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27315 Commits (5909bdc88735c2c1bd9f44eb6a1b518785144292)

Author SHA1 Message Date
Ricardo Wurmus 420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 6fd71f1b6a
gnu: r-biobase: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e51afc63b7
gnu: r-genomicranges: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus c2401d06c5
gnu: r-xvector: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 0a465e5694
gnu: r-limma: Update to 3.36.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d358a5a0c1
gnu: r-variantannotation: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 4639025284
gnu: r-edger: Update to 3.22.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 953c8b18f8
gnu: r-genomeinfodb: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 8b44c28f5d
gnu: r-iranges: Update to 2.14.10. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 33cd15fa84
gnu: r-s4vectors: Update to 0.18.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 607acf3194
gnu: r-dnacopy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 3679a2fec4
gnu: r-bioccheck: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus dc6c168ac1
gnu: r-biocstyle: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5f52b692a
gnu: r-biocviews: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 97af51ef40
gnu: r-biocinstaller: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5907a44e1
gnu: r-biocgenerics: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9370b8ee9f
gnu: r-grohmm: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 712fe39680
gnu: r-systempiper: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus eabe78faca
gnu: r-shortread: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9da8e275ca
gnu: r-gostats: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus d8410d6610
gnu: r-category: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus f1094f50a7
gnu: r-gseabase: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9177ac2295
gnu: r-rbgl: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 5516db9e70
gnu: r-annotationforge: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 16da69b5e6
gnu: r-dexseq: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 51c1f96ebc
gnu: r-deseq2: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 41657b15f4
gnu: r-genefilter: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 4d70c8c486
gnu: r-geneplotter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 14e9235f0c
gnu: r-copynumber: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 02be818044
gnu: r-annotate: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 81b0181b6f
gnu: r-qdnaseq: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 5c0df206cf
gnu: r-cghcall: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 205df4a4cb
gnu: r-cghbase: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 6748708883
gnu: r-marray: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0.
[propagated-inputs]: Remove r-biobase.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus f794e85daa
gnu: r-chippeakanno: Update to 3.14.0. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0.
[propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges,
r-iranges, and r-s4vectors.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 43734b4727
gnu: r-ripseeker: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 45bbccf4e7
gnu: r-diffbind: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0.
[propagated-inputs]: Add r-genomicranges, r-ggplot2, and
r-summarizedexperiment.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 72427c721d
gnu: r-regioner: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0.
[propagated-inputs]: Add r-s4vectors.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 2f5b3d8e90
gnu: r-hpar: Update to 1.22.2. 
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus d22546cf80
gnu: r-minimal: Update to 3.5.0. 
* gnu/packages/statistics.scm (r-with-tests): New variable derived from
r-minimal; update to 3.5.0.
[arguments]: Build recommended packages.
(r-minimal): Inherit from r-with-tests.
[arguments]: Disable recommended packages and tests.
 2018-06-02 13:39:06 +02:00
Clément Lassieur d5452aa201
gnu: emacs-elfeed: Update to 3.0.0. 
* gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0.
 2018-06-02 13:05:08 +02:00
Ludovic Courtès a13c1bf4ca
Merge branch 'master' into core-updates 2018-06-01 23:41:40 +02:00
Mark H Weaver 1a3e3162ac
gnu: icecat: Add more fixes from upstream esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from
the upstream mozilla-esr52 repository.
 2018-06-01 12:51:43 -04:00
Ricardo Wurmus 65a9f6b6cf
gnu: qtbase: Fix build on older kernels. 
* gnu/packages/qt.scm (qtbase)[arguments]: Add configure flags
"-no-feature-getentropy" and "-no-feature-renameat2".
 2018-06-01 17:33:25 +02:00
Ludovic Courtès 9f160a0d3c
vm: Use 'with-extensions'. 
* gnu/system/vm.scm (system-docker-image)[build]: Use
'with-extensions'.  Remove 'add-to-load-path' calls.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès 33d8a87104
bootloader: grub: Use 'with-extensions'. 
* gnu/bootloader/grub.scm (svg->png): Use 'with-extensions'.  Remove
'add-to-load-path' calls.
* gnu/build/svg.scm: Use (rsvg) and (cairo) the normal way.  Remove
'module-autoload!' calls.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès 31a5d694a3
bootloader: grub: Simplify 'svg->png'. 
* gnu/bootloader/grub.scm (svg->png): Remove now unneeded
  #:guile-for-build argument.
 2018-06-01 15:21:28 +02:00
Ludovic Courtès ff913cf514
tests: ssh: Use 'with-extensions'. 
* gnu/tests/ssh.scm (run-ssh-test)[test]: Wrap body in
'with-extensions'.  Remove %load-path manipulation code.
 2018-06-01 15:21:28 +02:00
Robin Templeton 514026d7de
gnu: rust: Add support for building 32-bit packages on 64-bit hosts. 
* gnu/packages/rust.scm (rust-bootstrap, rust-1.23): Use
nix-system->gnu-triplet to determine the system type.
(rust-1.19): Use readelf instead of nm in the atomic-lock-free test.
(rust-1.23): Disable the cargo_test_env test. Disable parallel execution of
tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample a078a6ec3b
gnu: Add git-annex. 
* gnu/packages/version-control.scm (git-annex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 4e5d9bf20e
gnu: Add ghc-disk-free-space. 
* gnu/packages/haskell.scm (ghc-disk-free-space): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 1ea3971992
gnu: ghc-psqueues: Allow building with newer versions of QuickCheck. 
* gnu/packages/haskell.scm (ghc-psqueues)[arguments]: Add configure
flag to allow newer versions of QuickCheck.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 6950a45073
gnu: Add ghc-safesemaphore. 
* gnu/packages/haskell.scm (ghc-safesemaphore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:27 +02:00
Timothy Sample 92c2097bc2
gnu: Add ghc-esqueleto. 
* gnu/packages/haskell.scm (ghc-esqueleto): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample a39e6faee9
gnu: Add ghc-ifelse. 
* gnu/packages/haskell.scm (ghc-ifelse): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample e3aae496f9
gnu: Add ghc-feed. 
* gnu/packages/haskell.scm (ghc-feed): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Timothy Sample 4c798726b4
gnu: Add ghc-bloomfilter. 
* gnu/package/haskell.scm (ghc-bloomfilter): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Rouby Pierre-Antoine 93b83eb31e
services: Add hpcguix-web. 
* gnu/service/web.scm (<hpcguix-web-configuration>): New record-type.
  (%hpcguix-web-accounts): New variable.
  (%hpcguix-web-activation,hpcguix-web-shepherd-service,
  hpcguix-web-service-type): New procedures.
* gnu/tests/web.scm (run-hpcguix-web-server-test): New procedure.
  (%hpcguix-web-specs, %hpcguix-web-os, %test-hpcguix-web): New variable.
* doc/guix.texi (Web Services): Add 'hpcguix-web'.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-06-01 13:50:26 +02:00
Rouby Pierre-Antoine d6a4dfec90
gnu: Add hpcguix-web. 
* gnu/package/web.scm (hpcguix-web): New variable.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-06-01 13:50:26 +02:00
Ludovic Courtès 7a4e2eaab3
marionette: Add 'wait-for-tcp-port'. 
* gnu/build/marionette.scm (wait-for-tcp-port): New procedure.
* gnu/tests/dict.scm (run-dicod-test)["connect inside"]: Use it instead
of the inline loop.
 2018-06-01 13:50:26 +02:00
Ludovic Courtès 5ede50b850
gnu: emacs-w3m: Update and allow builds with Emacs 26. 
* gnu/packages/emacs.scm (emacs-w3m)[source]: Grab the source from
github.com.
[native-inputs]: Add TEXINFO.
[arguments]: Add 'support-emacs!' phase.  In 'patch-exec-paths' phase,
make w3m.el and w3m-image.el writable.  Remove substitution for
'w3m-image-viewer', which no longer exists.
 2018-06-01 13:50:26 +02:00
Stefan Stefanović 8674abb1dd
gnu: sddm: Fix CMake build. 
* gnu/packages/display-managers.scm (sddm): Fix CMake build.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/patches/sddm-fix-build-with-qt-5.11-1024.patch: New file.

Signed-off-by: Rutger Helling <rhelling@mykolab.com>
 2018-06-01 12:17:00 +02:00
Leo Famulari e90322d201
gnu: prosody: Update to 0.10.2 [fixes CVE-2018-10847]. 
* gnu/packages/messaging.scm (prosody): Update to 0.10.2.
 2018-05-31 20:31:46 -04:00
Konrad Hinsen 555ab0853b
gnu: Add emacs-zotxt. 
* gnu/packages/emacs.scm (emacs-zotxt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:09 +02:00
Konrad Hinsen 45dca193a4
gnu: Add emacs-org-caldav. 
* gnu/packages/emacs.scm (emacs-org-caldav): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Konrad Hinsen ec8a9892d1
gnu: Add python-bigfloat. 
* gnu/packages/python.scm (python-bigfloat, python2-bigfloat): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Fis Trivial 73d854232f
gnu: bear: Fix python path. 
* gnu/packages/build-tools.scm (bear)
[inputs]: Add python-wrapper.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-31 18:13:08 +02:00
Ludovic Courtès b1059b38b2
system: 'read-boot-parameters' provides a more meaningful warning. 
'system' here was bound to Guile's 'system' procedure.

* gnu/system.scm (read-boot-parameters): Fix argument for fallback
warning.
 2018-05-31 18:13:08 +02:00
Ludovic Courtès 69a05eab35
file-systems: Always wait for devices to show up. 
Previously, 'canonicalize-device-spec' would wait for devices when they
were specified as a label or UUID, but would not wait when the user
passed a "/dev" file name directly.  This could cause problems when
the /dev node takes a while to show up.

* gnu/build/file-systems.scm (canonicalize-device-spec): Add 'resolve'
call in the 'string?' case.
 2018-05-31 18:13:08 +02:00
Ricardo Wurmus 59f87b44da
Merge branch 'master' into core-updates 2018-05-31 13:23:49 +02:00
Ricardo Wurmus 404e5c7d7d
gnu: r-servr: Update to 0.10. 
* gnu/packages/web.scm (r-servr): Update to 0.10.
[native-inputs]: Remove r-rcpp.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus ce8b9e3b1c
gnu: r-seurat: Update to 2.3.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 508dd24abe
gnu: r-shiny: Update to 1.1.0. 
* gnu/packages/web.scm (r-shiny): Update to 1.1.0.
[source]: Fetch from git.
[propagated-inputs]: Add r-crayon.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus eb0d599a67
gnu: r-rjson: Update to 0.2.19. 
* gnu/packages/web.scm (r-rjson): Update to 0.2.19.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 71644c0ee8
gnu: r-htmltable: Update to 1.12. 
* gnu/packages/web.scm (r-htmltable): Update to 1.12.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus beb0878fe5
gnu: r-directlabels: Update to 2018.05.22. 
* gnu/packages/statistics.scm (r-directlabels): Update to 2018.05.22.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 089e037638
gnu: r-ranger: Update to 0.10.0. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.10.0.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 14bb6f5f83
gnu: r-tclust: Update to 1.4-1. 
* gnu/packages/statistics.scm (r-tclust): Update to 1.4-1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9fad62743c
gnu: r-caret: Update to 6.0-80. 
* gnu/packages/statistics.scm (r-caret): Update to 6.0-80.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9bcc68fbf6
gnu: r-quantreg: Update to 5.36. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.36.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 13dc492435
gnu: r-rrcov: Update to 1.4-4. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.4-4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 6f96c2d89e
gnu: r-ggthemes: Update to 3.5.0. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 3.5.0.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 366dd8d7cb
gnu: r-runit: Update to 0.4.32. 
* gnu/packages/statistics.scm (r-runit): Update to 0.4.32.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus edb29f2986
gnu: r-purrr: Update to 0.2.5. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.5.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus e94d827440
gnu: r-tidyr: Update to 0.8.1. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 1957c20e0c
gnu: r-synchronicity: Update to 1.3.4. 
* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 7da0790e2a
gnu: r-rngtools: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-rngtools): Update to 1.3.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3a6051659d
gnu: r-pkgmaker: Update to 0.27. 
* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.27.
[propagated-inputs]: Add r-bibtex, r-magrittr, r-stringi, and r-withr.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus b4ca0076bd
gnu: r-lambda-r: Update to 1.2.3. 
* gnu/packages/statistics.scm (r-lambda-r): Update to 1.2.3.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus a52bb97a79
gnu: r-plotrix: Update to 3.7-2. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-2.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 1ce6be5ee2
gnu: r-data-table: Update to 1.11.4. 
* gnu/packages/statistics.scm (r-data-table): Update to 1.11.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 2d7758c1d6
gnu: r-rlang: Update to 0.2.1. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.2.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 624283a107
gnu: r-knitrbootstrap: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.2.
[propagated-inputs]: Add r-markdown.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 22cdc16fa4
gnu: r-pheatmap: Update to 1.0.10. 
* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.10.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 99b225f3eb
gnu: r-bit: Update to 1.1-14. 
* gnu/packages/statistics.scm (r-bit): Update to 1.1-14.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3c441be0f3
gnu: r-kernlab: Update to 0.9-26. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-26.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus ad016826c9
gnu: r-rmysql: Update to 0.10.15. 
* gnu/packages/databases.scm (r-rmysql): Update to 0.10.15.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus aea3be250c
gnu: r-mice: Update to 3.0.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.0.0.
[propagated-inputs]: Add r-broom, r-dplyr, r-mitml, and r-rlang.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 6034a62a1b
gnu: r-callr: Update to 2.0.4. 
* gnu/packages/cran.scm (r-callr): Update to 2.0.4.
[propagated-inputs]: Add r-processx; remove r-assertthat, r-crayon, r-debugme,
and r-testthat.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus a8b4677b7c
gnu: r-openxlsx: Update to 4.1.0. 
* gnu/packages/cran.scm (r-openxlsx): Update to 4.1.0.
[propagated-inputs]: Add r-zip.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus e86d3cc501
gnu: r-shinyace: Update to 0.3.1. 
* gnu/packages/cran.scm (r-shinyace): Update to 0.3.1.
[propagated-inputs]: Add r-jsonlite.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus a80606308a
gnu: r-processx: Update to 3.1.0. 
* gnu/packages/cran.scm (r-processx): Update to 3.1.0.
[propagated-inputs]: Remove r-debugme; add r-testthat.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9944399ae3
gnu: r-ggally: Update to 1.4.0. 
* gnu/packages/cran.scm (r-ggally): Update to 1.4.0.
[inputs]: Add libressl.
[propagated-inputs]: Add r-rlang.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 13079c143b
gnu: r-psych: Update to 1.8.4. 
* gnu/packages/cran.scm (r-psych): Update to 1.8.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus aadb9ee6df
gnu: r-pillar: Update to 1.2.3. 
* gnu/packages/cran.scm (r-pillar): Update to 1.2.3.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 65ea783f6c
gnu: r-utf8: Update to 1.1.4. 
* gnu/packages/cran.scm (r-utf8): Update to 1.1.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus c36745cf95
gnu: r-ggjoy: Update to 0.4.1. 
* gnu/packages/cran.scm (r-ggjoy): Update to 0.4.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus cda93e8399
gnu: r-dtw: Update to 1.20-1. 
* gnu/packages/cran.scm (r-dtw): Update to 1.20-1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus fabf09934b
gnu: r-ica: Update to 1.0-2. 
* gnu/packages/cran.scm (r-ica): Update to 1.0-2.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 1e31e8bc74
gnu: r-sm: Update to 2.2-5.5. 
* gnu/packages/cran.scm (r-sm): Update to 2.2-5.5.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus da5cca36b7
gnu: r-hardyweinberg: Update to 1.6.1. 
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.1.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 0759d87dfc
gnu: r-ggrepel: Update to 0.8.0. 
* gnu/packages/cran.scm (r-ggrepel): Update to 0.8.0.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus b13b56743b
gnu: r-cvst: Update to 0.2-2. 
* gnu/packages/cran.scm (r-cvst): Update to 0.2-2.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 975ea10d6f
gnu: r-energy: Update to 1.7-4. 
* gnu/packages/cran.scm (r-energy): Update to 1.7-4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 90f1ecb939
gnu: r-emdbook: Update to 1.3.10. 
* gnu/packages/cran.scm (r-emdbook): Update to 1.3.10.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 0acbf8bbb7
gnu: r-inline: Update to 0.3.15. 
* gnu/packages/cran.scm (r-inline): Update to 0.3.15.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 207c497e14
gnu: r-ff: Update to 2.2-14. 
* gnu/packages/cran.scm (r-ff): Update to 2.2-14.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus c81497b141
gnu: r-rcpp: Update to 0.12.17. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.17.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 5479e3e639
gnu: r-abbyyr: Update to 0.5.4. 
* gnu/packages/cran.scm (r-abbyyr): Update to 0.5.4.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 11de8673d1
gnu: Add r-bibtex. 
* gnu/packages/cran.scm (r-bibtex): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 9f56ceecf3
gnu: Add r-reticulate. 
* gnu/packages/cran.scm (r-reticulate): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus d182828f53
gnu: Add r-zip. 
* gnu/packages/cran.scm (r-zip): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 84e7147ae3
gnu: Add r-mitml. 
* gnu/packages/cran.scm (r-mitml): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 03e718fbb1
gnu: Add r-pan. 
* gnu/packages/cran.scm (r-pan): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus fe1495e35c
gnu: Add r-jomo. 
* gnu/packages/cran.scm (r-jomo): New variable.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3ca317359c
gnu: r-vegan: Update to 2.5-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-2.
 2018-05-31 13:21:31 +02:00
Mark H Weaver 966e9575a3
gnu: linux-libre@4.14: Update to 4.14.47. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.47.
(%linux-libre-4.14-hash): Update hash.
(linux-libre-arm-generic-4.14, linux-libre-arm-omap2plus-4.14)
(linux-libre-4.14): Remove patch.
 2018-05-31 04:17:22 -04:00
Mark H Weaver 55b68174aa
gnu: linux-libre@4.9: Update to 4.9.105. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.105.
Remove patch.
 2018-05-31 04:16:05 -04:00
Mark H Weaver 2aab213e36
gnu: linux-libre@4.4: Update to 4.4.135. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.135.
Remove patch.
 2018-05-31 04:14:57 -04:00
Ricardo Wurmus 1e341fa508
gnu: powertabeditor: Fix build with Qt 5.11. 
Fixes <https://bugs.gnu.org/31659>.

* gnu/packages/music.scm (powertabeditor)[arguments]: Add build phase
"add-missing-headers".
 2018-05-31 08:30:45 +02:00
Efraim Flashner d2dde99e99
gnu: mariadb: Update to 10.1.33. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.33.
 2018-05-31 08:45:58 +03:00
Mark H Weaver 0d6f84aab1
Merge branch 'master' into core-updates 2018-05-31 00:27:03 -04:00
Mark H Weaver 88a3465e4a
gnu: linux-libre: Revert bad upstream patch in 4.14/4.9/4.4 kernels. 
Apply the 1-line revert from upstream that was the sole fix in 4.14.47,
4.9.105, and 4.4.135.  Here we cherry-pick the patch until the corresponding
linux-libre versions are released.

* gnu/packages/linux.scm (linux-libre-4.14, linux-libre-4.9)
(linux-libre-arm-generic-4.14, linux-libre-arm-omap2plus-4.14)
(linux-libre-4.4): Add the patch.
 2018-05-31 00:23:41 -04:00
Jonathan Brielmaier 706d6190ca
gnu: 0ad: Update to 0.0.23-alpha. 
* gnu/packages/games.scm (0ad-data, 0ad): Update to 0.0.23-alpha.
[source]: Use HTTPS URL.
[inputs]: Add libsodium.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-31 00:21:47 -04:00
Tobias Geerinckx-Rice e9ae846667
gnu: knot: Update to 2.6.7. 
* gnu/packages/dns.scm (knot): Update to 2.6.7.
 2018-05-31 04:54:58 +02:00
Tobias Geerinckx-Rice 51c4fb007a
gnu: duperemove: Update to 0.11. 
* gnu/packages/disk.scm (duperemove): Update to 0.11.
 2018-05-31 04:54:58 +02:00
Tobias Geerinckx-Rice 42d93a32ee
gnu: sakura: Update to 3.6.0. 
* gnu/packages/terminals.scm (sakura): Update to 3.6.0.
 2018-05-31 04:54:58 +02:00
Tobias Geerinckx-Rice 4ef1d9fd8b
gnu: stunnel: Update to 5.46. 
* gnu/packages/web.scm (stunnel): Update to 5.46.
 2018-05-31 04:54:57 +02:00
Tobias Geerinckx-Rice 6c4d1413f2
gnu: mkvtoolnix: Use INVOKE. 
* gnu/packages/video.scm (mkvtoolnix)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:57 +02:00
Tobias Geerinckx-Rice 8d5960d1b1
gnu: liba52: Use INVOKE. 
* gnu/packages/video.scm (liba52)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:57 +02:00
Tobias Geerinckx-Rice 3103101ec9
gnu: aalib: Use INVOKE. 
* gnu/packages/video.scm (aalib)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:56 +02:00
Tobias Geerinckx-Rice d840f6b98a
gnu: xapian: Use INVOKE. 
* gnu/packages/search.scm (xapian)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:56 +02:00
Tobias Geerinckx-Rice 6c738fe9e7
gnu: khal: Use INVOKE. 
* gnu/packages/calendar.scm (khal)[arguments]: Substitute INVOKE for
SYSTEM* and explicitly return #t from phases where needed.
 2018-05-31 04:54:56 +02:00
Tobias Geerinckx-Rice 4133914416
gnu: rss-bridge: Use INVOKE. 
* gnu/packages/web.scm (rss-bridge)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:55 +02:00
Tobias Geerinckx-Rice a145d7e9af
gnu: python-clf: Use INVOKE. 
* gnu/packages/web.scm (python-clf)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:55 +02:00
Tobias Geerinckx-Rice b8150fa091
gnu: python-internetarchive: Use INVOKE. 
* gnu/packages/web.scm (python-internetarchive)[arguments]: Substitute
INVOKE for SYSTEM*.
 2018-05-31 04:54:54 +02:00
Tobias Geerinckx-Rice 16b5dafc4d
gnu: httptunnel: Use INVOKE. 
* gnu/packages/web.scm (httptunnel)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:54 +02:00
Tobias Geerinckx-Rice 2cdc719193
gnu: surfraw: Use INVOKE. 
* gnu/packages/web.scm (surfraw)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:53 +02:00
Tobias Geerinckx-Rice 9cd760f13f
gnu: gumbo-parser: Use INVOKE. 
* gnu/packages/web.scm (gumbo-parser)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:53 +02:00
Tobias Geerinckx-Rice 7f4e5f19fa
gnu: sassc: Use INVOKE. 
* gnu/packages/web.scm (sassc)[arguments]: Substitute INVOKE for SYSTEM*
and its plumbing.
 2018-05-31 04:54:53 +02:00
Tobias Geerinckx-Rice b5d587055b
gnu: tidy: Use INVOKE. 
* gnu/packages/web.scm (tidy)[arguments]: Substitute INVOKE for SYSTEM*.
 2018-05-31 04:54:52 +02:00
Tobias Geerinckx-Rice 946e5e8aa1
gnu: tipp10: Use INVOKE. 
* gnu/packages/education.scm (tipp10)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:52 +02:00
Tobias Geerinckx-Rice aa0771556e
gnu: krona-tools: Use INVOKE. 
* gnu/packages/web.scm (krona-tools)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:51 +02:00
Tobias Geerinckx-Rice 359375e649
gnu: fcgiwrap: Use INVOKE. 
* gnu/packages/web.scm (fcgiwrap)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:51 +02:00
Tobias Geerinckx-Rice e80c05ac3e
gnu: ffmpeg: Use INVOKE. 
* gnu/packages/video.scm (ffmpeg)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-05-31 04:54:50 +02:00
Tobias Geerinckx-Rice 512f22f9e8
gnu: r-dplyr: Update to 0.7.5. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.5.
[propagated-inputs]: Add r-tidyselect.
 2018-05-31 04:54:50 +02:00
Tobias Geerinckx-Rice fc55fe2ef7
gnu: s6-rc: Update to 0.4.0.1. 
* gnu/packages/skarnet.scm (s6-rc): Update to 0.4.0.1.
 2018-05-31 04:54:50 +02:00
Tobias Geerinckx-Rice 1608969b03
gnu: skalibs: Update to 2.6.4.0. 
* gnu/packages/skarnet.scm (skalibs): Update to 2.6.4.0.
 2018-05-31 04:54:49 +02:00
Tobias Geerinckx-Rice 2c65c085f9
gnu: lchat: Mark up description. 
* gnu/packages/suckless.scm (lchat)[description]: Use @code.
 2018-05-31 04:54:48 +02:00
Tobias Geerinckx-Rice 82f22fac9f
gnu: lchat: Update to 0.0.0-3.f951919. 
* gnu/packages/suckless.scm (lchat): Update to 0.0.0-3.f951919.
[arguments]: Run tests.  Install man page.
 2018-05-31 04:54:48 +02:00
Tobias Geerinckx-Rice aa945bf637
gnu: human: Update to 0.3. 
* gnu/packages/suckless.scm (human): Update to 0.3.
[source]: Use version as the tag, and GIT-FILE-NAME.
 2018-05-31 04:54:48 +02:00
Tobias Geerinckx-Rice 8f7c6a5ff7
gnu: sent: Update to 1. 
* gnu/packages/suckless.scm (sent): Update to 1.
[source]: Switch to URL-FETCH/TARBALL.
 2018-05-31 04:54:47 +02:00
Tobias Geerinckx-Rice fc1a7b58d7
gnu: st: Update to 0.8.1. 
* gnu/packages/suckless.scm (st): Update to 0.8.1.
[arguments]: Relax ‘inhibit-terminfo-install’ regular expression.
 2018-05-31 04:54:47 +02:00
Tobias Geerinckx-Rice 504d16dd04
gnu: spoon: Update to 0.6. 
* gnu/packages/suckless.scm (spoon): Update to 0.6.
 2018-05-31 04:54:46 +02:00
Tobias Geerinckx-Rice a66fb3a14e
gnu: isync: Add zlib compression support. 
This adds ~400 KiB (.5%) to isync's now-73.1 MiB closure.

* gnu/packages/mail.scm (isync)[inputs]: Add ZLIB.
 2018-05-30 23:46:53 +02:00
Efraim Flashner 03d9031962
gnu: mariadb: Update to 10.1.33. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.33.
 2018-05-30 22:46:31 +03:00
Mark H Weaver 370e87fdbb
gnu: linux-libre: Update to 4.16.13. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.16.13.
(%linux-libre-hash): Update hash.
 2018-05-30 14:59:47 -04:00
Mark H Weaver 49e67982eb
gnu: linux-libre@4.14: Update to 4.14.46. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.46.
(%linux-libre-4.14-hash): Update hash.
 2018-05-30 14:58:49 -04:00
Mark H Weaver f9e1c2d72a
gnu: linux-libre@4.9: Update to 4.9.104. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.104.
 2018-05-30 14:58:09 -04:00
Mark H Weaver 13fcbf3cce
gnu: linux-libre@4.4: Update to 4.4.134. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.134.
 2018-05-30 14:57:22 -04:00
Clément Lassieur 6f8f98df7f
gnu: scribus: Fix build against Qt 5.11. 
* gnu/packages/scribus.scm (scribus)[arguments]: Add a 'patch-source' phase
that includes missing headers.
 2018-05-30 20:45:17 +02:00
Ludovic Courtès 9ab0627eee
gnu: glibc-locales: Adjust patch that no longer applied. 
* gnu/packages/patches/glibc-locales.patch: Adjust for glibc 2.27.
 2018-05-30 15:21:27 +02:00
Ricardo Wurmus 80c0f69c50
gnu: emms: Fix build. 
* gnu/packages/emacs.scm (emms)[arguments]: Reset time stamps of files to be
gzipped; let post-install phase return #t.
 2018-05-30 14:54:53 +02:00
Ricardo Wurmus bc73f673e8
gnu: icedtea-7: Build with gcc-4.9. 
* gnu/packages/java.scm (icedtea-7)[native-inputs]: Add gcc-4.9.
 2018-05-30 12:29:14 +02:00
Ricardo Wurmus bcb078a4dc
gnu: icedtea-6: Build with gcc-4.9. 
* gnu/packages/java.scm (icedtea-6)[native-inputs]: Add gcc-4.9 and libnsl.
 2018-05-30 11:06:21 +02:00
Mark H Weaver d0e23e3940
gnu: vlc: Update to 3.0.3, and add more inputs. 
Co-authored-by: Roel Janssen <roel@gnu.org>

* gnu/packages/video.scm (vlc): Update to 3.0.3.
[native-inputs]: Add flex, bison, and gettext-minimal.
[inputs]: Replace ffmpeg-2.8 with the latest ffmpeg.  Replace lua-5.1 with
lua-5.2.  Add eudev, fribidi, libarchive, libass, libavc1394, libbluray,
libcaca, libdca, libdvdnav, libdvdread, libebml, libidn, libmatroska,
libmodplug, libmpeg2, libraw1394, librsvg, libsecret, libupnp, libva,
libvdpau, libvpx, libx264, qtsvg, samba, speexdsp, taglib, twolame, unzip,
wayland, and wayland-protocols.
[arguments]: Add BUILDCC=gcc to configure-flags.  In the 'patch-source' phase,
remove a vestigial substitution fix, enable the use of fribidi deprecated
interfaces, and adjust the file names in substitutions from "gui/qt4" to
"gui/qt".  Move the 'regenerate-plugin-cache' phase after 'strip', and in it,
set the timestamps to 1 second after the epoch, and use 'invoke'.  Add new
'wrap-executable' phase.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2018-05-30 11:02:57 +02:00
Clément Lassieur cfcd9a4551
gnu: wireshark: End phase with #t. 
* gnu/packages/networking.scm (wireshark)[arguments]: End 'patch-source' phase
with #t.
 2018-05-30 11:02:52 +02:00
Tobias Geerinckx-Rice 3fe0d36027
gnu: perl-text-format: Update to 0.61. 
* gnu/packages/perl.scm (perl-text-format): Update to 0.61.
 2018-05-30 10:06:57 +02:00
Tobias Geerinckx-Rice 2847d833be
gnu: python-oslo.utils: Update to 3.36.2. 
* gnu/packages/openstack.scm (python-oslo.utils): Update to 3.36.2.
 2018-05-30 10:06:57 +02:00
Ricardo Wurmus 14e2f61ada
gnu: gtkglext: Fix build. 
* gnu/packages/gnome.scm (gtkglext)[arguments]: Add build phase to fix name
collision.
 2018-05-30 08:57:33 +02:00
Mark H Weaver 341a36b32c
Merge branch 'master' into core-updates 2018-05-30 02:21:29 -04:00
Mark H Weaver a21bcd7079
Revert "gnu: swig: Patch for Octave 4.4." 
This reverts commit 3771000f89.
 2018-05-30 02:18:26 -04:00
Rutger Helling bfc25e015d
gnu: xpra: Update to 2.3.1. 
* gnu/packages/xorg.scm (xpra): Update to 2.3.1.
[inputs]: Add libxi.
 2018-05-30 08:14:23 +02:00
Ricardo Wurmus b3e23b0216
gnu: ibus-libpinyin: Update to 1.10.0. 
* gnu/packages/ibus.scm (ibus-libpinyin): Update to 1.10.0.
[arguments]: Remove "autogen" phase.
[native-inputs]: Remove autoconf, automake, and libtool.
 2018-05-30 07:42:20 +02:00
Ricardo Wurmus 8738c2b342
gnu: libpinyin: Update to 2.2.0. 
* gnu/packages/ibus.scm (libpinyin): Update to 2.2.0.
[arguments]: Remove.
[inputs]: Remove model.
[native-inputs]: Remove autoconf, automake, and libtool.
 2018-05-30 07:42:19 +02:00
Mark H Weaver 7627705293
gnu: vlc: Update to 3.0.3, and add more inputs. 
Co-authored-by: Roel Janssen <roel@gnu.org>

* gnu/packages/video.scm (vlc): Update to 3.0.3.
[native-inputs]: Add flex, bison, and gettext-minimal.
[inputs]: Replace ffmpeg-2.8 with the latest ffmpeg.  Replace lua-5.1 with
lua-5.2.  Add eudev, fribidi, libarchive, libass, libavc1394, libbluray,
libcaca, libdca, libdvdnav, libdvdread, libebml, libidn, libmatroska,
libmodplug, libmpeg2, libraw1394, librsvg, libsecret, libupnp, libva,
libvdpau, libvpx, libx264, qtsvg, samba, speexdsp, taglib, twolame, unzip,
wayland, and wayland-protocols.
[arguments]: Add BUILDCC=gcc to configure-flags.  In the 'patch-source' phase,
remove a vestigial substitution fix, enable the use of fribidi deprecated
interfaces, and adjust the file names in substitutions from "gui/qt4" to
"gui/qt".  Move the 'regenerate-plugin-cache' phase after 'strip', and in it,
set the timestamps to 1 second after the epoch, and use 'invoke'.  Add new
'wrap-executable' phase.
 2018-05-30 00:17:35 -04:00
Mark H Weaver 7cb8d092d5
gnu: linux-libre@4.1: Update to 4.1.52. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.52.
 2018-05-29 23:16:14 -04:00
Mark H Weaver c0d7c1244a
Merge branch 'master' into core-updates 2018-05-29 21:20:47 -04:00
David Thompson f274f0774d
gnu: tiled: Update to 1.1.5. 
* gnu/packages/game-development.scm (tiled): Update to 1.1.5.
 2018-05-29 21:20:27 -04:00
Rouby Pierre-Antoine 9cf879a573
gnu: Add go-github-com-gorilla-context. 
* gnu/packages/golang.scm (go-github-com-gorilla-context): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:08 -04:00
Rouby Pierre-Antoine daed2c5e6a
gnu: Add go-github-com-google-gofuzz. 
* gnu/packages/golang.scm (go-github-com-google-gofuzz): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:08 -04:00
Rouby Pierre-Antoine 73fe19ef28
gnu: Add go-github-com-google-cadvisor. 
* gnu/packages/golang.scm (go-github-com-google-cadvisor): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:08 -04:00
Rouby Pierre-Antoine 7979f7df9a
gnu: Add go-github-com-emicklei-go-restful. 
* gnu/packages/golang.scm (go-github-com-emicklei-go-restful): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:08 -04:00
Rouby Pierre-Antoine 67836c5956
gnu: Add go-github-com-blang-semver. 
* gnu/packages/golang.scm (go-github-com-blang-semver): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:08 -04:00
Rouby Pierre-Antoine 7c2ebbd4a6
gnu: Add go-github-com-urfave-cli. 
* gnu/packages/golang.scm (go-github-com-urfave-cli): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-29 18:39:05 -04:00
Kei Kebreau 5a14e81e41
gnu: Update shogun to 6.1.3. 
* gnu/packages/machine-learning.scm (shogun): Update to 6.1.3.
[source]: Update snippet to remove proprietary software.
[arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase.
Rewrite file lists given to substitute* in 'change-R-target-path' and
'fix-octave-modules' phases.  Adjust 'fix-octave-modules' for the update.
Add 'move-rxcpp' phase.  Rewrite configure-flags for the update.
[inputs]: Add eigen.
[native-inputs]: Add rxcpp.
 2018-05-29 18:20:38 -04:00
Kei Kebreau 3771000f89
gnu: swig: Patch for Octave 4.4. 
* gnu/packages/swig.scm (swig)[source]: Add patch.
* gnu/packages/patches/swig-octave-patches.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2018-05-29 18:20:38 -04:00
Ricardo Wurmus 44884a9df8
gnu: eigen: Include unsupported features. 
* gnu/packages/algebra.scm (eigen)[source]: Do not build the tests for
unsupported features, but include the files.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2018-05-29 18:20:38 -04:00
Kei Kebreau 3a354e104a
gnu: Add rxcpp. 
* gnu/packages/machine-learning.scm (rxcpp): New variable.
 2018-05-29 18:20:37 -04:00
Kei Kebreau de658cc2f8
gnu: octave: Update to 4.4.0. 
* gnu/packages/maths.scm (octave): Update to 4.4.0.
 2018-05-29 18:20:37 -04:00
Leo Famulari f0dd127d0a
gnu: mpd: Update to 0.20.20. 
* gnu/packages/mpd.scm (mpd): Update to 0.20.20.
 2018-05-29 18:00:34 -04:00
Ricardo Wurmus e5bbfc7df0
gnu: mypaint-brushes: Fetch source from git. 
* gnu/packages/gimp.scm (mypaint-brushes)[source]: Fetch source from git.
 2018-05-29 23:24:32 +02:00
Ricardo Wurmus 5686be393b
gnu: mypaint-brushes: Fix build. 
* gnu/packages/gimp.scm (mypaint-brushes)[arguments]: Remove bootstrap phase;
add "relax-dependency-version" phase.
 2018-05-29 23:24:32 +02:00
Ricardo Wurmus d2e1da18b0
gnu: python-pygobject: Delete broken tests. 
* gnu/packages/glib.scm (python-pygobject)[arguments]: Add phase
"delete-broken-tests".
 2018-05-29 23:24:32 +02:00
Ricardo Wurmus 1b043aeb85
gnu: python2-pygobject: Add native-inputs. 
* gnu/packages/glib.scm (python2-pygobject)[native-inputs]: New field.
 2018-05-29 23:17:48 +02:00
Ricardo Wurmus 59f6dfe552
gnu: python-pygobject: Update to 3.28.2. 
* gnu/packages/glib.scm (python-pygobject): Update to 3.28.2.
[native-inputs]: Add python-pytest.
 2018-05-29 22:43:00 +02:00
Ricardo Wurmus 660c9b4788
gnu: modem-manager: Fix build. 
* gnu/packages/freedesktop.scm (modem-manager)[arguments]: Add configure flag
to avoid aborting on certain warnings.
 2018-05-29 22:11:04 +02:00
Leo Famulari b50196c3a4
gnu: Git: Update to 2.17.1 [fixes CVE 2018-{11234,11235}]. 
* gnu/packages/version-control.scm (git): Update to 2.17.1.
 2018-05-29 16:00:02 -04:00
Tobias Geerinckx-Rice 0eeade9b53
gnu: pan: Update to 0.145. 
* gnu/packages/mail.scm (pan): Update to 0.145.
 2018-05-29 20:43:38 +02:00
Tobias Geerinckx-Rice 3b68a9b66e
gnu: disorderfs: Update to 0.5.3. 
* gnu/packages/file-systems.scm (disorderfs): Update to 0.5.3.
[source]: Update upstream URI and re-use VERSION.
 2018-05-29 20:43:37 +02:00
Tobias Geerinckx-Rice e5ab03b51d
gnu: thefuck: Update to 3.27. 
* gnu/packages/admin.scm (thefuck): Update to 3.27.
 2018-05-29 20:43:37 +02:00
Leo Famulari e3d779cc93
gnu: Wireshark: Update to 2.6.1. 
* gnu/packages/networking.scm (wireshark): Update to 2.6.1.
 2018-05-29 14:39:22 -04:00
Leo Famulari 4d0f463d6b
gnu: xdg-utils: Update to 1.1.3 [fixes CVE-2017-18266]. 
* gnu/packages/freedesktop.scm (xdg-utils): Update to 1.1.3.
 2018-05-29 14:39:22 -04:00
Ludovic Courtès 201f2c8769
vm: Remove unneeded dependency on Guile-JSON. 
Fixes <https://bugs.gnu.org/31581>.
Reported by Leo Famulari <leo@famulari.name>.

* gnu/system/vm.scm: Remove unneeded (guix docker) import.
 2018-05-29 18:29:36 +02:00
Clément Lassieur 7c1445f86a
gnu: Add missing copyright line. 
* gnu/packages/engineering.scm: Add missing copyright line for commit 6cedd61.
 2018-05-29 15:43:13 +02:00
Ricardo Wurmus b347317ae6
Merge branch 'master' into core-updates 2018-05-29 15:41:06 +02:00
Clément Lassieur 6cedd61177
gnu: librecad: Fix build against Qt 5.11. 
* gnu/packages/engineering.scm (librecad)[arguments]: Add missing headers.
 2018-05-29 15:25:23 +02:00
Ludovic Courtès 0d56d9c714
services: fstab: Properly handle file system labels. 
Fixes a regression introduced in
a5acc17a3c.

Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

* gnu/services/base.scm (file-system->fstab-entry): Pass LABEL, not
FILE-SYSTEM, to 'file-system-label->string'.
 2018-05-29 15:09:44 +02:00
Ricardo Wurmus 80e99aa467
gnu: emacs-s: Fix tests. 
* gnu/packages/emacs.scm (emacs-s)[arguments]: Use full emacs package to fix
tests.
 2018-05-29 14:05:11 +02:00
Ricardo Wurmus 06f863791a
gnu: emacs-dash: Update to 2.14.1. 
* gnu/packages/emacs.scm (emacs-dash): Update to 2.14.1.
[source]: Fetch from git.
 2018-05-29 14:05:11 +02:00
Ricardo Wurmus bd6a699d73
gnu: emacs-minimal: Fix build by disabling gnutls support. 
This is a follow-up to bb82c3d42b.

* gnu/packages/emacs.scm (emacs-minimal)[arguments]: Pass configure flag to
indicate that gnutls support has intentionally been disabled.
 2018-05-29 14:05:11 +02:00
Mathieu Othacehe 2206c7ad93
gnu: emacs: Update to 26.1. 
* gnu/packages/emacs.scm (emacs): Update to 26.1,
[arguments]: disable tests as they do not exist in release.
* gnu/packages/patches/emacs-fix-scheme-indent-function.patch: Update patch
indentation and line numbers.
 2018-05-29 14:05:11 +02:00
Vagrant Cascadian 6fe1657705
system: Add u-boot-puma-rk3399. 
* gnu/packages/bootloaders.scm (u-boot-puma-rk3399): New variable.
(make-u-boot-package)[arguments]: Add '.rksd' files to the files installed
during custom 'install phase.
* gnu/bootloader/u-boot.scm (u-boot-puma-rk3399-bootloader):
New exported variable.
* gnu/system/install.scm (rk3399-puma-installation-os):
New exported variable.
* gnu/packages/firmware.scm (arm-trusted-firmware-puma-rk3399): New variable.
(rk3399-cortex-m0): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2018-05-29 10:46:13 +02:00
Leo Famulari 2a49aee4d1
gnu: khal: Update to 0.9.9. 
* gnu/packages/calendar.scm (khal): Update to 0.9.9.
 2018-05-29 00:41:32 -04:00
Mark H Weaver 82b695b834
Merge branch 'master' into core-updates 2018-05-28 20:45:37 -04:00
Danny Milosavljevic ee3c8fbee2
gnu: make-u-boot-package: Sort printed configurations case-insensitively. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Sort printed
configurations case-insensitively.
 2018-05-29 00:37:10 +02:00
Danny Milosavljevic 65212c42cd
gnu: u-boot-tools: Enable tests. 
* gnu/packages/bootloaders.scm (u-boot-tools)[native-inputs]: Add openssl,
python2-coverage, python2-pytest, sdl.
[arguments]<#:make-flags>: Remove NO_SDL.
[arguments]<#:test-target>: Change to "tests".
[arguments]<#:phases>[patch]: New phase.
[arguments]<#:phases>[check]: Replace and move.
 2018-05-28 23:52:07 +02:00
Clément Lassieur a234ae38ba
gnu: wireshark: Fix build against Qt 5.11. 
* gnu/packages/networking.scm (wireshark)[arguments]: Add a 'patch-source'
phase that includes missing headers.
 2018-05-28 23:45:50 +02:00
Clément Lassieur 77cc8778a3
gnu: supercollider: Remove broken Qt dependency. 
As suggested by Ricardo Wurmus.

This also removes IDE support.

* gnu/packages/audio.scm (supercollider)[arguments]: Add "-DSC_QT=off" to
configure flags.
[native-inputs]: Remove QTTOOLS.
[inputs]: Remove QTBASE, QTWEBKIT, QTSENSORS, QTDECLARATIVE and QTLOCATION.
 2018-05-28 22:49:55 +02:00
Clément Lassieur c7d901c130
gnu: vlc: Fix build against Qt 5.11. 
* gnu/packages/video.scm (vlc)[arguments]: Add missing headers.
 2018-05-28 22:40:53 +02:00
Mathieu Othacehe a338b6f51d
Revert "gnu: emacs: Update to 26.1." 
This reverts commit bb82c3d42b. This commit
needs probably to be done on core-updates.
 2018-05-28 19:10:17 +02:00
Mathieu Othacehe bb82c3d42b
gnu: emacs: Update to 26.1. 
* gnu/packages/emacs.scm (emacs): Update to 26.1,
[arguments]: disable tests as they do not exist in release.
* gnu/packages/patches/emacs-fix-scheme-indent-function.patch: Update patch
indentation and line numbers.
 2018-05-28 18:40:21 +02:00
Ricardo Wurmus 3ec07ced8a
gnu: Add singularity. 
* gnu/packages/linux.scm (singularity): New variable.
 2018-05-28 17:36:09 +02:00
Ricardo Wurmus e580597d25
gnu: Add squashfs-tools-next. 
* gnu/packages/compression.scm (squashfs-tools-next): New variable.
 2018-05-28 17:36:08 +02:00
Clément Lassieur fdb85546dd
gnu: gajim: Update to 1.0.3. 
* gnu/packages/messaging.scm (gajim): Update to 1.0.3.
 2018-05-28 16:44:05 +02:00
Clément Lassieur 135745939d
gnu: python-nbxmpp: Update to 0.6.6. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.6.
 2018-05-28 16:43:55 +02:00
Mark H Weaver fe365a3d0e
gnu: libssh2: Fix build on MIPS systems. 
* gnu/packages/ssh.scm (libssh2)[arguments]: When building for MIPS, replace
the existing bootstrap phase instead of adding a new 'autoreconf' phase (in
the wrong place).
 2018-05-28 09:06:13 -04:00
Mark H Weaver 073cc31313
gnu: Fix typo. 
Fix a typo introduced in commit 2101cc3fb6.

* gnu/local.mk: Add back the missing comment character.
 2018-05-28 09:04:44 -04:00
Fis Trivial 70770b9381
gnu: Add xtensor. 
* gnu/packages/algebra.scm (xtensor): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 14:20:50 +02:00
Fis Trivial 6f3c850618
gnu: Add xtl. 
* gnu/packages/cpp.scm (xtl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 14:19:29 +02:00
Fis Trivial e3c0676adf
gnu: Add json-modern-cxx. 
* gnu/packages/cpp.scm (json-modern-cxx): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 14:18:51 +02:00
Fis Trivial 385357c0d7
gnu: Add fifo-map. 
* gnu/packages/cpp.scm (fifo-map): New variable.
* gnu/packages/patches/fifo-map-fix-flags-for-gcc.patch: New file.
* gnu/packages/patches/fifo-map-remove-catch.hpp.patch: New file.
* gnu/local.mk: Add new patch files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 13:48:52 +02:00
Fis Trivial ad8a4d6dc8
gnu: Add amalgamate. 
This commit also re-orders some module statements.

* gnu/packages/code.scm (amalgamate): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 13:45:39 +02:00
Fis Trivial 56e72c0084
gnu: Add catch-framework2. 
* gnu/packages/check.scm (catch-framework2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-28 13:39:57 +02:00
Ludovic Courtès 9ceeca0880
system: Remove uses of the 'title' field of <file-system>. 
* gnu/system/install.scm (installation-os): Remove uses of the 'title'
field of 'file-system'; use 'file-system-label' as appropriate.
* gnu/system/vm.scm (system-disk-image, system-qemu-image): Likewise.
* gnu/tests.scm (%simple-os): Likewise.
* gnu/tests/install.scm (%minimal-os, %minimal-extlinux-os)
(%minimal-os-on-vda, %separate-home-os, %separate-store-os)
(%raid-root-os, %encrypted-root-os, %btrfs-root-os): Likewise.
* gnu/build/shepherd.scm (default-mounts)[tmpfs]: Likewise.
* tests/guix-system.sh: Likewise.
* tests/system.scm (%root-fs): Likewise.
("operating-system-boot-mapped-devices, implicit dependency"): Likewise.
 2018-05-28 13:24:19 +02:00
Ludovic Courtès a5acc17a3c
file-systems: Remove 'title' field and add <file-system-label>. 
The 'title' field was easily overlooked and was an endless source of
confusion.  Now, the value of the 'device' field is self-contained.

* gnu/system/file-systems.scm (<file-system>): Change constructor name
to '%file-system'.
[title]: Remove.
(<file-system-label>): New record type with printer.
(report-deprecation, device-expression)
(process-file-system-declaration, file-system): New macros.
(file-system-title): New procedure.
(file-system->spec, spec->file-system): Adjust to handle
<file-system-label>.
* gnu/system.scm (bootable-kernel-arguments): Add case for
'file-system-label?'.
(read-boot-parameters): Likewise.
(mapped-device-user): Avoid 'file-system-title'.
(fs->boot-device): Remove.
(operating-system-boot-parameters): Use 'file-system-device' instead of
'fs->boot-device'.
(device->sexp): Add case for 'file-system-label?'.
* gnu/bootloader/grub.scm (grub-root-search): Add case for
'file-system-label?'.
* gnu/system/examples/bare-bones.tmpl,
gnu/system/examples/beaglebone-black.tmpl,
gnu/system/examples/lightweight-desktop.tmpl,
gnu/system/examples/vm-image.tmpl: Remove uses of 'title'.
* gnu/system/vm.scm (virtualized-operating-system): Remove uses of
'file-system-title'.
* guix/scripts/system.scm (check-file-system-availability): Likewise,
and adjust fix-it hint.
(check-initrd-modules)[file-system-/dev]: Likewise.
* gnu/build/file-systems.scm (canonicalize-device-spec): Remove 'title'
parameter.
[canonical-title]: Remove.
Match on SPEC's type rather than on CANONICAL-TITLE.
(mount-file-system): Adjust caller.
* gnu/build/linux-boot.scm (boot-system): Interpret ROOT here.
* gnu/services/base.scm (file-system->fstab-entry): Remove use of
'file-system-title'.
* doc/guix.texi (File Systems): Remove documentation of the 'title'
field.  Rewrite documentation of 'device' and document
'file-system-label'.
 2018-05-28 13:24:11 +02:00
Mark H Weaver 25816c4306
gnu: icecat: Add more fixes from upstream mozilla-esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from
the upstream mozilla-esr52 repository.
 2018-05-27 17:39:29 -04:00
Pierre Langlois 8a6d16b897
gnu: clementine: Update snapshot. 
* gnu/package/music.scm (clementine): Update snapshot to 4619a4c1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2018-05-27 22:33:06 +03:00
Pierre Langlois 1222a64c02
gnu: libechonest: Remove package. 
It appears the "EchoNest" service isn't available anymore which makes this
package obsolete.

* gnu/packages/music.scm (libechonest): Remove variable.
(clementine)[inputs]: Remove libechonest.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2018-05-27 22:33:05 +03:00
Pierre Langlois 01c4869003
gnu: libmygpo-qt: Fix Qt 5.11 build. 
The update to Qt 5.11.0 broke libmygpo-qt. It turned it was using a deprecated
CMake function (qt5_use_moduldes).  Let's pick up two upstream patches that
fix the issue: https://github.com/gpodder/libmygpo-qt/pull/15

As mentioned in the the pull request, there is now a test failure but it looks
harmless.

* gnu/packages/patches/libmygpo-qt-fix-qt-5.11.patch,
gnu/packages/patches/libmygpo-qt-missing-qt5-modules.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/music.scm (libmygpo-qt)[source]: Add patches.
[arguments]: Build tests but do not run them.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2018-05-27 22:33:01 +03:00
Julien Lepiller 2101cc3fb6
gnu: gnu: Make alsa find its plugins by setting ALSA_PLUGIN_DIR. 
* gnu/packages/patches/alsa-lib-add-environment-variable.patch: New
file.
* gnu/packages/linux.scm (alsa-lib)[source]: Use it.
[native-search-paths]: Add ALSA_PLUGIN_DIR.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-05-27 19:05:34 +02:00
Julien Lepiller 3a69f5f2d3
gnu: Add java-logback-classic. 
* gnu/packages/java.scm (java-logback-classic): New variable.
 2018-05-27 18:47:15 +02:00
Julien Lepiller 7d8207a4c1
gnu: Add java-logback-core. 
* gnu/packages/java.scm (java-logback-core): New variable.
 2018-05-27 18:47:09 +02:00
Julien Lepiller 3402e651c8
gnu: Add java-janino. 
* gnu/packages/java.scm (java-janino): New variable.
 2018-05-27 18:47:07 +02:00
Julien Lepiller 3fa18fe796
gnu: Add java-commons-compiler. 
* gnu/packages/java.scm (java-commons-compiler): New variable.
 2018-05-27 18:47:05 +02:00
Julien Lepiller 66006fe526
gnu: Add java-commons-jxpath. 
* gnu/packages/java.scm (java-commons-jxpath): New variable.
 2018-05-27 18:47:03 +02:00
Julien Lepiller 7049dea185
gnu: Add java-eclipse-sisu-plexus. 
* gnu/packages/java.scm (java-eclipse-sisu-plexus): New variable.
 2018-05-27 18:47:01 +02:00
Julien Lepiller 1a1810f534
gnu: Add java-eclipse-sisu-inject. 
* gnu/packages/java.scm (java-eclipse-sisu-inject): New variable.
 2018-05-27 18:46:58 +02:00
Julien Lepiller a1a5ef2094
gnu: Add java-jsr250. 
* gnu/packages/java.scm (java-jsr250): New variable.
 2018-05-27 18:46:38 +02:00
Rutger Helling 9b9db6c482
gnu: xonotic: Correct licenses. 
* gnu/packages/games.scm (xonotic-data)[license]: Refer to correct file.
* gnu/packages/games.scm (xonotic)[license]: Refer to correct file.
 2018-05-27 10:24:06 +02:00
Efraim Flashner 865003433f
gnu: qtconnectivity: Enable previously failing test. 
* gnu/packages/qt.scm (qtconnectivity)[arguments]: Remove custom
'disable-failing-tests phase.
 2018-05-27 10:21:33 +03:00
Efraim Flashner 1f52eb7be7
gnu: qt: Update to 5.11.0. 
* gnu/packages/qt.scm (qtbase, qtsvg, qtimageformats, qtx11extras,
qtxmlpatterns, qtdeclarative, qtconnectivity, qtwebsockets, qtsensors,
qtmultimedia, qtwayland, qtserialport, qtserialbus, qtwebchannel,
qtlocation, qttools, qtscript, qtquickcontrols, qtquickcontrols2,
qtgraphicaleffects, qtgamepad, qtscxml, qtpurchasing, qtcanvas3d,
qtcharts, qtdatavis3d, qtnetworkauth, qtremoteobjects, qtspeech):
Update to 5.11.0.
[source]: Update source uri.
(qtbase)[source]: Don't remove bundled sqlite.
[inputs]: Remove sqlite.
[arguments]: Use 'invoke'. Use bundled sqlite.
(qtsvg, qtmultimedia, qtcanvas3d)[arguments]: Use 'invoke'.
(qtremoteobjects)[arguments]: Skip new integration test.
 2018-05-27 09:05:56 +03:00
Mark H Weaver 1640f16e78
Merge branch 'master' into core-updates 2018-05-27 01:26:09 -04:00
Mark H Weaver a4e45acdc0
gnu: linux-libre: Update to 4.16.12. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.16.12.
(%linux-libre-hash): Update hash.
 2018-05-27 01:23:26 -04:00
Mark H Weaver 52a1379814
gnu: linux-libre@4.14: Update to 4.14.44. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.44.
(%linux-libre-4.14-hash): Update hash.
 2018-05-27 01:22:36 -04:00
Mark H Weaver ce9484d851
gnu: linux-libre@4.9: Update to 4.9.103. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.103.
 2018-05-27 01:21:55 -04:00
Mark H Weaver ab7da7bc39
gnu: linux-libre@4.4: Update to 4.4.133. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.133.
 2018-05-27 01:20:01 -04:00
Fis Trivial e8f4d53e03
gnu: Add pybind11. 
* gnu/packages/python.scm (pybind11): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-26 22:24:23 +02:00
Pierre Neidhardt 0d529a7c6a
gnu: gifsicle: New variable. 
* gnu/packages/image.scm (gifsicle): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-26 22:22:16 +02:00
Pierre Neidhardt 5735256d0b
gnu: Add upx. 
* gnu/packages/compression.scm (upx): New variable.
 2018-05-26 22:11:18 +02:00
Pierre Neidhardt 719871771d
gnu: Add ucl. 
* gnu/packages/compression.scm (ucl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-26 22:00:59 +02:00
Adam Massmann e0f415b2b5
gnu: xapers: Fix recommended packages 
* gnu/packages/search.scm (xapers): [inputs]: remove python, poppler
[propagated-inputs]: add poppler, xclip, xdg-utils.
[arguments]: modify-phases to disable x-terminal options.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-26 21:48:38 +02:00
Nils Gillmann dc70ff2a86
gnu: Add xonotic. 
* gnu/packages/games.scm (xonotic, xonotic-data): New variables.

Signed-off-by: Rutger Helling <rhelling@mykolab.com>
 2018-05-26 18:15:39 +02:00
Marius Bakke b9d562284c
gnu: x265: Update to 2.8. 
* gnu/packages/video.scm (x265): Update to 2.8.
 2018-05-26 17:13:20 +02:00
Marius Bakke d5c472a216
gnu: p11-kit: Update to 0.23.11. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.11.
[arguments]: Add #:phases.  Drop new "runtime" test.
 2018-05-26 17:04:18 +02:00
Marius Bakke 26633cb8b3
gnu: samba: Update to 4.8.2. 
* gnu/packages/samba.scm (samba): Update to 4.8.2.
 2018-05-26 17:04:18 +02:00
Marius Bakke 6ce76bdc31
gnu: whois: Update to 5.3.1. 
* gnu/packages/networking.scm (whois): Update to 5.3.1.
[inputs]: Change from LIBIDN to LIBIDN2.
 2018-05-26 17:04:17 +02:00
Marius Bakke 80746f97f1
gnu: vte: Update to 0.52.2. 
* gnu/packages/gnome.scm (vte): Update to 0.52.2.
 2018-05-26 17:04:17 +02:00
Marius Bakke bbb56dc7b6
gnu: feh: Update to 2.26.3. 
* gnu/packages/image-viewers.scm (feh): Update to 2.26.3.
 2018-05-26 17:04:17 +02:00
Marius Bakke b3884bbfc5
gnu: rust: Fix typo. 
* gnu/packages/rust.scm (rust-bootstrap)[description]: s/manaer/manager.
 2018-05-26 17:04:17 +02:00
Rutger Helling 385f8a0930
gnu: wine-staging: Update to 3.9. 
* gnu/packages/wine.scm (wine-staging): Update to 3.9.
 2018-05-26 16:45:47 +02:00
Rutger Helling 84fbe00a8b
gnu: wine-staging-patchset-data: Update to 3.9. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.9.
 2018-05-26 16:45:46 +02:00
Nicolas Goaziou 4c40ed9d37
gnu: Add scummvm. 
* gnu/packages/emulators.scm (scummvm): New variable.
 2018-05-25 23:19:58 +02:00
Mark H Weaver 0ff4e49a95
gnu: boost: Re-enable context and coroutine libraries on MIPS. 
* gnu/packages/boost.scm (boost)[arguments]: Remove the extra make-flags
"--without-context", "--without-coroutine", and "--without-coroutine2" that
were previously added on mips64 systems.
 2018-05-25 14:07:28 -04:00
Andreas Enge 43a776e294
gnu: mpfrcx: Update to 0.5. 
* gnu/packages/algebra.scm (mpfrcx): Update to 0.5 and change licence to
lgpl3+.
 2018-05-25 19:52:15 +02:00
Jelle Licht c53fa8c83a
gnu: mps-youtube: Update to 0.2.8. 
* gnu/packages/video.scm (mps-youtube): Update to 0.2.8.
 2018-05-25 14:01:57 +02:00
Jelle Licht e7ca985973
gnu: footswitch: Update to ca43d53f. 
* gnu/packages/accessibility.scm (footswitch): Update to ca43d53f.
 2018-05-25 14:01:40 +02:00
Ludovic Courtès fbe1b85b63
gnu: openmpi: Add PSM2 (Intel OmniPath) support. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM2 on supported systems.
 2018-05-25 13:43:03 +02:00
Ludovic Courtès a560641a60
gnu: openmpi: Reintroduce PSM (Intel TrueScale) support. 
Fixes a regression introduced in
9129804230 whereby PSM would never be
added as an input.

* gnu/packages/mpi.scm (openmpi)[inputs]: Re-add PSM on supported
systems.
 2018-05-25 13:43:03 +02:00
Ludovic Courtès 6df2a50ac4
gnu: openmpi: Update to 3.0.1. 
* gnu/packages/mpi.scm (openmpi): Update to 3.0.1.
[arguments]: In 'remove-absolute' phase, adjust romio file name.
* gnu/packages/maths.scm (scalapack)[arguments]: Add
'set-test-environment' phase.
(slepc-openmpi)[arguments]: Likewise.
(mumps-openmpi)[arguments]: Likewise.
(superlu-dist)[arguments]: In 'check' phase, set
'OMPI_MCA_plm_rsh_agent'.
(scotch)[arguments]: In 'build-esmumps', likewise.
(p4est)[arguments]: Add 'set-test-environment' phase.
(hypre-openmpi)[arguments]: Likewise.
 2018-05-25 13:43:03 +02:00
Ludovic Courtès 0921eff2a8
gnu: superlu-dist: Update to 5.3.0. 
* gnu/packages/maths.scm (superlu-dist): Update to 5.3.0.
[source](snippet): Adapt file name and function names to new version.
Remove 'delete-file' call.
 2018-05-25 13:43:03 +02:00
Ludovic Courtès 98e0b1288f
vm: Pass "panic=1" to Linux. 
* gnu/build/vm.scm (load-in-linux-vm): Always pass "panic=1" after '-append'.
 2018-05-25 13:43:03 +02:00
Mathieu Othacehe 4806d390cb
gnu: Add python2-gdrivefs. 
* gnu/packages/python.scm (python2-gdrivefs): New variable.
 2018-05-25 10:36:43 +02:00
Mathieu Othacehe a037a59f83
gnu: Add python-fusepy. 
* gnu/packages/python.scm (python-fusepy): New variable,
(python2-fusepy): new variable.
 2018-05-25 10:36:43 +02:00
Mathieu Othacehe b5a9f49b49
gnu: Add python-gipc. 
* gnu/packages/python.scm (python-gipc): New variable,
(python2-gipc): new variable.
 2018-05-25 10:36:43 +02:00
Mathieu Othacehe 961bcdf5ac
gnu: Add python-google-api-client. 
* gnu/packages/python-web.scm (python-google-api-client): New variable,
(python2-google-api-client): new variable.
 2018-05-25 10:36:43 +02:00
Mathieu Othacehe 1ceca46b06
gnu: Add python2-oauth2client. 
* gnu/packages/python-web.scm (python2-oauth2client): New variable.
 2018-05-25 10:36:43 +02:00
Danny Milosavljevic c75c9b05e1
gnu: mrustc: Update to 0.0.0-3.b5b7089. 
* gnu/packages/rust.scm (mrustc): Update to 0.0.0-3.b5b7089.
 2018-05-25 00:59:41 +02:00
Fis Trivial 655ca71329
gnu: Add xsimd. 
* gnu/packages/cpp.scm (xsimd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-24 23:38:48 +02:00
Pierre Neidhardt 914205214c
gnu: ntfs-3g: Link 'mount.ntfs' to 'mount.ntfs-3g'. 
* gnu/packages/linux.scm (ntfs-3g)[arguments]: Add #:phases.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-05-24 23:38:47 +02:00
Julien Lepiller 109f022e9d
gnu: gdal: Fix configure flags. 
* gnu/packages/geo.scm (gdal)[arguments]: Fix configure flags.
 2018-05-24 22:14:31 +02:00
Nils Gillmann c10679f5f1
gnu: gnurl: Update to 7.60.0. 
* gnu/packages/gnunet.scm (gnurl): Update to 7.60.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-05-24 12:13:52 -04:00
Ricardo Wurmus a1b802454a
gnu: Add fastp. 
* gnu/packages/bioinformatics.scm (fastp): New variable.
 2018-05-24 17:49:32 +02:00
Rutger Helling 26bcd2a2b2
gnu: weston: Disable parallel tests. 
* gnu/packages/freedesktop.scm (weston): Disable parallel tests.
 2018-05-24 15:13:13 +02:00
Ricardo Wurmus 217af8ae71
gnu: qsynth: Update to 0.5.1. 
* gnu/packages/audio.scm (qsynth): Update to 0.5.1.
 2018-05-24 12:08:52 +02:00
Ricardo Wurmus 04e7cd8d80
gnu: qjackctl: Update to 0.5.1. 
* gnu/packages/audio.scm (qjackctl): Update to 0.5.1.
 2018-05-24 12:08:52 +02:00
Rutger Helling f035e5d0bc
gnu: weston: Update to 4.0.0. 
* gnu/packages/freedesktop.scm (weston): Update to 4.0.0.
[arguments]: Disable tests.
 2018-05-24 12:04:49 +02:00
Ricardo Wurmus fd29faa8d6
gnu: Add emacs-desktop-environment. 
* gnu/packages/emacs.scm (emacs-desktop-environment): New variable.
 2018-05-24 10:59:00 +02:00
Ricardo Wurmus a31d7334c2
gnu: mate-desktop-service-type: Add description. 
* gnu/services/desktop.scm (mate-desktop-service-type): Add description.
 2018-05-24 10:15:51 +02:00