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29800 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice 207e4d2705
gnu: python-oslo.i18n: Update to 3.20.0. 
* gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.20.0.
 2018-03-19 13:24:28 +01:00
Tobias Geerinckx-Rice bae598d6c9
gnu: r-withr: Update to 2.1.2. 
* gnu/packages/statistics.scm (r-withr): Update to 2.1.2.
 2018-03-19 13:24:27 +01:00
Efraim Flashner 9760061315
gnu: tilda: Update to 1.4.1. 
* gnu/packages/terminals.scm (tilda): Update to 1.4.1.
[arguments]: Rename 'autogen phase to 'bootstrap.  Clean up 'bootstrap
phase.
 2018-03-19 14:22:28 +02:00
Ricardo Wurmus 32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus fd757a8f21
gnu: pigx-chipseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:54 +01:00
Ricardo Wurmus 8c6117ee22
gnu: Add ghc-pandoc-citeproc-with-pandoc-1. 
* gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable.
 2018-03-19 11:07:54 +01:00
Marius Bakke 4eade64706
Merge branch 'master' into staging 2018-03-19 03:50:39 +01:00
Eric Bavier be95bcf088
git-download: Fix recursive checkouts. 
* guix/git-download.scm (git-fetch)<build>: Fix match on INPUTS, which may
contain package outputs.
 2018-03-18 20:00:44 -05:00
Vijayalakshmi Vedantham 109b2f7c93
gnu: Add r-abbyyr. 
* gnu/packages/cran.scm (r-abbyyr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-03-19 01:06:41 +01:00
Ludovic Courtès 71e08fde28
glob: Add an extra glob pattern compilation stage. 
* guix/glob.scm (compile-glob-pattern): Rename to...
(string->sglob): ... this.
(compile-sglob, string->compiled-sglob): New procedures.
(glob-match?): Replace '?, 'range, and 'set with a single clause.
* tests/glob.scm (test-compile-glob-pattern): Rename to...
(test-string->sglob): ... this.  Adjust accordingly.
(test-glob-match): Use 'string->compiled-sglob' instead of
'compile-glob-pattern'.
* gnu/build/linux-modules.scm (read-module-aliases): Use
'string->compiled-sglob' instead of 'compile-glob-pattern'.
 2018-03-18 22:57:17 +01:00
Ludovic Courtès e914b398af
glob: Support square brackets in patterns. 
* guix/glob.scm (wildcard-indices): Remove.
(parse-bracket): New procedure.
(compile-glob-pattern): Rewrite.  Support square brackets for sets and
ranges.
(glob-match?): Support sets and ranges.
* tests/glob.scm (test-compile-glob-pattern)
(test-glob-match): New macros.
Use them to rewrite the existing tests, and add new tests.
 2018-03-18 22:35:36 +01:00
Ludovic Courtès 675e81a082
linux-modules: 'load-linux-module*' honors BLACK-LIST in recursive calls. 
* gnu/build/linux-modules.scm (load-linux-module*): Pass BLACK-LIST in
recursive call.
 2018-03-18 22:35:27 +01:00
Ludovic Courtès a57df67b59
linux-modules: Add 'current-kernel-directory'. 
* gnu/build/linux-modules.scm (current-kernel-directory): New procedure.
(current-alias-file): Use it.
 2018-03-18 22:35:03 +01:00
Ludovic Courtès 248db51c7e
vm: Display a backtrace upon error by default. 
* gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass
 #:on-error to 'base-initrd'.
 2018-03-18 22:34:40 +01:00
Ludovic Courtès 17cdd3d0fe
tests: elpa: Don't actually download files. 
* tests/elpa.scm (eval-test-with-elpa): Mock 'url-fetch'.
 2018-03-18 22:33:41 +01:00
Ludovic Courtès 9bb1838c3f
import: elpa: Return 'license:gpl3+ for ELPA only. 
Fixes <https://bugs.gnu.org/30836>.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.

* guix/import/elpa.scm (elpa-package->sexp): Add LICENSE parameter and
honor it.
(elpa->guix-package): Pass 'license:gpl3+ only when REPO is 'gnu.
 2018-03-18 22:26:34 +01:00
Ludovic Courtès e5425ed950
import: elpa: Adjust test for HTTPS URLs. 
This is a followup to 44dd3d579d.

* tests/elpa.scm (eval-test-with-elpa): Use https.
 2018-03-18 22:25:54 +01:00
Sohom Bhattacharjee 14f2105dc6
gnu: youtube-dl: Update to 2018.03.14. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.03.14.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-03-18 18:47:16 +01:00
Christopher Baines 72406062b9
gnu: shotwell: Update to 0.28.0. 
* gnu/packages/gnome.scm (shotwell): Update to 0.28.0.
 2018-03-18 10:35:23 +00:00
Ben Woodcroft e218b0c8b3
gnu: Add ruby-ruby-engine. 
* gnu/packages/ruby.scm (ruby-ruby-engine): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 670ee20a57
gnu: Add ruby-rake. 
* gnu/packages/ruby.scm (ruby-rake): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft d64ebebd8e
gnu: Add ruby-erubis. 
* gnu/packages/ruby.scm (ruby-erubis): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft b88502c95c
gnu: Add ruby-sporkmonger-rack-mount. 
* gnu/packages/ruby.scm (ruby-sporkmonger-rack-mount): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft c4550f7568
gnu: Add ruby-creole. 
* gnu/packages/ruby.scm (ruby-creole): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 6ef8525607
gnu: Add ruby-contest. 
* gnu/packages/ruby.scm (ruby-contest): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft a0a7e6903a
gnu: Add ruby-rack-protection. 
* gnu/packages/ruby.scm (ruby-rack-protection): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 20a0f80414
gnu: Add ruby-rack-test. 
* gnu/packages/ruby.scm (ruby-rack-test): New variable.
 2018-03-18 10:23:51 +00:00
Ben Woodcroft 34138e42ba
gnu: Add ruby-asciidoctor. 
* gnu/packages/ruby.scm (ruby-asciidoctor): New variable.
 2018-03-18 10:23:51 +00:00
Ben Woodcroft 63e07468b3
gnu: Add ruby-asciimath. 
* gnu/packages/maths.scm (ruby-asciimath): New variable.
 2018-03-18 10:23:49 +00:00
Mark H Weaver cc4c8a576c
gnu: icecat: Fix CVE-2018-{5146,5147}, etc. 
Includes fixes for CVE-2018-5146 and CVE-2018-5147.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from
the upstream mozilla-esr52 repository.
 2018-03-17 21:44:23 -04:00
Marius Bakke 7ace97395f
Merge branch 'master' into staging 2018-03-18 01:09:25 +01:00
Christopher Baines be5ed14213
gnu: Add terraform-docs. 
* gnu/packages/terraform.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2018-03-17 23:04:29 +00:00
Christopher Baines ed0c6a768e
gnu: Add go-github-com-hashicorp-hcl. 
* gnu/packages/golang.scm (go-github-com-hashicorp-hcl): New variable.
 2018-03-17 23:04:29 +00:00
Christopher Baines c4d2cffae7
gnu: Add go-github-com-tj-docopt. 
* gnu/packages/golang.scm (go-github-com-tj-docopt): New variable.
 2018-03-17 23:04:29 +00:00
Ludovic Courtès 95bd9f65a8
git: 'switch-to-ref' accepts short commit IDs. 
Fixes <https://bugs.gnu.org/30716>.
Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

* guix/git.scm (switch-to-ref): When REF is a commit, check the length
of COMMIT and use 'object-lookup-prefix' if available.
 2018-03-18 00:02:06 +01:00
Ludovic Courtès 44efe67ed0
gnu: guile-git: Update to 2bb9fbb. 
* gnu/packages/guile.scm (guile-git): Update to 2bb9fbb.
 2018-03-18 00:02:06 +01:00
Ludovic Courtès b34ac82482
gnu: nss-mdns: Adjust Avahi socket file name. 
Fixes <https://bugs.gnu.org/30613>.
Regression introduced in 550f4509ac.
Reported by George myglc2 Clemmer <myglc2@gmail.com>.

* gnu/packages/avahi.scm (nss-mdns)[arguments]: Remove
 #:configure-flags.  Add #:phases.
 2018-03-18 00:02:06 +01:00
Ludovic Courtès 80f565d313
gnu: datamash: Update to 1.3. 
* gnu/packages/datamash.scm (datamash): Update to 1.3.
 2018-03-18 00:02:06 +01:00
ng0 c217df913e
gnu: fvwm: Add '.desktop' file. 
* gnu/packages/fvwm.scm (fvwm)[arguments]: Add new phase to create '.desktop' file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Konrad Hinsen 07d2fed2f6
import: elpa: Fix typos in documentation strings 
* guix/import/elpa.scm: Fix typos in docstrings.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Konrad Hinsen 44dd3d579d
import: elpa: use https in download URLs 
* guix/import/elpa.scm (elpa-url): Use HTTPS.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Martin Castillo 985934cb21
services: openssh: Add 'accepted-environment' field. 
* gnu/services/ssh.scm (<openssh-configuration>)[accepted-environment]: New field.
(openssh-config-file): Honor 'acccepted-environment'.
* doc/guix.texi (Networking Services): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Gábor Boskovits 3c27414968
gnu: java-simple-xml: Fix java8 test failures. 
* gnu/packages/patches/javas-simple-xml-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/java.scm (java-simple-xml)[source](patches): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Efraim Flashner 5983b78368
gnu: shaderc: Clean up package arguments. 
* gnu/packages/vulkan.scm (shaderc)[version]: Remove extra '-'.
[arguments]: Remove extra 'mkdir-p' calls and refer to inputs directly.
 2018-03-17 23:15:34 +02:00
Rutger Helling 308b17f676
Revert "gnu: shaderc: Use more standard keys." 
This reverts commit 9bc0591bc1.
This commit broke 'shaderc'.
 2018-03-17 21:59:27 +01:00
Christopher Baines fb6f35ba1d
gnu: Add python-prometheus-client. 
* gnu/packages/monitoring.scm (python-prometheus-client,
python2-prometheus-client): New variables.
 2018-03-17 20:44:50 +00:00
Christopher Baines 533808383f
services: databases: Change quote' to single-quote. 
In the postgresql-config-file gexp compiler.

* gnu/services/databases.scm (postgresql-config-file-compiler): Change quote'
to single-quote.
 2018-03-17 20:31:37 +00:00