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34062 Commits

Author SHA1 Message Date
Christopher Baines f694b4ba9c
gnu: Remove duplicated ghc-time-locale-compat. 
It was first added in 5e51bcf7b3, then again in
c56a30b3ba.

* gnu/packages/haskell.scm (ghc-time-locale-compat): Remove duplicated package
definition.
 2018-07-29 17:57:52 +01:00
Christopher Baines 89b4882176
gnu: Remove duplicated ghc-th-lift-instances. 
It was first added in a6d1c4e75a, then again in
ff7dd11f0a.

* gnu/packages/haskell.scm (ghc-th-lift-instances): Remove duplicated package
definition.
 2018-07-29 17:57:52 +01:00
Christopher Baines cfa6cc4d9a
gnu: Remove duplicated r-psych package. 
It was first added in cdc129dc53, then again in
db80dd4a1d.

* gnu/packages/cran.scm (r-psych): Remove duplicated package definition.
 2018-07-29 17:57:52 +01:00
Christopher Baines d493d59a7f
gnu: Remove duplicated emacs-load-relative. 
It was first added in fa1a17b786, and then again
in f8a88f223e.

* gnu/packages/emacs.scm (emacs-load-relative): Remove duplicated package
definition.
 2018-07-29 17:57:52 +01:00
Christopher Baines 26b8cd1a5a
gnu: Remove duplicated emacs-csv-mode. 
It was first added in 9faa46ee48, and then again
in 8bc8efc753.

* gnu/packages/emacs.scm (emacs-csv-mode): Remove duplicated package
definition.
 2018-07-29 17:57:52 +01:00
Ludovic Courtès 99b78ba498
linux-initrd: Report only missing modules, not all needed modules. 
Previously the warning would list all the required modules rather than
just those that are missing.

* gnu/system/mapped-devices.scm (check-device-initrd-modules): Compute
'missing' and report it.
 2018-07-29 18:50:28 +02:00
Ludovic Courtès fcd068e984
linux-initrd: Try several file names when looking up modules. 
Fixes <https://bugs.gnu.org/31714>.
Reported by Tonton <tonton@riseup.net>.

* gnu/build/linux-modules.scm (find-module-file): New procedure.
* gnu/system/linux-initrd.scm (flat-linux-module-directory)[build-exp]:
Remove 'lookup' procedure and use 'find-module-file' instead.
* gnu/system/mapped-devices.scm (check-device-initrd-modules): Add
comment.
 2018-07-29 18:50:28 +02:00
Ludovic Courtès d2a1cf45f7
linux-initrd: Improve check of initrd modules. 
Previously we would not strip the ".ko" suffix if present.

* gnu/build/linux-modules.scm (file-name->module-name): Export.
* gnu/system/mapped-devices.scm (check-device-initrd-modules): Use
'file-name->module-name' instead of 'normalize-module-name'.
 2018-07-29 18:50:28 +02:00
Eric Brown 5b68239072
services: openssh: Add forwarding options. 
* gnu/services/ssh.scm (<openssh-configuration>)[allow-agent-forwarding?]
[allow-tcp-forwarding?, gateway-ports?]: New fields.
(openssh-config-file): Handle them.
* doc/guix.texi (Networking Services): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-07-29 18:50:28 +02:00
Ludovic Courtès b90d97ec2e
ssh: Display the size of the store items being sent. 
* guix/ssh.scm (send-files): Compute the size of MISSING and display
it.
 2018-07-29 18:50:28 +02:00
Ben Woodcroft 3f8c82e6d3
gnu: taxtastic: Add missing propagated-inputs. 
* gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add
python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2,
python-dendropy.
 2018-07-29 22:53:10 +10:00
Ben Woodcroft 9e0c135c39
gnu: python-dendropy: Update to 4.4.0. 
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy):
Update to 4.4.0.
[source]: Use GitHub URI. Remove patch.
[properties]: Remove field.
(python2-dendropy)[arguments]: Run tests with setup.py.
[native-inputs]: Remove 'python2-nose.
* gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Delete it.
 2018-07-29 22:53:10 +10:00
Ben Woodcroft 19601e895b
gnu: python2-psycopg2: Update to 2.7.5. 
* gnu/packages/bioinformatics.scm (python2-psycopg2): Update to 2.7.5.
 2018-07-29 22:53:10 +10:00
Ben Woodcroft 5d5a02dd4c
gnu: Add python-fastalite. 
* gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite):
New variables.
 2018-07-29 21:58:00 +10:00
Christopher Lemmer Webber 10d5315361
gnu: Add chroma. 
* gnu/packages/games.scm (chroma): New variable.
 2018-07-29 09:37:20 +02:00
Mark H Weaver f8e2df9851
gnu: linux-libre: Update to 4.17.11. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.11.
(%linux-libre-hash): Update hash.
 2018-07-29 03:32:03 -04:00
Mark H Weaver c85a76cc00
gnu: linux-libre@4.14: Update to 4.14.59. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.59.
(%linux-libre-4.14-hash): Update hash.
 2018-07-29 03:31:10 -04:00
Mark H Weaver 8b30bc82dc
gnu: linux-libre@4.9: Update to 4.9.116. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.116.
 2018-07-29 03:30:32 -04:00
Mark H Weaver 4262a491ce
gnu: linux-libre@4.4: Update to 4.4.145. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.145.
 2018-07-29 03:29:42 -04:00
Gábor Boskovits 6219685922
gnu: clojure: Fix index generation. 
* gnu/packages/java.scm (clojure)[arguments]: Add phase 'fix-manifest-classpath to remove
offending directory entry making indexing fail.
 2018-07-29 08:41:34 +02:00
Marius Bakke 48d7ac175f
gnu: openlibm: Update to 0.6.0. 
* gnu/packages/maths.scm (openlibm): Update to 0.6.0.
 2018-07-28 18:12:13 +02:00
Marius Bakke 46bda5eb7a
gnu: glm: Update home page. 
* gnu/packages/maths.scm (glm)[home-page]: Use HTTPS.
 2018-07-28 17:56:59 +02:00
Marius Bakke 5ea4b5943d
gnu: glm: Update to 0.9.9.0. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.0.
[source](uri): Change to new download location.
 2018-07-28 17:55:04 +02:00
Marius Bakke 71de61c353
gnu: libjpeg-turbo: Update license. 
* gnu/packages/image.scm (libjpeg-turbo)[license]: Add ZLIB.
 2018-07-28 17:27:16 +02:00
Marius Bakke 6871121be0
gnu: libjpeg-turbo: Update to 2.0.0. 
* gnu/packages/image.scm (libjpeg-turbo): Update to 2.0.0.
[build-system]: Change to CMAKE-BUILD-SYSTEM.
[arguments]: Adjust accordingly.
 2018-07-28 17:27:16 +02:00
Marius Bakke 0981ec1300
gnu: accountsservice: Update to 0.6.50. 
* gnu/packages/freedesktop.scm (accountsservice): Update to 0.6.50.
[arguments]: Add "--enable-elogind" and "--disable-systemd" to #:configure-flags.
[inputs]: Add ELOGIND.
 2018-07-28 17:27:15 +02:00
Marius Bakke 35fa923d8b
gnu: dconf: Update to 0.28.0. 
* gnu/packages/gnome.scm (dconf): Update to 0.28.0.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[arguments]: Adjust accordingly.
[native-inputs]: Add VALA and GLIB:BIN.
 2018-07-28 17:27:15 +02:00
Marius Bakke e20e6b4061
gnu: dconf: Update license. 
* gnu/packages/gnome.scm (dconf)[license]: Change from LGPL2.1 to LGPL2.1+.
 2018-07-28 17:27:15 +02:00
Marius Bakke 03676d6f35
gnu: dconf: Install GTK documentation. 
* gnu/packages/gnome.scm (dconf)[native-inputs]: Add GTK-DOC.
[arguments]: Adjust #:configure-flags accordingly.
 2018-07-28 17:27:15 +02:00
Marius Bakke bc036f4c99
gnu: dconf: Adjust inputs and remove obsolete workaround. 
* gnu/packages/gnome.scm (dconf)[inputs]: Remove GLIB and LIBXML2.
[propagated-inputs]: Add GLIB.
[native-inputs]: Add LIBXML2.  Remove INTLTOOL.
[arguments]: Remove #:phases.
 2018-07-28 17:27:15 +02:00
Ludovic Courtès c95c9032b4
gnu: x265: Fix compilation on ARMv7. 
* gnu/packages/patches/x265-arm-asm-primitives.patch: New file.
* gnu/packages/video.scm (x265)[sources](patches): Add it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-07-28 15:08:07 +02:00
Ludovic Courtès 5193ae64ca
gnu: mariadb: Work around GCC ICE on armhf-linux. 
* gnu/packages/patches/mariadb-gcc-ice.patch: New file.
* gnu/packages/databases.scm (mariadb)[arguments]: Conditionally add
'apply-patch' phase.
[native-inputs]: Conditionally add "gcc-ice-patch" input.
 2018-07-28 15:08:07 +02:00
Chris Marusich 346a632144
doc: Clarify some of guix-daemon's GC options. 
Reported by Pierre Neidhardt <ambrevar@gmail.com>.

* doc/guix.texi (Invoking guix-daemon): Fix an incorrect statement
regarding --gc-keep-outputs.  Add a little to the description of this
option and --gc-keep-derivations.
 2018-07-28 03:00:16 -07:00
Kei Kebreau b15a020dd5
gnu: allegro: Update to 5.2.4.0. 
* gnu/packages/game-development.scm (allegro): Update to 5.2.4.0.
[source]: Update URL.
 2018-07-27 14:30:49 -04:00
Ludovic Courtès 74a4fa5040
gnu: gcc@8: Update to 8.2.0. 
* gnu/packages/gcc.scm (gcc-8): Update to 8.2.0.
 2018-07-27 18:52:58 +02:00
Ludovic Courtès f00d66b12c
gnu: Add font-blackfoundry-inria. 
* gnu/packages/fonts.scm (font-blackfoundry-inria): New file.
 2018-07-27 18:00:06 +02:00
Ludovic Courtès 223779c4c5
gnu: emacs-flycheck: Don't rely on pkg-info.el for 'flycheck-version'. 
* gnu/packages/emacs.scm (flycheck)[source]: Add 'modules' and
'snippet'.
 2018-07-27 18:00:06 +02:00
Ricardo Wurmus 26fd7b24ec
gnu: pigx-scrnaseq: Disable another expensive test. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
 2018-07-27 15:44:23 +02:00
Ricardo Wurmus ed2dfe3955
gnu: Add snakemake-4. 
* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
 2018-07-27 15:30:38 +02:00
Ricardo Wurmus 269f100330
gnu: snakemake: Add missing dependencies. 
* gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-datrie,
python-docutils, python-jinja2, python-jsonschema, and python-networkx.
 2018-07-27 15:30:38 +02:00
Ricardo Wurmus 216a72a957
gnu: Add python-datrie. 
* gnu/packages/python.scm (python-datrie): New variable.
 2018-07-27 15:30:38 +02:00
Marius Bakke beb8511c73
gnu: imagemagick: Update to 6.9.10-8. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-8.
 2018-07-27 14:43:43 +02:00
Marius Bakke 2fcbc572f9
gnu: mbedtls-apache: Update to 2.7.5. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.5.
 2018-07-27 14:43:43 +02:00
Ricardo Wurmus b62715aa82
gnu: snakemake: Update to 5.2.0. 
* gnu/packages/python.scm (snakemake): Update to 5.2.0.
 2018-07-27 14:19:43 +02:00
Ricardo Wurmus 22305f859b
gnu: guile-sdl2: Update to 0.3.0. 
* gnu/packages/sdl.scm (guile-sdl2): Update to 0.3.0.
[arguments]: Remove "patch-makefile" phase.
 2018-07-27 14:19:33 +02:00
Danny Milosavljevic d804d0b9ef
import: hackage: Emit native-inputs in the importer. 
* guix/import/cabal.scm (cabal-custom-setup-dependencies): Export.
(cabal-package-custom-setup): Export.
(<cabal-package>): New field "custom-setup".
(make-cabal-package): Modify.
(eval-cabal): Modify.
* guix/import/hackage.scm (cabal-dependencies->names): Factor out...
(cabal-test-dependencies->names): ...this.
(cabal-custom-setup-dependencies->names): New procedure.
(hackage-module->sexp): Modify.
 2018-07-27 11:42:53 +02:00
Kei Kebreau 9dafb64711
gnu: tiled: Update to 1.1.6. 
* gnu/packages/game-development.scm (tiled): Update to 1.1.6.
[arguments]: Substitute invoke for system*.
 2018-07-27 00:17:06 -04:00
Kei Kebreau 6e92fba4b0
gnu: python-xsge: Update to 2018.02.26. 
* gnu/packages/game-development.scm (python-xsge, python2-xsge): Update to
2018.02.26.
[arguments]: Substitute invoke for system*.
 2018-07-26 23:35:45 -04:00
Kei Kebreau d36b98ad95
gnu: freeciv: Update to 2.6.0. 
* gnu/packages/games.scm (freeciv): Update to 2.6.0.
 2018-07-26 14:43:10 -04:00
Brendan Tildesley e8ec2dda08
gnu: ecryptfs-utils: Patch more hardcoded paths. 
* gnu/packages/linux.scm (ecryptfs-utils): [arguments]: Add an additional file
to be patched that was missing in the last fix. Ecryptfs will now find the
umount binary path as well as mount and others. Re-sort the list of files to be
substituted.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-07-26 13:19:57 -04:00