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Ludovic Courtès
5ca2b3c245 build: Add rsem patch to the distribution. 
This file was added in commit 66e3eff1.

* gnu-system.am (dist_patch_DATA): Add rsem-makefile.patch.
 2015-11-24 13:15:38 +01:00
Ludovic Courtès
38b92daa81 graph: Add '%bag-with-origins-node-type'. 
* guix/scripts/graph.scm (bag-node-edges): Remove 'filter' call.  Add
case for 'origin'.
(%bag-node-type)[edges]: Add filtering here.
(%bag-with-origins-node-type): New variable.
(%node-types): Add it.
* tests/graph.scm ("bag DAG, including origins"): New test.
* tests/guix-graph.sh: Add 'bag-with-origins'.
* doc/guix.texi (Invoking guix graph): Document it.
 2015-11-23 23:34:15 +01:00
Ludovic Courtès
961d0d2d22 doc: Mention the 'NIX_REMOTE' variable for 'guix import nix'. 
Suggested by rgrau on #guix.

* doc/guix.texi (Invoking guix import): Document 'NIX_REMOTE'.
 2015-11-23 23:20:41 +01:00
Ludovic Courtès
2d7fc7daf1 refresh: Add '--expression'. 
* guix/scripts/refresh.scm (%options, show-help): Add --expression.
(guix-refresh): Honor it.
* doc/guix.texi (Invoking guix refresh): Document it.
 2015-11-23 17:48:35 +01:00
Ludovic Courtès
160b0ef3fd Thank Jan. 2015-11-23 17:48:35 +01:00
Ludovic Courtès
86cdfc451b guix download: Fail when more than one URL is passed. 
* guix/scripts/download.scm (guix-download)[parse-option]: Call 'leave'
when passed an extra argument.
* tests/guix-download.sh: Add test.
 2015-11-23 17:48:35 +01:00
Ludovic Courtès
71ae18ee52 guix download: Gracefully handle missing arguments. 
Fixes <http://bugs.gnu.org/21991>.
Reported by Jan Synáček <jan.synacek@gmail.com>.

* guix/scripts/download.scm (guix-download): Call 'leave' when OPTS does
not contain an 'argument' key.
 2015-11-23 17:48:35 +01:00
Taylan Ulrich Bayırlı/Kammer
bbee7bd765 gnu: enca: Add file-name field to source. 
* gnu/packages/textutils.scm (enca): Add file-name field to source.
 2015-11-23 13:46:31 +01:00
Taylan Ulrich Bayırlı/Kammer
6f323b0773 gnu: recode: Add file-name field to source. 
* gnu/packages/textutils.scm (recode): Add file-name field to source.
 2015-11-23 12:05:55 +01:00
Ludovic Courtès
821f4dc287 gnu: Fix a few 'source-file-name' lint warnings. 
* gnu/packages/firmware.scm (ath9k-htc-firmware)[source](file-name): New
field.
* gnu/packages/gnunet.scm (guile-gnunet)[source](file-name): New field.
* gnu/packages/guile.scm (guile-next)[source](file-name): New field.
(guile-minikanren)[source](file-name): New field
(guile-gdbm-ffi)[source](file-name): New field.
* gnu/packages/ssh.scm (guile-ssh)[source](file-name): New field.
 2015-11-23 10:52:32 +01:00
Alex Kost
59dc56390d emacs: Expand 'guix-load-path'. 
Reported by Mathieu Lirzin <mthl@gnu.org> at
<http://lists.gnu.org/archive/html/guix-devel/2015-11/msg00585.html>.

* emacs/guix-backend.el (guix-start-repl): Expand 'guix-load-path' to
  avoid a potentially relative directory name in Guile %load-path.
 2015-11-23 11:33:55 +03:00
Ludovic Courtès
862d2479f6 ftp-client: Default port for 'ftp-open' is now "ftp". 
* guix/ftp-client.scm (ftp-open): Change default #:port to "ftp".
* guix/scripts/lint.scm (probe-uri): Remove 'port' parameter to
'ftp-open'.
 2015-11-22 14:35:28 +01:00
Ludovic Courtès
d6d33984df ftp-client: Fix off-by-one when trying addresses in 'ftp-open'. 
* guix/ftp-client.scm (ftp-open): Change to use 'match' instead of
car/cdr, and fix off-by-one (was '(null? addresses)' instead of
'(null? (cdr addresses))'.)
 2015-11-22 14:16:36 +01:00
Ludovic Courtès
5fb95cc592 doc: Mention 'guix environment guix'. 
* doc/contributing.texi (Building from Git): Mention 'guix environment
guix'.  Remove outdated description of ./bootstrap.  Clarify a few
things.
 2015-11-22 14:14:25 +01:00
Ludovic Courtès
82e64fc14e environment: Correctly handle abnormal exits. 
Fixes <http://bugs.gnu.org/21958>.

* guix/scripts/environment.scm (status->exit-code): New procedure.
(exit/status, primitive-exit/status): Use it.
* tests/guix-environment-container.sh: Add test.
 2015-11-21 22:26:13 +01:00
Ludovic Courtès
6493fd0458 tests: Skip 'guix-container-environment.sh' when support is missing. 
Fixes <http://bugs.gnu.org/21410>.
Reported by Alex Vong <alexvong1995@gmail.com>.

* tests/guix-environment-container.sh: Exit with 77 when
'((@@ (guix scripts environment) assert-container-features))' fails.
 2015-11-21 22:26:13 +01:00
Ludovic Courtès
aabe6d3801 doc: Remove extraneous "See." 
* doc/contributing.texi (Building from Git): Remove extra "See" and use
@xref instead of @pxref.
 2015-11-21 22:26:13 +01:00
Efraim Flashner
92d9a36e97 gnu: tig: Update to 2.1.1. 
* gnu/packages/version-control.scm (tig): Update to 2.1.1.
 2015-11-21 23:03:11 +02:00
Efraim Flashner
7fbbd3e7a0 gnu: cvs: Use external zlib. 
* gnu/packages/version-control.scm (cvs)[arguments]: add configure flag
  --with-exernal-zlib.
 2015-11-21 21:43:11 +02:00
Efraim Flashner
f94f481988 gnu: nano: Update to 2.4.3. 
* gnu/packages/nano.scm (nano): Update to 2.4.3.
 2015-11-21 20:56:08 +02:00
Ludovic Courtès
a51cbecb44 refresh: Rewrite '--list-dependent' in terms of (guix graph). 
* guix/scripts/refresh.scm (all-packages, list-dependents): New
procedures.
(guix-refresh): Use it.
 2015-11-21 16:27:34 +01:00
Ludovic Courtès
923d846c4d graph: Add procedures to query a node's edges. 
* guix/graph.scm (%node-edges, node-edges, node-back-edges)
(node-transitive-edges): New procedures.
* tests/graph.scm ("node-edges")
("node-transitive-edges + node-back-edges"): New tests.
 2015-11-21 16:26:43 +01:00
Ludovic Courtès
8fb583714f Add (guix graph). 
* guix/scripts/graph.scm (<node-type>, <graph-backend>, emit-prologue)
(emit-epilogue, emit-node, emit-edge, %graphviz-backend, export-graph):
Move to...
* guix/graph.scm: ... here.  New file.
* guix/scripts/system.scm, tests/graph.scm: Use it.
* Makefile.am (MODULES): Add it.
 2015-11-21 16:26:43 +01:00
Mathieu Lirzin
1b933e62dc gnu: parted: Update to 3.2. 
* gnu/packages/disk.scm (parted): Update to 3.2.
[inputs]: Add lvm2 and remove check.  Replace readline-6.2 with its
latest version.
[native-inputs]: Add perl and python for the tests.
[arguments]: Use `modify-phases' and adapt to the new tests.
[home-page]: Use https.
 2015-11-21 13:10:27 +01:00
Ludovic Courtès
06da1a6b4f gnu: Add qemu-minimal. 
* gnu/packages/qemu.scm (qemu): Exchange with former QEMU-HEADLESS.
(qemu-headless): Rename to...
(qemu-minimal): ... this.  New variable.  Pass --target-list.
* gnu/packages/debug.scm (qemu-2.3.0): Inherit from QEMU-MINIMAL.
* gnu/packages/grub.scm (qemu-for-tests): Likewise.
* gnu/system/vm.scm (expression->derivation-in-linux-vm, qemu-image):
Update to name change.
 2015-11-21 00:36:23 +01:00
Alex Kost
bb38ece458 doc: Fix 'geiser-guile-load-path' example. 
Reported by marusich on #guix.

* doc/contributing.texi (The Perfect Setup): Wrap modifying
  'geiser-guile-load-path' into 'with-eval-after-load'.
 2015-11-21 02:19:04 +03:00
Ricardo Wurmus
56215e4154 gnu: Add Synfig Studio. 
* gnu/packages/animation.scm (synfigstudio): New variable.
 2015-11-20 20:23:03 +01:00
Ricardo Wurmus
7775a18690 gnu: Add Synfig. 
* gnu/packages/animation.scm (synfig): New variable.
* gnu/packages/patches/synfig-build-fix.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
 2015-11-20 20:23:03 +01:00
Ricardo Wurmus
c1fbc66a77 gnu: Add ETL. 
* gnu/packages/animation.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-11-20 20:23:03 +01:00
Ricardo Wurmus
307ad140db gnu: Add MLT. 
* gnu/packages/video.scm (mlt): New variable.
 2015-11-20 20:23:03 +01:00
Ricardo Wurmus
561965941c gnu: Add libxml++. 
* gnu/packages/gnome.scm (libxml++): New variable.
 2015-11-20 20:23:03 +01:00
Eric Bavier
9cf5245497 gnu: slepc: Update to 3.6.2. 
* gnu/packages/maths.scm (slepc): Update to 3.6.2.
  [arguments]: Append "/lib" to arpack configure flag.  Use 'inputs'
  rather than '%build-inputs' in 'configure phase.
 2015-11-20 11:58:40 -06:00
Eric Bavier
32187d99bb gnu: petsc: Update to 3.6.2. 
* gnu/packages/maths.scm (petsc): Update to 3.6.2.
 2015-11-20 11:58:40 -06:00
Eric Bavier
c69fa4380a gnu: mumps: Update to 5.0.1. 
* gnu/packages/maths.scm (mumps): Update to 5.0.1.
 2015-11-20 11:58:40 -06:00
Eric Bavier
ac356fd6ab gnu: openmpi: Update to 1.10.1. 
* gnu/packages/mpi.scm (openmpi): Update to 1.10.1.
  [arguments]: Remove now-unsupported configure flags.  Add
  --enable-builtin-atomics.  Remove development-oriented
  --enable-debug.
 2015-11-20 11:58:40 -06:00
Eric Bavier
2f5b6a1f18 gnu: hwloc: Update to 1.11.1. 
* gnu/packages/mpi.scm (hwloc): Update to 1.11.1.
  [source]: Remove patch.
* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: Delete it.
* gnu-system.am (dist_patch_DATA): Remove it.
 2015-11-20 11:58:40 -06:00
Ricardo Wurmus
0297966495 gnu: guitarix: Update to 0.34.0. 
* gnu/packages/audio.scm (guitarix): Update to 0.34.0.
[source]: Remove patch.
[inputs]: Add webkitgtk/gtk+-2.
* gnu/packages/patches/guitarix-c++11: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
 2015-11-20 18:19:30 +01:00
David Thompson
a907d9973a gnu: services: Fix typo in gpm-dmd-service. 
* gnu/services/base.scm (gpm-dmd-service): s/dmd/gpm/
 2015-11-20 09:56:41 -05:00
David Thompson
3307c7877e gnu: Add emulation-station. 
* gnu/packages/games.scm (emulation-station): New variable.
 2015-11-20 09:27:15 -05:00
Ricardo Wurmus
b49c5a58dc gnu: preseq: Update to 2.0. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
  file.
* gnu-system.am (dist_patch_DATA): Remove them.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus
c6a24d6e92 gnu: Add smithlab-cpp. 
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus
3d51ec919e gnu: edirect: Update home page. 
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
c52a382c4a gnu: sra-tools: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
9e5ef614aa gnu: ncbi-vdb: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
614a8977cb gnu: ngs-java: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
d6a1cd7cae gnu: ngs-sdk: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
2c84ba7e11 gnu: Add ruby-net-ssh. 
* gnu/packages/ruby.scm (ruby-net-ssh): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
4f2a52aeb5 gnu: Add ruby-mocha. 
* gnu/packages/ruby.scm (ruby-mocha): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
d93062fd5c gnu: Add ruby-redcarpet. 
* gnu/packages/ruby.scm (ruby-redcarpet): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus
97aee8d3eb gnu: Add ruby-introspection. 
* gnu/packages/ruby.scm (ruby-introspection): New variable.
 2015-11-20 15:21:24 +01:00