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Author SHA1 Message Date
Ricardo Wurmus 94e907b962
import cran: Add recursive importer. 
* guix/import/cran.scm (recursive-import): New variable.
(cran->guix-package): Memoize the procedure.
 2016-12-17 19:12:55 +01:00
Ricardo Wurmus b26abe4f14
import cran: Ignore default R packages. 
* guix/import/cran.scm (default-r-packages): New variable.
(description->package): Drop default R packages from list of inputs.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus ad68f7fa58
import cran: description->package: Also return package dependencies. 
* guix/import/cran.scm (description->package): Return package
  dependencies in addition to generated package expression.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus bfa0c752bc
import cran: Move guix-name to top-level. 
* guix/import/cran.scm (guix-name): Move to top-level.
 2016-12-17 15:56:48 +01:00
Ricardo Wurmus 2e5f32ce1b
import cran: Remove more invalid characters from package names. 
* guix/import/cran.scm (guix-name): Replace period and underscore with
  dash; always prepend package names with "r-".
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus 576eda6d02
import cran: Handle BSD licenses with LICENSE file. 
* guix/import/cran.scm (string->license): Add cases for BSD licenses
with LICENSE file.
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus 741d68c20d
import cran: Translate MIT to the Expat license. 
* guix/import/cran.scm (string->license): Translate "MIT" license to
Expat license.
 2016-12-17 15:56:47 +01:00
Ricardo Wurmus 13f54d081b
import cran: Do not use "or later" licenses by default. 
* guix/import/cran.scm (string->license): Use exact license versions.
 2016-12-17 15:56:39 +01:00
Ludovic Courtès aaee461b9d
doc: Update dot graphs. 
* doc/images/bootstrap-packages.dot,
doc/images/coreutils-bag-graph.dot, doc/images/coreutils-graph.dot,
doc/images/shepherd-graph.dot: Regenerate.
 2016-12-17 14:46:42 +01:00
Ludovic Courtès a6562c7e20
profiles: Remove dependency on 'glibc-utf8-locales' for tests. 
Commit 1af0860e8b added a mandatory
dependency on 'glibc-utf8-locales', which entails long rebuilds for
tests.

* guix/profiles.scm (profile-derivation): Add #:locales? parameter.
Add 'set-utf8-locale' variable.  Use it when LOCALES? is true.
(link-to-empty-profile): Pass #:locales? #f.
* guix/scripts/environment.scm (inputs->profile-derivation): Pass
  #:locales?.
* guix/scripts/package.scm (build-and-use-profile): Likewise.
* tests/packages.scm ("--search-paths with pattern"): Pass #:locales? #f.
* tests/profiles.scm ("profile-derivation")
("profile-derivation, inputs", "profile-manifest, search-paths")
("etc/profile", "etc/profile when etc/ already exists"):
("etc/profile when etc/ is a symlink"): Likewise.
 2016-12-17 14:46:42 +01:00
Ludovic Courtès d44fb7dd60
gnu: bootstrap: Add FTP URL for bootstrap binaries. 
* gnu/packages/bootstrap.scm (%bootstrap-base-urls): Add
ftp://alpha.gnu.org (http://alpha.gnu.org is currently unresponsive.)
 2016-12-17 14:46:42 +01:00
Raoul Bonnal c9e9154e99
gnu: star: Update to 2.5.2b. 
* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2016-12-17 23:26:35 +10:00
Marius Bakke 51ad11ad62
gnu: Add fatfsck-static. 
* gnu/packages/disk.scm (dosfstools/static): New private variable.
(fatfsck/static): New variable.
 2016-12-17 10:13:22 +01:00
Alex Kost 64e43c674e
gnu: Add emacs-guix. 
* gnu/packages/emacs.scm (emacs-guix): New variable.
 2016-12-17 10:56:39 +03:00
Alex Kost 753baf775f
gnu: Add emacs-bui. 
* gnu/packages/emacs.scm (emacs-bui): New variable.
 2016-12-17 10:56:39 +03:00
Leo Famulari c7ec7c9926
gnu: imagemagick: Update to 6.9.6-8. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.6-8.
 2016-12-17 00:46:48 -05:00
Leo Famulari 7c1a7bf484
gnu: acme-client: Provide path to certificates. 
* gnu/packages/tls.scm (acme-client)[arguments]: Add 'patch-paths' phase.
 2016-12-17 00:09:10 -05:00
Ricardo Wurmus 76b3fbbce6
build: assert-no-store-file-names: Ignore ChangeLog. 
* Makefile.am (assert-no-store-file-names): Ignore /gnu/store file names
in the ChangeLog, because they might be examples in commit messages.
 2016-12-17 00:21:23 +01:00
Leo Famulari f8faf537ca
gnu: libupnp: Fix CVE-2016-8863. 
* gnu/packages/patches/libupnp-CVE-2016-8863.patch: New file.
* gnu/local.mk (dist_patch_DATA): Use it.
* gnu/packages/libupnp.scm (libupnp)[source]: Use it.
 2016-12-16 15:28:02 -05:00
Theodoros Foradis 850812decf
gnu: Add Greek Aspell dictionary 
* gnu/packages/aspell.scm (aspell-dict-el): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-16 18:04:55 +01:00
Ludovic Courtès 1af0860e8b
profiles: Build profiles in a UTF-8 locale. 
Fixes <http://bugs.gnu.org/25213>.
Reported by Christopher Baines <mail@cbaines.net>.

* guix/profiles.scm (profile-derivation)[glibc-utf8-locales]: New
variable.
[builder]: Use it to set 'LOCPATH'.
 2016-12-16 18:01:08 +01:00
Ludovic Courtès 580deec5b4
download: Protect against dangling symlinks in $SSL_CERT_DIR. 
Reported by Christopher Baines <mail@cbaines.net>
in <https://bugs.gnu.org/25213>.

* guix/build/download.scm (make-credendials-with-ca-trust-files): Check
whether FILE exists before calling
'set-certificate-credentials-x509-trust-file!'.
 2016-12-16 18:00:01 +01:00
Ludovic Courtès 99ec0cb397
refresh: Make dependency on (guix import crates) weak. 
Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

* guix/scripts/refresh.scm: Do not explicitly import (guix import crates).
 2016-12-16 17:38:39 +01:00
Ludovic Courtès f731529e2a
install: Add dosfstools. 
* gnu/system/install.scm (installation-os)[packages]: Add DOSFSTOOLS.
 2016-12-16 17:37:28 +01:00
ng0 fc9286d03a
gnu: tor: Recommend torsocks. 
* gnu/packages/tor.scm (tor)[description]: Recommend torsocks.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>
 2016-12-16 10:49:01 -05:00
Ludovic Courtès 3eee16130d
gnu: grub: Add dependency on efibootmgr. 
Suggested by Marius Bakke <mbakke@fastmail.com>.

* gnu/packages/grub.scm (grub)[arguments]: In 'patch-stuff', set
efibootmgr absolute file name in 'platform.c'.
[inputs]: Add EFIBOOTMGR.
 2016-12-16 14:45:56 +01:00
Ludovic Courtès 5597b3ae08
doc: "Nar" now means "normalized archive". 
* doc/guix.texi (Invoking guix archive): Mention "normalized archive"
and add index entries.
 2016-12-16 14:45:56 +01:00
Tobias Geerinckx-Rice c8502d9ec1
Revert "gnu: kmod: Update to 23." 
This should have been pushed to the ‘staging’ branch first.

This reverts commit 1e1cd41629.
 2016-12-16 12:19:50 +01:00
Tobias Geerinckx-Rice 7c58c852c4
gnu: libraw1394: Update to 2.1.2. 
* gnu/packages/linux.scm (libraw1394): Update to 2.1.2.
 2016-12-16 03:08:43 +01:00
Tobias Geerinckx-Rice 1e1cd41629
gnu: kmod: Update to 23. 
* gnu/packages/linux.scm (kmod): Update to 23.
 2016-12-16 03:08:42 +01:00
Tobias Geerinckx-Rice 3fe7cb872a
gnu: ethtool: Update to 4.8. 
* gnu/packages/networking.scm (ethtool): Update to 4.8.
 2016-12-16 03:08:42 +01:00
Tobias Geerinckx-Rice 7d162df8ce
gnu: mcelog: Update to 146. 
* gnu/packages/linux.scm (mcelog): Update to 146.
 2016-12-16 03:08:41 +01:00
Mark H Weaver 0eb36dd17f
gnu: linux-libre@4.4: Update to 4.4.39. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.39.
 2016-12-15 20:35:24 -05:00
Leo Famulari fb73f07a0f
gnu: guile-irregex: Update to 0.9.6 [fixes CVE-2016-9954]. 
* gnu/packages/guile.scm (guile-irregex): Update to 0.9.6.
 2016-12-15 18:40:19 -05:00
Mathieu Lirzin 57aa94bd7e
services: cuirass: Put specifications in the store. 
* gnu/services/cuirass.scm (<cuirass-configuration>): Change type of
'specifications' field to an alist to match the documentation example.
(cuirass-shepherd-service): Store the provided specifications in a file.  Use
that file as the "--specification" argument.
 2016-12-15 22:50:27 +01:00
Mathieu Lirzin 44ccd9622e
gnu: cuirass: Update to revision 2. 
* gnu/packages/ci.scm (cuirass): Update to revision 2.
[native-inputs]: Add texinfo.
 2016-12-15 22:50:24 +01:00
Tobias Geerinckx-Rice 177de53784
gnu: libpsl: Update to 0.16.0. 
* gnu/packages/web.scm (libpsl): Update to 0.16.0.
 2016-12-15 21:05:05 +01:00
Tobias Geerinckx-Rice 426aecfd48
gnu: openconnect: Update to 7.08. 
* gnu/packages/vpn.scm (openconnect): Update to 7.09.
 2016-12-15 19:31:45 +01:00
John Darrington 7d73b2c6d0
gnu: Add system test for the rpcbind-daemon service. 
* gnu/tests/nfs.scm: New file.
* gnu/local.mk: Add it.
 2016-12-15 19:13:46 +01:00
Thomas Danckaert 7781afde65
gnu: Add kdevelop. 
* gnu/packages/kde.scm (kdevelop): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 17:11:32 +01:00
Thomas Danckaert c02c8cf4a8
gnu: Add kdevplatform. 
* gnu/packages/kde.scm (kdevplatform): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 17:09:27 +01:00
Thomas Danckaert 7c1a52090d
gnu: libksysguard: Correct inputs. 
* gnu/packages/kde.scm (libksysguard)[inputs]: Remove kdbusaddons,
  kdoctools, kinit, knewstruff, knotifications, kio; add kauth,
  kcompletion, kconfig, kcoreaddons, kwidgetsaddons.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 17:06:49 +01:00
Christopher Baines e05b780a58
services: postgresql: Add locale to configuration 
* gnu/services/databases.scm (<postgresql-configuration>): Add locale
  field.
  (postgresql-shepherd-service): Pass locale to initdb.
  (postgresql-service): Add locale default.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 16:55:02 +01:00
Christopher Baines 2d3d5cc5ea
services: postgresql: Add port to configuration 
* gnu/services/databases.scm (<postgresql-configuration>): Add port
  field.
  (postgresql-shepherd-service): Pass port to postgres.
  (postgresql-service): Add port default.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 16:54:22 +01:00
Chris Marusich eee7878f4e
gnu: gnome-settings-daemon: Add dependency on NetworkManager. 
* gnu/packages/gnome.scm (gnome-settings-daemon)[arguments]: Remove
"--disable-network-manager".
[inputs]: Add NETWORK-MANAGER.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 16:51:11 +01:00
Chris Marusich fd070f35d3
gnu: network-manager: Enable session tracking with elogind. 
* gnu/packages/gnome.scm (network-manager): Add configuration options
  "--with-systemd-logind=yes" (so we can use elogind to track login sessions)
  and "--with-consolekit=no" (so we don't use consolekit to track sessions,
  since it isn't packaged yet).  Add elogind as an input, and add a snippet to
  replace some references to systemd with elogind.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-12-15 16:50:48 +01:00
David Craven 6976c68158
upstream: Determine archive type correctly. 
* guix/upstream.scm (package-update): Take the basename of the uri
  before trying to determine the extension.
 2016-12-15 05:57:03 +01:00
Eric Bavier 200cdf81c6
doc: mention cpan updater. 
* doc/guix.texi (Invoking guix refresh): Mention cpan updater.
 2016-12-14 21:13:19 -06:00
Mark H Weaver 48ef3f9d9c
gnu: icecat: Label patches that have since been assigned CVEs. 
Document that the following CVEs are fixed: CVE-2016-9893, CVE-2016-9895,
CVE-2016-9897, CVE-2016-9898, CVE-2016-9899, CVE-2016-9900, CVE-2016-9901,
CVE-2016-9902, CVE-2016-9904, and CVE-2016-9905.  Note that these are all of
the CVEs fixed in Firefox ESR 45.6.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add comments to patches that
have since been assigned CVEs.
 2016-12-14 19:55:26 -05:00
Tobias Geerinckx-Rice 0c6c9c00ab
gnu: Update more dead Google Code home pages. 
* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
 2016-12-14 22:08:51 +01:00