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35675 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice ccfac015bf
gnu: wcslib: Update to 5.20. 
* gnu/packages/astronomy.scm (wcslib): Update to 5.20.
[arguments]: Build parallelly.
 2018-10-06 23:29:31 +02:00
Leo Famulari e90ce11577
gnu: git: Update to 2.19.1 [fixes CVE-2018-17456]. 
* gnu/packages/version-control.scm (git): Update to 2.19.1.
 2018-10-06 04:11:26 -04:00
Ricardo Wurmus d71078bc75
gnu: Add ngless. 
* gnu/packages/bioinformatics.scm (ngless): New variable.
 2018-10-05 23:59:27 +02:00
Ricardo Wurmus b1f9cc88c4
gnu: Add ghc-safeio. 
* gnu/packages/haskell.scm (ghc-safeio): New variable.
 2018-10-05 23:59:27 +02:00
Ricardo Wurmus ea202046fa
gnu: Add ghc-file-embed. 
* gnu/packages/haskell.scm (ghc-file-embed): New variable.
 2018-10-05 23:59:27 +02:00
Ricardo Wurmus c7e400b1ee
gnu: Add ghc-configurator. 
* gnu/packages/haskell.scm (ghc-configurator): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus d453b89944
gnu: Add ghc-bytestring-lexing. 
* gnu/packages/haskell.scm (ghc-bytestring-lexing): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus d9ee3e375c
gnu: Add ghc-inline-c-cpp. 
* gnu/packages/haskell.scm (ghc-inline-c-cpp): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 9ef95a196f
gnu: Add ghc-safe-exceptions. 
* gnu/packages/haskell.scm (ghc-safe-exceptions): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 88189099df
gnu: Add ghc-inline-c. 
* gnu/packages/haskell.scm (ghc-inline-c): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 52f5114d01
gnu: Add ghc-raw-string-qq. 
* gnu/packages/haskell.scm (ghc-raw-string-qq): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 5e6bf3e2da
gnu: Add ghc-hpack. 
* gnu/packages/haskell.scm (ghc-hpack): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 320323141f
gnu: Add ghc-interpolate. 
* gnu/packages/haskell.scm (ghc-interpolate): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus a933cbfb61
gnu: Add ghc-conduit-algorithms. 
* gnu/packages/haskell.scm (ghc-conduit-algorithms): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 71c2e3e1a1
gnu: Add ghc-pqueue. 
* gnu/packages/haskell.scm (ghc-pqueue): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 4fc161b9c6
gnu: Add ghc-bzlib-conduit. 
* gnu/packages/haskell.scm (ghc-bzlib-conduit): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 44c6180b3f
gnu: Add ghc-lzma-conduit. 
* gnu/packages/haskell.scm (ghc-lzma-conduit): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 38757d610e
gnu: Add ghc-bindings-dsl. 
* gnu/packages/haskell.scm (ghc-bindings-dsl): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 80588cfccf
gnu: Add ghc-stm-conduit. 
* gnu/packages/haskell.scm (ghc-stm-conduit): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 36ec599e78
gnu: Add ghc-lzma. 
* gnu/packages/haskell.scm (ghc-lzma): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus d05ed20ef1
gnu: Add ghc-cereal-conduit. 
* gnu/packages/haskell.scm (ghc-cereal-conduit): New variable.
 2018-10-05 23:59:26 +02:00
Ricardo Wurmus 6c8197783d
gnu: Add ghc-atomic-write. 
* gnu/packages/haskell.scm (ghc-atomic-write): New variable.
 2018-10-05 23:59:25 +02:00
Ricardo Wurmus 562cfae330
gnu: Add ghc-chart-cairo. 
* gnu/packages/haskell.scm (ghc-chart-cairo): New variable.
 2018-10-05 23:59:25 +02:00
Ricardo Wurmus 7df25c77c5
gnu: Add ghc-cairo. 
* gnu/packages/haskell.scm (ghc-cairo): New variable.
 2018-10-05 23:59:25 +02:00
Ricardo Wurmus 279c97dba8
gnu: ghc-regex: Fix build. 
* gnu/packages/haskell.scm (ghc-regex)[arguments]: Add build phase to relax
version checks.
 2018-10-05 23:59:25 +02:00
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