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* gnu: Add R.oo.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-oo): New variable.
* gnu: Add R.methodsS3.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-methodss3): New variable.
* gnu: Add base64enc.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-base64enc): New variable.
* gnu: Add DT.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-dt): New variable.
* gnu: Add SparseM.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-sparsem): New variable.
* gnu: Add GO.db.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-go-db): New variable.
* gnu: Add GenomicFeatures.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
* gnu: Add rtracklayer.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
* gnu: Add GenomicAlignments.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
* gnu: Add SummarizedExperiment.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
* gnu: Add Rsamtools.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
* gnu: Add Biostrings.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): New variable.
* gnu: Add BiocParallel.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
* gnu: Add biomaRt.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biomart): New variable.
* gnu: Add AnnotationDbi.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
* gnu: Add Biobase.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biobase): New variable.
* gnu: Add snow.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-snow): New variable.
* gnu: Add futile.logger.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-futile-logger): New variable.
* gnu: Add futile.options.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-futile-options): New variable.
* gnu: Add lambda.r.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-lambda-r): New variable.
* gnu: Add r-xml.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-xml): New variable.
* gnu: Add RCurl.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-rcurl): New variable.
* gnu: Add RSQLite.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-rsqlite): New variable.
* import: Rename "cran-fetch" to "fetch-description".Ricardo Wurmus2016-01-07
| | | | | * guix/import/cran.scm (cran-fetch): Rename procedure ... (fetch-description): ... to this.
* import: Add package->upstream-name procedure.Ricardo Wurmus2016-01-07
| | | | * guix/import/cran.scm (package->upstream-name): New procedure.
* gnu: Add xmlstarlet.Raimon Grau2016-01-07
| | | | * gnu/packages/xml.scm (xmlstarlet): New variable.
* gnu: zita-convolver: Drop the '-march=native' optimization.宋文武2016-01-07
| | | | * gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
* gnu: zita-resampler: Drop the '-march=native' optimization.宋文武2016-01-07
| | | | * gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
* gnu: Add ruby-ansi.Ben Woodcroft2016-01-07
| | | | * gnu/packages/ruby.scm (ruby-ansi): New variable.
* gnu: edirect: Update to 3.50.Ricardo Wurmus2016-01-07
| | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip".
* gnu: w3m: Enable SSL, disable broken protocols and ciphers.Leo Famulari2016-01-07
| | | | | | | | | | 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.
* gnu: w3m: Update patch to use '-p1'.Leo Famulari2016-01-07
| | | | | | | | | * 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.
* build-system/gnu: Make 'package-with-explicit-inputs' idempotent.Ludovic Courtès2016-01-06
| | | | | | | * 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.
* utils: Add 'ensure-keyword-arguments'.Ludovic Courtès2016-01-06
| | | | | * guix/utils.scm (delkw, ensure-keyword-arguments): New procedures. * tests/utils.scm ("ensure-keyword-arguments"): New test.
* http-client: Work around <http://bugs.gnu.org/22273>.Ludovic Courtès2016-01-06
| | | | * guix/http-client.scm (read-header-line): New procedure. Use it.
* gnu: guix: Update development snapshot to f888c0b.Ludovic Courtès2016-01-06
| | | | * gnu/packages/package-management.scm (guix-devel): Update to f888c0b.
* http-client: Fix erroneous comment.Ludovic Courtès2016-01-06
| | | | | * guix/http-client.scm: Fix Guile version number in comment for Guile commit 5a10e41.
* gnu: gmsh: Update to 2.11.0.Eric Bavier2016-01-06
| | | | | * gnu/packages/maths.scm (gmsh): Update to 2.11.0. [arguments]: Replace 'check phase.
* lint: cve: Catch host name lookup errors.Ludovic Courtès2016-01-06
| | | | | * guix/scripts/lint.scm (package-vulnerabilities): Catch 'getaddrinfo-error'.
* gnu: sudo: Use /var/run/sudo instead of /run/sudo.Ludovic Courtès2016-01-06
| | | | | | * 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.
* services: cleanup-service: Catch 'system-error' instead of everything.Ludovic Courtès2016-01-06
| | | | | | | | 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'.
* gnu: ldc: Fix license.Ludovic Courtès2016-01-06
| | | | | * gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of 'license:x11-style' by LICENSE:BOOST1.0.
* build: ruby: Remove cached gem after install.Ben Woodcroft2016-01-06
| | | | | | | | | 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.
* gnu: icedtea7: Rename to icedtea-7.Ricardo Wurmus2016-01-06
| | | | | | * gnu/packages/java.scm (icedtea7): Rename variable to... (icedtea-7): ...this. (icedtea): Refer to "icedtea-7".
* gnu: icedtea6: Rename to icedtea-6.Ricardo Wurmus2016-01-06
| | | | | * gnu/packages/java.scm (icedtea6): Rename variable to... (icedtea-6): ...this.
* gnu: icedtea6, icedtea7: Rename package to "icedtea".Ricardo Wurmus2016-01-06
| | | | | * gnu/packages/java.scm (icedtea6): Change package name to "icedtea". (icedtea7): Inherit package name.
* gnu: Add and use default IcedTea.Ricardo Wurmus2016-01-06
| | | | | | | | | | | * 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".
* gnu: icedtea6, icedtea7: Unpack to "openjdk.src".Ricardo Wurmus2016-01-06
| | | | | | | | * 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".
* gnu: Add Jellyfish.Ricardo Wurmus2016-01-06
| | | | * gnu/packages/bioinformatics.scm (jellyfish): New variable.
* build: Bump version number.Ludovic Courtès2016-01-05
| | | | * configure.ac: Change version to 0.9.1.
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