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Author SHA1 Message Date
Efraim Flashner 7fc944273d
gnu: masscan: Declare a source file-name. 
* gnu/packages/admin.scm (masscan)[source]: Declare a source file-name.
 2018-03-04 11:01:36 +02:00
Christopher Baines bc037c1bd1
services: redis: Add a default-value to the redis-service-type. 
* gnu/packages/databases.scm (redis-service-type)[default-value]: Set
  to (redis-configuration).
 2018-03-03 23:52:26 +00:00
Christopher Baines e903738f86
services: mysql: Add a default-value to the mysql-service-type. 
* gnu/services/databases.scm (mysql-service-type)[default-value]: Set
  to (mysql-configuration).
 2018-03-03 23:52:25 +00:00
Christopher Baines 1e6b9c6e16
services: postgresql: Add a default-value to the postgresql-service-type. 
* gnu/packages/databases.scm (<postgresql-configuration>)
  [config-file,data-directory]: Add default.
  (postgresql-service-type)[default-value]:
  Set to (postgresql-configuration).
 2018-03-03 23:52:23 +00:00
Danny Milosavljevic 8b2219d847
linux-modules: Add module-aliases. 
* gnu/build/linux-modules.scm (module-aliases): New variable.
 2018-03-03 23:40:02 +01:00
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
Ludovic Courtès 3cb3a4e6e5
linux-initrd: 'file-system-modules' returns the right module list. 
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.
 2018-03-03 09:41:21 +01:00
Ricardo Wurmus 3ede1550e8
gnu: cutadapt: Update to 1.16. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus 62a4b952c0
gnu: python-xopen: Update to 0.3.2. 
* gnu/packages/python.scm (python-xopen): Update to 0.3.2.
 2018-03-02 23:43:55 +01:00
Ricardo Wurmus fa5965990d
gnu: Add r-hpar. 
* gnu/packages/bioconductor.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2018-03-02 23:24:57 +01:00
Ricardo Wurmus 2a112be09a
gnu: Add r-powerplus. 
* gnu/packages/cran.scm (r-powerplus): New variable.
 2018-03-02 23:07:26 +01:00
Ricardo Wurmus d976454c6b
gnu: Add r-np. 
* gnu/packages/cran.scm (r-np): New variable.
 2018-03-02 23:07:20 +01:00
Ricardo Wurmus 7b81a7eabf
gnu: Add r-phontools. 
* gnu/packages/cran.scm (r-phontools): New variable.
 2018-03-02 23:07:12 +01:00
Ricardo Wurmus 68b6a67e94
gnu: Add r-complexplus. 
* gnu/packages/cran.scm (r-complexplus): New variable.
 2018-03-02 23:07:04 +01:00
Ricardo Wurmus f96eda90d5
gnu: Add r-expm. 
* gnu/packages/cran.scm (r-expm): New variable.
 2018-03-02 23:06:57 +01:00
Ricardo Wurmus 7531ee842c
gnu: Add r-trend. 
* gnu/packages/cran.scm (r-trend): New variable.
 2018-03-02 23:06:50 +01:00
Ricardo Wurmus d32e572489
gnu: Add r-cubature. 
* gnu/packages/cran.scm (r-cubature): New variable.
 2018-03-02 23:06:41 +01:00
Ricardo Wurmus 6615a36421
gnu: Add r-urca. 
* gnu/packages/cran.scm (r-urca): New variable.
 2018-03-02 23:06:33 +01:00
Ricardo Wurmus 5b25bc55dc
gnu: Add r-fractal. 
* gnu/packages/cran.scm (r-fractal): New variable.
 2018-03-02 23:06:26 +01:00
Ricardo Wurmus 19da7fe314
gnu: Add r-extradistr. 
* gnu/packages/cran.scm (r-extradistr): New variable.
 2018-03-02 23:06:17 +01:00
Ricardo Wurmus 4993a02ad7
gnu: Add r-tsa. 
* gnu/packages/cran.scm (r-tsa): New variable.
 2018-03-02 23:06:10 +01:00
Ricardo Wurmus a2c079a780
gnu: Add r-wmtsa. 
* gnu/packages/cran.scm (r-wmtsa): New variable.
 2018-03-02 23:06:00 +01:00
Ricardo Wurmus b6dc325538
gnu: Add r-tseries. 
* gnu/packages/cran.scm (r-tseries): New variable.
 2018-03-02 23:05:52 +01:00
Ricardo Wurmus dceb159206
gnu: Add r-quantmod. 
* gnu/packages/cran.scm (r-quantmod): New variable.
 2018-03-02 23:05:43 +01:00
Ricardo Wurmus 0be7effefa
gnu: Add r-sapa. 
* gnu/packages/cran.scm (r-sapa): New variable.
 2018-03-02 23:05:35 +01:00
Ricardo Wurmus 034ac9d67a
gnu: Add r-ifultools. 
* gnu/packages/cran.scm (r-ifultools): New variable.
 2018-03-02 23:05:14 +01:00
Ricardo Wurmus d3cb62e58d
gnu: Add r-splus2r. 
* gnu/packages/cran.scm (r-splus2r): New variable.
 2018-03-02 23:05:02 +01:00
Ricardo Wurmus 0b64332c74
gnu: Add r-leaps. 
* gnu/packages/cran.scm (r-leaps): New variable.
 2018-03-02 23:03:10 +01:00
Ricardo Wurmus 93c21ddc86
gnu: Add r-ttr. 
* gnu/packages/cran.scm (r-ttr): New variable.
 2018-03-02 22:55:10 +01:00
Ricardo Wurmus 4e35c4290e
gnu: Add r-rbiofabric. 
* gnu/packages/graph.scm (r-rbiofabric): New variable.
 2018-03-02 22:23:18 +01:00
Ricardo Wurmus 1088744d87
gnu: Add r-sna. 
* gnu/packages/cran.scm (r-sna): New variable.
 2018-03-02 22:23:18 +01:00
Ricardo Wurmus 07a2f34d5c
gnu: Add r-statnet-common. 
* gnu/packages/cran.scm (r-statnet-common): New variable.
 2018-03-02 22:23:18 +01:00
Ricardo Wurmus 5f4565b18f
gnu: Add r-network. 
* gnu/packages/cran.scm (r-network): New variable.
 2018-03-02 22:23:18 +01:00
Tobias Geerinckx-Rice b01a1b34f2
gnu: nghttp2: Update to 1.31.0. 
* gnu/packages/web.scm (nghttp2): Update to 1.31.0.
 2018-03-02 15:52:57 +01:00
Tobias Geerinckx-Rice 6fda93e6c8
gnu: libpsl: Update to 0.20.1. 
* gnu/packages/web.scm (libpsl): Update to 0.20.1.
 2018-03-02 15:52:57 +01:00
Tobias Geerinckx-Rice 5658b4ce69
gnu: zerofree: Update to 1.1.1. 
* gnu/packages/linux.scm (zerofree): Update to 1.1.1.
 2018-03-02 15:52:57 +01:00
Tobias Geerinckx-Rice a40f732bb6
gnu: python-webencodings: Fix typo in description. 
* gnu/packages/python-web.scm (python-webencodings)[description]: Fix typo.
 2018-03-02 15:52:57 +01:00
Tobias Geerinckx-Rice 139ecdee8e
gnu: delta: Remove redundant code. 
* gnu/packages/debug.scm (delta)[arguments]: Remove unneeded MKDIR-P
calls.
 2018-03-02 15:52:56 +01:00
Tobias Geerinckx-Rice defe0282c2
gnu: perl-mozilla-ca: Update to 20180117. 
* gnu/packages/perl.scm (perl-mozilla-ca): Update to 20180117.
 2018-03-02 15:52:56 +01:00
Tobias Geerinckx-Rice dc8584d2b1
gnu: perl-test-harness: Update to 3.41. 
* gnu/packages/perl-check.scm (perl-test-harness): Update to 3.41.
 2018-03-02 15:52:56 +01:00
Tobias Geerinckx-Rice 6e48fbb19a
gnu: highlight: Don't hard-code Lua version. 
* gnu/packages/pretty-print.scm (highlight)[arguments]: Construct the
Lua prefix programatically instead of hard-coding it.
 2018-03-02 15:52:56 +01:00
Tobias Geerinckx-Rice 3a5c02777d
gnu: highlight: Update to 3.42. 
* gnu/packages/pretty-print.scm (highlight): Update to 3.42.
 2018-03-02 15:52:55 +01:00
Tobias Geerinckx-Rice 467834d550
gnu: ghc-abstract-deque: Fix typos in description. 
* gnu/packages/haskell.scm (ghc-abstract-deque)[description]: Fix typos.
 2018-03-02 15:52:55 +01:00
Tobias Geerinckx-Rice d338321ddb
gnu: qscintilla: Use HTTPS home page. 
* gnu/packages/qt.scm (qscintilla)[home-page]: Use HTTPS.
 2018-03-02 15:52:55 +01:00
Tobias Geerinckx-Rice 2c1cc27f8f
gnu: fortify-headers: Update to 0.9. 
* gnu/packages/suckless.scm (fortify-headers): Update to 0.9.
 2018-03-02 15:52:55 +01:00
Tobias Geerinckx-Rice 5c0f68e844
gnu: fossil: Update phase style. 
* gnu/packages/version-control.scm (fossil)[arguments]: Substitute
INVOKE for SYSTEM* and end phases with #t.
 2018-03-02 15:52:54 +01:00
Tobias Geerinckx-Rice f136c8f23d
gnu: gnome-mpv: Update to 0.14. 
* gnu/packages/video.scm (gnome-mpv): Update to 0.14.
 2018-03-02 15:52:54 +01:00
Tobias Geerinckx-Rice 65a3c342b0
gnu: ath9k-htc-firmware: Use INSTALL-FILE. 
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Substitute
INSTALL-FILE for COPY-FILE with MKDIR-P.
 2018-03-02 15:52:54 +01:00
Tobias Geerinckx-Rice f563d19904
gnu: ovmf: Update phase style. 
* gnu/packages/firmware.scm (ovmf): Substitute INVOKE for SYSTEM* and
end phases with #t.
 2018-03-02 15:52:54 +01:00
Tobias Geerinckx-Rice 0dae492195
gnu: ovmf: Use HTTPS home page. 
* gnu/packages/firmware.scm (ovmf)[home-page]: Use HTTPS.
 2018-03-02 15:52:54 +01:00
Tobias Geerinckx-Rice 3ebf12ea0e
gnu: b43-tools: Use HTTPS home page. 
* gnu/packages/firmware.scm (b43-tools)[home-page]: Use HTTPS.
 2018-03-02 15:52:53 +01:00