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
22c09c335b
gnu: Add java-biojava-alignment.
...
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03 21:27:48 +01:00
b28c803708
gnu: Add java-biojava-phylo.
...
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03 21:27:46 +01:00
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
f09d16e594
gnu: Add java-forester.
...
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03 21:27:41 +01:00
93abc975fe
gnu: Add java-openchart2.
...
* gnu/packages/java.scm (java-openchart2): New variable.
2018-03-03 21:27:39 +01:00
5fef15e506
gnu: Add java-biojava-core.
...
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
2018-03-03 21:27:36 +01:00
dbb3581383
gnu: Add java-jdistlib.
...
* gnu/packages/statistics.scm (java-jdistlib): New variable.
2018-03-03 21:27:33 +01:00
4e92911c82
gnu: Add java-jtransforms.
...
* gnu/packages/algebra.scm (java-jtransforms): New variable.
2018-03-03 21:27:30 +01:00
24074b0bdd
gnu: Add java-jlargearrays.
...
* gnu/packages/algebra.scm (java-jlargearrays): New variable.
2018-03-03 21:27:27 +01:00
c8d996080e
gnu: Add java-la4j.
...
* gnu/packages/algebra.scm (java-la4j): New variable.
2018-03-03 21:27:21 +01:00
bd975831c6
gnu: Add fastqc.
...
* gnu/packages/bioinformatics.scm (fastqc): New variable.
2018-03-03 21:21:48 +01:00
2f0d041816
gnu: Add java-cisd-jhdf5.
...
* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
2018-03-03 21:21:48 +01:00
04ddca26e6
gnu: Add java-cisd-args4j.
...
* gnu/packages/java.scm (java-cisd-args4j): New variable.
2018-03-03 21:21:47 +01:00
30d554732a
gnu: Add java-cisd-base.
...
* gnu/packages/java.scm (java-cisd-base): New variable.
2018-03-03 21:21:47 +01:00
f9e0fcb28f
gnu: Add texlive-fonts-iwona.
...
* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.
2018-03-03 21:21:47 +01:00
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
fb547c3429
gnu: dictionaries: Add copyright line.
...
* gnu/packages/dictionaries.scm: Add copyright line.
2018-03-03 14:23:17 +01:00
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
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
62b138caf5
gnu: Add ruby-iruby.
...
* gnu/packages/ruby.scm (ruby-iruby): New variable.
2018-03-03 12:51:27 +00:00
8279b1d3b1
gnu: Add ruby-mimemagic.
...
* gnu/packages/ruby.scm (ruby-mimemagic): New variable.
2018-03-03 12:51:26 +00:00
b03eb6acb4
gnu: Add ruby-data_uri.
...
* gnu/packages/ruby.scm (ruby-data_uri): New variable.
2018-03-03 12:51:26 +00:00
d0afff263c
gnu: Add ruby-cztop.
...
* gnu/packages/ruby.scm (ruby-cztop): New variable.
2018-03-03 12:51:26 +00:00
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
afdb437c82
gnu: Add ruby-bond.
...
* gnu/packages/ruby.scm (ruby-bond): New variable.
2018-03-03 12:51:26 +00:00
a8d2bf3cab
gnu: Add ruby-bacon-bits.
...
* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.
2018-03-03 12:51:26 +00:00
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
433dc74611
gnu: networking: Add czmq.
...
* gnu/packages/networking.scm (czmq): New variable.
2018-03-03 12:51:23 +00:00
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
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
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
9d13f82da8
gnu: sslh: Update to 1.19c.
...
* gnu/packages/networking.scm (sslh): Update to 1.19c.
2018-03-03 13:27:16 +01:00
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
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
74a2f8ff1f
gnu: hdparm: Update to 9.54.
...
* gnu/packages/linux.scm (hdparm): Update to 9.54.
2018-03-03 13:27:16 +01:00
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
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
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
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
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
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
5a3716aebf
vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd.
...
Fixes a regression introduced in
bc499b113a
2018-03-03 09:41:21 +01:00
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
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
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
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
2a112be09a
gnu: Add r-powerplus.
...
* gnu/packages/cran.scm (r-powerplus): New variable.
2018-03-02 23:07:26 +01:00
d976454c6b
gnu: Add r-np.
...
* gnu/packages/cran.scm (r-np): New variable.
2018-03-02 23:07:20 +01:00
7b81a7eabf
gnu: Add r-phontools.
...
* gnu/packages/cran.scm (r-phontools): New variable.
2018-03-02 23:07:12 +01:00
68b6a67e94
gnu: Add r-complexplus.
...
* gnu/packages/cran.scm (r-complexplus): New variable.
2018-03-02 23:07:04 +01:00
f96eda90d5
gnu: Add r-expm.
...
* gnu/packages/cran.scm (r-expm): New variable.
2018-03-02 23:06:57 +01:00
7531ee842c
gnu: Add r-trend.
...
* gnu/packages/cran.scm (r-trend): New variable.
2018-03-02 23:06:50 +01:00
d32e572489
gnu: Add r-cubature.
...
* gnu/packages/cran.scm (r-cubature): New variable.
2018-03-02 23:06:41 +01:00
6615a36421
gnu: Add r-urca.
...
* gnu/packages/cran.scm (r-urca): New variable.
2018-03-02 23:06:33 +01:00
5b25bc55dc
gnu: Add r-fractal.
...
* gnu/packages/cran.scm (r-fractal): New variable.
2018-03-02 23:06:26 +01:00
19da7fe314
gnu: Add r-extradistr.
...
* gnu/packages/cran.scm (r-extradistr): New variable.
2018-03-02 23:06:17 +01:00
4993a02ad7
gnu: Add r-tsa.
...
* gnu/packages/cran.scm (r-tsa): New variable.
2018-03-02 23:06:10 +01:00
a2c079a780
gnu: Add r-wmtsa.
...
* gnu/packages/cran.scm (r-wmtsa): New variable.
2018-03-02 23:06:00 +01:00
b6dc325538
gnu: Add r-tseries.
...
* gnu/packages/cran.scm (r-tseries): New variable.
2018-03-02 23:05:52 +01:00
dceb159206
gnu: Add r-quantmod.
...
* gnu/packages/cran.scm (r-quantmod): New variable.
2018-03-02 23:05:43 +01:00
0be7effefa
gnu: Add r-sapa.
...
* gnu/packages/cran.scm (r-sapa): New variable.
2018-03-02 23:05:35 +01:00
034ac9d67a
gnu: Add r-ifultools.
...
* gnu/packages/cran.scm (r-ifultools): New variable.
2018-03-02 23:05:14 +01:00
d3cb62e58d
gnu: Add r-splus2r.
...
* gnu/packages/cran.scm (r-splus2r): New variable.
2018-03-02 23:05:02 +01:00
0b64332c74
gnu: Add r-leaps.
...
* gnu/packages/cran.scm (r-leaps): New variable.
2018-03-02 23:03:10 +01:00
93c21ddc86
gnu: Add r-ttr.
...
* gnu/packages/cran.scm (r-ttr): New variable.
2018-03-02 22:55:10 +01:00
4e35c4290e
gnu: Add r-rbiofabric.
...
* gnu/packages/graph.scm (r-rbiofabric): New variable.
2018-03-02 22:23:18 +01:00
1088744d87
gnu: Add r-sna.
...
* gnu/packages/cran.scm (r-sna): New variable.
2018-03-02 22:23:18 +01:00
07a2f34d5c
gnu: Add r-statnet-common.
...
* gnu/packages/cran.scm (r-statnet-common): New variable.
2018-03-02 22:23:18 +01:00
5f4565b18f
gnu: Add r-network.
...
* gnu/packages/cran.scm (r-network): New variable.
2018-03-02 22:23:18 +01:00
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
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
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
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
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
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
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
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
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
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
d338321ddb
gnu: qscintilla: Use HTTPS home page.
...
* gnu/packages/qt.scm (qscintilla)[home-page]: Use HTTPS.
2018-03-02 15:52:55 +01:00
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
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
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
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
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
0dae492195
gnu: ovmf: Use HTTPS home page.
...
* gnu/packages/firmware.scm (ovmf)[home-page]: Use HTTPS.
2018-03-02 15:52:54 +01:00
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
315c89f5ba
gnu: b43-tools: Update phase style.
...
* gnu/packages/firmware.scm (b43-tools)[arguments]: Substitute INVOKE
for SYSTEM* and FOR-EACH for EVERY, and end phases with #t.
2018-03-02 15:52:53 +01:00
bb5c358204
gnu: b43-tools: Update to 0.0.0-1.27892ef.
...
* gnu/packages/firmware.scm (b43-tools): Update to 0.0.0-1.27892ef.
[version]: Use our standard versioning scheme.
2018-03-02 15:52:53 +01:00
12adfdf0b6
gnu: Update (gnu packages python-web) phase styles.
...
* gnu/packages/python-web.scm (python-openid, python-terminado)
(python-geventhttpclient, python-cachecontrol, python-webencodings)
(python-s3transfer)[arguments]: Substitute INVOKE for SYSTEM* and end
phases with #t.
2018-03-02 15:52:53 +01:00
6a192184ec
gnu: python-flask-script: Update to 2.0.6.
...
* gnu/packages/python-web.scm (python-flask-script): Update to 2.0.6.
2018-03-02 15:52:52 +01:00
05075433a2
gnu: python-htmlmin: Update to 0.1.12.
...
* gnu/packages/python-web.scm (python-htmlmin): Update to 0.1.12.
2018-03-02 15:52:52 +01:00
bda82eff18
gnu: python-s3transfer: Update to 0.1.13.
...
* gnu/packages/python-web.scm (python-s3transfer): Update to 0.1.13.
2018-03-02 15:52:52 +01:00
e46dd02d99
gnu: python-webtest: Update to 2.0.29.
...
* gnu/packages/python-web.scm (python-webtest): Update to 2.0.29.
2018-03-02 15:52:52 +01:00
6f21aca728
gnu: python-ndg-httpsclient: Update to 0.4.4.
...
* gnu/packages/python-web.scm (python-ndg-httpsclient): Update to 0.4.4.
2018-03-02 15:52:51 +01:00
3c5658c596
gnu: python-cssutils: Update to 1.0.2.
...
* gnu/packages/python-web.scm (python-cssutils): Update to 1.0.2.
2018-03-02 15:52:51 +01:00
1a6fb8dac1
gnu: python-flask-babel: Update to 0.11.2.
...
* gnu/packages/python-web.scm (python-flask-babel): Update to 0.11.2.
2018-03-02 15:52:51 +01:00
424cea8083
guix system: Check for the lack of modules in the initrd.
...
* guix/scripts/system.scm (check-mapped-devices): Take an OS instead of
a list of <mapped-device>. Pass #:needed-for-boot? and #:initrd-modules
to CHECK.
(check-initrd-modules): New procedure.
(perform-action): Move 'check-mapped-devices' call first. Add call to
'check-initrd-modules'.
* gnu/system/mapped-devices.scm (check-device-initrd-modules): New
procedure.
(check-luks-device): Add #:initrd-modules and #:needed-for-boot?. Use
them to call 'check-device-initrd-modules'.
2018-03-02 13:53:15 +01:00
bc499b113a
system: Add 'initrd-modules' field.
...
* gnu/system.scm (<operating-system>)[initrd-modules]: New field.
(operating-system-initrd-file): Pass #:linux-modules to 'make-initrd'.
* gnu/system/linux-initrd.scm (default-initrd-modules): New procedure.
(%base-initrd-modules): New macro.
(base-initrd): Add #:linux-modules and honor it.
* gnu/system/install.scm (embedded-installation-os): Use
'initrd-modules' instead of 'initrd'.
* gnu/tests/install.scm (%raid-root-os): Likewise.
* doc/guix.texi (operating-system Reference): Add 'initrd-modules'.
(Initial RAM Disk): Document it. Adjust example to not use
#:extra-modules.
2018-03-02 13:53:10 +01:00
Ricardo Wurmus