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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
2016-01-07gnu: 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
2016-01-06gnu: guix: Update development snapshot to f888c0b....* gnu/packages/package-management.scm (guix-devel): Update to f888c0b. 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
2016-01-06gnu: 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
2016-01-06gnu: 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
2016-01-06gnu: 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". Ricardo Wurmus
2016-01-06gnu: Add Jellyfish....* gnu/packages/bioinformatics.scm (jellyfish): New variable. Ricardo Wurmus
2016-01-05gnu: calibre: Update to 2.48.0....* gnu/packages/ebook.scm (calibre): Update to 2.48.0. Andreas Enge
2016-01-05gnu: Add LDC....* 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. Roel Janssen
2016-01-05gnu: Add emacs-undo-tree.... * gnu/packages/emacs.scm (emacs-undo-tree): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Dmitry Bogatov
2016-01-05gnu: emacs: Remove 'info.info'....* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'. Add 'remove-info.info' phase. Ludovic Courtès
2016-01-05linux-boot: Remove verbose output for module loads....* 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'. Ludovic Courtès
2016-01-05services: Move /tmp cleanup to a separate service....* 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. Ludovic Courtès
2016-01-05services: boot: Reinstate /tmp and /var/run deletion....For some time /tmp and /var/run were not being deleted because 'delete-file-recursively' was unbound. * gnu/services.scm (compute-boot-script)[%modules, modules, compiled]: New variables. Use them to augment the module search path. Ludovic Courtès
2016-01-04gnu: gtk+: Add patch to support GUIX_GTK3_PATH....* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK3_PATH. Ricardo Wurmus
2016-01-04gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH....* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gtk+-2) [source]: Add patch. [native-search-paths]: Add search path for GUIX_GTK2_PATH. Ricardo Wurmus
2016-01-04gnu: julia: Update to 0.4.2....* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/julia.scm (julia): Update to 0.4.2. [arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase "patch-include-path" with "fix-include-and-link-paths"; add phase "hardcode-paths"; add missing make-flags. [inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add "coreutils"; add "libuv-julia"; add "wget"; add "which". [native-inputs]: Remove "which". Ricardo Wurmus
2016-01-04gnu: Add libuv-julia....* gnu/packages/julia.scm (libuv-julia): New variable. Ricardo Wurmus
2016-01-04gnu: utf8proc: Update to 1.3.1....* gnu/packages/textutils.scm (utf8proc): Update to 1.3.1. [arguments]: Remove custom "install" phase. Ricardo Wurmus
2016-01-03gnu: samba: Update to 4.3.3....Fixes CVE-2015-{3223,5252,5299,5296,8467,5330}. * gnu/packages/samba.scm (samba): Update to 4.3.3. Leo Famulari
2016-01-03gnu: ldb: Update to 1.1.24....Required for samba-4.3.3 in order to fix CVE-2015-5330 and CVE-2015-3223. * gnu/packages/samba.scm (ldb): Update to 1.2.24. Leo Famulari
2016-01-02gnu: Add Asymptote....* gnu/packages/bdw-gc.scm (libgc-for-c++): New variable. * gnu/packages/plotutils.scm (asymptote): New variable. * gnu/packages/patches/asymptote-gsl2.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Eric Bavier
2016-01-02gnu: Add python-markdown....* gnu/packages/python.scm (python-markdown, python2-markdown): New variables. Signed-off-by: Leo Famulari <leo@famulari.name> Erik Edrosa
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