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Author SHA1 Message Date
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
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 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
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 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