ac8d738b97
gnu: r-mgcv: Move to set of recommended R packages.
...
* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.
2017-03-17 10:14:01 +01:00
248f65269a
gnu: Add r-nlme.
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* gnu/packages/statistics.scm (r-nlme): New variable.
2017-03-17 10:14:01 +01:00
69e14f9ec7
gnu: r-matrix: Move to set of recommended R packages.
...
* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.
2017-03-17 10:14:01 +01:00
060c12868b
gnu: r-lattice: Move to other recommended R packages.
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* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
2017-03-17 10:14:01 +01:00
e88bad6ddb
gnu: Add r-kernsmooth.
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* gnu/packages/statistics.scm (r-kernsmooth): New variable.
2017-03-17 10:14:00 +01:00
69fddd2d6e
gnu: Add r-foreign.
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* gnu/packages/statistics.scm (r-foreign): New variable.
2017-03-17 10:14:00 +01:00
c1999c5910
gnu: Add r-codetools.
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* gnu/packages/statistics.scm (r-codetools): New variable.
2017-03-17 10:14:00 +01:00
a27bfb8484
gnu: Add r-cluster.
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* gnu/packages/statistics.scm (r-cluster): New variable.
2017-03-17 10:14:00 +01:00
7489258751
gnu: Add r-class.
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* gnu/packages/statistics.scm (r-class): New variable.
2017-03-17 10:14:00 +01:00
c7e80a7e0d
gnu: Add r-mass.
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* gnu/packages/statistics.scm (r-mass): New variable.
2017-03-17 10:14:00 +01:00
8f0069170c
gnu: Add r-boot.
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* gnu/packages/statistics.scm (r-boot): New variable.
2017-03-17 10:14:00 +01:00
708b54a992
doc: Really document 'guix pack --format'.
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* doc/guix.texi (Invoking guix pack): Properly document --format.
2017-03-17 09:46:13 +01:00
54d556bdd7
gnu: youtube-dl: Update to 2017.03.16.
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* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
2017-03-17 03:11:35 +01:00
3078821d13
gnu: asciidoc: Use local docbook-xml package.
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* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
2017-03-16 21:35:50 -04:00
f9cdf1c15b
gnu: Add knot.
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* gnu/packages/dns.scm (knot): New variable.
2017-03-17 02:32:01 +01:00
754667f0eb
gnu: Add liburcu.
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* gnu/packages/datastructures.scm (liburcu): New variable.
2017-03-17 02:32:00 +01:00
366efcb2fb
gnu: dns: Fix typo and use @dfn in descriptions.
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* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms.
(yadifa)[description]: Likewise, and fix a typo.
2017-03-17 02:32:00 +01:00
2ec5ba859f
gnu: linux-libre: Update to 4.10.3.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3.
(%linux-libre-hash): Update hash.
2017-03-16 19:40:40 -04:00
2044306f05
gnu: linux-libre@4.4: Update to 4.4.54.
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* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
2017-03-16 19:40:39 -04:00
bcc5b74173
gnu: linux-libre@4.9: Update to 4.9.15.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
2017-03-16 19:40:39 -04:00
49ac6dbb0a
gnu: qemu: Fix CVE-2017-{2620,2630}.
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* gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Use them.
2017-03-16 19:40:08 -04:00
1e5b8beeff
gnu: virglrenderer: Fix CVE-2017-6386.
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* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/spice.scm (virglrenderer)[source]: Use it.
2017-03-16 19:39:55 -04:00
ad172c4a76
doc: Reorganize categories.
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* doc/guix.texi: Move "guix build" to the "Software Development"
category; add "guix pack".
2017-03-16 23:03:40 +01:00
107b8da622
doc: Mention 'guix pack' reproducibility.
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* doc/guix.texi (Invoking guix pack): Mention reproducibility.
2017-03-16 22:59:33 +01:00
38c4ca4141
gnu: mesa: Fix typo.
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The typo caused the configure phase to fail like this:
"configure: error: classic DRI driver '915' does not exist"
This is a followup to commit c5e91014a2
2017-03-16 17:51:56 -04:00
db3f2b61ad
pack: Allow for "-S /opt/foo=".
...
Reported by Andy Wingo.
* guix/scripts/pack.scm (%options): Use 'string-split' instead of
'string-tokenize'.
2017-03-16 22:50:15 +01:00
9e84ea3673
pack: Honor symlinks in the Docker back-end.
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* guix/docker.scm (symlink-source, topmost-component): New procedures.
(build-docker-image): Add #:symlinks parameter and honor it. Remove
hard-coded /bin symlink.
* guix/scripts/pack.scm (docker-image): Pass #:symlinks to
'build-docker-image'.
2017-03-16 22:50:15 +01:00
54241dc8e6
docker: Build images in a reproducible fashion.
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* guix/docker.scm (%tar-determinism-options): New variable.
(build-docker-image): Use it on the two 'tar' invocations.
2017-03-16 22:50:15 +01:00
84dda5a9c0
pack: Use a fixed timestamp in Docker images.
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* guix/docker.scm (build-docker-image): Add #:creation-time parameter.
Use SRFI-19 'date->string' instead of 'strftime' et al.
* guix/scripts/pack.scm (docker-image)[build]: Pass #:creation-time to
'build-docker-image'.
2017-03-16 22:50:15 +01:00
b1edfbc37f
pack: Add '--format' option and Docker output support.
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* guix/docker.scm: Remove dependency on (guix store) and (guix utils).
Use (guix build store-copy). Load (json) lazily.
(build-docker-image): Remove #:system. Add #:closure, #:compressor, and
'image' parameters. Use 'uname' to determine the architecture. Remove
use of 'call-with-temporary-directory'. Use 'read-reference-graph' to
compute ITEMS. Honor #:compressor.
* guix/scripts/pack.scm (docker-image): New procedure.
(%default-options): Add 'format'.
(%formats): New variable.
(%options, show-help): Add '--format'.
(guix-pack): Honor '--format'.
* guix/scripts/archive.scm: Remove '--format' option. This reverts
commits 1545a012cb01445711db03476a23ff
2017-03-16 22:50:15 +01:00
2971f39c33
pack: Honor command-line options related to the store.
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* guix/scripts/pack.scm (guix-pack): Call
'set-build-options-from-command-line'.
2017-03-16 22:50:15 +01:00
146db52a18
memoization: Micro-optimize code produced by 'define-cache-procedure'.
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* guix/memoization.scm (%nothing): Remove.
(define-cache-procedure): Make '%nothing' a local variable, with a
literal list.
2017-03-16 22:50:15 +01:00
34d60c49cb
services: connman: Rework service.
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* gnu/services/networking.scm (connman-service): Remove.
(<connman-configuration>): New record specifying the package
to be used (connman) and whether vpn plugin shall be
disabled (disable-vpn?).
(connman-configuration): New exported variable.
(connman-configuration?): New exported variable.
(connman-service-type): Export it.
* doc/guix.texi (Networking Services): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-03-16 22:50:14 +01:00
d938a58bee
gexp: Add '=>' syntax to import computed modules.
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* guix/gexp.scm (imported-files)[file-pair]: Add case for pairs where
the cdr is not a string.
(imported-modules): Support '=>' syntax in MODULES.
* tests/gexp.scm ("imported-files with file-like objects")
("gexp->derivation & with-imported-module & computed module"): New tests.
* doc/guix.texi (G-Expressions): Document '=>' syntax for
'with-imported-modules'.
2017-03-16 22:50:14 +01:00
4c0c4db070
utils: Move base16 procedures to (guix base16).
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* guix/utils.scm (bytevector->base16-string, base16-string->bytevector):
Move to...
* guix/base16.scm: ... here. New file.
* tests/utils.scm ("bytevector->base16-string->bytevector"): Move to...
* tests/base16.scm: ... here. New file.
* Makefile.am (MODULES): Add guix/base16.scm.
(SCM_TESTS): Add tests/base16.scm.
* build-aux/download.scm, guix/derivations.scm,
guix/docker.scm, guix/import/snix.scm, guix/pk-crypto.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/store.scm, tests/hash.scm,
tests/pk-crypto.scm: Adjust imports accordingly.
2017-03-16 22:50:14 +01:00
2c715a9223
gnu: password-store: Fix compatibility with GnuPG 2.1.19.
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* gnu/packages/patches/password-store-gnupg-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/password-utils.scm (password-store)[source]: Use it.
Signed-off-by: Clément Lassieur <clement@lassieur.org>
2017-03-16 19:58:43 +01:00
2441c28414
gnu: Add r-seurat.
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* gnu/packages/bioinformatics.scm (r-seurat): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16 14:54:58 +01:00
79849358f8
gnu: sra-tools: Update to 2.8.2-1.
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* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
2017-03-16 13:40:36 +01:00
d5e1716239
gnu: ncbi-vdb: Install configuration files.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
2017-03-16 13:39:53 +01:00
558e23074e
gnu: ncbi-vdb: Override search path for java-ngs.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
2017-03-16 13:38:39 +01:00
4cacd87e4d
Merge remote-tracking branch 'origin/master' into core-updates
2017-03-16 13:11:28 +02:00
701111989e
gnu: ncbi-vdb: Use modify-phases syntax.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
2017-03-16 10:20:56 +01:00
5021f54787
gnu: ncbi-vdb: Update to 2.8.2.
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* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
2017-03-16 10:19:25 +01:00
6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0.
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* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
2017-03-16 10:18:48 +01:00
56f76b08be
gnu: jack-2: Fix build by patching fast_rand.
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* gnu/packages/audio.scm (jack-2)[arguments]: Add phase "patch-fast_rand" to
apply upstream fixes.
2017-03-16 09:41:20 +01:00
5707ce6e4b
Revert "gnu: bdftopcf: Use libxfont2."
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Building with libxfont2 leads to an error in the configure phase:
"No package 'xfont' found"
This reverts commit 2060b4d95f
2017-03-16 02:06:56 -04:00
0f03c53168
gnu: Add pzstd.
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* gnu/packages/compression.scm (pzstd): New variable.
2017-03-16 05:44:02 +01:00
f6ac3101ff
gnu: Add zstd.
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* gnu/packages/compression.scm (zstd): New variable.
2017-03-16 05:44:02 +01:00
9186216268
gnu: python-publicsuffix2: Update to 2.20160818.
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* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
2017-03-16 05:44:02 +01:00
192b887a03
gnu: awscli: Update to 1.11.63.
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* gnu/packages/python.scm (awscli): Update to 1.11.63.
2017-03-16 05:44:01 +01:00
Ricardo Wurmus