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Author SHA1 Message Date
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
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