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2016-01-07gnu: Add GenomicAlignments.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07gnu: Add SummarizedExperiment.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07gnu: Add Rsamtools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07gnu: Add Biostrings.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07gnu: Add BiocParallel.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07gnu: Add biomaRt.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07gnu: Add AnnotationDbi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07gnu: Add Biobase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07gnu: Add snow.Ricardo Wurmus
* gnu/packages/statistics.scm (r-snow): New variable.
2016-01-07gnu: Add futile.logger.Ricardo Wurmus
* gnu/packages/statistics.scm (r-futile-logger): New variable.
2016-01-07gnu: Add futile.options.Ricardo Wurmus
* gnu/packages/statistics.scm (r-futile-options): New variable.
2016-01-07gnu: Add lambda.r.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lambda-r): New variable.
2016-01-07gnu: Add r-xml.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): New variable.
2016-01-07gnu: Add RCurl.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcurl): New variable.
2016-01-07gnu: Add RSQLite.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): New variable.
2016-01-07import: Rename "cran-fetch" to "fetch-description".Ricardo Wurmus
* guix/import/cran.scm (cran-fetch): Rename procedure ... (fetch-description): ... to this.
2016-01-07import: Add package->upstream-name procedure.Ricardo Wurmus
* guix/import/cran.scm (package->upstream-name): New procedure.
2016-01-07gnu: Add xmlstarlet.Raimon Grau
* gnu/packages/xml.scm (xmlstarlet): New variable.
2016-01-07gnu: zita-convolver: Drop the '-march=native' optimization.宋文武
* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
2016-01-07gnu: zita-resampler: Drop the '-march=native' optimization.宋文武
* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
2016-01-07gnu: Add ruby-ansi.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-ansi): New variable.
2016-01-07gnu: edirect: Update to 3.50.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip".
2016-01-07gnu: w3m: Enable SSL, disable broken protocols and ciphers.Leo Famulari
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.
2016-01-07gnu: w3m: Update patch to use '-p1'.Leo Famulari
* 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.
2016-01-06build-system/gnu: Make 'package-with-explicit-inputs' idempotent.Ludovic Courtès
* 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.
2016-01-06utils: Add 'ensure-keyword-arguments'.Ludovic Courtès
* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures. * tests/utils.scm ("ensure-keyword-arguments"): New test.
2016-01-06http-client: Work around <http://bugs.gnu.org/22273>.Ludovic Courtès
* guix/http-client.scm (read-header-line): New procedure. Use it.
2016-01-06gnu: guix: Update development snapshot to f888c0b.Ludovic Courtès
* gnu/packages/package-management.scm (guix-devel): Update to f888c0b.
2016-01-06http-client: Fix erroneous comment.Ludovic Courtès
* guix/http-client.scm: Fix Guile version number in comment for Guile commit 5a10e41.
2016-01-06gnu: gmsh: Update to 2.11.0.Eric Bavier
* gnu/packages/maths.scm (gmsh): Update to 2.11.0. [arguments]: Replace 'check phase.
2016-01-06lint: cve: Catch host name lookup errors.Ludovic Courtès
* guix/scripts/lint.scm (package-vulnerabilities): Catch 'getaddrinfo-error'.
2016-01-06gnu: sudo: Use /var/run/sudo instead of /run/sudo.Ludovic Courtès
* 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.
2016-01-06services: cleanup-service: Catch 'system-error' instead of everything.Ludovic Courtès
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'.
2016-01-06gnu: ldc: Fix license.Ludovic Courtès
* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of 'license:x11-style' by LICENSE:BOOST1.0.
2016-01-06build: ruby: Remove cached gem after install.Ben Woodcroft
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.
2016-01-06gnu: icedtea7: Rename to icedtea-7.Ricardo Wurmus
* gnu/packages/java.scm (icedtea7): Rename variable to... (icedtea-7): ...this. (icedtea): Refer to "icedtea-7".
2016-01-06gnu: icedtea6: Rename to icedtea-6.Ricardo Wurmus
* gnu/packages/java.scm (icedtea6): Rename variable to... (icedtea-6): ...this.
2016-01-06gnu: icedtea6, icedtea7: Rename package to "icedtea".Ricardo Wurmus
* gnu/packages/java.scm (icedtea6): Change package name to "icedtea". (icedtea7): Inherit package name.
2016-01-06gnu: Add and use default IcedTea.Ricardo Wurmus
* 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".
2016-01-06gnu: icedtea6, icedtea7: Unpack to "openjdk.src".Ricardo Wurmus
* 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".
2016-01-06gnu: Add Jellyfish.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
2016-01-05build: Bump version number.Ludovic Courtès
* configure.ac: Change version to 0.9.1.
2016-01-05doc: Remove double occurrence of words.Michael Vetter
* doc/guix.texi: substitute 'the the' with 'the'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-01-05build: pull: Compile .scm files in one process.Taylan Ulrich Bayırlı/Kammer
* guix/build/pull.scm (call-with-process, report-build-progress) (p-for-each): Remove. (build-guix): Load and compile files in one process.
2016-01-05gnu: calibre: Update to 2.48.0.Andreas Enge
* gnu/packages/ebook.scm (calibre): Update to 2.48.0.
2016-01-05gnu: Add LDC.Roel Janssen
* gnu/packages/ldc.scm: New file. * gnu/packages/patches/ldc-disable-tests.patch: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm. (dist_patch_DATA): Add patch file.
2016-01-05gnu: Add emacs-undo-tree.Dmitry Bogatov
* gnu/packages/emacs.scm (emacs-undo-tree): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-01-05gnu: emacs: Remove 'info.info'.Ludovic Courtès
* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'. Add 'remove-info.info' phase.
2016-01-05linux-boot: Remove verbose output for module loads.Ludovic Courtès
* gnu/build/linux-boot.scm (boot-system): Leave 'current-module-debugging-port' unchanged. * gnu/build/linux-modules.scm (load-linux-module*): Update comment about 'mmap'.
2016-01-05services: Move /tmp cleanup to a separate service.Ludovic Courtès
* gnu/services.scm (compute-boot-script): Remove /tmp and /var/run deletion code from here. (cleanup-gexp): New procedure with /tmp and /var/run deletion code formerly in 'compute-boot-script'. (cleanup-service-type): New variable. * gnu/system.scm (essential-services): Add an instance of CLEANUP-SERVICE-TYPE.
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