Commit Graph

19550 Commits

Author SHA1 Message Date
Ricardo Wurmus 60c9190e21
gnu: r-minimal: Fix remaining reproducibility problems.
Fixes <https://bugs.gnu.org/25598>.

* gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining
reproducibility fixes to "build-reproducibly" phase.
2017-03-17 10:14:02 +01:00
Ricardo Wurmus 2d7c4ae3ee
gnu: r: Rename to r-minimal.
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
2017-03-17 10:14:02 +01:00
Ricardo Wurmus f1fe5283c9
gnu: Add r-with-recommended-packages.
* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
2017-03-17 10:14:02 +01:00
Ricardo Wurmus aeb64f3cb2
gnu: r: Do not build recommended packages.
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
2017-03-17 10:14:02 +01:00
Ricardo Wurmus 6eaa9bfba6
gnu: r-survival: Move to set of recommended R packages.
* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
packages.
2017-03-17 10:14:02 +01:00
Ricardo Wurmus 4b005c7a75
gnu: Add r-spatial.
* gnu/packages/statistics.scm (r-spatial): New variable.
2017-03-17 10:14:01 +01:00
Ricardo Wurmus 567b154fb0
gnu: r-rpart: Move to the set of recommended packages.
* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.
2017-03-17 10:14:01 +01:00
Ricardo Wurmus a5a343656b
gnu: r-nnet: Move to set of recommended R packages.
* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.
2017-03-17 10:14:01 +01:00
Ricardo Wurmus 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
Ricardo Wurmus 248f65269a
gnu: Add r-nlme.
* gnu/packages/statistics.scm (r-nlme): New variable.
2017-03-17 10:14:01 +01:00
Ricardo Wurmus 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
Ricardo Wurmus 060c12868b
gnu: r-lattice: Move to other recommended R packages.
* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
2017-03-17 10:14:01 +01:00
Ricardo Wurmus e88bad6ddb
gnu: Add r-kernsmooth.
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus 69fddd2d6e
gnu: Add r-foreign.
* gnu/packages/statistics.scm (r-foreign): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus c1999c5910
gnu: Add r-codetools.
* gnu/packages/statistics.scm (r-codetools): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus a27bfb8484
gnu: Add r-cluster.
* gnu/packages/statistics.scm (r-cluster): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus 7489258751
gnu: Add r-class.
* gnu/packages/statistics.scm (r-class): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus c7e80a7e0d
gnu: Add r-mass.
* gnu/packages/statistics.scm (r-mass): New variable.
2017-03-17 10:14:00 +01:00
Ricardo Wurmus 8f0069170c
gnu: Add r-boot.
* gnu/packages/statistics.scm (r-boot): New variable.
2017-03-17 10:14:00 +01:00
Ludovic Courtès 708b54a992
doc: Really document 'guix pack --format'.
* doc/guix.texi (Invoking guix pack): Properly document --format.
2017-03-17 09:46:13 +01:00
Tobias Geerinckx-Rice 54d556bdd7
gnu: youtube-dl: Update to 2017.03.16.
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
2017-03-17 03:11:35 +01:00
Kei Kebreau 3078821d13
gnu: asciidoc: Use local docbook-xml package.
* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
2017-03-16 21:35:50 -04:00
Tobias Geerinckx-Rice f9cdf1c15b
gnu: Add knot.
* gnu/packages/dns.scm (knot): New variable.
2017-03-17 02:32:01 +01:00
Tobias Geerinckx-Rice 754667f0eb
gnu: Add liburcu.
* gnu/packages/datastructures.scm (liburcu): New variable.
2017-03-17 02:32:00 +01:00
Tobias Geerinckx-Rice 366efcb2fb
gnu: dns: Fix typo and use @dfn in descriptions.
* 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
Leo Famulari 2ec5ba859f
gnu: linux-libre: Update to 4.10.3.
* 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
Leo Famulari 2044306f05
gnu: linux-libre@4.4: Update to 4.4.54.
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
2017-03-16 19:40:39 -04:00
Leo Famulari bcc5b74173
gnu: linux-libre@4.9: Update to 4.9.15.
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
2017-03-16 19:40:39 -04:00
Leo Famulari 49ac6dbb0a
gnu: qemu: Fix CVE-2017-{2620,2630}.
* 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
Leo Famulari 1e5b8beeff
gnu: virglrenderer: Fix CVE-2017-6386.
* 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
Ludovic Courtès ad172c4a76
doc: Reorganize categories.
* doc/guix.texi: Move "guix build" to the "Software Development"
category; add "guix pack".
2017-03-16 23:03:40 +01:00
Ludovic Courtès 107b8da622
doc: Mention 'guix pack' reproducibility.
* doc/guix.texi (Invoking guix pack): Mention reproducibility.
2017-03-16 22:59:33 +01:00
Leo Famulari 38c4ca4141
gnu: mesa: Fix typo.
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.

* gnu/packages/gl.scm (mesa)[arguments]: Fix typo in #:configure-flags.
2017-03-16 17:51:56 -04:00
Ludovic Courtès 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
Ludovic Courtès 9e84ea3673
pack: Honor symlinks in the Docker back-end.
* 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
Ludovic Courtès 54241dc8e6
docker: Build images in a reproducible fashion.
* 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
Ludovic Courtès 84dda5a9c0
pack: Use a fixed timestamp in Docker images.
* 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
Ludovic Courtès b1edfbc37f
pack: Add '--format' option and Docker output support.
* 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 1545a012cb,
01445711db, and
03476a23ff.
* doc/guix.texi (Invoking guix pack): Document '--format'.
(Invoking guix archive): Remove documentation of '--format'.
2017-03-16 22:50:15 +01:00
Ludovic Courtès 2971f39c33
pack: Honor command-line options related to the store.
* guix/scripts/pack.scm (guix-pack): Call
'set-build-options-from-command-line'.
2017-03-16 22:50:15 +01:00
Ludovic Courtès 146db52a18
memoization: Micro-optimize code produced by 'define-cache-procedure'.
* 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
Mathieu Othacehe 34d60c49cb
services: connman: Rework service.
* 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
Ludovic Courtès d938a58bee
gexp: Add '=>' syntax to import computed modules.
* 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
Ludovic Courtès 4c0c4db070
utils: Move base16 procedures to (guix base16).
* 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
Clément Lassieur 2c715a9223
gnu: password-store: Fix compatibility with GnuPG 2.1.19.
* 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
Raoul Jean Pierre Bonnal 2441c28414
gnu: Add r-seurat.
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16 14:54:58 +01:00
Ricardo Wurmus 79849358f8
gnu: sra-tools: Update to 2.8.2-1.
* 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
Ricardo Wurmus d5e1716239
gnu: ncbi-vdb: Install configuration files.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
2017-03-16 13:39:53 +01:00
Ricardo Wurmus 558e23074e
gnu: ncbi-vdb: Override search path for java-ngs.
* 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
Efraim Flashner 4cacd87e4d
Merge remote-tracking branch 'origin/master' into core-updates 2017-03-16 13:11:28 +02:00
Ricardo Wurmus 701111989e
gnu: ncbi-vdb: Use modify-phases syntax.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
2017-03-16 10:20:56 +01:00