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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
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
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Mark H Weaver
99654a1685
gnu: icecat: Add more fixes from upstream mozilla-esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the
upstream mozilla-esr52 repository.
 2018-03-02 01:31:30 -05:00
Mark H Weaver
8863f2f051
gnu: icecat: Update to 52.6.0-gnu1. 
* gnu/packages/gnuzilla.scm (icecat): Update to 52.6.0-gnu1.
[source]: Remove patches that are no longer needed.
* gnu/packages/patches/icecat-bug-1348660-pt5.patch,
gnu/packages/patches/icecat-bug-1414945.patch,
gnu/packages/patches/icecat-bug-1415133.patch,
gnu/packages/patches/icecat-bug-1424373-pt2.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2018-03-02 01:31:19 -05:00
Leo Famulari
703a8b7dc5
gnu: postgresql@9.6: Update to 9.6.8 [fixes CVE-2018-1058]. 
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.8.
 2018-03-01 20:01:48 -05:00
Leo Famulari
bb17b2be49
gnu: postgresql: Update to 10.3 [fixes CVE-2018-1058]. 
* gnu/packages/databases.scm (postgresql): Update to 10.3.
 2018-03-01 20:01:48 -05:00
Leo Famulari
e9802319f7
gnu: memcached: Update to 1.5.6. 
* gnu/packages/databases.scm (memcached): Update to 1.5.6.
 2018-03-01 20:00:12 -05:00
Mark H Weaver
da525e714a
gnu: linux-libre: Update to 4.15.7. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.7.
(%linux-libre-hash): Update hash.
 2018-03-01 17:59:21 -05:00
Mark H Weaver
433765e599
gnu: linux-libre@4.14: Update to 4.14.23. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.23.
(%linux-libre-4.14-hash): Update hash.
 2018-03-01 17:58:35 -05:00
Mark H Weaver
8b1f76c443
gnu: linux-libre@4.9: Update to 4.9.85. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.85.
 2018-03-01 17:58:04 -05:00
Mark H Weaver
5026696033
gnu: linux-libre@4.4: Update to 4.4.119. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.119.
 2018-03-01 17:57:22 -05:00
Julien Lepiller
8147d7c675
gnu: php: Fix test failure. 
* gnu/packages/php.scm (php)[inputs]: Use gd-for-php.
(gd-for-php): New private variable.
* gnu/packages/patches/gd-CVE-2018-5711.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-03-01 22:25:28 +01:00
Tobias Geerinckx-Rice
738aa0ca1d
gnu: sdcc: Fix typo in description. 
* gnu/packages/sdcc.scm (sdcc)[description]: Fix (upstream) typo.  Add
hyphens.
 2018-03-01 22:21:02 +01:00
Tobias Geerinckx-Rice
1ff14bf2cd
gnu: sdcc: Update to 3.7.0. 
* gnu/packages/sdcc.scm (sdcc): Update to 3.7.0.
 2018-03-01 22:21:02 +01:00
Tobias Geerinckx-Rice
bb47da4a6a
gnu: php: Update to 7.2.3. 
* gnu/packages/php.scm (php): Update to 7.2.3.
 2018-03-01 22:21:01 +01:00
Tobias Geerinckx-Rice
a9c0a133c0
gnu: python-stem: Update to 1.6.0. 
* gnu/packages/python.scm (python-stem): Update to 1.6.0.
[arguments]: Add ‘fix-test-environment’ phase.
 2018-03-01 22:21:01 +01:00
Tobias Geerinckx-Rice
68e7632db0
gnu: onionshare: Update phase style. 
* gnu/packages/tor.scm (onionshare)[arguments]: Substitute INVOKE for
SYSTEM* and end phase with #t.
 2018-03-01 22:21:01 +01:00
Tobias Geerinckx-Rice
fbb0164a5f
gnu: privoxy: Update phase style. 
* gnu/packages/tor.scm (privoxy)[arguments]: Substitute INVOKE for
SYSTEM* and end phase with #t.
 2018-03-01 22:21:01 +01:00
Tobias Geerinckx-Rice
66b89ee28e
gnu: python-stem: Update phase style. 
* gnu/packages/python.scm (python-stem)[arguments]: Substitute INVOKE
for SYSTEM* and end phase with #t.
 2018-03-01 22:21:00 +01:00
Tobias Geerinckx-Rice
57c734a628
gnu: liblo: Update to 0.29. 
* gnu/packages/audio.scm (liblo): Update to 0.29.
 2018-03-01 22:21:00 +01:00
Tobias Geerinckx-Rice
4972f9cc0a
gnu: nagios: Update to 4.3.4. 
* gnu/packages/monitoring.scm (nagios): Update to 4.3.4.
 2018-03-01 22:21:00 +01:00
Tobias Geerinckx-Rice
4f5452ab3a
gnu: libftdi: Use HTTPS home page. 
* gnu/packages/libftdi.scm (libftdi)[home-page]: Use HTTPS.
 2018-03-01 22:21:00 +01:00
Tobias Geerinckx-Rice
7314a5475e
gnu: dbacl: Use HTTPS home page. 
* gnu/packages/textutils.scm (dbacl)[home-page]: Use HTTPS.
 2018-03-01 22:20:59 +01:00
Tobias Geerinckx-Rice
db317b38dc
gnu: dbacl: Update phase style. 
* gnu/packages/textutils.scm (dbacl)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t.
 2018-03-01 22:20:59 +01:00
Ricardo Wurmus
b672a81607
gnu: Graft glibc to allow execution on Linux 2.6.32. 
* gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/base.scm (glibc/linux)[replacement]: New field.
(glibc-2.26-patched): New variable.
 2018-03-01 21:32:36 +01:00
Ricardo Wurmus
b79e1fbe96
gnu: r-httpuv: Update to 1.3.6.1. 
* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.1.
 2018-03-01 21:28:54 +01:00
Ricardo Wurmus
bfae3f7121
gnu: r-lubridate: Update to 1.7.3. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
eaf0905970
gnu: r-tidyselect: Update to 0.2.4. 
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.4.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
35d12b05f0
gnu: r-rmarkdown: Update to 1.9. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
dafd13d5b2
gnu: r-rcpparmadillo: Update to 0.8.400.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.8.400.0.0.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
36e1202b2c
gnu: r-yaml: Update to 2.1.17. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.1.17.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
e3ddb56329
gnu: r-gdtools: Update to 0.1.7. 
* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.7.
[inputs]: Add zlib.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
e24ccf46f1
gnu: r-rpart: Update to 4.1-13. 
* gnu/packages/statistics.scm (r-rpart): Update to 4.1-13.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
744e06e717
gnu: r-mass: Update to 7.3-49. 
* gnu/packages/statistics.scm (r-mass): Update to 7.3-49.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
29c9c9c2c1
gnu: r-rmysql: Update to 0.10.14. 
* gnu/packages/databases.scm (r-rmysql): Update to 0.10.14.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
5e38673455
gnu: r-pillar: Update to 1.2.1. 
* gnu/packages/cran.scm (r-pillar): Update to 1.2.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
9d6f392529
gnu: r-truncnorm: Update to 1.0-8. 
* gnu/packages/cran.scm (r-truncnorm): Update to 1.0-8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
9aaf2813e2
gnu: r-scran: Update to 1.6.8. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
6a0e13906b
gnu: r-wgcna: Update to 1.63. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
61cbd49b30
gnu: r-topgo: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
535014ce60
gnu: r-genomicranges: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
eb8971b742
gnu: r-limma: Update to 3.34.9. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
22d96920d3
gnu: r-edger: Update to 3.20.9. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
99e4b11d81
gnu: r-shortread: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus
b180893289
gnu: r-dexseq: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
 2018-03-01 21:28:52 +01:00
Efraim Flashner
360ea2bbd5
gnu: efl: Use separate "include" output. 
* gnu/packages/enlightenment.scm (efl)[outputs]: Add 'include' output.
 2018-03-01 22:19:37 +02:00
Efraim Flashner
40a7997e63
gnu: efl: Update to 1.20.7. 
* gnu/packages/enlightenment.scm (efl): Update to 1.20.7.
 2018-03-01 22:18:58 +02:00
Ricardo Wurmus
643817e445
gnu: Add patchmatrix. 
* gnu/packages/music.scm (patchmatrix): New variable.
 2018-03-01 21:12:59 +01:00
Ricardo Wurmus
1debc5b9d2
gnu: ghc-uuid: Fix build. 
* gnu/packages/haskell.scm (ghc-uuid)[arguments]: Allow building with a newer
version of QuickCheck.
 2018-03-01 21:11:43 +01:00
Christopher Lemmer Webber
04e7b1e7f9
gnu: golly: Fix source url. 
* gnu/packages/games.scm (golly): Fix source url.
 2018-03-01 11:19:56 -06:00
Marius Bakke
52fb59ef25
gnu: imagemagick: Update to 6.9.9-36. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-36.
 2018-03-01 17:40:49 +01:00
Marius Bakke
fe29681717
gnu: libe-book: Update to 0.1.3. 
* gnu/packages/libreoffice.scm (libe-book): Update to 0.1.3.
[propagated-inputs]: Add LIBLANGTAG.
 2018-03-01 17:40:49 +01:00
Marius Bakke
814bc35d55
gnu: libabw: Update to 0.1.2. 
* gnu/packages/libreoffice.scm (libabw): Update to 0.1.2.
 2018-03-01 17:40:48 +01:00
Marius Bakke
c7cc1fcbe0
gnu: libpagemaker: Update to 0.0.4. 
* gnu/packages/libreoffice.scm (libpagemaker): Update to 0.0.4.
[source](uri): Use HTTPS.
 2018-03-01 17:40:48 +01:00
Marius Bakke
9ed31fca81
gnu: libmspub: Update to 0.1.4. 
* gnu/packages/libreoffice.scm (libmspub): Update to 0.1.4.
[source](uri): Use HTTPS.
 2018-03-01 17:40:48 +01:00
Marius Bakke
789445a10a
gnu: xorgproto: Update to 2018.4. 
* gnu/packages/xorg.scm (xorgproto): Update to 2018.4.
 2018-03-01 17:40:48 +01:00
Ludovic Courtès
21b5fc253e
gnu: cuirass: Update to aa4c778. 
* gnu/packages/ci.scm (cuirass): Update to aa4c778.
 2018-03-01 17:38:55 +01:00
Rene
35e2d0cfae
gnu: nautilus: Use meson-build-system, update to 3.26.2. 
* gnu/packages/gnome.scm (nautilus): Update to 3.26.2.
[build-system]: Use meson-build-system.
[native-inputs]: Add desktop-file-utils and gtk+:bin.
[inputs]: Add libselinux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-01 14:00:21 +01:00
Leo Famulari
acb59d99db
gnu: Fix Borg crashes with Python msgpack > 0.5 
The Python msgpack library changed its name, but borg (and possibly
other packages) still uses the old name.

Fixes <https://bugs.gnu.org/30662>.

* gnu/packages/python.scm (python-msgpack-transitional): New variable.
* gnu/packages/backup.scm (borg)[inputs]: Use it.
 2018-02-28 23:43:23 -05:00
Ricardo Wurmus
2adfe819f0
gnu: Remove duplicate definition of emacs-esxml. 
* gnu/packages/emacs.scm (emacs-esxml): Remove.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
c1d2236569
gnu: Remove emacs-nov. 
The package already exists with the name "emacs-nov-el".

* gnu/packages/emacs.scm (emacs-nov): Remove.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
201084ac1f
gnu: java-bouncycastle-bcpkix: Use invoke. 
* gnu/packages/java.scm (java-bouncycastle-bcpkix)[arguments]: Use invoke.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
9be4b9fa58
gnu: java-bouncycastle-bcprov: Use invoke. 
* gnu/packages/java.scm (java-bouncycastle-bcprov)[arguments]: Use invoke.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
1b6bc51675
gnu: java-lz4: Use invoke. 
* gnu/packages/java.scm (java-lz4)[arguments]: Use invoke.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
ec32bc9860
gnu: antlr3-3.1: Remove version from package name. 
* gnu/packages/java.scm (antlr3-3.1)[name]: Remove.
[arguments]: Adjust accordingly.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
13f38d31a4
gnu: antlr3-3.1: Use invoke. 
* gnu/packages/java.scm (antlr3-3.1)[arguments]: Use invoke.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
e85c1bf6cd
gnu: java-jansi-native: Simplify. 
* gnu/packages/java.scm (java-jansi-native)[arguments]: Use "invoke"; remove
useless "mkdir-p".
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
3d6925ef51
gnu: java-jansi-native: Fix description. 
* gnu/packages/java.scm (java-jansi-native)[description]: Replace placeholder
text with an actual description.
 2018-02-28 23:05:06 +01:00
Ricardo Wurmus
6338ea9a88
gnu: java-hawtjni: Simplify build phases. 
* gnu/packages/java.scm (java-hawtjni)[arguments]: Use "invoke" instead of
"system*"; use "install-file" instead of "mkdir-p" and "copy-file".
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
080d0b605a
gnu: java-commons-jexl-2: Use invoke. 
* gnu/packages/java.scm (java-commons-jexl-2)[arguments]: Use invoke.
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
8c7d32e07c
gnu: java-jnacl: Do not prefix jar with "java-". 
* gnu/packages/java.scm (java-jnacl)[arguments]: Rename jar to "jnacl.jar".
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
3e87923a67
gnu: java-jnacl: Update to 0.1.0-2.094e819. 
* gnu/packages/java.scm (java-jnacl): Update to 0.1.0-2.094e819.
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
8333c206a9
gnu: java-jnacl: Simplify build phase. 
* gnu/packages/java.scm (java-jnacl)[arguments]: Simplify "fix-tests" phase.
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
e158642816
gnu: java-jnacl: Correct license. 
* gnu/packages/java.scm (java-jnacl)[license]: Change to BSD-2.
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
602f54f436
gnu: java-jnacl: Use invoke. 
* gnu/packages/java.scm (java-jnacl)[arguments]: Use "invoke".
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
f201b18ed7
gnu: Add java-ecj-3.5. 
* gnu/packages/java.scm (java-ecj-3.5): New variable.
 2018-02-28 23:05:05 +01:00
Ricardo Wurmus
c1cb857645
gnu: Add java-ecj-3. 
* gnu/packages/java.scm (java-ecj-3): New variable.
 2018-02-28 23:05:05 +01:00
Tobias Geerinckx-Rice
9d43579f2d
gnu: dovecot: Update to 2.3.0.1 [fixes CVE-2017-14461]. 
* gnu/packages/mail.scm (dovecot): Update to 2.3.0.1.
[source]: Remove upstreamed patch.
* gnu/packages/patches/dovecot-CVE-2017-15132.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-02-28 22:58:23 +01:00
Tobias Geerinckx-Rice
4321aeb6d3
gnu: html-xml-utils: Update to 7.6. 
* gnu/packages/xml.scm (html-xml-utils): Update to 7.6.
 2018-02-28 22:58:23 +01:00
Tobias Geerinckx-Rice
0828bd82bd
gnu: libftdi: Update to 1.4. 
* gnu/packages/libftdi.scm (libftdi): Update to 1.4.
 2018-02-28 22:58:23 +01:00
Tobias Geerinckx-Rice
30bbb86ae3
gnu: git-remote-gcrypt: Update to 1.0.2. 
* gnu/packages/version-control.scm (git-remote-gcrypt): Update to 1.0.2.
 2018-02-28 22:58:23 +01:00
Tobias Geerinckx-Rice
aa08ab38cd
gnu: dropbear: Update to 2018.76. 
* gnu/packages/ssh.scm (dropbear): Update to 2018.76.
 2018-02-28 22:58:23 +01:00
Konrad Hinsen
649eb8b567
gnu: Add sala. 
* gnu/packages/password-utils.scm (sala): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-02-28 22:47:48 +01:00
Ludovic Courtès
4c853b7c11
gnu: guile-static-stripped: Add 'finit_module' wrapper. 
* gnu/packages/patches/guile-linux-syscalls.patch: Add
'load-linux-module/fd' procedure.
 2018-02-28 22:47:48 +01:00
Ludovic Courtès
63e48300d1
gnu: guile-static-stripped: Remove dependency on bash-minimal. 
Previously guile-static-stripped, which is embedded in the initrd, would
depend on 'bash-minimal' and 'glibc'; the closure size was 77 MiB.  Now
the closure size is down to 45.7 MiB.

Reported by Danny Milosavljevic <dannym@scratchpost.org> in
<https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00505.html>.

* gnu/packages/make-bootstrap.scm (%guile-static): Remove the
'pre-configure' phase.
(%guile-static-stripped)[arguments]: Add #:allowed-references.
 2018-02-28 22:47:48 +01:00
Efraim Flashner
bcc6551083
gnu: ccl: Patch absolute file-name. 
* gnu/packages/lisp.scm (ccl)[arguments]: In 'pre-build add substitution
for /bin/pwd.
 2018-02-28 22:11:21 +02:00
Efraim Flashner
da1b30bd93
gnu: keepassxc: Enable various plugins. 
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add
configure-flags to enable favicons, browser integration and ssh-agent.
[inputs]: Add curl, libsodium.
 2018-02-28 22:11:21 +02:00
Efraim Flashner
3374dcc78c
gnu: keepassxc: Update to 2.3.0. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.0.
 2018-02-28 22:11:17 +02:00
Marius Bakke
53453d7acc
gnu: wavpack: Fix CVE-2018-6767. 
* gnu/packages/patches/wavpack-CVE-2018-6767.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/audio.scm (wavpack)[source](patches): Add it.
 2018-02-28 20:29:46 +01:00
Marius Bakke
6b3ee23b7a
gnu: ldb: Update to 1.3.2. 
* gnu/packages/samba.scm (ldb): Update to 1.3.2.
 2018-02-28 20:17:31 +01:00
Marius Bakke
954b677195
gnu: p11-kit: Update to 0.23.10. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.10.
 2018-02-28 20:13:41 +01:00
Marius Bakke
f03ec1e595
gnu: feh: Update to 2.24. 
* gnu/packages/image-viewers.scm (feh): Update to 2.24.
 2018-02-28 20:01:03 +01:00
Alex Vong
6f45e45d4d
gnu: Add youtube-viewer. 
* gnu/packages/video.scm (youtube-viewer): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-02-28 16:59:55 +01:00
Alex Vong
b5bbcda3ee
gnu: Add perl-gtk2. 
* gnu/packages/gtk.scm (perl-gtk2): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-02-28 16:59:55 +01:00
Alex Vong
ee6911c7c0
gnu: Add perl-pango. 
* gnu/packages/gtk.scm (perl-pango): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-02-28 16:59:55 +01:00
Alex Vong
451f6e30eb
gnu: Add perl-glib. 
* gnu/packages/glib.scm (perl-glib): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-02-28 16:57:33 +01:00
Alex Vong
4e028d7ad2
gnu: Add perl-cairo. 
* gnu/packages/gtk.scm (perl-cairo): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-02-28 16:57:33 +01:00
Marius Bakke
b0a2c9cbe9
gnu: python-webencodings: Update to 0.5.1. 
* gnu/packages/python-web.scm (python-webencodings): Update to 0.5.1.
 2018-02-28 16:02:55 +01:00
Marius Bakke
4ef80b2f58
gnu: python-html5lib: Update to 1.0.1. 
* gnu/packages/python-web.scm (python-html5lib): Update to 1.0.1.
 2018-02-28 16:01:43 +01:00
Marius Bakke
a846f29dff
gnu: python-netifaces: Update to 0.10.6. 
* gnu/packages/python.scm (python-netifaces): Update to 0.10.6.
[source](uri): Use PYPI-URI.
[home-page]: Update.
 2018-02-28 15:40:44 +01:00
Marius Bakke
fb2477f6d2
gnu: python-psutil: Update to 5.4.3. 
* gnu/packages/python.scm (python-psutil): Update to 5.4.3.
[properties]: Declare python2 variant.
(python2-psutil): Propagate PYTHON2-ENUM34.
 2018-02-28 14:17:55 +01:00
Marius Bakke
836de07a47
gnu: python-wrapt: Update to 1.10.11. 
* gnu/packages/python.scm (python-wrapt): Update to 1.10.11.
 2018-02-28 13:59:03 +01:00