jackhill/guix/guix.git
8 years agognu: Add Pfff.
Pjotr Prins [Sun, 3 Jan 2016 05:41:49 +0000 (06:41 +0100)]
gnu: Add Pfff.

* gnu/packages/textutils.scm (pfff): New variable.

8 years agognu: mpv: Remove 'samba' input.
Alex Kost [Thu, 7 Jan 2016 18:27:14 +0000 (21:27 +0300)]
gnu: mpv: Remove 'samba' input.

This is a heavy-weight and uncommon feature.  See
<http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>.

* gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.

8 years agoemacs: Display supported systems in "Package Info".
Alex Kost [Mon, 28 Dec 2015 18:40:06 +0000 (21:40 +0300)]
emacs: Display supported systems in "Package Info".

* emacs/guix-main.scm (%package-param-alist): Add 'systems'.
* emacs/guix-ui-package.el (guix-package-info-insert-systems): New
  procedure.
  (guix-package-info-format): Add it.
  (guix-output-info-format): Likewise.
  (guix-package-info-titles): Add "Supported systems" title.

8 years agognu: Add genomation.
Ricardo Wurmus [Wed, 23 Dec 2015 16:35:04 +0000 (17:35 +0100)]
gnu: Add genomation.

* gnu/packages/bioinformatics.scm (r-genomation): New variable.

8 years agognu: Add seqPattern.
Ricardo Wurmus [Wed, 23 Dec 2015 16:34:45 +0000 (17:34 +0100)]
gnu: Add seqPattern.

* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.

8 years agognu: Add impute.
Ricardo Wurmus [Wed, 23 Dec 2015 16:34:27 +0000 (17:34 +0100)]
gnu: Add impute.

* gnu/packages/bioinformatics.scm (r-impute): New variable.

8 years agognu: Add BSgenome.
Ricardo Wurmus [Wed, 23 Dec 2015 16:34:07 +0000 (17:34 +0100)]
gnu: Add BSgenome.

* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.

8 years agognu: Add plotly.
Ricardo Wurmus [Wed, 23 Dec 2015 16:33:36 +0000 (17:33 +0100)]
gnu: Add plotly.

* gnu/packages/statistics.scm (r-plotly): New variable.

8 years agognu: Add viridis.
Ricardo Wurmus [Wed, 23 Dec 2015 16:33:15 +0000 (17:33 +0100)]
gnu: Add viridis.

* gnu/packages/statistics.scm (r-viridis): New variable.

8 years agognu: Add topGO.
Ricardo Wurmus [Wed, 23 Dec 2015 16:31:03 +0000 (17:31 +0100)]
gnu: Add topGO.

* gnu/packages/bioinformatics.scm (r-topgo): New variable.

8 years agognu: Add matrixStats.
Ricardo Wurmus [Wed, 23 Dec 2015 16:29:51 +0000 (17:29 +0100)]
gnu: Add matrixStats.

* gnu/packages/statistics.scm (r-matrixstats): New variable.

8 years agognu: Add R.rsp.
Ricardo Wurmus [Wed, 23 Dec 2015 16:29:28 +0000 (17:29 +0100)]
gnu: Add R.rsp.

* gnu/packages/statistics.scm (r-r-rsp): New variable.

8 years agognu: Add R.cache.
Ricardo Wurmus [Wed, 23 Dec 2015 16:29:08 +0000 (17:29 +0100)]
gnu: Add R.cache.

* gnu/packages/statistics.scm (r-r-cache): New variable.

8 years agognu: Add R.utils.
Ricardo Wurmus [Wed, 23 Dec 2015 16:28:47 +0000 (17:28 +0100)]
gnu: Add R.utils.

* gnu/packages/statistics.scm (r-r-utils): New variable.

8 years agognu: Add R.oo.
Ricardo Wurmus [Wed, 23 Dec 2015 16:28:26 +0000 (17:28 +0100)]
gnu: Add R.oo.

* gnu/packages/statistics.scm (r-r-oo): New variable.

8 years agognu: Add R.methodsS3.
Ricardo Wurmus [Wed, 23 Dec 2015 16:27:51 +0000 (17:27 +0100)]
gnu: Add R.methodsS3.

* gnu/packages/statistics.scm (r-r-methodss3): New variable.

8 years agognu: Add base64enc.
Ricardo Wurmus [Wed, 23 Dec 2015 16:27:28 +0000 (17:27 +0100)]
gnu: Add base64enc.

* gnu/packages/statistics.scm (r-base64enc): New variable.

8 years agognu: Add DT.
Ricardo Wurmus [Wed, 23 Dec 2015 16:27:12 +0000 (17:27 +0100)]
gnu: Add DT.

* gnu/packages/statistics.scm (r-dt): New variable.

8 years agognu: Add SparseM.
Ricardo Wurmus [Wed, 23 Dec 2015 16:26:50 +0000 (17:26 +0100)]
gnu: Add SparseM.

* gnu/packages/statistics.scm (r-sparsem): New variable.

8 years agognu: Add GO.db.
Ricardo Wurmus [Wed, 23 Dec 2015 16:25:59 +0000 (17:25 +0100)]
gnu: Add GO.db.

* gnu/packages/bioinformatics.scm (r-go-db): New variable.

8 years agognu: Add GenomicFeatures.
Ricardo Wurmus [Fri, 18 Dec 2015 13:09:18 +0000 (14:09 +0100)]
gnu: Add GenomicFeatures.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.

8 years agognu: Add rtracklayer.
Ricardo Wurmus [Fri, 18 Dec 2015 13:09:00 +0000 (14:09 +0100)]
gnu: Add rtracklayer.

* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.

8 years agognu: Add GenomicAlignments.
Ricardo Wurmus [Fri, 18 Dec 2015 13:08:36 +0000 (14:08 +0100)]
gnu: Add GenomicAlignments.

* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.

8 years agognu: Add SummarizedExperiment.
Ricardo Wurmus [Fri, 18 Dec 2015 13:08:17 +0000 (14:08 +0100)]
gnu: Add SummarizedExperiment.

* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.

8 years agognu: Add Rsamtools.
Ricardo Wurmus [Fri, 18 Dec 2015 13:07:56 +0000 (14:07 +0100)]
gnu: Add Rsamtools.

* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.

8 years agognu: Add Biostrings.
Ricardo Wurmus [Fri, 18 Dec 2015 13:07:32 +0000 (14:07 +0100)]
gnu: Add Biostrings.

* gnu/packages/bioinformatics.scm (r-biostrings): New variable.

8 years agognu: Add BiocParallel.
Ricardo Wurmus [Fri, 18 Dec 2015 13:07:08 +0000 (14:07 +0100)]
gnu: Add BiocParallel.

* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.

8 years agognu: Add biomaRt.
Ricardo Wurmus [Fri, 18 Dec 2015 13:06:52 +0000 (14:06 +0100)]
gnu: Add biomaRt.

* gnu/packages/bioinformatics.scm (r-biomart): New variable.

8 years agognu: Add AnnotationDbi.
Ricardo Wurmus [Fri, 18 Dec 2015 13:06:28 +0000 (14:06 +0100)]
gnu: Add AnnotationDbi.

* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.

8 years agognu: Add Biobase.
Ricardo Wurmus [Fri, 18 Dec 2015 13:06:09 +0000 (14:06 +0100)]
gnu: Add Biobase.

* gnu/packages/bioinformatics.scm (r-biobase): New variable.

8 years agognu: Add snow.
Ricardo Wurmus [Fri, 18 Dec 2015 13:05:29 +0000 (14:05 +0100)]
gnu: Add snow.

* gnu/packages/statistics.scm (r-snow): New variable.

8 years agognu: Add futile.logger.
Ricardo Wurmus [Fri, 18 Dec 2015 13:05:07 +0000 (14:05 +0100)]
gnu: Add futile.logger.

* gnu/packages/statistics.scm (r-futile-logger): New variable.

8 years agognu: Add futile.options.
Ricardo Wurmus [Fri, 18 Dec 2015 13:04:49 +0000 (14:04 +0100)]
gnu: Add futile.options.

* gnu/packages/statistics.scm (r-futile-options): New variable.

8 years agognu: Add lambda.r.
Ricardo Wurmus [Fri, 18 Dec 2015 13:03:47 +0000 (14:03 +0100)]
gnu: Add lambda.r.

* gnu/packages/statistics.scm (r-lambda-r): New variable.

8 years agognu: Add r-xml.
Ricardo Wurmus [Fri, 18 Dec 2015 13:03:26 +0000 (14:03 +0100)]
gnu: Add r-xml.

* gnu/packages/statistics.scm (r-xml): New variable.

8 years agognu: Add RCurl.
Ricardo Wurmus [Fri, 18 Dec 2015 13:03:08 +0000 (14:03 +0100)]
gnu: Add RCurl.

* gnu/packages/statistics.scm (r-rcurl): New variable.

8 years agognu: Add RSQLite.
Ricardo Wurmus [Fri, 18 Dec 2015 13:02:40 +0000 (14:02 +0100)]
gnu: Add RSQLite.

* gnu/packages/statistics.scm (r-rsqlite): New variable.

8 years agoimport: Rename "cran-fetch" to "fetch-description".
Ricardo Wurmus [Wed, 16 Dec 2015 13:28:43 +0000 (14:28 +0100)]
import: Rename "cran-fetch" to "fetch-description".

* guix/import/cran.scm (cran-fetch): Rename procedure ...
(fetch-description): ... to this.

8 years agoimport: Add package->upstream-name procedure.
Ricardo Wurmus [Wed, 16 Dec 2015 13:22:17 +0000 (14:22 +0100)]
import: Add package->upstream-name procedure.

* guix/import/cran.scm (package->upstream-name): New procedure.

8 years agognu: Add xmlstarlet.
Raimon Grau [Mon, 28 Dec 2015 11:51:59 +0000 (11:51 +0000)]
gnu: Add xmlstarlet.

* gnu/packages/xml.scm (xmlstarlet): New variable.

8 years agognu: zita-convolver: Drop the '-march=native' optimization.
宋文武 [Wed, 6 Jan 2016 15:23:26 +0000 (23:23 +0800)]
gnu: zita-convolver: Drop the '-march=native' optimization.

* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.

8 years agognu: zita-resampler: Drop the '-march=native' optimization.
宋文武 [Wed, 6 Jan 2016 15:04:14 +0000 (23:04 +0800)]
gnu: zita-resampler: Drop the '-march=native' optimization.

* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.

8 years agognu: Add ruby-ansi.
Ben Woodcroft [Tue, 29 Dec 2015 04:11:21 +0000 (14:11 +1000)]
gnu: Add ruby-ansi.

* gnu/packages/ruby.scm (ruby-ansi): New variable.

8 years agognu: edirect: Update to 3.50.
Ricardo Wurmus [Thu, 7 Jan 2016 10:04:38 +0000 (11:04 +0100)]
gnu: edirect: Update to 3.50.

* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".

8 years agognu: w3m: Enable SSL, disable broken protocols and ciphers.
Leo Famulari [Wed, 6 Jan 2016 00:26:25 +0000 (19:26 -0500)]
gnu: w3m: Enable SSL, disable broken protocols and ciphers.

Fixes <http://bugs.gnu.org/16791>.

* gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file.
* gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file.
* gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file.
* gnu/packages/w3m.scm (w3m)[source]: Add patches.
* gnu-system.am (dist_patch_DATA): Add the new files.

8 years agognu: w3m: Update patch to use '-p1'.
Leo Famulari [Wed, 6 Jan 2016 15:43:18 +0000 (10:43 -0500)]
gnu: w3m: Update patch to use '-p1'.

* gnu/packages/patches/w3m-fix-compile.patch: Rename this file...
* gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch
prefix level to '-p1'.
* gnu-system.am (dist_patch_DATA): Update patch name.
* gnu/packages/w3m.scm (w3m)[source]: Update patch name.
[source]: Drop patch flag -p0.

8 years agobuild-system/gnu: Make 'package-with-explicit-inputs' idempotent.
Ludovic Courtès [Wed, 6 Jan 2016 21:56:01 +0000 (22:56 +0100)]
build-system/gnu: Make 'package-with-explicit-inputs' idempotent.

* guix/build-system/gnu.scm (package-with-explicit-inputs): Use
  'ensure-keyword-arguments' instead of appending to ARGS.
* gnu/packages/commencement.scm (static-bash-for-glibc): Add missing
  #:guile argument.

8 years agoutils: Add 'ensure-keyword-arguments'.
Ludovic Courtès [Wed, 6 Jan 2016 21:42:09 +0000 (22:42 +0100)]
utils: Add 'ensure-keyword-arguments'.

* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures.
* tests/utils.scm ("ensure-keyword-arguments"): New test.

8 years agohttp-client: Work around <http://bugs.gnu.org/22273>.
Ludovic Courtès [Wed, 6 Jan 2016 20:36:15 +0000 (21:36 +0100)]
http-client: Work around <bugs.gnu.org/22273>.

* guix/http-client.scm (read-header-line): New procedure.  Use it.

8 years agognu: guix: Update development snapshot to f888c0b.
Ludovic Courtès [Wed, 6 Jan 2016 20:24:01 +0000 (21:24 +0100)]
gnu: guix: Update development snapshot to f888c0b.

* gnu/packages/package-management.scm (guix-devel): Update to f888c0b.

8 years agohttp-client: Fix erroneous comment.
Ludovic Courtès [Wed, 6 Jan 2016 17:04:36 +0000 (18:04 +0100)]
http-client: Fix erroneous comment.

* guix/http-client.scm: Fix Guile version number in comment for Guile
commit 5a10e41.

8 years agognu: gmsh: Update to 2.11.0.
Eric Bavier [Tue, 1 Dec 2015 23:41:52 +0000 (17:41 -0600)]
gnu: gmsh: Update to 2.11.0.

* gnu/packages/maths.scm (gmsh): Update to 2.11.0.
  [arguments]: Replace 'check phase.

8 years agolint: cve: Catch host name lookup errors.
Ludovic Courtès [Wed, 6 Jan 2016 14:53:20 +0000 (15:53 +0100)]
lint: cve: Catch host name lookup errors.

* guix/scripts/lint.scm (package-vulnerabilities): Catch
'getaddrinfo-error'.

8 years agognu: sudo: Use /var/run/sudo instead of /run/sudo.
Ludovic Courtès [Wed, 6 Jan 2016 14:51:31 +0000 (15:51 +0100)]
gnu: sudo: Use /var/run/sudo instead of /run/sudo.

* gnu/packages/admin.scm (sudo)[arguments]: Pass
--with-rundir=/var/run/sudo since /var/run is cleaned up at boot time on
GuixSD whereas /run is not.

8 years agoservices: cleanup-service: Catch 'system-error' instead of everything.
Ludovic Courtès [Wed, 6 Jan 2016 13:49:48 +0000 (14:49 +0100)]
services: cleanup-service: Catch 'system-error' instead of everything.

This makes sure that critical errors such as unbound-variable do not go
undetected.

* gnu/services.scm (cleanup-gexp): Introduce local 'fail-safe' macro and
use it.  Remove uses of 'false-if-exception'.

8 years agognu: ldc: Fix license.
Ludovic Courtès [Wed, 6 Jan 2016 13:21:53 +0000 (14:21 +0100)]
gnu: ldc: Fix license.

* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of
'license:x11-style' by LICENSE:BOOST1.0.

8 years agobuild: ruby: Remove cached gem after install.
Ben Woodcroft [Wed, 30 Dec 2015 00:27:33 +0000 (10:27 +1000)]
build: ruby: Remove cached gem after install.

The .gem file stored in GEM_HOME after install is both redundant and an
archive that stores timestamped files which makes builds
non-deterministic, so delete it after 'gem install'.

* guix/build/ruby-build-system.scm (install): Remove cached gem after
  install.

8 years agognu: icedtea7: Rename to icedtea-7.
Ricardo Wurmus [Wed, 30 Dec 2015 13:34:25 +0000 (14:34 +0100)]
gnu: icedtea7: Rename to icedtea-7.

* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".

8 years agognu: icedtea6: Rename to icedtea-6.
Ricardo Wurmus [Wed, 30 Dec 2015 13:33:11 +0000 (14:33 +0100)]
gnu: icedtea6: Rename to icedtea-6.

* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.

8 years agognu: icedtea6, icedtea7: Rename package to "icedtea".
Ricardo Wurmus [Wed, 30 Dec 2015 13:31:16 +0000 (14:31 +0100)]
gnu: icedtea6, icedtea7: Rename package to "icedtea".

* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.

8 years agognu: Add and use default IcedTea.
Ricardo Wurmus [Wed, 30 Dec 2015 13:25:09 +0000 (14:25 +0100)]
gnu: Add and use default IcedTea.

* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".

8 years agognu: icedtea6, icedtea7: Unpack to "openjdk.src".
Ricardo Wurmus [Wed, 30 Dec 2015 13:04:04 +0000 (14:04 +0100)]
gnu: icedtea6, icedtea7: Unpack to "openjdk.src".

* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to
"openjdk.src".
(icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to
"openjdk.src" in build phases; simplify "unpack" phase.
[native-inputs]: Rename "openjdk-drop" to "openjdk-src".

8 years agognu: Add Jellyfish.
Ricardo Wurmus [Fri, 18 Dec 2015 16:40:02 +0000 (17:40 +0100)]
gnu: Add Jellyfish.

* gnu/packages/bioinformatics.scm (jellyfish): New variable.

8 years agobuild: Bump version number.
Ludovic Courtès [Tue, 5 Jan 2016 22:54:53 +0000 (23:54 +0100)]
build: Bump version number.

* configure.ac: Change version to 0.9.1.

8 years agodoc: Remove double occurrence of words.
Michael Vetter [Tue, 5 Jan 2016 08:37:05 +0000 (09:37 +0100)]
doc: Remove double occurrence of words.

* doc/guix.texi: substitute 'the the' with 'the'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
8 years agobuild: pull: Compile .scm files in one process.
Taylan Ulrich Bayırlı/Kammer [Fri, 27 Nov 2015 08:27:55 +0000 (09:27 +0100)]
build: pull: Compile .scm files in one process.

* guix/build/pull.scm (call-with-process, report-build-progress)
(p-for-each): Remove.
(build-guix): Load and compile files in one process.

8 years agognu: calibre: Update to 2.48.0.
Andreas Enge [Tue, 5 Jan 2016 21:46:54 +0000 (22:46 +0100)]
gnu: calibre: Update to 2.48.0.

* gnu/packages/ebook.scm (calibre): Update to 2.48.0.

8 years agognu: Add LDC.
Roel Janssen [Tue, 5 Jan 2016 14:43:50 +0000 (15:43 +0100)]
gnu: Add LDC.

* gnu/packages/ldc.scm: New file.
* gnu/packages/patches/ldc-disable-tests.patch: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm.
  (dist_patch_DATA): Add patch file.

8 years agognu: Add emacs-undo-tree.
Dmitry Bogatov [Wed, 30 Dec 2015 18:06:49 +0000 (21:06 +0300)]
gnu: Add emacs-undo-tree.

 * gnu/packages/emacs.scm (emacs-undo-tree): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
8 years agognu: emacs: Remove 'info.info'.
Ludovic Courtès [Mon, 4 Jan 2016 22:32:29 +0000 (23:32 +0100)]
gnu: emacs: Remove 'info.info'.

* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'.  Add
'remove-info.info' phase.

8 years agolinux-boot: Remove verbose output for module loads.
Ludovic Courtès [Mon, 4 Jan 2016 22:04:21 +0000 (23:04 +0100)]
linux-boot: Remove verbose output for module loads.

* gnu/build/linux-boot.scm (boot-system): Leave
'current-module-debugging-port' unchanged.
* gnu/build/linux-modules.scm (load-linux-module*): Update comment about
'mmap'.

8 years agoservices: Move /tmp cleanup to a separate service.
Ludovic Courtès [Mon, 4 Jan 2016 21:58:05 +0000 (22:58 +0100)]
services: Move /tmp cleanup to a separate service.

* gnu/services.scm (compute-boot-script): Remove /tmp and /var/run
deletion code from here.
(cleanup-gexp): New procedure with /tmp and /var/run deletion code
formerly in 'compute-boot-script'.
(cleanup-service-type): New variable.
* gnu/system.scm (essential-services): Add an instance of
CLEANUP-SERVICE-TYPE.

8 years agoservices: boot: Reinstate /tmp and /var/run deletion.
Ludovic Courtès [Mon, 4 Jan 2016 21:42:09 +0000 (22:42 +0100)]
services: boot: Reinstate /tmp and /var/run deletion.

For some time /tmp and /var/run were not being deleted because
'delete-file-recursively' was unbound.

* gnu/services.scm (compute-boot-script)[%modules, modules, compiled]:
New variables.  Use them to augment the module search path.

8 years agoguix package: Allow multiple '--search' flags.
Ludovic Courtès [Mon, 4 Jan 2016 21:27:38 +0000 (22:27 +0100)]
guix package: Allow multiple '--search' flags.

* guix/scripts/package.scm (find-packages-by-description): Change 'rx'
parameter to 'regexps'.
[matches-all?, matches-one?]: New procedures.
Use them.
(process-query): Collect regexps from all 'search' queries, and pass
them to 'find-packages-by-description'.
* tests/guix-package.sh: Add tests.
* doc/guix.texi (Invoking guix package): Document it.

8 years agoui: Update copyright year in '--version' output.
Ludovic Courtès [Mon, 4 Jan 2016 21:11:57 +0000 (22:11 +0100)]
ui: Update copyright year in '--version' output.

* guix/ui.scm (show-version-and-exit): Increment copyright year.

8 years agogit-download: Correctly implement recursive checkouts.
Ludovic Courtès [Mon, 4 Jan 2016 21:10:03 +0000 (22:10 +0100)]
git-download: Correctly implement recursive checkouts.

Previously, the 'git checkout' invocation would remove sub-modules that
had been initialized by 'git clone --recursive'.

* guix/build/git.scm (git-fetch): Never use "git clone --recursive".
Invoke "git submodule update --init --recursive" after "git checkout".
Remove '.git' directories as the last step.

8 years agognu: gtk+: Add patch to support GUIX_GTK3_PATH.
Ricardo Wurmus [Thu, 3 Dec 2015 07:32:06 +0000 (08:32 +0100)]
gnu: gtk+: Add patch to support GUIX_GTK3_PATH.

* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK3_PATH.

8 years agognu: gtk+-2: Add patch to support GUIX_GTK2_PATH.
Ricardo Wurmus [Thu, 3 Dec 2015 07:30:04 +0000 (08:30 +0100)]
gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH.

* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+-2) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK2_PATH.

8 years agognu: julia: Update to 0.4.2.
Ricardo Wurmus [Mon, 30 Nov 2015 13:25:53 +0000 (14:25 +0100)]
gnu: julia: Update to 0.4.2.

* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/julia.scm (julia): Update to 0.4.2.
[arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase
"patch-include-path" with "fix-include-and-link-paths"; add phase
"hardcode-paths"; add missing make-flags.
[inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add
"coreutils"; add "libuv-julia"; add "wget"; add "which".
[native-inputs]: Remove "which".

8 years agognu: Add libuv-julia.
Ricardo Wurmus [Mon, 30 Nov 2015 13:22:18 +0000 (14:22 +0100)]
gnu: Add libuv-julia.

* gnu/packages/julia.scm (libuv-julia): New variable.

8 years agognu: utf8proc: Update to 1.3.1.
Ricardo Wurmus [Mon, 30 Nov 2015 13:31:02 +0000 (14:31 +0100)]
gnu: utf8proc: Update to 1.3.1.

* gnu/packages/textutils.scm (utf8proc): Update to 1.3.1.
[arguments]: Remove custom "install" phase.

8 years agognu: samba: Update to 4.3.3.
Leo Famulari [Sun, 3 Jan 2016 19:53:12 +0000 (14:53 -0500)]
gnu: samba: Update to 4.3.3.

Fixes CVE-2015-{3223,5252,5299,5296,8467,5330}.

* gnu/packages/samba.scm (samba): Update to 4.3.3.

8 years agognu: ldb: Update to 1.1.24.
Leo Famulari [Sun, 3 Jan 2016 19:55:55 +0000 (14:55 -0500)]
gnu: ldb: Update to 1.1.24.

Required for samba-4.3.3 in order to fix CVE-2015-5330 and
CVE-2015-3223.

* gnu/packages/samba.scm (ldb): Update to 1.2.24.

8 years agognu: Add Asymptote.
Eric Bavier [Sun, 20 Dec 2015 22:24:24 +0000 (16:24 -0600)]
gnu: Add Asymptote.

* gnu/packages/bdw-gc.scm (libgc-for-c++): New variable.
* gnu/packages/plotutils.scm (asymptote): New variable.
* gnu/packages/patches/asymptote-gsl2.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

8 years agograph: %BAG-WITH-ORIGINS-NODE-TYPE includes the origin's guile.
Ludovic Courtès [Sat, 2 Jan 2016 21:22:57 +0000 (22:22 +0100)]
graph: %BAG-WITH-ORIGINS-NODE-TYPE includes the origin's guile.

Before that it would include #f for most origins since that the default
value of 'origin-patch-guile'.

* guix/scripts/graph.scm (bag-node-edges): When 'origin-patch-guile'
returns #f, use (default-guile).
* tests/graph.scm ("bag DAG, including origins"): Check for an edge from
O to (default-guile).

8 years agograph: %BAG-EMERGED-NODE-TYPE filters out origins.
Ludovic Courtès [Sat, 2 Jan 2016 21:12:36 +0000 (22:12 +0100)]
graph: %BAG-EMERGED-NODE-TYPE filters out origins.

Fixes <http://bugs.gnu.org/22280>.
Reported by Leo Famulari <leo@famulari.name>.

* guix/scripts/graph.scm (%bag-emerged-node-type)[edges]: Mimic
%BAG-NODE-TYPE.  This is a followup to 38b92da.

8 years agoUpdate NEWS.
Alex Kost [Thu, 31 Dec 2015 19:42:03 +0000 (22:42 +0300)]
Update NEWS.

* NEWS: Mention Emacs interface for Hydra and changes in variables.

8 years agoemacs: Use "B" key in "Package List" to display latest builds.
Alex Kost [Fri, 11 Dec 2015 11:09:27 +0000 (14:09 +0300)]
emacs: Use "B" key in "Package List" to display latest builds.

* emacs/guix-ui-package.el (guix-package-list-latest-builds): New
  procedure.
  (guix-package-list-mode-map): Bind "B" key to it.
  (guix-output-list-mode-map): Likewise.
* doc/emacs.texi (Emacs List buffer): Document it.

8 years agoemacs: Add Hydra interface.
Alex Kost [Fri, 11 Dec 2015 11:01:35 +0000 (14:01 +0300)]
emacs: Add Hydra interface.

* emacs/guix-utils.el (guix-hexify, guix-number->bool): New procedures.
  (guix-while-null): New macro.
* emacs/guix-hydra.el: New file.
* emacs/guix-hydra-build.el: New file.
* emacs/guix-hydra-jobset.el: New file.
* emacs.am (ELFILES): Add them.
* doc/emacs.texi (Emacs Hydra): New node.
  (Emacs Interface): Add it.
* doc/guix.texi (Top): Add it.
  (Substitutes): Mention Emacs interface.

8 years agoemacs: Add 'guix-ui-read-profile'.
Alex Kost [Fri, 18 Dec 2015 08:34:48 +0000 (11:34 +0300)]
emacs: Add 'guix-ui-read-profile'.

* emacs/guix-ui.el (guix-ui-read-profile): New procedure.
* emacs/guix-ui-package.el (guix-search-by-name)
  (guix-search-by-regexp, guix-installed-packages)
  (guix-obsolete-packages, guix-all-available-packages)
  (guix-newest-available-packages): Use it.
* emacs/guix-ui-generation.el (guix-generations)
  (guix-last-generations, guix-generations-by-time): Use it.

8 years agoemacs: Add hierarchy of customization groups.
Alex Kost [Fri, 18 Dec 2015 08:19:12 +0000 (11:19 +0300)]
emacs: Add hierarchy of customization groups.

* emacs/guix-buffer.el (guix-define-groups, guix-define-entry-type)
  (guix-define-buffer-type): New macros.
  (guix-buffer-define-interface): Add parent groups for the generated
  custom groups.
* emacs/guix-info.el: Use 'guix-define-buffer-type' to generate custom
  groups.
* emacs/guix-list.el: Likewise.
* emacs/guix-ui.el: Use 'guix-define-groups' to generate custom groups.
  (guix-ui-define-entry-type): New macro.
* emacs/guix-ui-package.el: Use it.
* emacs/guix-ui-generation.el: Use it.

8 years agoemacs: Return nil instead of "" in completing readers.
Alex Kost [Fri, 11 Dec 2015 09:36:56 +0000 (12:36 +0300)]
emacs: Return nil instead of "" in completing readers.

* emacs/guix-utils.el (guix-completing-read): New procedure.
  (guix-define-readers): Use it.

8 years agoemacs: Add 'guix-list-get-display-entries'.
Alex Kost [Wed, 9 Dec 2015 20:19:17 +0000 (23:19 +0300)]
emacs: Add 'guix-list-get-display-entries'.

* emacs/guix-list.el (guix-list-get-display-entries): New procedure.
* emacs/guix-ui-generation.el (guix-generation-get-display): Use it.

8 years agoemacs: Add 'list-single' variables.
Alex Kost [Wed, 9 Dec 2015 18:58:36 +0000 (21:58 +0300)]
emacs: Add 'list-single' variables.

* emacs/guix-list.el (guix-list-single-entry?): New procedure.
  (guix-list-define-interface): Add ':list-single?' key and generate
  'guix-ENTRY-TYPE-list-single' variables.
* emacs/guix-ui-package.el (guix-package-list-single): Remove.

8 years agoemacs: Reorganize package/generation UI code.
Alex Kost [Wed, 9 Dec 2015 11:44:34 +0000 (14:44 +0300)]
emacs: Reorganize package/generation UI code.

Move the code for packages/generations interface from "guix-info.el",
"guix-list.el", "guix-base.el" and "guix.el" to "guix-ui-package.el" and
"guix-ui-generation.el".

* emacs/guix-base.el (guix-package-entry->name-specification)
  (guix-package-entries->name-specifications)
  (guix-package-id-and-output-by-output-id)
  (guix-package-installed-outputs, guix-process-package-actions)
  (guix-package-list-type, guix-package-info-type)
  (guix-continue-package-operation-p, guix-get-package-strings)
  (guix-insert-package-strings): Move to "guix-ui-package.el".
  (guix-generation-packages-buffer-name-function, guix-output-name-width)
  (guix-generation-packages-update-buffer, guix-generation-packages)
  (guix-generation-packages-buffer-name-default)
  (guix-generation-packages-buffer-name-long)
  (guix-generation-packages-buffer-name, guix-generation-packages-buffer)
  (guix-generation-insert-packages, guix-generation-insert-package)
  (guix-profile-generation-manifest-file, guix-delete-generations)
  (guix-profile-generation-packages-buffer, guix-switch-to-generation):
  Move to "guix-ui-generation.el".
* emacs/guix-info.el (guix-package-location, guix-package-name)
  (guix-package-source, guix-package-info-source)
  (guix-package-info-heading, guix-package-info-license)
  (guix-package-info-name, guix-package-info-name-button)
  (guix-package-info-version, guix-package-info-location)
  (guix-package-info-synopsis, guix-package-info-description)
  (guix-package-info-obsolete, guix-package-info-installed-outputs)
  (guix-package-info-uninstalled-outputs)
  (guix-package-info-insert-heading)
  (guix-package-info-define-insert-inputs)
  (guix-package-info-obsolete-string)
  (guix-package-info-insert-obsolete-text)
  (guix-package-info-insert-non-unique-text)
  (guix-package-info-insert-outputs, guix-package-info-insert-output)
  (guix-package-info-insert-action-button)
  (guix-package-info-auto-find-source)
  (guix-package-info-auto-download-source)
  (guix-package-info-download-buffer, guix-package-info-show-source)
  (guix-package-info-download-source, guix-package-info-insert-source)
  (guix-package-info-redisplay-after-download)
  (guix-output-info-insert-version, guix-output-info-insert-output):
  Move to "guix-ui-package.el".
  (guix-generation-info-number, guix-generation-info-current)
  (guix-generation-not-current, guix-generation-info-insert-number)
  (guix-generation-info-insert-current): Move to "guix-ui-generation.el".
* emacs/guix-list.el (guix-package-list-generation-marking-enabled)
  (guix-package-list-installed, guix-package-list-obsolete)
  (guix-package-list-get-name, guix-package-list-get-installed-outputs)
  (guix-package-list-marking-check, guix-package-list-mark-outputs)
  (guix-package-list-mark-install, guix-package-list-mark-delete)
  (guix-package-list-mark-upgrade, guix-package-list-mark-upgrades)
  (guix-list-mark-package-upgrades, guix-list-execute-package-actions)
  (guix-package-list-execute, guix-package-list-make-action)
  (guix-package-list-edit, guix-output-list-mark-install)
  (guix-output-list-mark-delete, guix-output-list-mark-upgrade)
  (guix-output-list-mark-upgrades, guix-output-list-make-action)
  (guix-output-list-describe, guix-output-list-edit): Move to
  "guix-ui-package.el".
  (guix-generation-list-get-current, guix-generation-list-switch)
  (guix-generation-list-generations-to-compare)
  (guix-generation-list-compare, guix-generation-list-show-packages)
  (guix-generation-list-show-added-packages)
  (guix-generation-list-show-removed-packages)
  (guix-generation-list-diff, guix-generation-list-diff-manifests)
  (guix-generation-list-ediff, guix-generation-list-ediff-manifests)
  (guix-generation-list-diff-packages)
  (guix-generation-list-ediff-packages)
  (guix-generation-list-mark-delete, guix-generation-list-execute): Move
  to "guix-ui-generation.el".
* emacs/guix.el: Remove.
  (guix, guix-faces, guix-edit): Move to "guix-base.el".
  (guix-list-single-package, guix-search-params, guix-search-history)
  (guix-get-show-packages, guix-search-by-name, guix-search-by-regexp)
  (guix-installed-packages, guix-obsolete-packages)
  (guix-all-available-packages, guix-newest-available-packages): Move
  to "guix-ui-package.el".
  (guix-get-show-generations, guix-generations, guix-last-generations)
  (guix-generations-by-time): Move to "guix-ui-generation.el".
* emacs.am (ELFILES): Remove "guix.el".  Add "guix-ui-package.el" and
  "guix-ui-generation.el".
* doc/emacs.texi (Emacs Appearance): Adjust accordingly.

8 years agoemacs: Reorganize 'readers' code.
Alex Kost [Wed, 9 Dec 2015 11:12:00 +0000 (14:12 +0300)]
emacs: Reorganize 'readers' code.

* emacs/guix-base.el (guix-graph-type-names, guix-refresh-updater-names)
  (guix-lint-checker-names, guix-package-names): Move to...
* emacs/guix-read.el: ... here.
  (guix-read-file-name, guix-define-reader, guix-define-readers): Move to...
* emacs/guix-utils.el: ... here.

8 years agoemacs: Generalize buffer interface.
Alex Kost [Wed, 2 Dec 2015 12:24:07 +0000 (15:24 +0300)]
emacs: Generalize buffer interface.

Extract the code for defining buffer interface from "guix-base.el",
generalize it and move to "guix-buffer.el".

* emacs.am (ELFILES): Add "emacs/guix-buffer.el".
* emacs/guix-base.el (guix-profile, guix-entries, guix-buffer-type)
  (guix-entry-type, guix-search-type, guix-search-vals, guix-set-vars)
  (guix-get-symbol, guix-show-entries, guix-get-show-entries)
  (guix-set-buffer, guix-history-call, guix-make-history-item)
  (guix-get-params-for-receiving): Remove.
  (guix-switch-to-buffer): Rename to 'guix-buffer-display' and move to
  "guix-buffer.el".
  (guix-get-entries): Rename to 'guix-ui-get-entries' and move to
  "guix-ui.el".
  (guix-buffer-data, guix-buffer-value, guix-buffer-param-title)
  (guix-buffer-name, guix-buffer-history-size)
  (guix-buffer-revert-confirm?, guix-buffer-map, guix-buffer-revert)
  (guix-buffer-after-redisplay-hook, guix-buffer-redisplay)
  (guix-buffer-redisplay-goto-button): Move to...
* emacs/guix-buffer.el: ... here.  New file.
  (guix-buffer-item): New variable.
  (guix-buffer-with-item, guix-buffer-with-current-item)
  (guix-buffer-define-current-item-accessor)
  (guix-buffer-define-current-item-accessors)
  (guix-buffer-define-current-args-accessor)
  (guix-buffer-define-current-args-accessors): New macros.
  (guix-buffer-get-entries, guix-buffer-mode-enable)
  (guix-buffer-mode-initialize, guix-buffer-insert-entries)
  (guix-buffer-show-entries-default, guix-buffer-show-entries)
  (guix-buffer-message, guix-buffer-history-item, guix-buffer-set)
  (guix-buffer-display-entries-current)
  (guix-buffer-get-display-entries-current)
  (guix-buffer-display-entries, guix-buffer-get-display-entries): New
  procedures.
* emacs/guix-info.el: Adjust for the procedures renaming.
  (guix-info-define-interface): Add ':show-entries-function' keyword.
* emacs/guix-list.el: Likewise.
* emacs/guix-ui.el (guix-ui-define-interface): Generate
  'guix-ENTRY-TYPE-BUFFER-TYPE-get-entries' procedure based on
  'guix-ui-get-entries'.
* emacs/guix.el (guix-get-show-packages, guix-get-show-generations):
  Adjust for the procedures renaming.

8 years agoemacs: info: Get rid of syntactic fontification.
Alex Kost [Fri, 27 Nov 2015 13:01:20 +0000 (16:01 +0300)]
emacs: info: Get rid of syntactic fontification.

* emacs/guix-info.el (guix-info-mode-initialize): New procedure.  Set
  'font-lock-defaults' to avoid syntactic fontification.
  (guix-info-define-interface): Use it.

8 years agoemacs: Generalize buffer naming.
Alex Kost [Mon, 23 Nov 2015 13:41:58 +0000 (16:41 +0300)]
emacs: Generalize buffer naming.

* emacs/guix-base.el (guix-buffer-name): New procedure.
  (guix-buffer-define-interface): Make ':buffer-name' a required keyword.
  (guix-update-after-operation, guix-buffer-name-function)
  (guix-buffer-name-simple, guix-buffer-name-default, guix-buffer-name)
  (guix-buffer-p, guix-buffers, guix-update-buffer)
  (guix-update-buffers-maybe-after-operation): Adjust, move and rename to...
* emacs/guix-ui.el (guix-ui-update-after-operation)
  (guix-ui-buffer-name-function, guix-ui-buffer-name-simple)
  (guix-ui-buffer-name-default, guix-ui-buffer-name)
  (guix-ui-buffer?, guix-ui-buffers, guix-ui-update-buffer)
  (guix-ui-update-buffers-after-operation): ... this.
  (guix-ui-define-interface): Generate
  'guix-ENTRY-TYPE-BUFFER-TYPE-buffer-name' procedure and pass it as
  ':buffer-name' argument.
  (guix-ui): New custom group.
* emacs/guix-info.el: Specify ':buffer-name' for the defined interfaces.
* emacs/guix-list.el: Likewise.
* doc/emacs.texi (Emacs Appearance): Adjust accordingly.

8 years agoemacs: info: Buttonize package name heading.
Alex Kost [Sun, 22 Nov 2015 21:18:38 +0000 (00:18 +0300)]
emacs: info: Buttonize package name heading.

* emacs/guix-info.el (guix-package-info-insert-heading): Insert
  buttonized name specification.