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2016-01-07gnu: Add R.rsp.•••* gnu/packages/statistics.scm (r-r-rsp): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.cache.•••* gnu/packages/statistics.scm (r-r-cache): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.utils.•••* gnu/packages/statistics.scm (r-r-utils): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.oo.•••* gnu/packages/statistics.scm (r-r-oo): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.methodsS3.•••* gnu/packages/statistics.scm (r-r-methodss3): New variable. Ricardo Wurmus
2016-01-07gnu: Add base64enc.•••* gnu/packages/statistics.scm (r-base64enc): New variable. Ricardo Wurmus
2016-01-07gnu: Add DT.•••* gnu/packages/statistics.scm (r-dt): New variable. Ricardo Wurmus
2016-01-07gnu: Add SparseM.•••* gnu/packages/statistics.scm (r-sparsem): New variable. Ricardo Wurmus
2016-01-07gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable. Ricardo Wurmus
2016-01-07gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable. Ricardo Wurmus
2016-01-07gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable. Ricardo Wurmus
2016-01-07gnu: Add Rsamtools.•••* gnu/packages/bioinformatics.scm (r-rsamtools): New variable. Ricardo Wurmus
2016-01-07gnu: Add Biostrings.•••* gnu/packages/bioinformatics.scm (r-biostrings): New variable. Ricardo Wurmus
2016-01-07gnu: Add BiocParallel.•••* gnu/packages/bioinformatics.scm (r-biocparallel): New variable. Ricardo Wurmus
2016-01-07gnu: Add biomaRt.•••* gnu/packages/bioinformatics.scm (r-biomart): New variable. Ricardo Wurmus
2016-01-07gnu: Add AnnotationDbi.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable. Ricardo Wurmus
2016-01-07gnu: Add Biobase.•••* gnu/packages/bioinformatics.scm (r-biobase): New variable. Ricardo Wurmus
2016-01-07gnu: Add snow.•••* gnu/packages/statistics.scm (r-snow): New variable. Ricardo Wurmus
2016-01-07gnu: Add futile.logger.•••* gnu/packages/statistics.scm (r-futile-logger): New variable. Ricardo Wurmus
2016-01-07gnu: Add futile.options.•••* gnu/packages/statistics.scm (r-futile-options): New variable. Ricardo Wurmus
2016-01-07gnu: Add lambda.r.•••* gnu/packages/statistics.scm (r-lambda-r): New variable. Ricardo Wurmus
2016-01-07gnu: Add r-xml.•••* gnu/packages/statistics.scm (r-xml): New variable. Ricardo Wurmus
2016-01-07gnu: Add RCurl.•••* gnu/packages/statistics.scm (r-rcurl): New variable. Ricardo Wurmus
2016-01-07gnu: Add RSQLite.•••* gnu/packages/statistics.scm (r-rsqlite): New variable. Ricardo Wurmus
2016-01-07import: Rename "cran-fetch" to "fetch-description".•••* guix/import/cran.scm (cran-fetch): Rename procedure ... (fetch-description): ... to this. Ricardo Wurmus
2016-01-07import: Add package->upstream-name procedure.•••* guix/import/cran.scm (package->upstream-name): New procedure. Ricardo Wurmus
2016-01-07gnu: Add xmlstarlet.•••* gnu/packages/xml.scm (xmlstarlet): New variable. Raimon Grau
2016-01-07gnu: zita-convolver: Drop the '-march=native' optimization.•••* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet. 宋文武
2016-01-07gnu: zita-resampler: Drop the '-march=native' optimization.•••* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet. 宋文武
2016-01-07gnu: Add ruby-ansi.•••* gnu/packages/ruby.scm (ruby-ansi): New variable. Ben Woodcroft
2016-01-07gnu: edirect: Update to 3.50.•••* gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip". Ricardo Wurmus
2016-01-07gnu: 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. Leo Famulari
2016-01-07gnu: 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. Leo Famulari
2016-01-06build-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. Ludovic Courtès
2016-01-06utils: Add 'ensure-keyword-arguments'.•••* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures. * tests/utils.scm ("ensure-keyword-arguments"): New test. Ludovic Courtès
2016-01-06http-client: Work around <http://bugs.gnu.org/22273>.•••* guix/http-client.scm (read-header-line): New procedure. Use it. Ludovic Courtès
2016-01-06gnu: guix: Update development snapshot to f888c0b.•••* gnu/packages/package-management.scm (guix-devel): Update to f888c0b. Ludovic Courtès
2016-01-06http-client: Fix erroneous comment.•••* guix/http-client.scm: Fix Guile version number in comment for Guile commit 5a10e41. Ludovic Courtès
2016-01-06gnu: gmsh: Update to 2.11.0.•••* gnu/packages/maths.scm (gmsh): Update to 2.11.0. [arguments]: Replace 'check phase. Eric Bavier
2016-01-06lint: cve: Catch host name lookup errors.•••* guix/scripts/lint.scm (package-vulnerabilities): Catch 'getaddrinfo-error'. Ludovic Courtès
2016-01-06gnu: 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. Ludovic Courtès
2016-01-06services: 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'. Ludovic Courtès
2016-01-06gnu: ldc: Fix license.•••* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of 'license:x11-style' by LICENSE:BOOST1.0. Ludovic Courtès
2016-01-06build: 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. Ben Woodcroft
2016-01-06gnu: icedtea7: Rename to icedtea-7.•••* gnu/packages/java.scm (icedtea7): Rename variable to... (icedtea-7): ...this. (icedtea): Refer to "icedtea-7". Ricardo Wurmus
2016-01-06gnu: icedtea6: Rename to icedtea-6.•••* gnu/packages/java.scm (icedtea6): Rename variable to... (icedtea-6): ...this. Ricardo Wurmus
2016-01-06gnu: icedtea6, icedtea7: Rename package to "icedtea".•••* gnu/packages/java.scm (icedtea6): Change package name to "icedtea". (icedtea7): Inherit package name. Ricardo Wurmus
2016-01-06gnu: 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". Ricardo Wurmus
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