
1d0be47ab6 whereby the total size for
directories (coming from substitutes) would be 4KiB.  This led the
progress bar to go back to the start, typically.

* guix/progress.scm (progress-reporter/trace): Add 'total'.  In 'start',
initialize it.  Adjust 'report' to update it.  Adjust 'stop' to prefer
SIZE as the actual size and then TOTAL.  Do not use the size of FILE as
the total since that could be 4KiB when FILE is a directory.
 2018-10-05 23:54:18 +02:00
Christopher Baines 11ff2adc74
gnu: ruby-sass: Update to 3.6.0. 
* gnu/packages/ruby.scm (ruby-sass)[version]: Update to 3.6.0.
[source]: Update sha256.
[native-inputs]: Add ruby-mathn, as this is needed when using Ruby 2.5.
 2018-10-05 21:25:42 +01:00
Christopher Baines 4d372cb9a2
gnu: Add ruby-mathn. 
* gnu/packages/ruby.scm (ruby-mathn): New variable.
 2018-10-05 21:25:42 +01:00
Christopher Baines 2c7cb711e9
gnu: ruby-sass-spec: Fix spec expectation. 
This fixes building ruby-sass with Ruby 2.5.

* gnu/packages/ruby.scm (ruby-sass-spec)[arguments]: Add patch-test phase to
fix the expectation of one of the tests. Also change the comment regarding the
tests not being run.
 2018-10-05 21:25:42 +01:00
Christopher Baines 39ecb977d3
gnu: ruby-term-ansicolor: Fix test for Ruby 2.5. 
* gnu/packages/ruby.scm (ruby-term-ansicolor)[arguments]: Add new fix-test
phase to fix a test that fails under Ruby 2.5.
 2018-10-05 21:25:41 +01:00
Christopher Baines 0b060e3486
gnu: ruby-shindo: Remove -rubygems flags. 
These have been removed in Ruby 2.5.

* gnu/packages/ruby.scm (ruby-shindo)[arguments]: Change fix-tests phase to
also remove the -rubygems flags.
 2018-10-05 21:25:41 +01:00
Christopher Baines 357450dca0
gnu: bioruby: Update to 1.5.2. 
This works with Ruby 2.5.

* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
 2018-10-05 21:25:39 +01:00
Kei Kebreau b0e829c632
gnu: gnucash-docs: Update to 3.3. 
The documentation on SourceForge is now located in the same directory as the
source code.

* gnu/packages/gnucash.scm (gnucash-docs): Update to 3.3.
 2018-10-05 14:28:44 -04:00
Kei Kebreau 73ca145a7e
gnu: gnucash: Update to 3.3. 
* gnu/packages/patches/gnucash-disable-failing-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gnucash.scm (gnucash): Update to 3.3.
[source]: Add patch.
[arguments]: Add 'set-env-vars', 'glib-or-gtk-compile-schemas', and
'glib-or-gtk-wrap' phases.
 2018-10-05 13:41:08 -04:00
Tobias Geerinckx-Rice fc4738149f
gnu: Add bastet. 
* gnu/packages/games.scm (bastet): New public variable.
* gnu/packages/patches/bastet-change-source-of-unordered_set.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-10-05 19:32:45 +02:00
Tobias Geerinckx-Rice b008a12ae7
gnu: fdroidserver: Update to 1.0.10. 
* gnu/packages/android.scm (fdroidserver): Update to 1.0.10.
 2018-10-05 19:30:09 +02:00
Tobias Geerinckx-Rice 8713c03e55
gnu: audacity: Don't use unstable tarball. 
* gnu/packages/audio.scm (audacity)[source]: Use GIT-FETCH and GIT-FILE-NAME.
 2018-10-05 19:30:09 +02:00
Tobias Geerinckx-Rice 3f90445692
gnu: filezilla: Update to 3.37.4. 
* gnu/packages/ftp.scm (filezilla): Update to 3.37.4.
 2018-10-05 19:30:09 +02:00
Tobias Geerinckx-Rice 38aca674c3
gnu: libfilezilla: Update to 0.14.0. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.14.0.
 2018-10-05 19:30:08 +02:00
Ricardo Wurmus a6798218be
gnu: samtools-0.1: Adjust to match changes in samtools. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 8e72f0f319
gnu: deeptools: Update to 3.1.2. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 1a28b9ab55
gnu: python-plotly: Add python-pandas to inputs. 
* gnu/packages/graph.scm (python-plotly)[propagated-inputs]: Add
python-pandas.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus bd5f5eece9
gnu: htslib: Update to 1.9. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
 2018-10-05 09:21:50 +02:00
Mark H Weaver 4a5e2a90d8
gnu: icecat: Add fixes from mozilla-esr60 [security fixes]. 
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
Mark H Weaver 2e073dc23c
gnu: linux-libre: Update to 4.18.12. 
* 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
Mark H Weaver 2195636cc1
gnu: linux-libre@4.14: Update to 4.14.74. 
* 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
Mark H Weaver 45f4ddd7c0
gnu: linux-libre@4.9: Update to 4.9.131. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.131.
 2018-10-04 20:36:28 -04:00
Paul Garlick 9e2aa70bad
gnu: petsc-openmpi: Configure with support for MUMPS solver. 
* 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
Tobias Geerinckx-Rice d8b042326d
gnu: hiawatha: Set sane run-time directory defaults. 
* 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
Tobias Geerinckx-Rice b9b53fb4ff
gnu: hwloc: Update to 2.0.2. 
* gnu/packages/mpi.scm (hwloc): Update to 2.0.2.
 2018-10-04 21:28:24 +02:00
Tobias Geerinckx-Rice 7382ecd818
gnu: Add nsd. 
* gnu/packages/dns.scm (nsd): New public variable.
 2018-10-04 21:10:34 +02:00
David Thompson 55b616fd15
gnu: guile-next: Update to commit 6f3357b0df64c4be17e72079864c09a542f1c779. 
* gnu/packages/guile.scm (guile-next): Update to commit
6f3357b0df64c4be17e72079864c09a542f1c779.
 2018-10-04 13:22:02 -04:00
David Thompson e14b3067e3
gnu: guile-next: Add the correct native search paths. 
* gnu/packages/guile.scm (guile-next): Add native search paths for version 3.0.
 2018-10-04 13:21:50 -04:00
Tobias Geerinckx-Rice aff91b0d0b
gnu: hiawatha: Support HTTP/2. 
* gnu/packages/web.sck (hiawatha)[arguments]: USE_SYSTEM_NGHTTP2
to ENABLE_HTTP2.
[inputs]: Add nghttp2:lib.
 2018-10-04 19:06:06 +02:00
Tobias Geerinckx-Rice 8e87aa0497
gnu: hiawatha: Update to 10.8.3. 
* 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
Tobias Geerinckx-Rice 38a9bf805d
gnu: mbedtls-apache: Update to 2.13.0 [security fixes]. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.13.0.
[native-inputs]: Add python.
 2018-10-04 17:42:30 +02:00
Arun Isaac 68c0a6260f
gnu: geos: Update to 3.7.0. 
* gnu/packages/geo.scm (geos): Update to 3.7.0.
 2018-10-04 20:01:06 +05:30
Tobias Geerinckx-Rice 0136fbd167
gnu: hexedit: Update to 1.4.2. 
* 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
Tobias Geerinckx-Rice 4fab0da096
gnu: html-xml-utils: Update to 7.7. 
* gnu/packages/xml.scm (html-xml-utils): Update to 7.7.
 2018-10-04 15:59:08 +02:00
Tobias Geerinckx-Rice ddf72f5059
gnu: perl-xml-feed: Update to 0.54. 
* gnu/packages/xml.scm (perl-xml-feed): Update to 0.54.
 2018-10-04 15:59:07 +02:00
Ludovic Courtès ca91d35225
gnu: guix: Update to 1d0be47. 
* gnu/packages/package-management.scm (guix): Update to 1d0be47.
 2018-10-04 11:21:37 +02:00
Ludovic Courtès 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
Diego Nicola Barbato ff30bb010b
gnu: escpr: Update to 1.6.30. 
* 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
Björn Höfling 63856931db
gnu: opencv: Update to 3.4.3. 
[[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
Ludovic Courtès 666fb2884a
gnu: r-acclma: Fix uses of @acronym in description. 
* 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
Ludovic Courtès 89fdd9ee0c
services: rottlog: Use command strings in the mcron jobs. 
* 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
Rutger Helling cd81c9e2a7
gnu: mpv: Update to 0.29.1. 
* gnu/packages/video.scm (mpv): Update to 0.29.1.
 2018-10-04 08:13:57 +02:00
Tobias Geerinckx-Rice 689ca9ba23
gnu: retroarch: Update to 1.7.5. 
* gnu/packages/emulators.scm (retroarch): Update to 1.7.5.
 2018-10-04 06:28:27 +02:00
Tobias Geerinckx-Rice 1fc346de4e
gnu: retroarch: Don't use unstable tarball. 
* gnu/packages/emulators.scm (retroarch)[source]: Use GIT-FETCH and GIT-FILE-NAME.
 2018-10-04 06:28:27 +02:00
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 104f475f9b
gnu: perl-string-copyright: Update to 0.003006. 
* gnu/packages/license.scm (perl-string-copyright): Update to 0.003006.
 2018-10-04 06:28:26 +02:00