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2018-03-03gnu: Add java-picard-2.10.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
2018-03-03gnu: Add java-htsjdk-2.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
2018-03-03gnu: Add java-htsjdk-latest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
2018-03-03gnu: Add java-biojava-alignment-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
2018-03-03gnu: Add java-biojava-phylo-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
2018-03-03gnu: Add java-biojava-core-4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
2018-03-03gnu: Add java-biojava-alignment.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03gnu: Add java-biojava-phylo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03gnu: Add java-forester-1.005.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
2018-03-03gnu: Add java-forester.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03gnu: Add java-openchart2.Ricardo Wurmus
* gnu/packages/java.scm (java-openchart2): New variable.
2018-03-03gnu: Add java-biojava-core.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
2018-03-03gnu: Add java-jdistlib.Ricardo Wurmus
* gnu/packages/statistics.scm (java-jdistlib): New variable.
2018-03-03gnu: Add java-jtransforms.Ricardo Wurmus
* gnu/packages/algebra.scm (java-jtransforms): New variable.
2018-03-03gnu: Add java-jlargearrays.Ricardo Wurmus
* gnu/packages/algebra.scm (java-jlargearrays): New variable.
2018-03-03gnu: Add java-la4j.Ricardo Wurmus
* gnu/packages/algebra.scm (java-la4j): New variable.
2018-03-03gnu: Add fastqc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastqc): New variable.
2018-03-03gnu: Add java-cisd-jhdf5.Ricardo Wurmus
* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
2018-03-03gnu: Add java-cisd-args4j.Ricardo Wurmus
* gnu/packages/java.scm (java-cisd-args4j): New variable.
2018-03-03gnu: Add java-cisd-base.Ricardo Wurmus
* gnu/packages/java.scm (java-cisd-base): New variable.
2018-03-03gnu: Add texlive-fonts-iwona.Ricardo Wurmus
* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.
2018-03-03services: messaging: Prosody config supports file-like objects.Clément Lassieur
* doc/guix.texi (Messaging Services): Update accordingly. * gnu/services/configuration.scm (serialize-configuration, serialize-maybe-stem, serialize-package): Return strings or string-valued gexps (these procedures were only used for their side-effects). * gnu/services/messaging.scm (serialize-field, serialize-field-list, enclose-quotes, serialize-raw-content, serialize-ssl-configuration, serialize-virtualhost-configuration-list, serialize-int-component-configuration-list, serialize-ext-component-configuration-list, serialize-virtualhost-configuration, serialize-int-component-configuration, serialize-ext-component-configuration, serialize-prosody-configuration): Return strings or string-valued gexps and stop printing. (prosody-activation): Use SERIALIZE-PROSODY-CONFIGURATION's return value with MIXED-TEXT-FILE instead of using its output with PLAIN-FILE. (serialize-non-negative-integer, serialize-non-negative-integer-list): Convert numbers to strings. (file-object?, serialize-file-object, file-object-list?, serialize-file-object-list): New procedures. (ssl-configuration)[capath, cafile], (prosody-configuration)[plugin-paths, groups-file]: Replace FILE-NAME with FILE-OBJECT. * guix/gexp.scm (file-like?): New exported procedure.
2018-03-03gnu: dictionaries: Add copyright line.Nicolas Goaziou
* gnu/packages/dictionaries.scm: Add copyright line.
2018-03-03gnu: wireshark: Update to 2.4.5.Nicolas Goaziou
* gnu/packages/networking.scm (wireshark): Update to 2.4.5.
2018-03-03gnu: grammalecte: Update to 0.6.2.Nicolas Goaziou
* gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2. [arguments]: Remove.
2018-03-03gnu: Add ruby-iruby.Christopher Baines
* gnu/packages/ruby.scm (ruby-iruby): New variable.
2018-03-03gnu: Add ruby-mimemagic.Christopher Baines
* gnu/packages/ruby.scm (ruby-mimemagic): New variable.
2018-03-03gnu: Add ruby-data_uri.Christopher Baines
* gnu/packages/ruby.scm (ruby-data_uri): New variable.
2018-03-03gnu: Add ruby-cztop.Christopher Baines
* gnu/packages/ruby.scm (ruby-cztop): New variable.
2018-03-03gnu: Add ruby-czmq-ffi-gen.Christopher Baines
* gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable.
2018-03-03gnu: Add ruby-bond.Christopher Baines
* gnu/packages/ruby.scm (ruby-bond): New variable.
2018-03-03gnu: Add ruby-bacon-bits.Christopher Baines
* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.
2018-03-03gnu: Add ruby-mocha-on-bacon.Christopher Baines
* gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable.
2018-03-03gnu: networking: Add czmq.Christopher Baines
* gnu/packages/networking.scm (czmq): New variable.
2018-03-03gnu: ghc-refact: Fix typo in description.Tobias Geerinckx-Rice
* gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo.
2018-03-03gnu: quagga: Update to 1.2.4.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (quagga): Update to 1.2.4.
2018-03-03gnu: conky: Remove redundant MKDIR-P.Tobias Geerinckx-Rice
* gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P.
2018-03-03gnu: sslh: Update to 1.19c.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (sslh): Update to 1.19c.
2018-03-03gnu: wv: Edit description.Tobias Geerinckx-Rice
Wv is still unmaintained – this just makes it more obvious. * gnu/packages/wv.scm (wv)[description]: Mention the product versions in addition to internal file format ones. Align more closely with the upstream description.
2018-03-03gnu: libseccomp: Update to 2.3.3.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (libseccomp): Update to 2.3.3.
2018-03-03gnu: hdparm: Update to 9.54.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (hdparm): Update to 9.54.
2018-03-03gnu: sdl2: Update to 2.0.8.Tobias Geerinckx-Rice
* gnu/packages/sdl.scm (sdl2): Update to 2.0.8.
2018-03-03gnu: r-httpuv: Update to 1.3.6.2.Ricardo Wurmus
* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2.
2018-03-03gnu: r-dbi: Update to 0.8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbi): Update to 0.8.
2018-03-03gnu: r-performanceanalytics: Update to 1.5.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.2. [propagated-inputs]: Add r-quadprog. [native-inputs]: Remove gfortran.
2018-03-03linux-initrd: Add virtio modules to '%base-initrd-modules'.Ludovic Courtès
Fixes a regression in installation tests, whereby 'guix system init' would report that virtio modules are missing for the target devices. In practice virtio modules were always available since 'base-initrd' was always called with #:virtio? #t. This commit simply moves them to '%base-initrd-modules' so that 'guix system' knows they're available. Reported by Danny Milosavljevic <dannym@scratchpost.org> at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#112>. * gnu/system/linux-initrd.scm (default-initrd-modules): Add virtio modules. (base-initrd): Remove #:virtio? and 'virtio-modules'. * gnu/system/vm.scm (expression->derivation-in-linux-vm) (system-qemu-image, virtualized-operating-system): Remove uses of #:virtio?. * doc/guix.texi (Initial RAM Disk): Update 'base-initrd' doc.
2018-03-03system: beaglebone-black: Use 'initrd-modules'.Ludovic Courtès
* gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules' instead of 'initrd'.
2018-03-03vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.Ludovic Courtès
Fixes a regression introduced in bc499b113a598c0e7863da9887a4133472985713, whereby the default initrd used by 'expression->derivation-in-linux-vm' would lack all the usual modules: virtio, nls_iso8859-1, etc. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass #:linux-modules to 'base-initrd'.
2018-03-03linux-initrd: 'file-system-modules' returns the right module list.Ludovic Courtès
Fixes a bug whereby, for an "iso9660" file system, it would return '("iso9660" "isofs"), i.e., both the key and the value. Reported by Danny Milosavljevic <dannym@scratchpost.org> at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=30629#115>. * gnu/system/linux-initrd.scm (lookup-procedure): 'vhash-assoc' returns a key/value pair; match it.
2018-03-02gnu: cutadapt: Update to 1.16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16. [source]: Fetch via git. [arguments]: Remove. [native-inputs]: Replace python-nose with python-pytest.
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