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10052 Commits

Author SHA1 Message Date
Ricardo Wurmus e7173df87a gnu: icedtea6: Update to 1.13.9. 
* gnu/packages/java.scm (icedtea6): Update to 1.13.9.
 2015-12-23 14:57:58 +01:00
Efraim Flashner a9257a873f gnu: libmicrohttpd: Update to 0.9.48. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.48.
 2015-12-22 22:50:58 +02:00
Efraim Flashner 0877ef4342 gnu: parallel: Update to 20151222. 
* gnu/packages/parallel.scm (parallel): Update to 20151222.
 2015-12-22 22:47:44 +02:00
Efraim Flashner 419fa59b17 gnu: sipwitch: Update to 1.9.15. 
* gnu/packages/telephony.scm (sipwitch): Update to 1.9.15.
 2015-12-22 22:45:41 +02:00
Efraim Flashner 99e6f9c828 gnu: ucommon: Update to 7.0.0. 
* gnu/packages/telephony.scm (ucommon): Update to 7.0.0.
[inputs]: Add gnutls.
 2015-12-22 22:39:48 +02:00
Mark H Weaver e54465ff85 gnu: isc-dhcp: Disable parallel build. 
* gnu/packages/admin.scm (isc-dhcp)[arguments]: Disable parallel build.
 2015-12-22 10:45:13 -05:00
Mark H Weaver 6548b1e122 gnu: isc-dhcp: Update to 4.3.3; update bundled bind to 9.9.8-P2. 
Fixes CVE-2015-8000 and CVE-2015-8461.

* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3.
  [inputs]: Add 'bind-source-tarball'.
  [arguments]: Use modify-phases.  Add 'replace-bundled-bind' phase.
  In 'post-configure' phase, avoid hard-coding version numbers of
  bundled bind.
 2015-12-21 19:47:27 -05:00
Mark H Weaver f9a5b18897 gnu: bind-utils: Update to 9.10.3-P2. 
* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P2.
  [source]: Use HTTP URI instead of FTP.
 2015-12-21 19:47:26 -05:00
Ludovic Courtès ab64483f64 file-systems: The 'device' field can be a UUID (bytevector). 
Previously a wrong-type-arg error would be raised when a file system
with a UUID (bytevector) field was encountered.

* gnu/system.scm (other-file-system-services)[device-mappings]: Check
whether FS's device is a string.
 2015-12-22 00:29:43 +01:00
Ludovic Courtès be21979d85 file-systems: Add a 'mount?' field. 
Fixes <http://bugs.gnu.org/22176>.
Reported by Florian Paul Schmidt <mista.tapas@gmx.net>.

* gnu/system/file-systems.scm (<file-system>)[mount?]: New field.
(file-system->spec): Adjust accordingly.
* gnu/services/base.scm (file-system-dmd-service): Return the empty list
when FILE-SYSTEM has 'mount?' set to false.
(user-processes-service): Select the subset of FILE-SYSTEMS that matches
'file-system-mount?'.
* doc/guix.texi (File Systems): Document it.
 2015-12-22 00:29:21 +01:00
Ludovic Courtès e43e84ba7a services: Add 'fstab-service-type'. 
* gnu/services/base.scm (file-system->fstab-entry)
(file-systems->fstab): New procedures.
(fstab-service-type): New variable.
* gnu/services/base.scm (file-system-dmd-service): New procedure, taken
from...
(file-system-service-type): ... here.
* gnu/system.scm (essential-services): Add FSTAB-SERVICE-TYPE instance.
 2015-12-22 00:04:36 +01:00
Ricardo Wurmus 12d38e8d43 build: Add bioconductor-uri procedure. 
* guix/build-system/r.scm (bioconductor-uri): New procedure.
 2015-12-21 22:32:01 +01:00
Ricardo Wurmus 8e92cfb101 gnu: Add vmpk. 
* gnu/packages/music.scm (vmpk): New variable.
 2015-12-21 22:09:47 +01:00
Ricardo Wurmus bf76d7802c gnu: Add drumstick. 
* gnu/packages/music.scm (drumstick): New variable.
 2015-12-21 22:09:47 +01:00
Leo Famulari ef9006451f gnu: letsencrypt and acme: Update to 0.1.1. 
These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.1.1.
[source]: Use pypi-uri.
* gnu/packages/tls.scm (acme): Update to 0.1.1.
[source]: Use pypi-uri.
 2015-12-21 14:35:58 -05:00
Efraim Flashner 704989660f gnu: ffmpeg: Update to 2.8.4. 
* gnu/packages/video.scm (ffmpeg): Update to 2.8.4.
 2015-12-21 21:30:46 +02:00
Leo Famulari d12717cba0 doc: Be more explicit in example of file-systems configuration. 
* gnu/system/examples/bare-bones.tmpl (file-systems): Change device
label.
* gnu/system/examples/desktop.tmpl (file-systems): Likewise.
 2015-12-21 13:12:07 -05:00
Leo Famulari dd81635571 doc: Explain significance of partition labels. 
* doc/guix.texi (Preparing for Installation): Point out relationship
between partition labels and the file-system configuration.
 2015-12-21 12:53:12 -05:00
Leo Famulari f0150f8724 gnu: grub: Add fix for CVE-2015-8730. 
* gnu/packages/patches/grub-CVE-2015-8370.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.
* gnu/packages/grub.scm: Apply patch.
 2015-12-21 12:33:55 -05:00
Ricardo Wurmus e2cd1d0fb9 gnu: Add GenomicRanges. 
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 0e7d5560de gnu: Add XVector. 
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus bf7764b74f gnu: Add GenomeInfoDb. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 78addcb0eb gnu: Add IRanges. 
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 7485129e4f gnu: Add S4Vectors. 
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus d29b25c490 gnu: Add BiocGenerics. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
 2015-12-21 17:22:16 +01:00
Ricardo Wurmus 9fba89e829 gnu: Add r-acsnminer. 
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 9e47f30b08 gnu: Add r-gridextra. 
* gnu/packages/statistics.scm (r-gridextra): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus b73751c8ff gnu: Add r-gtable. 
* gnu/packages/statistics.scm (r-gtable): New variable.
 2015-12-21 17:21:26 +01:00
Ricardo Wurmus 77bdb276e9 gnu: Add r-rmarkdown. 
* gnu/packages/statistics.scm (r-rmarkdown): New variable.
* gnu/packages/haskell.scm: Do not select libxml2 from the xml module to
  prevent circular package module imports.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 4c1f2705b5 gnu: Add r-catools. 
* gnu/packages/statistics.scm (r-catools): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus bb6d2dadf7 gnu: Add r-bitops. 
* gnu/packages/statistics.scm (r-bitops): New variable.
 2015-12-21 17:13:44 +01:00
Ricardo Wurmus 8406138b72 gnu: Add AdaptiveSparsity. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
 2015-12-21 16:05:38 +01:00
Ricardo Wurmus e22d4ca4c4 gnu: Add r-rcpparmadillo. 
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
* gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
 2015-12-21 16:05:37 +01:00
Ricardo Wurmus b15e47f9e6 gnu: Add armadillo. 
* gnu/packages/maths.scm (armadillo): New variable.
 2015-12-21 15:47:40 +01:00
Ricardo Wurmus b1186502a4 doc: Fix outdated claim about CRAN importer. 
* doc/guix.texi: The CRAN importer no longer extracts information from
  the HTML package description but from the package's DESCRIPTION file.
 2015-12-21 15:25:10 +01:00
Ricardo Wurmus be036757bd import: Drop empty list items. 
* guix/import/cran.scm (listify): Remove empty strings from result list.
 2015-12-21 15:24:54 +01:00
Ricardo Wurmus 0cb5bc2cff http-client: Support basic authentication. 
* guix/http-client.scm (http-fetch): Add Authorization header to request
  when the URI contains userinfo.
 2015-12-21 15:24:44 +01:00
Ricardo Wurmus 086e498bcf gnu: Add libgit2. 
* gnu/packages/version-control.scm (libgit2): New variable.
 2015-12-21 15:22:14 +01:00
Ben Woodcroft 02f35bb5a7 gnu: mafft: Update to 7.267. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
 2015-12-21 15:16:01 +01:00
Mathieu Lirzin 1ef3f91a70 gnu: rxvt-unicode: Install the terminal capability data. 
This provides the necessary terminal capability data, which are required
by ncurses-based applications.

* gnu/packages/xdisorg.scm (rxvt-unicode)[native-inputs]: Add ncurses.
[arguments]: Set the destination of the terminfo files.
[native-search-path]: New field.  Make them automatically available to
the user.
 2015-12-21 13:35:34 +01:00
Efraim Flashner 72d8b5baf4 gnu: msmtp: Update to 1.6.3. 
* gnu/packages/mail.scm (msmtp): Update to 1.6.3.
[inputs]: Add libsecret.
 2015-12-21 09:36:15 +02:00
Efraim Flashner ec92806ae5 gnu: claws-mail: Update to 3.13.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.13.1.
 2015-12-21 09:17:47 +02:00
Efraim Flashner 56918e26cf gnu: python-cython: Update to 0.23.4. 
* gnu/packages/python.scm (python-cython): Update to 0.23.4.
 2015-12-21 06:55:13 +02:00
David Thompson e99711af22 gnu: ruby: Update to 2.2.4. 
This version fixes CVE-2015-7551.

* gnu/packages/ruby.scm (ruby): Update to 2.2.4.
 2015-12-20 22:40:53 -05:00
Ludovic Courtès c5b303c57f lint: The CPE name of GRUB is "grub2". 
Reported by Leo Famulari.

* guix/scripts/lint.scm (package-name->cpe-name): Add "grub".
 2015-12-20 22:34:22 +01:00
Ludovic Courtès 724a7d9c74 packages: Remove now redundant graph procedures. 
These procedures are now redundant with those in (guix graph) and are no
longer used since commit a51cbecb.

* gnu/packages.scm (vhash-refq, package-dependencies)
(package-direct-dependents, package-transitive-dependents)
(package-covering-dependents): Remove.
 2015-12-20 22:34:22 +01:00
Ludovic Courtès ccda8f7d7f profiles: Honor search paths of propagated inputs. 
Fixes <http://bugs.gnu.org/22073>.
Reported by Federico Beffa <beffa@ieee.org>.

* guix/profiles.scm (package->manifest-entry): Use
'package-transitive-native-search-paths' when computing
'search-paths' field.
* tests/profiles.scm ("package->manifest-entry, search paths"): New test.
 2015-12-20 22:34:22 +01:00
Ludovic Courtès aa8e051532 packages: Add 'package-transitive-native-search-paths'. 
* guix/packages.scm (package-transitive-native-search-paths): New
procedure.
* tests/packages.scm ("package-transitive-native-search-paths"): New
test.
 2015-12-20 22:34:22 +01:00
Efraim Flashner 54b7f63a72 gnu: offlineimap: Update to 6.6.0. 
* gnu/packages/mail.scm (offlineimap): Update to 6.6.0.
 2015-12-20 21:39:18 +02:00
Efraim Flashner b5d47a5a53 gnu: gnupg: Update to 1.4.20. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.20.
 2015-12-20 20:07:31 +02:00