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10124 Commits

Author SHA1 Message Date
Ricardo Wurmus 8bfe007c9c gnu: Add R.methodsS3. 
* gnu/packages/statistics.scm (r-r-methodss3): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus a69a593595 gnu: Add base64enc. 
* gnu/packages/statistics.scm (r-base64enc): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus a8227e4ae9 gnu: Add DT. 
* gnu/packages/statistics.scm (r-dt): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus d706257b5b gnu: Add SparseM. 
* gnu/packages/statistics.scm (r-sparsem): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus fb25d8803f gnu: Add GO.db. 
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 2fd7c04984 gnu: Add GenomicFeatures. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 317755ff0f gnu: Add rtracklayer. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus d8a828af78 gnu: Add GenomicAlignments. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 6e76dda2d0 gnu: Add SummarizedExperiment. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus f8d74f7018 gnu: Add Rsamtools. 
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus bf15935337 gnu: Add Biostrings. 
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus e91d362e48 gnu: Add BiocParallel. 
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus c465fa72ed gnu: Add biomaRt. 
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 8b7bce740d gnu: Add AnnotationDbi. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 555e3399dc gnu: Add Biobase. 
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus bc899123e7 gnu: Add snow. 
* gnu/packages/statistics.scm (r-snow): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 6b82f56cf9 gnu: Add futile.logger. 
* gnu/packages/statistics.scm (r-futile-logger): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus b9ff33b50e gnu: Add futile.options. 
* gnu/packages/statistics.scm (r-futile-options): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus ca65d387fd gnu: Add lambda.r. 
* gnu/packages/statistics.scm (r-lambda-r): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 543ded3619 gnu: Add r-xml. 
* gnu/packages/statistics.scm (r-xml): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus cefaa79c9e gnu: Add RCurl. 
* gnu/packages/statistics.scm (r-rcurl): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus 21e4d6a9cf gnu: Add RSQLite. 
* gnu/packages/statistics.scm (r-rsqlite): New variable.
 2016-01-07 17:18:15 +01:00
Ricardo Wurmus 34a75d35bb import: Rename "cran-fetch" to "fetch-description". 
* guix/import/cran.scm (cran-fetch): Rename procedure ...
(fetch-description): ... to this.
 2016-01-07 17:18:04 +01:00
Ricardo Wurmus d1c116089b import: Add package->upstream-name procedure. 
* guix/import/cran.scm (package->upstream-name): New procedure.
 2016-01-07 17:18:02 +01:00
Raimon Grau fe9451c50a gnu: Add xmlstarlet. 
* gnu/packages/xml.scm (xmlstarlet): New variable.
 2016-01-07 16:00:00 +01:00
宋文武 29e255ca83 gnu: zita-convolver: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
宋文武 6dff495580 gnu: zita-resampler: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
Ben Woodcroft 7d3a1a2dd2 gnu: Add ruby-ansi. 
* gnu/packages/ruby.scm (ruby-ansi): New variable.
 2016-01-07 15:36:05 +01:00
Ricardo Wurmus 5dfd276602 gnu: edirect: Update to 3.50. 
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
 2016-01-07 11:25:24 +01:00
Leo Famulari 62339e2d49 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.
 2016-01-07 02:35:38 -05:00
Leo Famulari e6352001c4 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.
 2016-01-07 02:35:38 -05:00
Ludovic Courtès d4aaf95401 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.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès 6071122b71 utils: Add 'ensure-keyword-arguments'. 
* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures.
* tests/utils.scm ("ensure-keyword-arguments"): New test.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès 793a43f409 http-client: Work around <http://bugs.gnu.org/22273>. 
* guix/http-client.scm (read-header-line): New procedure.  Use it.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès dff9141c5e gnu: guix: Update development snapshot to f888c0b. 
* gnu/packages/package-management.scm (guix-devel): Update to f888c0b.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès 1c63dafce6 http-client: Fix erroneous comment. 
* guix/http-client.scm: Fix Guile version number in comment for Guile
commit 5a10e41.
 2016-01-06 23:08:22 +01:00
Eric Bavier c7b08410de gnu: gmsh: Update to 2.11.0. 
* gnu/packages/maths.scm (gmsh): Update to 2.11.0.
  [arguments]: Replace 'check phase.
 2016-01-06 10:49:23 -06:00
Ludovic Courtès f888c0b120 lint: cve: Catch host name lookup errors. 
* guix/scripts/lint.scm (package-vulnerabilities): Catch
'getaddrinfo-error'.
 2016-01-06 15:54:12 +01:00
Ludovic Courtès 7b78f359d1 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.
 2016-01-06 15:51:31 +01:00
Ludovic Courtès 3c4c8c3e06 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'.
 2016-01-06 14:49:48 +01:00
Ludovic Courtès 341ae58213 gnu: ldc: Fix license. 
* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of
'license:x11-style' by LICENSE:BOOST1.0.
 2016-01-06 14:21:53 +01:00
Ben Woodcroft 7266848ace 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.
 2016-01-06 12:42:41 +01:00
Ricardo Wurmus a243e12aba gnu: icedtea7: Rename to icedtea-7. 
* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d028740622 gnu: icedtea6: Rename to icedtea-6. 
* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus 5452588c1a gnu: icedtea6, icedtea7: Rename package to "icedtea". 
* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d2540f80c2 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".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus d91488908b 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".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus 43c565d2e7 gnu: Add Jellyfish. 
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
 2016-01-06 11:10:46 +01:00
Ludovic Courtès 03cea32031 build: Bump version number. 
* configure.ac: Change version to 0.9.1.
 2016-01-05 23:55:26 +01:00
Michael Vetter f9b9a0330d doc: Remove double occurrence of words. 
* doc/guix.texi: substitute 'the the' with 'the'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-01-05 23:55:26 +01:00