8bfe007c9c
gnu: Add R.methodsS3.
...
* gnu/packages/statistics.scm (r-r-methodss3): New variable.
2016-01-07 17:18:16 +01:00
a69a593595
gnu: Add base64enc.
...
* gnu/packages/statistics.scm (r-base64enc): New variable.
2016-01-07 17:18:16 +01:00
a8227e4ae9
gnu: Add DT.
...
* gnu/packages/statistics.scm (r-dt): New variable.
2016-01-07 17:18:16 +01:00
d706257b5b
gnu: Add SparseM.
...
* gnu/packages/statistics.scm (r-sparsem): New variable.
2016-01-07 17:18:16 +01:00
fb25d8803f
gnu: Add GO.db.
...
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2016-01-07 17:18:16 +01:00
2fd7c04984
gnu: Add GenomicFeatures.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
2016-01-07 17:18:16 +01:00
317755ff0f
gnu: Add rtracklayer.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
2016-01-07 17:18:16 +01:00
d8a828af78
gnu: Add GenomicAlignments.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07 17:18:16 +01:00
6e76dda2d0
gnu: Add SummarizedExperiment.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07 17:18:16 +01:00
f8d74f7018
gnu: Add Rsamtools.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07 17:18:16 +01:00
bf15935337
gnu: Add Biostrings.
...
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07 17:18:16 +01:00
e91d362e48
gnu: Add BiocParallel.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07 17:18:16 +01:00
c465fa72ed
gnu: Add biomaRt.
...
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07 17:18:16 +01:00
8b7bce740d
gnu: Add AnnotationDbi.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07 17:18:16 +01:00
555e3399dc
gnu: Add Biobase.
...
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07 17:18:16 +01:00
bc899123e7
gnu: Add snow.
...
* gnu/packages/statistics.scm (r-snow): New variable.
2016-01-07 17:18:16 +01:00
6b82f56cf9
gnu: Add futile.logger.
...
* gnu/packages/statistics.scm (r-futile-logger): New variable.
2016-01-07 17:18:16 +01:00
b9ff33b50e
gnu: Add futile.options.
...
* gnu/packages/statistics.scm (r-futile-options): New variable.
2016-01-07 17:18:16 +01:00
ca65d387fd
gnu: Add lambda.r.
...
* gnu/packages/statistics.scm (r-lambda-r): New variable.
2016-01-07 17:18:16 +01:00
543ded3619
gnu: Add r-xml.
...
* gnu/packages/statistics.scm (r-xml): New variable.
2016-01-07 17:18:16 +01:00
cefaa79c9e
gnu: Add RCurl.
...
* gnu/packages/statistics.scm (r-rcurl): New variable.
2016-01-07 17:18:16 +01:00
21e4d6a9cf
gnu: Add RSQLite.
...
* gnu/packages/statistics.scm (r-rsqlite): New variable.
2016-01-07 17:18:15 +01:00
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
d1c116089b
import: Add package->upstream-name procedure.
...
* guix/import/cran.scm (package->upstream-name): New procedure.
2016-01-07 17:18:02 +01:00
fe9451c50a
gnu: Add xmlstarlet.
...
* gnu/packages/xml.scm (xmlstarlet): New variable.
2016-01-07 16:00:00 +01:00
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
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
7d3a1a2dd2
gnu: Add ruby-ansi.
...
* gnu/packages/ruby.scm (ruby-ansi): New variable.
2016-01-07 15:36:05 +01:00
b24765139c
gnu: sqlite: Update to 3.10.0.
...
* gnu/packages/databases.scm (sqlite): Update to 3.10.0.
2016-01-07 12:37:37 +02:00
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
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
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
93b3a8b0ee
gnu: flex: Update to 2.6.0.
...
* gnu/packages/flex.scm (flex): Update to 2.6.0.
[source]: Remove flex-bison-tests.patch.
* gnu-system.am (dist_patch_DATA): Remove flex-bison-tests.patch.
* gnu/packages/patches/flex-bison-tests.patch: Remove it.
2016-01-07 08:42:15 +02:00
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
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
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
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
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
bfcb7bcb73
gnu: libffi: Update to 3.2.1.
...
* gnu/packages/libffi.scm (libffi): Update to 3.2.1.
2016-01-06 20:28:57 +02:00
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
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
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
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
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
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
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
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
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
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
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