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38087 Commits

Author SHA1 Message Date
Christopher Baines fe5969656a
gnu: mongo-tools: Fix build. 
I guess this broke when upgrading go. I did try upgrading to the later patch
and minor releases, but they had similar problems, so lets upgrade separately.

* gnu/packages/databases.scm (mongo-tools)[arguments]: Add patch-source phase.
 2018-12-04 20:27:04 +00:00
Marius Bakke b4c684cdf3
gnu: mbedtls-apache: Update to 2.14.1 [fixes CVE-2018-19608]. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.14.1.
 2018-12-04 21:13:31 +01:00
Marius Bakke 17074cae32
gnu: samba.scm: Sort module imports. 
* gnu/packages/samba.scm (gnu): Sort imports.
 2018-12-04 21:13:31 +01:00
Marius Bakke bdf161251a
gnu: ldb: Update to 1.4.3. 
* gnu/packages/samba.scm (ldb): Update to 1.4.3.
[inputs]: Add LMDB.
 2018-12-04 21:13:31 +01:00
Marius Bakke 44eff75ea3
gnu: samba: Update to 4.9.3. 
* gnu/packages/samba.scm (samba): Update to 4.9.3.
[inputs]: Add GPGME, JANSSON, LIBARCHIVE and LMDB.
 2018-12-04 21:13:31 +01:00
Marius Bakke 69d30ba280
gnu: re2: Update to 2018-12-01. 
* gnu/packages/regex.scm (re2): Update to 2018-12-01.
 2018-12-04 21:13:31 +01:00
Marius Bakke 56302fc1ec
gnu: re2: Download sources from git. 
* gnu/packages/regex.scm (re2)[source]: Change to GIT-FETCH.
 2018-12-04 21:13:31 +01:00
Marius Bakke db2db1296b
gnu: python-django: Update to 1.11.17. 
* gnu/packages/django.scm (python-django): Update to 1.11.17.
 2018-12-04 21:13:31 +01:00
Christopher Baines 69a64ecd66
gnu: go-gopkg.in-tomb.v2: Fix build. 
Looks like this test isn't compiling with newer versions of go, so fix it to
get the package building again.

* gnu/packages/golang.scm (go-gopkg.in-tomb.v2)[arguments]: Add new
patch-source phase.
 2018-12-04 19:53:04 +00:00
Ludovic Courtès 040ae18819
tests: Increase root partitions size to 1.2G. 
The system closure has grown slightly above 1GiB so adjust accordingly.

* gnu/tests/install.scm (%simple-installation-script): Increase vdb2 size of
1.2G,
(%extlinux-gpt-installation-script); ditto
(%simple-installation-script-for-/dev/vda): ditto,
(%separate-store-installation-script): ditto for vdb3,
(%encrypted-root-installation-script): ditto.
 2018-12-04 20:30:50 +01:00
Arun Isaac 30a1f6e214
gnu: Add apertium. 
* gnu/packages/dictionaries.scm (apertium): New variable.
 2018-12-04 23:08:45 +05:30
Arun Isaac d2e1d02253
gnu: Add lttoolbox. 
* gnu/packages/dictionaries.scm (lttoolbox): New variable.
 2018-12-04 23:08:45 +05:30
Arun Isaac 5790d163a4
gnu: dictionaries: Use license prefix. 
* gnu/packages/dictionaries.scm: Import (guix licenses) with license:
prefix. Fix all license fields.
 2018-12-04 23:08:33 +05:30
Ricardo Wurmus 42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
 2018-12-04 16:21:50 +01:00
Ludovic Courtès 606b1a1e6b
doc: Update substitute server. 
Fixes an accidental revert in commit
0a5fa004f7.

* doc/guix.texi (SUBSTITUTE-SERVER): Really change to ci.guix.info.
 2018-12-04 15:28:07 +01:00
Andreas Enge 4ebfe99a3f
gnu: pari-gp: Update to 2.11.1. 
* gnu/packages/algebra.scm (pari-gp): Update to 2.11.1.
 2018-12-04 13:38:16 +01:00
Tim Gesthuizen f5a15a86b0
gnu: emacs-irony-mode: Fetch source using git. 
* gnu/packages/emacs.scm (emacs-irony-mode)[source]: Rewrite in terms of GIT-FETCH.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-12-04 11:14:21 +01:00
Timo Eisenmann 3a1835128d
gnu: enlightenment: Use absolute path to 'edje_cc'. 
* gnu/packages/enlightenment.scm (enlightenment)[arguments]: In
'set-system-actions', set absolute file name to 'edje_cc'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-12-04 11:06:00 +01:00
Paul Garlick dd6cb4a0af
gnu: fenics: Skip extra demo in 'check' phase. 
* gnu/packages/simulation.scm (fenics)[arguments]: Add 'curl-curl'
demo to list of demos that require meshes supplied by git-lfs.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-12-04 10:58:56 +01:00
Paul Garlick af5236739e
gnu: petsc-openmpi: Configure with support for HYPRE preconditioner. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hypre-openmpi.
[arguments]: Add 'with-hypre=1' flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-12-04 10:58:50 +01:00
Ludovic Courtès 7bc5657f84
grafts: Mark as non substitutable. 
* guix/grafts.scm (graft-derivation/shallow): Pass #:substitutable? to
'build-expression->derivation'.
 2018-12-04 10:57:56 +01:00
Ludovic Courtès 9300e2e893
refresh: '--list-dependents' ignores deprecated packages. 
* guix/scripts/refresh.scm (all-packages): Filter out deprecated packages.
 2018-12-04 10:57:56 +01:00
Ludovic Courtès 0a5fa004f7
build: Default to https://ci.guix.info for substitutes. 
* config-daemon.ac (guix_substitute_urls): Always default to
"https://ci.guix.info".
* doc/guix.texi (SUBSTITUTE-SERVER): Switch to ci.guix.info.
* guix/scripts/build.scm (%default-log-urls): Likewise.
* guix/scripts/substitute.scm (%default-substitute-urls): Likewise.
* guix/store.scm (%default-substitute-urls): Likewise.
 2018-12-04 10:57:56 +01:00
Ludovic Courtès 0bc02becca
Remove most references to hydra.gnu.org. 
* Makefile.am (assert-binaries-available): Don't mention hydra.gnu.org
in comment.
* build-aux/check-available-binaries.scm: Likewise.
* build-aux/check-final-inputs-self-contained.scm: Likewise.
* doc/guix.texi (SUBSTITUTE-SERVER): New variable.
Use it throughout instead of "mirror.hydra.gnu.org".
* doc/contributing.texi (Submitting Patches): Likewise.
* gnu/services/base.scm (hydra-key-authorization)
(guix-activation): Remove mentions of "hydra.gnu.org" in comments and
messages.
* gnu/system/install.scm (%installation-services): Likewise.
* guix/scripts/size.scm (guix-size): Likewise.
 2018-12-04 10:57:56 +01:00
Ludovic Courtès 6a837b6062
etc: Add "ci.guix.info.pub" public key file. 
* etc/substitutes/ci.guix.info.pub: New file.
* Makefile.am (dist_pkgdata_DATA): Add it.
* guix/self.scm (miscellaneous-files): Add
"share/guix/ci.guix.info.pub".
 2018-12-04 10:57:56 +01:00
Rutger Helling 1f51f0d975
gnu: dolphin-emu: Update to commit 2c57e70. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 2c57e70.
 2018-12-04 10:03:55 +01:00
Oleg Pykhalov 9325533bd0
services: ddclient: Fix unrecognized keywords. 
This patch fixes warnings about unrecognized keywords in logs.

* gnu/services/dns.scm (serialize-field): Skip some field names.
 2018-12-04 07:16:00 +03:00
Leo Famulari 191c439e79
gnu: Beets: Update to 1.4.7. 
* gnu/packages/music.scm (beets): Update to 1.4.7.
 2018-12-03 18:54:53 -05:00
Leo Famulari ca45e49404
gnu: python-unidecode: Update to 1.0.23. 
* gnu/packages/python.scm (python-unidecode, python2-unidecode): Update to
1.0.23.
 2018-12-03 18:54:50 -05:00
Leo Famulari c05c1910db
gnu: Beets: Fix compatibility with Python 3.7. 
* gnu/packages/patches/beets-python-3.7-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
*  gnu/packages/music.scm (beets)[source]: Use it.
 2018-12-03 17:30:30 -05:00
Ludovic Courtès 91a4863d9d
gnu: Add hnsd. 
Thank you, Handshake!

* gnu/packages/dns.scm (hnsd): New variable.
 2018-12-03 21:57:49 +01:00
Julien Lepiller e08da7e231
nls: Update 'fr' translation. 2018-12-03 21:02:11 +01:00
Marius Bakke 4f03aa23e8
gnu: python-cryptography: Update to 2.4.2. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.4.2.
 2018-12-03 17:44:14 +01:00
Marius Bakke cee3d7136b
gnu: python-statsmodels: Update to 0.9.0. 
* gnu/packages/statistics.scm (python-statsmodels): Update to 0.9.0.
[arguments]: Remove obsolete workaround.
 2018-12-03 17:44:14 +01:00
Marius Bakke 650bc94216
gnu: python-scikit-learn: Update source hash. 
The upstream git tag moved from 6ccb5e44b188059e9b7459ac02ec97e32a9ab7ba to
55bf5d93e5674f13a1134d93a11fd0cd11aabcd1 two days later...

* gnu/packages/machine-learning.scm (python-scikit-learn)[source](sha256):
Update for upstream tag change.
 2018-12-03 17:44:14 +01:00
Marius Bakke 635d29c244
gnu: python-scikit-image: Propagate six and numpy. 
* gnu/packages/python.scm (python-scikit-image)[native-inputs]: Move
PYTHON-NUMPY and PYTHON-SIX ...
[propagated-inputs]: ... here.
 2018-12-03 17:44:14 +01:00
Marius Bakke fcb5409438
gnu: python-scikit-image: Update to 0.14.1. 
Also add explicit Python2 variants for its dependency closure.

* gnu/packages/python.scm (python-scikit-image): Update to 0.14.1.
[source](uri): Use PYPI-URI.
[propagated-inputs]: Add PYTHON-CLOUDPICKLE, PYTHON-DASK, PYTHON-MATPLOTLIB
and PYTHON-PYWAVELETS.
(python2-toolz, python2-cloudpickle, python2-locket, python2-blosc,
python2-partd, python2-dask): New public variables.
 2018-12-03 17:44:14 +01:00
Marius Bakke 947ee67d4b
gnu: python-dask: Update to 1.0.0. 
* gnu/packages/python.scm (python-dask): Update to 1.0.0.
[arguments]: Disable one test for Python2, and override 'check' phase.
 2018-12-03 17:44:14 +01:00
Marius Bakke 03bfbe2f10
gnu: python-cloudpickle: Update to 0.6.1. 
* gnu/packages/python.scm (python-cloudpickle): Update to 0.6.1.
 2018-12-03 17:44:14 +01:00
Marius Bakke 36c90dda38
gnu: Add python-pywavelets. 
* gnu/packages/python.scm (python-pywavelets, python2-pywavelets): New public
variables.
 2018-12-03 17:44:14 +01:00
Marius Bakke 8aaec042d4
gnu: kicad: Fix build with Boost >= 1.68. 
* gnu/packages/engineering.scm (kicad)[arguments]: Add phase 'adjust-boost-include'.
 2018-12-03 17:44:13 +01:00
Marius Bakke aefcdea199
gnu: python-greenlet: Update to 0.4.15. 
* gnu/packages/python.scm (python-greenlet): Update to 0.4.15.
 2018-12-03 17:44:13 +01:00
Marius Bakke 0e02e81936
gnu: python-geventhttpclient: Fix test failure. 
* gnu/packages/python-web.scm (python-geventhttpclient)[arguments]: Add
"--import-mode=append" to pytest invokation.
 2018-12-03 17:44:13 +01:00
Eric Bavier a8fdca11d8
doc: Remove footnotes about guile-json requirements. 
Follow-up to 6efccabe4e.

* doc/guix.texi (Invoking guix import)[pypi, gem, cpan, json]: Remove
footnotes mentioning requirement for Guile-JSON.
 2018-12-03 08:56:06 -06:00
Laura Lazzati b9914c4794
doc: Fix "desktop" OS config example. 
* gnu/system/examples/desktop.tmpl (file-systems): Add
'file-system-label' call in 'device' field.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-12-03 14:27:24 +01:00
Björn Höfling b8ca5b3146
hg-fetch: Remove .hg directories of sub-repositories. 
* guix/build/hg.scm (hg-fetch): Remove all .hg directories recursively.
 2018-12-03 12:29:08 +01:00
Pierre Neidhardt a03894416e
gnu: emacs-helm-company: Update to 0.2.3. 
* gnu/packages/emacs.scm (emacs-helm-company): Update to 0.2.3.
 2018-12-03 11:21:06 +01:00
Ludovic Courtès 194451347d
Merge branch 'core-updates' 2018-12-03 08:52:17 +01:00
Oleg Pykhalov 37c6f11f8d
repl: Load user's initialization file. 
* guix/scripts/repl.scm (guix-repl): Load user's initialization file.
 2018-12-03 08:04:51 +03:00
Eric Bavier 6efccabe4e
guile-json: Download source from savannah. 
* gnu/packages/guile.scm (guile-json)[source]: Download tarball from
savannah.  Remove 'file-name' field.
[native-inputs]: Remove autoconf and automake; tarball is bootstrapped.
 2018-12-02 17:56:05 -06:00