Commit Graph

29112 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice c94752ad22
gnu: tor: Update to 0.3.2.10 [security fixes].
This release fixes TROVE-2018-001 (also tracked as CVE-2018-0490),
TROVE-2018-002 (CVE-2018-049), and TROVEs-2018-00{3,4} as well.

* gnu/packages/tor.scm (tor): Update to 0.3.2.10.
2018-03-03 21:31:08 +01:00
Ricardo Wurmus 1adeef3194
gnu: Add dropseq-tools.
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
2018-03-03 21:28:05 +01:00
Ricardo Wurmus 72299db9fe
gnu: Add java-picard-2.10.3.
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
2018-03-03 21:28:02 +01:00
Ricardo Wurmus 719fa958f3
gnu: Add java-htsjdk-2.10.1.
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
2018-03-03 21:27:59 +01:00
Ricardo Wurmus 9a599c17b7
gnu: Add java-htsjdk-latest.
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
2018-03-03 21:27:57 +01:00
Ricardo Wurmus 9ac7db1830
gnu: Add java-biojava-alignment-4.0.
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
2018-03-03 21:27:56 +01:00
Ricardo Wurmus 5528f9e8f0
gnu: Add java-biojava-phylo-4.0.
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
2018-03-03 21:27:53 +01:00
Ricardo Wurmus e44da58c16
gnu: Add java-biojava-core-4.0.
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
2018-03-03 21:27:51 +01:00
Ricardo Wurmus 22c09c335b
gnu: Add java-biojava-alignment.
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03 21:27:48 +01:00
Ricardo Wurmus b28c803708
gnu: Add java-biojava-phylo.
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03 21:27:46 +01:00
Ricardo Wurmus 10645b9212
gnu: Add java-forester-1.005.
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
2018-03-03 21:27:44 +01:00
Ricardo Wurmus f09d16e594
gnu: Add java-forester.
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03 21:27:41 +01:00
Ricardo Wurmus 93abc975fe
gnu: Add java-openchart2.
* gnu/packages/java.scm (java-openchart2): New variable.
2018-03-03 21:27:39 +01:00
Ricardo Wurmus 5fef15e506
gnu: Add java-biojava-core.
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
2018-03-03 21:27:36 +01:00
Ricardo Wurmus dbb3581383
gnu: Add java-jdistlib.
* gnu/packages/statistics.scm (java-jdistlib): New variable.
2018-03-03 21:27:33 +01:00
Ricardo Wurmus 4e92911c82
gnu: Add java-jtransforms.
* gnu/packages/algebra.scm (java-jtransforms): New variable.
2018-03-03 21:27:30 +01:00
Ricardo Wurmus 24074b0bdd
gnu: Add java-jlargearrays.
* gnu/packages/algebra.scm (java-jlargearrays): New variable.
2018-03-03 21:27:27 +01:00
Ricardo Wurmus c8d996080e
gnu: Add java-la4j.
* gnu/packages/algebra.scm (java-la4j): New variable.
2018-03-03 21:27:21 +01:00
Ricardo Wurmus bd975831c6
gnu: Add fastqc.
* gnu/packages/bioinformatics.scm (fastqc): New variable.
2018-03-03 21:21:48 +01:00
Ricardo Wurmus 2f0d041816
gnu: Add java-cisd-jhdf5.
* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
2018-03-03 21:21:48 +01:00
Ricardo Wurmus 04ddca26e6
gnu: Add java-cisd-args4j.
* gnu/packages/java.scm (java-cisd-args4j): New variable.
2018-03-03 21:21:47 +01:00
Ricardo Wurmus 30d554732a
gnu: Add java-cisd-base.
* gnu/packages/java.scm (java-cisd-base): New variable.
2018-03-03 21:21:47 +01:00
Ricardo Wurmus f9e0fcb28f
gnu: Add texlive-fonts-iwona.
* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.
2018-03-03 21:21:47 +01:00
Clément Lassieur bdcf0e6fd4
services: messaging: Prosody config supports file-like objects.
* 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.
2018-03-03 18:21:52 +01:00
Nicolas Goaziou fb547c3429
gnu: dictionaries: Add copyright line.
* gnu/packages/dictionaries.scm: Add copyright line.
2018-03-03 14:23:17 +01:00
Nicolas Goaziou 5e332c57d1
gnu: wireshark: Update to 2.4.5.
* gnu/packages/networking.scm (wireshark): Update to 2.4.5.
2018-03-03 14:21:20 +01:00
Nicolas Goaziou 0645da3fe3
gnu: grammalecte: Update to 0.6.2.
* gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2.
[arguments]: Remove.
2018-03-03 14:06:43 +01:00
Christopher Baines 62b138caf5
gnu: Add ruby-iruby.
* gnu/packages/ruby.scm (ruby-iruby): New variable.
2018-03-03 12:51:27 +00:00
Christopher Baines 8279b1d3b1
gnu: Add ruby-mimemagic.
* gnu/packages/ruby.scm (ruby-mimemagic): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines b03eb6acb4
gnu: Add ruby-data_uri.
* gnu/packages/ruby.scm (ruby-data_uri): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines d0afff263c
gnu: Add ruby-cztop.
* gnu/packages/ruby.scm (ruby-cztop): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines fe5dd5f446
gnu: Add ruby-czmq-ffi-gen.
* gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines afdb437c82
gnu: Add ruby-bond.
* gnu/packages/ruby.scm (ruby-bond): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines a8d2bf3cab
gnu: Add ruby-bacon-bits.
* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.
2018-03-03 12:51:26 +00:00
Christopher Baines cf646acf96
gnu: Add ruby-mocha-on-bacon.
* gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable.
2018-03-03 12:51:25 +00:00
Christopher Baines 433dc74611
gnu: networking: Add czmq.
* gnu/packages/networking.scm (czmq): New variable.
2018-03-03 12:51:23 +00:00
Tobias Geerinckx-Rice add928d35f
gnu: ghc-refact: Fix typo in description.
* gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo.
2018-03-03 13:28:22 +01:00
Tobias Geerinckx-Rice 75377c6c48
gnu: quagga: Update to 1.2.4.
* gnu/packages/networking.scm (quagga): Update to 1.2.4.
2018-03-03 13:28:22 +01:00
Tobias Geerinckx-Rice e6d30cf755
gnu: conky: Remove redundant MKDIR-P.
* gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P.
2018-03-03 13:27:17 +01:00
Tobias Geerinckx-Rice 9d13f82da8
gnu: sslh: Update to 1.19c.
* gnu/packages/networking.scm (sslh): Update to 1.19c.
2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice dbefd3ff72
gnu: wv: Edit description.
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.
2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice 83a9003c5d
gnu: libseccomp: Update to 2.3.3.
* gnu/packages/linux.scm (libseccomp): Update to 2.3.3.
2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice 74a2f8ff1f
gnu: hdparm: Update to 9.54.
* gnu/packages/linux.scm (hdparm): Update to 9.54.
2018-03-03 13:27:16 +01:00
Tobias Geerinckx-Rice f4009ade25
gnu: sdl2: Update to 2.0.8.
* gnu/packages/sdl.scm (sdl2): Update to 2.0.8.
2018-03-03 13:27:15 +01:00
Ricardo Wurmus ec8b3d48ff
gnu: r-httpuv: Update to 1.3.6.2.
* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2.
2018-03-03 10:46:35 +01:00
Ricardo Wurmus fac40f38fe
gnu: r-dbi: Update to 0.8.
* gnu/packages/statistics.scm (r-dbi): Update to 0.8.
2018-03-03 10:46:35 +01:00
Ricardo Wurmus 081d143d3b
gnu: r-performanceanalytics: Update to 1.5.2.
* gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.2.
[propagated-inputs]: Add r-quadprog.
[native-inputs]: Remove gfortran.
2018-03-03 10:46:35 +01:00
Ludovic Courtès eac026e5c8
linux-initrd: Add virtio modules to '%base-initrd-modules'.
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.
2018-03-03 09:41:21 +01:00
Ludovic Courtès f850e0da8e
system: beaglebone-black: Use 'initrd-modules'.
* gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules'
instead of 'initrd'.
2018-03-03 09:41:21 +01:00
Ludovic Courtès 5a3716aebf
vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.
Fixes a regression introduced in
bc499b113a, 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'.
2018-03-03 09:41:21 +01:00