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Author SHA1 Message Date
Ricardo Wurmus c28d8d8db0
gnu: r-kernlab: Update to 0.9-27. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c0608f815c
gnu: r-adaptivesparsity: Update to 1.6. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a207bca2ad
gnu: r-codedepends: Move from cran to bioconductor. 
* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus caaec88651
gnu: r-ggpubr: Update to 0.1.8. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a9b02ddd73
gnu: r-codedepends: Update to 0.6.5. 
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5.
[propagated-inputs]: Add r-graph.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 2e6909baf0
gnu: r-later: Update to 0.7.4. 
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 12132229b0
gnu: r-maptools: Update to 0.9-3. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 7a96c4e0a0
gnu: r-fnn: Update to 1.1.2.1. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 19950821d7
gnu: r-heatmaply: Update to 0.15.2. 
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 1fe9919a57
gnu: r-tsa: Update to 1.2. 
* gnu/packages/cran.scm (r-tsa): Update to 1.2.
[propagated-inputs]: Remove r-tseries.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus be5642eb69
gnu: r-statnet-common: Update to 4.1.4. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus e32368c130
gnu: r-metap: Update to 1.0. 
* gnu/packages/cran.scm (r-metap): Update to 1.0.
[propagated-inputs]: Add r-rdpack.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus d97d98e142
gnu: r-tinytex: Update to 0.8. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 6f5b157e3d
gnu: r-pillar: Update to 1.3.0. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0.
[propagated-inputs]: Add r-fansi.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 69bf449bf1
gnu: r-xts: Update to 0.11-0. 
* gnu/packages/cran.scm (r-xts): Update to 0.11-0.
[native-inputs]: Remove.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 1b3b2a72ee
gnu: r-mice: Update to 3.3.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus a7265593d3
gnu: r-pan: Update to 1.6. 
* gnu/packages/cran.scm (r-pan): Update to 1.6.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e7630cc931
gnu: r-jomo: Update to 2.6-4. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4.
[propagated-inputs]: Add r-ordinal.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b8f6e2f82a
gnu: Add r-ordinal. 
* gnu/packages/cran.scm (r-ordinal): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus dc66835226
gnu: Add r-ucminf. 
* gnu/packages/cran.scm (r-ucminf): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 45c156bf81
gnu: r-broom: Update to 0.5.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.0.
[propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove
r-plyr and r-psych.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2d2b95d151
gnu: r-ipred: Update to 0.9-7. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus c73752cac5
gnu: r-pls: Update to 2.7-0. 
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b00e8ae771
gnu: r-glue: Update to 1.3.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b72de5b3f6
gnu: r-callr: Update to 3.0.0. 
* gnu/packages/cran.scm (r-callr): Update to 3.0.0.
[propagated-inputs]: Add r-base64enc.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e3c1e93e35
gnu: r-reprex: Update to 0.2.0. 
* gnu/packages/cran.scm (r-reprex): Update to 0.2.0.
[propagated-inputs]: Add r-clipr, r-rlang, and r-withr.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2cdd9d4f83
gnu: r-reticulate: Update to 1.10. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.10.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus cb96d81be4
gnu: r-doby: Update to 4.6-2. 
* gnu/packages/cran.scm (r-doby): Update to 4.6-2.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 589bd1c426
gnu: Add r-flextable. 
* gnu/packages/cran.scm (r-flextable): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 78f2c08c0b
gnu: r-rmarkdown: Use latest version of Pandoc. 
* gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus f9f4578ba0
Revert "gnu: ghc-tasty: Update to 1.1.0.3." 
This reverts commit 3ad6b89090.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 90708323a1
Revert "gnu: ghc-base-compat: Update to 0.10.4." 
This reverts commit 0fa2c552fc.

We may not upgrade base-compat at this point because we haven't upgraded the
default GHC yet.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 0fd7d59dc3
gnu: Add r-moonbook. 
* gnu/packages/cran.scm (r-moonbook): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus aaed237d1b
gnu: Add r-nortest. 
* gnu/packages/cran.scm (r-nortest): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 1f560b9cdb
gnu: Add r-sjmisc. 
* gnu/packages/cran.scm (r-sjmisc): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus cfc0631433
gnu: Add r-sjlabelled. 
* gnu/packages/cran.scm (r-sjlabelled): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus de059e4bd3
gnu: Add r-prediction. 
* gnu/packages/cran.scm (r-prediction): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus bfee9ce88f
gnu: Add r-snakecase. 
* gnu/packages/cran.scm (r-snakecase): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus c183fa2688
gnu: Add r-officer. 
* gnu/packages/cran.scm (r-officer): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 5dbe7aa920
gnu: r-googlesheets: Update to 0.3.0. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.3.0.
[propagated-inputs]: Add r-tibble.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 88cb7aa9e7
gnu: r-plotly: Update to 4.8.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.8.0.
[propagated-inputs]: Add r-promises and r-rlang.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 195eec737c
gnu: r-matrixstats: Update to 0.54.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.54.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e2a2c3378e
gnu: r-r-rsp: Update to 0.43.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.43.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus eefa7c7f3d
gnu: r-r-utils: Update to 2.7.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.7.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e926159eb3
gnu: r-e1071: Update to 1.7-0. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2aafa73a94
gnu: r-xml: Update to 3.98-1.16. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.16.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 41f6685388
gnu: r-rcpparmadillo: Update to 0.9.100.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.100.5.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 19cb93be55
gnu: r-git2r: Update to 0.23.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.23.0.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2848c52c5e
gnu: r-roxygen2: Update to 6.1.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.0.
[propagated-inputs]: Add r-pkgload and r-purrr.
[native-inputs]: Add r-knitr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 9b7e8df85b
gnu: r-ade4: Update to 1.7-13. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-13.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 7f38b31ecb
gnu: r-xtable: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-xtable): Update to 1.8-3.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 6b02569f1d
gnu: r-dbplyr: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.2.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3299bc1c5e
gnu: r-yaml: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.2.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2a96a093ec
gnu: r-evaluate: Update to 0.11. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.11.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3bf390279d
gnu: r-scales: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-scales): Update to 1.0.0.
[propagated-inputs]: Remove r-dichromat and r-plyr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 97c81cc174
gnu: r-stringi: Update to 1.2.4. 
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e362be8e89
gnu: Add r-pkgload. 
* gnu/packages/cran.scm (r-pkgload): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 4f8247b54b
gnu: Add r-pkgbuild. 
* gnu/packages/cran.scm (r-pkgbuild): New variable.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 1ec1989f80
gnu: r-httpuv: Update to 1.4.5. 
* gnu/packages/web.scm (r-httpuv): Update to 1.4.5.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus f077174178
gnu: r-scran: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 8e44ff0c0d
gnu: r-scater: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e69c07e61a
gnu: r-hdf5array: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 16527f1cbc
gnu: r-ggbio: Update to 1.28.5. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 70daf9362b
gnu: r-biovizbase: Update to 1.28.2. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3c55304688
gnu: r-edaseq: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus eb251fe524
gnu: r-igraph: Update to 1.2.2. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus c273bcdfce
gnu: r-diffusionmap: Update to 1.1-0.1. 
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 6f6aef80e3
gnu: r-seurat: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 07bd90ce90
gnu: r-msnbase: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 4ee8c37cca
gnu: r-maldiquant: Update to 1.18. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 48b21f8b6b
gnu: r-seqminer: Update to 6.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus a02340058c
gnu: r-biocparallel: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 1d56c79f86
gnu: r-genomicranges: Update to 1.32.6. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 688cb08527
gnu: r-limma: Update to 3.36.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 33a103a543
gnu: r-variantannotation: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 1adf4596a6
gnu: r-edger: Update to 3.22.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 5728d9c6c0
gnu: r-iranges: Update to 2.14.11. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 3c04375614
gnu: r-biocviews: Update to 1.48.3. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 65050163e0
gnu: r-chippeakanno: Update to 3.14.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 88e4ed55d6
gnu: Add r-clipr. 
* gnu/packages/cran.scm (r-clipr): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 6a8469755c
gnu: Add r-rdpack. 
* gnu/packages/cran.scm (r-rdpack): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus dd954dd743
gnu: Add r-gbrd. 
* gnu/packages/cran.scm (r-gbrd): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 53718658d2
gnu: Add r-polynom. 
* gnu/packages/cran.scm (r-polynom): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 356230da4a
gnu: Add r-fansi. 
* gnu/packages/cran.scm (r-fansi): New variable.
 2018-09-05 20:03:03 +02:00
Ludovic Courtès 3b0153bd82
gnu: guix-daemon: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
made Guile-Gcrypt a hard dependency.

* gnu/packages/package-management.scm (guix-daemon)[inputs]: Add
GUILE-GCRYPT.
 2018-09-05 15:48:04 +02:00
Ludovic Courtès 7903f00a74
gnu: cuirass: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
added a hard dependency of Guix on Guile-Gcrypt.

* gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, use 'string-join' to compute
'mods'.  Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take
objects from lib/guile/X.Y/site-ccache.
 2018-09-05 15:35:54 +02:00
Ludovic Courtès 5e3082df1c
gnu: guile-fibers: Install .go files to "…/site-ccache". 
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
 2018-09-05 15:35:54 +02:00
Eric Bavier 3f5e6ccf9b
slepc: Upgrade to 3.9.2. 
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
 2018-09-05 08:10:38 -05:00
Eric Bavier c15be1280e
petsc: Upgrade to 3.9.3. 
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3.
[arguments]: Remove unnecessary configure flags.
 2018-09-05 08:10:37 -05:00
Eric Bavier a3a99e27bb
petsc: Move example code to "examples" output. 
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
 2018-09-05 08:10:37 -05:00
Eric Bavier b26e4f26ff
gnu: Add SUNDIALS. 
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
 2018-09-05 08:10:31 -05:00
Alex Vong 296f091b48
gnu: packages: mp3: Use HTTPS where possible. 
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS.
(libid3tag)[home-page]: Likewise.
(mp3info)[source, home-page]: Likewise.
(mpg123)[source]: Likewise.
(libmpcdec)[source, home-page]: Likewise.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Alex Vong 998100e6e8
gnu: eyed3: Update home page. 
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Ludovic Courtès 53166aec98
gnu: guix: Update to 3d43017. 
* gnu/packages/package-management.scm (guix): Update to 3d43017.
 2018-09-05 14:31:48 +02:00
Ludovic Courtès 185948b8a8
gnu: xorg: Fix typo. 
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
 2018-09-05 13:57:43 +02:00
Ricardo Wurmus 4fd2622df8
gnu: python-tables: Update to 3.4.4. 
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 8afdeb8751
gnu: python-pybigwig: Update to 0.3.12. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 0d7974c376
gnu: libbigwig: Update to 0.4.2. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus ca1dc4c76a
gnu: nss-pam-ldapd: Update to 0.9.10. 
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
 2018-09-05 11:44:52 +02:00
Rutger Helling fefe17b088
gnu: dolphin-emu: Update to commit 5f0d825. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
 2018-09-05 10:23:20 +02:00
Leo Famulari fcf4841c0e
gnu: Zsh: Patch some tests that began failing in 5.6. 
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting
them.
 2018-09-04 18:34:01 -04:00
Leo Famulari 95681e5586
gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}]. 
* gnu/packages/shells.scm (zsh): Update to 5.6.
[arguments]: Skip some tests.
 2018-09-04 18:10:53 -04:00
Ludovic Courtès ca71942445
Switch to Guile-Gcrypt. 
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)

* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt.  Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
 #:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions  Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules.  Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
 2018-09-04 17:25:11 +02:00
Alex Vong 1bf758767d
gnu: Add emacs-picpocket. 
* gnu/packages/emacs.scm (emacs-picpocket): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:39:43 +02:00
Paul Garlick 71ca16b58d
gnu: petsc-openmpi: Configure with support for hdf5 data format. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add
hdf5-parallel-openmpi.
[arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib'
flags.  Add 'set-test-environment' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:22:48 +02:00
Jonathan Brielmaier b50658fe8a
gnu: kicad: Update to 5.0.0. 
* gnu/packages/engineering.scm (kicad): Update to 5.0.0.
[source]: Change from git to url-fetch.
[arguments]: Remove now unneeded build version parameter.
[inputs]: Add opencascade-oce.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:02:59 +02:00
Arun Isaac 906a396bff
gnu: ghc-zlib: Enable tests. 
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building
with newer tasty.
[native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and
ghc-tasty-quickcheck.
 2018-09-04 17:31:09 +05:30
Arun Isaac 6300ba5b66
gnu: ghc-integer-logarithms: Allow building with newer tasty. 
* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building
with newer tasty.
 2018-09-04 15:24:32 +05:30
Arun Isaac 8374cc4b05
gnu: ghc-tasty-ant-xml: Update to 1.1.4. 
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml): Update to 1.1.4.
 2018-09-04 15:21:56 +05:30
Arun Isaac 3ad6b89090
gnu: ghc-tasty: Update to 1.1.0.3. 
* gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3.
[inputs]: Add ghc-wcwidth.
(ghc-attoparsec-bootstrap, ghc-integer-logarithms-bootstrap,
ghc-scientific-bootstrap): New variables.
(ghc-wcwidth)[inputs]: Replace ghc-attoparsec with ghc-attoparsec-bootstrap.
(ghc-scientific)[inputs]: Replace ghc-integer-logarithms with
ghc-integer-logarithms-bootstrap.
(ghc-attoparsec)[inputs]: Replace ghc-scientific with
ghc-scientific-bootstrap.
 2018-09-04 12:15:17 +05:30
Arun Isaac 9c4b522f15
gnu: Add ghc-wcwidth. 
* gnu/packages/haskell.scm (ghc-wcwidth): New variable.
 2018-09-04 12:15:10 +05:30
Ludovic Courtès fd95f37f36
Revert "gnu: perl: Add support for cross-compilation" 
This reverts commit 5108c18e7e, which was
accidentally committed.
 2018-09-03 23:49:12 +02:00
Raphaël Mélotte 5108c18e7e
gnu: perl: Add support for cross-compilation 
* gnu/packages/perl.scm (perl): use cross-libc when cross-compiling

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:41:08 +02:00
Benjamin Slade 38fe6449c0
gnu: Add transset-df. 
* gnu/packages/xorg.scm (transset-df): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-03 23:40:23 +02:00
Marius Bakke c702749dfd
gnu: arpack-ng: Update to 3.6.2. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.2.
 2018-09-03 19:09:01 +02:00
Marius Bakke 91bb495b85
gnu: arpack-ng: Drop redundant phase. 
* gnu/packages/maths.scm (arpack-ng)[arguments]: Remove.
 2018-09-03 19:09:01 +02:00
Marius Bakke 1f7d142000
gnu: python-matplotlib: Update to 2.2.3. 
* gnu/packages/python.scm (python-matplotlib): Update to 2.2.3.
 2018-09-03 19:09:00 +02:00
Marius Bakke cbd7c65709
gnu: ppp: Return #t from all phases. 
* gnu/packages/samba.scm (ppp)[arguments]: Return #t from phase.
 2018-09-03 18:58:47 +02:00
Marius Bakke 84aa18ff7f
gnu: re2: Update to 2018-09-01. 
* gnu/packages/regex.scm (re2): Update to 2018-09-01.
 2018-09-03 18:58:47 +02:00
Marius Bakke fcde1d27bb
gnu: openexr: Update to 2.3.0. 
* gnu/packages/graphics.scm (openexr): Update to 2.3.0.
[source](uri): Change to new download location.
[source](snippet): Remove workaround.
[source](patches): Remove.
* gnu/packages/patches/openexr-missing-samples.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-03 18:58:47 +02:00
Marius Bakke 1ae2c577a6
gnu: ilmbase: Update to 2.3.0. 
* gnu/packages/graphics.scm (ilmbase): Update to 2.3.0.
[source](uri): Change to new download location.
 2018-09-03 18:58:46 +02:00
Marius Bakke 9156206199
gnu: simplescreenrecorder: Build against modular Qt. 
* gnu/packages/video.scm (simplescreenrecorder)[inputs]: Remove QT.  Add
QTBASE and QTX11EXTRAS.
 2018-09-03 18:58:46 +02:00
Marius Bakke 65e686d6cb
Merge branch 'security-updates' 2018-09-03 18:58:20 +02:00
Efraim Flashner a5896da34e
gnu: gnu-pw-mgr: Update to 2.4.2. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.4.2.
 2018-09-03 19:34:24 +03:00
Tobias Geerinckx-Rice 38a8cd329d
gnu: python-nbxmpp: Update to 0.6.7. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.7.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice b619b7f67b
gnu: libircclient: Update to 1.10. 
* gnu/packages/messaging.scm (libircclient): Update to 1.10.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice cfcfc6ab62
Fix some typos. 
* doc/guix.texi (Sound Services, DNS Services): Fix typos.
* gnu/packages/cpp.scm (json-modern-cxx)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-fancy-narrow)[synopsis, description]:
Likewise. Edit & mark up while we're here.
* gnu/packages/mail.scm (alot)[synopsis, description]: Ditto.
 2018-09-03 18:21:43 +02:00
Tobias Geerinckx-Rice fb458bf3bc
gnu: sudo: Update to 1.8.25. 
* gnu/packages/admin.scm (sudo): Update to 1.8.25.
 2018-09-03 18:21:42 +02:00
Efraim Flashner 0cc6447669
gnu: python-efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (python-efl): Update to 1.21.0.
[source]: Don't use pypi source.
[arguments]: Delete network tests.
 2018-09-03 17:32:44 +03:00
Efraim Flashner 290bef39f6
gnu: efl: Update to 1.21.0. 
* gnu/packages/enlightenment.scm (efl): Update to 1.21.0.
 2018-09-03 17:32:44 +03:00
Ricardo Wurmus 02ddafef55
gnu: python-scipy: Disable broken tests. 
* gnu/packages/python.scm (python-scipy)[arguments]: Skip two broken tests.
 2018-09-03 13:49:32 +02:00
Rutger Helling 26baaaf49b
gnu: c-toxcore: Update to 0.2.7. 
* gnu/packages/messaging.scm (c-toxcore): Update to 0.2.7.
 2018-09-03 08:22:51 +02:00
Rutger Helling aa613d71ec
gnu: openrct2: Update to 0.2.1. 
* gnu/packages/games.scm (openrct2-objects): Update to 1.0.6.
* gnu/packages/games.scm (openrct2): Update to 0.2.1.
 2018-09-03 08:22:50 +02:00
Efraim Flashner 647465ace9
gnu: jellyfish: Update to 2.2.10. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
 2018-09-03 08:32:33 +03:00
Oleg Pykhalov 3910977823
gnu: monitoring.scm: Fix copyright line. 
This is a follow-up to ead46692ec.
 2018-09-02 19:18:16 +03:00
Alex Vong 2bd6ed9e4c
gnu: haskell-mode: Fix test failure. 
Fixes <https://bugs.gnu.org/31726>.

Thanks to Jack Hill <jackhill@jackhill.us> for exploring different solutions
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31726>.

* gnu/packages/patches/haskell-mode-unused-variables.patch,
gnu/packages/patches/haskell-mode-make-check.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/emacs.scm (haskell-mode)[source]: Use them.
[arguments]: Adjust 'pre-build' phase to embed file name.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 17:06:43 +02:00
Konrad Hinsen b21a55a9f2
gnu: emacs-helpful: Update to 0.13. 
* gnu/packages/emacs.scm (emacs-helpful): Update to 0.13.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:58:06 +02:00
Konrad Hinsen 351b6463af
gnu: emacs-elisp-refs: Update to 1.3. 
* gnu/packages/emacs.scm (emacs-elisp-refs): Update to 1.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-02 16:56:22 +02:00
Ludovic Courtès fe634eaf93
Add (guix describe) and use it to initialize '%package-search-path'. 
* guix/describe.scm: New file.
* Makefile.am (MODULES): Add it.
* gnu/packages.scm (%default-package-module-path): New variable.
(%package-module-path): Honor 'package-path-entries'.
* build-aux/update-NEWS.scm (main): Use %DEFAULT-PACKAGE-MODULE-PATH
instead of (last (%package-module-path)).
 2018-09-02 16:43:10 +02:00
Rutger Helling 87284c6b48
gnu: wine-staging: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging): Update to 3.15.
 2018-09-02 08:53:03 +02:00
Rutger Helling ab2e38e206
gnu: wine-staging-patchset-data: Update to 3.15. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.15.
 2018-09-02 08:53:03 +02:00
宋文武 9bf98520f2
gnu: rosegarden: Update to 18.06. 
* gnu/packages/music.scm (rosegarden): Update to 18.06.
[home-page]: Use HTTPS.
 2018-09-02 13:18:28 +08:00
Danny Milosavljevic 24d298b459
gnu: rust: Move rust-1.19 down. 2018-09-02 00:22:53 +02:00
Danny Milosavljevic 3159ef7c99
gnu: rust: Bootstrap (only) Rust 1.19.0 by mrustc. 
* gnu/packages/patches/rust-1.19-mrustc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rust.scm (rust-1.19)[source]: Add patch
"rust-1.19-mrustc.patch".
[arguments]<#:modules>: New field.
<#:phases>[patch-cargo-tomls]: New phase.
<#:phases>[build]: Modify.
<#:phases>[install]: Modify.
[native-inputs]: Replace rust-bootstrap by mrustc.
(rust-1.23)[native-inputs]: New field.
[arguments]<#:phases>: Delete phase "patch-cargo-tomls".
 2018-09-02 00:09:34 +02:00
Manuel Graf a0a273c1ee
gnu: Add perftest. 
* gnu/packages/linux.scm (perftest): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-01 17:51:29 -04:00
Julien Lepiller 37a0f47073
gnu: Add ruby-jekyll-paginate-v2. 
* gnu/packages/ruby.scm (ruby-jekyll-paginate-v2): New variable.
 2018-09-01 23:09:14 +02:00
Julien Lepiller 49e1dde53f
gnu: Add jekyll. 
* gnu/packages/ruby.scm (jekyll): New variable.
 2018-09-01 23:09:09 +02:00
Julien Lepiller 3729611379
gnu: Add ruby-pathutil. 
* gnu/packages/ruby.scm (ruby-pathutil): New variable.
 2018-09-01 23:09:06 +02:00
Julien Lepiller 49395112c4
gnu: Add ruby-forwardable-extended. 
* gnu/packages/ruby.scm (ruby-forwardable-extended): New variable.
 2018-09-01 23:09:04 +02:00
Julien Lepiller a13d451e18
gnu: Add ruby-liquid. 
* gnu/packages/ruby.scm (ruby-liquid): New variable.
 2018-09-01 23:09:02 +02:00
Julien Lepiller f1ec4d7611
gnu: Add ruby-mercenary. 
* gnu/packages/ruby.scm (ruby-mercenary): New variable.
 2018-09-01 23:09:00 +02:00
Julien Lepiller f8ae2ee528
gnu: Add ruby-safe-yaml. 
* gnu/packages/ruby.scm (ruby-safe-yaml): New variable.
 2018-09-01 23:08:58 +02:00
Julien Lepiller 73bfc125ef
gnu: Add ruby-heredoc-unindent. 
* gnu/packages/ruby.scm (ruby-heredoc-unindent): New variable.
 2018-09-01 23:08:56 +02:00
Julien Lepiller 2e072e37aa
gnu: Add ruby-hashie. 
* gnu/packages/ruby.scm (ruby-hashie): New variable.
 2018-09-01 23:08:55 +02:00
Julien Lepiller 2c5028bd97
gnu: Add ruby-rouge-2. 
* gnu/packages/ruby.scm (ruby-rouge-2): New variable.
 2018-09-01 23:08:53 +02:00
Julien Lepiller 4ce0414bca
gnu: Add ruby-rouge. 
* gnu/packages/ruby.scm (ruby-rouge): New variable.
 2018-09-01 23:08:46 +02:00
Julien Lepiller 5e2f74bdb8
gnu: Add ruby-em-websocket. 
* gnu/packages/ruby.scm (ruby-em-websocket): New variable.
 2018-09-01 23:08:44 +02:00
Julien Lepiller fa0063bcf4
gnu: Add ruby-http-parser.rb. 
* gnu/packages/ruby.scm (ruby-http-parser.rb): New variable.
 2018-09-01 23:08:42 +02:00
Julien Lepiller 0312706955
gnu: Add ruby-kramdown. 
* gnu/packages/ruby.scm (ruby-kramdown): New variable.
 2018-09-01 23:08:40 +02:00
Julien Lepiller 197ca8ecd2
gnu: Add ruby-prawn-table. 
* gnu/packages/ruby.scm (ruby-prawn-table): New variable.
 2018-09-01 23:08:38 +02:00
Julien Lepiller 7ad8dd086c
gnu: Add ruby-prawn. 
* gnu/packages/ruby.scm (ruby-prawn): New variable.
 2018-09-01 23:08:36 +02:00
Julien Lepiller 37fbced73c
gnu: Add ruby-yard. 
* gnu/packages/ruby.scm (ruby-yard): New variable.
 2018-09-01 23:08:34 +02:00
Julien Lepiller 770e3b535e
gnu: Add ruby-pdf-core. 
* gnu/packages/ruby.scm (ruby-pdf-core): New variable.
 2018-09-01 23:08:31 +02:00
Julien Lepiller 461fb8598e
gnu: Add ruby-pdf-inspector. 
* gnu/packages/ruby.scm (ruby-pdf-inspector): New variable.
 2018-09-01 23:08:29 +02:00
Julien Lepiller abbe629c6a
gnu: Add ruby-pdf-reader. 
* gnu/packages/ruby.scm (ruby-pdf-reader): New variable.
 2018-09-01 23:08:27 +02:00
Julien Lepiller 00d71efca6
gnu: Add ruby-morecane. 
* gnu/packages/ruby.scm (ruby-morecane): New variable.
 2018-09-01 23:08:10 +02:00
Julien Lepiller 83d9f67221
gnu: Add ruby-cane. 
* gnu/packages/ruby.scm (ruby-cane): New variable.
 2018-09-01 23:08:06 +02:00
Julien Lepiller 3224a5a84a
gnu: Add ruby-parallel. 
* gnu/packages/ruby.scm (ruby-parallel): New variable.
 2018-09-01 23:08:04 +02:00
Julien Lepiller ceac6f6f5b
gnu: Add ruby-jekyll-watch. 
* gnu/packages/ruby.scm (ruby-jekyll-watch): New variable.
 2018-09-01 23:08:02 +02:00
Julien Lepiller 88ed727fc5
gnu: Add ruby-listen-3.0. 
* gnu/packages/ruby.scm (ruby-listen-3.0): New variable.
 2018-09-01 23:08:00 +02:00
Julien Lepiller 5e242cb44c
gnu: Add ruby-jekyll-sass-converter. 
* gnu/packages/ruby.scm (ruby-jekyll-sass-converter): New variable.
 2018-09-01 23:07:58 +02:00
Julien Lepiller f00f449223
gnu: Add ruby-sass. 
* gnu/packages/ruby.scm (ruby-sass): New variable.
 2018-09-01 23:07:56 +02:00
Julien Lepiller 6456beef01
gnu: Add ruby-sass-spec. 
* gnu/packages/ruby.scm (ruby-sass-spec): New variable.
 2018-09-01 23:07:54 +02:00
Julien Lepiller ddc3a66798
gnu: Add ruby-diffy. 
* gnu/packages/ruby.scm (ruby-diffy): New variable.
 2018-09-01 23:07:52 +02:00
Julien Lepiller 0c8eedc153
gnu: Add ruby-terminfo. 
* gnu/packages/ruby.scm (ruby-terminfo): New variable.
 2018-09-01 23:07:50 +02:00
Julien Lepiller 18077ffc46
gnu: Add ruby-sass-listen. 
* gnu/packages/ruby.scm (ruby-sass-listen): New variable.
 2018-09-01 23:07:48 +02:00
Julien Lepiller 6bba8ecf7b
gnu: Add ruby-rdoc. 
* gnu/packages/ruby.scm (ruby-rdoc): New variable.
 2018-09-01 23:07:46 +02:00
Julien Lepiller f22c038799
gnu: Add ruby-command-line-reporter-3. 
* gnu/packages/ruby.scm (ruby-command-line-reporter-3): New variable.
 2018-09-01 23:07:44 +02:00
Julien Lepiller 78b9c291f6
gnu: Add ruby-command-line-reporter. 
* gnu/packages/ruby.scm (ruby-command-line-reporter): New variable.
 2018-09-01 23:07:42 +02:00
Julien Lepiller 9c7f15c048
gnu: Add ruby-colorator. 
* gnu/packages/ruby.scm (ruby-colorator): New variable.
 2018-09-01 23:07:39 +02:00
Julien Lepiller 6f2c4efb56
gnu: Add ruby-addressable. 
* gnu/package/ruby.scm (ruby-addressable): New variable.
 2018-09-01 23:07:37 +02:00
Julien Lepiller 0d16905b60
gnu: Add ruby-public-suffix. 
* gnu/packages/ruby.scm (ruby-public-suffix): New variable.
 2018-09-01 23:07:35 +02:00
Julien Lepiller afb7a3e8d5
gnu: ruby-ttfunk: Update to 1.5.1. 
* gnu/packages/ruby.scm (ruby-ttfunk): Update to 1.5.1.
 2018-09-01 23:07:32 +02:00
Julien Lepiller ef381322d5
gnu: ruby-activesupport: Update to 5.2.1. 
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.2.1.
 2018-09-01 23:07:30 +02:00
Julien Lepiller cbb50182ad
gnu: ruby-i18n: Update to 1.1.0. 
* gnu/packages/ruby.scm (ruby-i18n): Update to 1.1.0.
 2018-09-01 23:07:28 +02:00
Julien Lepiller 352b5d7e74
gnu: Add ruby-concurrent. 
* gnu/packages/ruby.scm (ruby-concurrent): New variable.
 2018-09-01 23:07:06 +02:00
Oleg Pykhalov ead46692ec
gnu: Add zabbix-agentd and zabbix-server. 
* gnu/packages/monitoring.scm (zabbix-agentd, zabbix-server): New variables.
 2018-09-01 19:01:36 +03:00
Marius Bakke e59588482b
gnu: nss, nss-certs: Update to 3.39 [fixes CVE-2018-12384]. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.39.
* gnu/packages/certs.scm (nss-certs): Likewise.
 2018-09-01 13:26:13 +02:00
Marius Bakke 7ea90c217f
gnu: nspr: Update to 4.20. 
* gnu/packages/gnuzilla.scm (nspr): Update to 4.20.
 2018-09-01 13:23:39 +02:00
Leo Famulari ea59f0487b
gnu: Remove Krita 3. 
Krita 3 fails to build with Qt 5.11.1. Since it's also unmaintained upstream,
remove it.

* gnu/packages/kde.scm (krita-3): Remove variable.
 2018-09-01 02:09:53 -04:00
Leo Famulari fd67d793c2
gnu: Krita: Build with libraw 0.18. 
Fixes <https://bugs.gnu.org/32467>.

Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

* gnu/packages/photo.scm (libraw-0.18): New variable.
* gnu/packages/kde.scm (krita)[inputs]: Use libraw-0.18.
 2018-09-01 02:09:52 -04:00
Leo Famulari 7ce9eaf013
gnu: Krita: Update to 4.1.1. 
* gnu/packages/kde.scm (krita): Update to 4.1.1.
 2018-09-01 02:09:52 -04:00
Leo Famulari d84a887a5f
gnu: libksysguard: Update to 5.13.4. 
* gnu/packages/kde.scm (libksysguard): Update to 5.13.4.
 2018-09-01 02:09:52 -04:00
Leo Famulari 600f1ad8e6
gnu: KDE: Update to 5.49.0. 
Fixes <https://bugs.gnu.org/32013>.

* gnu/packages/kde-frameworks.scm (attica, baloo, bluez-qt, breeze-icons,
extra-cmake-modules, kactivities, kactivities-stats, kapidox, karchive, kauth,
kbookmarks, kcmutils, kcodecs, kcompletion, kconfig, kconfigwidgets,
kcoreaddons, kcrash, kdbusaddons, kde-framework-integration, kdeclarative, kded,
kdesignerplugin, kdesu, kdewebkit, kdnssd, kdoctools, kemoticons, kfilemetadata,
kglobalaccel, kguiaddons, ki18n, kiconthemes, kidletime, kimageformats, kinit,
kio, kirigami, kitemmodels, kitemview, kjobwidgets, knewstuff, knotification,
knotifyconfig, kpackage, kparts, kpeople, kplotting, kpty, krunner, kservice,
ksyntaxhighlighting, ktexteditor, ktextwidgets, kunitcoversion, kwallet,
kwayland, kwidgetsaddons, kwindowsystem, kxmlgui, kxmlrpcclient,
modemmanager-qt, networkmanager-qt, oxygen-icons, plasma-framework, prison,
qqc2-desktop-style, solid, sonnet, threadweaver): Update to 5.49.0.
(extra-cmake-modules)[arguments]: Remove obsolete workaround.
(attica)[arguments]: Disable some new tests.

Co-authored-by: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 2018-09-01 02:09:49 -04:00
Eric Bavier 220458b098
gnu: hypre: Update to 2.14.0. 
* gnu/packages/maths.scm (hypre): Update to 2.14.0
 2018-08-31 10:08:00 -05:00
Ricardo Wurmus 9ce2f07ab6
gnu: python-matplotlib: Use python-pyqt-without-qtwebkit. 
* gnu/packages/python.scm (python-matplotlib)[propagated-inputs]: Replace
python-pyqt with python-pyqt-without-qtwebkit.
 2018-08-31 16:37:56 +02:00
Ricardo Wurmus 0e2d6d2698
gnu: Add python-pyqt-without-qtwebkit. 
* gnu/packages/qt.scm (python-pyqt-without-qtwebkit): New variable.
 2018-08-31 16:37:56 +02:00
Clément Lassieur 9fc2922794
services: nginx: Get the Shepherd to respawn NGINX. 
* gnu/services/web.scm (nginx-shepherd-service): Change 'start' (that is, all
actions that don't send a signal to the master process) to return the PID.
Wait until the PID file is created and contains an integer because it might be
created after the parent process exits.
 2018-08-31 16:35:39 +02:00
Rutger Helling 0b6678cd44
gnu: retroarch: Update to 1.7.4. 
* gnu/packages/emulators.scm (retroarch): Update to 1.7.4.
 2018-08-31 08:25:45 +02:00
Nicolas Goaziou be4c63f484
gnu: mame: Update to 0.201. 
* gnu/packages/emulators.scm (mame): Update to 0.201.
[arguments]: Remove unnecessary fix.
 2018-08-31 07:04:17 +02:00
Tobias Geerinckx-Rice 0c048c11a4
gnu: cmocka: Update to 1.1.2. 
* gnu/packages/check.scm (cmocka): Update to 1.1.2.
 2018-08-30 19:29:08 +02:00
Tobias Geerinckx-Rice 8a68b71d99
gnu: keyutils: Update to 1.5.11. 
* gnu/packages/crypto.scm (keyutils): Update to 1.5.11.
[inputs]: Add mit-krb5.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice d6d9ca1017
gnu: Don't use unstable tarballs in (packages opencl). 
* gnu/packages/opencl.scm (opencl-clhpp, clinfo, beignet, pocl)
[source]: Use GIT-FETCH and GIT-FILE-NAME.
(pocl)[arguments]: Remove ‘remove-headers’ phase.
(make-opencl-headers)[source]: Use GIT-FILE-NAME.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 8294362688
gnu: Add pipewalker. 
* gnu/packages/games.scm (pipewalker): New public variable.
 2018-08-30 19:28:11 +02:00
Tobias Geerinckx-Rice 6e8c75b884
gnu: Add msr-tools. 
* gnu/packages/hardware.scm (msr-tools): New public variable.
 2018-08-30 19:28:10 +02:00
Tobias Geerinckx-Rice aadd1d241c
gnu: Add ddcutil. 
* gnu/packages/hardware.scm: New file.
(ddcutil): New public variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add the new file.
 2018-08-30 19:28:10 +02:00
Marius Bakke 7693f678d1
gnu: pango: Replace with 1.42.4. 
Fixes <https://bugs.gnu.org/32594>.

* gnu/packages/gtk.scm (pango)[replacement]: New field.
(pango-1.42.4): New public variable.
 2018-08-30 18:57:10 +02:00
Marius Bakke 883832b480
gnu: appstream-glib: Update to 0.7.12. 
* gnu/packages/glib.scm (appstream-glib): Update to 0.7.12.
 2018-08-30 18:44:57 +02:00
Marius Bakke 4c13cb36f8
gnu: GnuPG: Update to 2.2.10. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.10.
 2018-08-30 18:44:57 +02:00
Marius Bakke e50c727878
gnu: rng-tools: Update to 6.4. 
* gnu/packages/linux.scm (rng-tools): Update to 6.4.
 2018-08-30 18:44:57 +02:00
Marius Bakke d3c1075c14
gnu: samba: Update to 4.8.5. 
* gnu/packages/samba.scm (samba): Update to 4.8.5.
 2018-08-30 18:44:57 +02:00
Marius Bakke 652940d060
gnu: ldb: Update to 1.3.6. 
* gnu/packages/samba.scm (ldb): Update to 1.3.6.
 2018-08-30 18:44:57 +02:00
Marius Bakke 99088aa751
gnu: p11-kit: Update to 0.23.14. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.14.
 2018-08-30 18:44:56 +02:00
Marius Bakke 471884ed11
gnu: lilv: Propagate LV2. 
* gnu/packages/audio.scm (lilv)[propagated-inputs]: Add LV2.
[inputs]: Remove.
 2018-08-30 18:44:51 +02:00
Oleg Pykhalov b5d1286f2d
gnu: net-snmp: Specify '--with-openssl' configuration flag. 
* gnu/packages/networking.scm (net-snmp)[arguments]: Add '--with-openssl'
flag.
 2018-08-30 14:46:15 +03:00
Eric Bavier f9e140a243
netsurf: Upgrade to 3.8. 
* gnu/packages/patches/netsurf-message-timestamp.patch: New patch.
* gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source.
* gnu/packages/web.scm (netsurf): Upgrade to 3.8.
[source]: Add the new patch.
 2018-08-30 00:44:40 -05:00
Eric Bavier c558113fb9
nsgenbind: Upgrade to 0.6. 
* gnu/packages/web.scm (nsgenbind): Upgrade to 0.6.
 2018-08-30 00:44:40 -05:00
Eric Bavier 1be7077572
libnspsl: Upgrade to 0.1.3. 
* gnu/packages/web.scm (libnspsl): Upgrade to 0.1.3.
 2018-08-30 00:44:40 -05:00
Eric Bavier 3e1035d738
libnsutils: Upgrade to 0.0.5. 
* gnu/packages/web.scm (libnsutils): Upgrade to 0.0.5.
 2018-08-30 00:44:40 -05:00
Eric Bavier 1dc02e727b
libnsgif: Upgrade to 0.2.1. 
* gnu/packages/web.scm (libnsgif): Upgrade to 0.2.1.
 2018-08-30 00:44:39 -05:00
Eric Bavier ef2198ac5b
libnsbmp: Upgrade to 0.1.5. 
* gnu/packages/web.scm (libnsbmp): Upgrade to 0.1.5.
 2018-08-30 00:44:39 -05:00
Eric Bavier bb38628fab
libsvgtiny: Upgrade to 0.1.7. 
* gnu/packages/web.scm (libsvgtiny): Upgrade to 0.1.7.
 2018-08-30 00:44:39 -05:00
Eric Bavier f8311c0fee
libdom: Upgrade to 0.3.3. 
* gnu/packages/web.scm (libdom): Upgrade to 0.3.3.
 2018-08-30 00:44:39 -05:00
Eric Bavier 2bb1752b7d
libcss: Upgrade to 0.8.0. 
* gnu/packages/web.scm (libcss): Upgrade to 0.8.0.
 2018-08-30 00:44:39 -05:00
Eric Bavier 60e411fc94
libwapcaplet: Upgrade to 0.4.1. 
* gnu/packages/web.scm (libwapcaplet): Upgrade to 0.4.1.
 2018-08-30 00:44:39 -05:00
Eric Bavier b06bf74b41
hubbub: Upgrade to 0.3.5. 
* gnu/packages/web.scm (hubbub): Upgrade to 0.3.5.
 2018-08-30 00:44:39 -05:00
Eric Bavier ea9b34c2f5
libparserutils: Upgrade to 0.2.4. 
* gnu/packages/web.scm (libparserutils): Upgrade to 0.2.4.
 2018-08-30 00:44:38 -05:00
Eric Bavier fa4131f2aa
netsurf-buildsystem: Upgrade to 1.7. 
* gnu/packages/web.scm (netsurf-buildsystem): Upgrade to 1.7.
 2018-08-30 00:44:33 -05:00
Mark H Weaver a28604ee81
gnu: linux-libre@4.4: Update to 4.4.153. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.153.
 2018-08-30 00:53:01 -04:00
Tobias Geerinckx-Rice 9986316618
gnu: mujs: Update to 1.0.4. 
* gnu/packages/javascript.scm (mujs): Update to 1.0.4.
 2018-08-30 04:42:54 +02:00
Tobias Geerinckx-Rice bfb994d8be
gnu: r-car: Update to 3.0-2. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-2.
 2018-08-30 04:42:52 +02:00
Tobias Geerinckx-Rice ad3306f62f
gnu: perl-gd: Update to 2.69. 
* gnu/packages/gd.scm (perl-gd): Update to 2.69.
 2018-08-30 04:42:51 +02:00
Tobias Geerinckx-Rice 33eea5c439
gnu: perl-sub-identify: Update to 0.14. 
* gnu/packages/perl.scm (perl-sub-identify): Update to 0.14.
 2018-08-30 04:42:51 +02:00
Tobias Geerinckx-Rice a82b561fef
gnu: robocut: Don't use unstable tarball. 
* gnu/packages/printers.scm (robocut)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2018-08-30 04:42:38 +02:00
Tobias Geerinckx-Rice 1f0f9514eb
gnu: gparted: Update to 0.32.0. 
* gnu/packages/disk.scm (gparted): Update to 0.32.0.
 2018-08-30 04:40:31 +02:00
Tobias Geerinckx-Rice 7bb7920f64
gnu: duplicity: Update to 0.7.18.1. 
* gnu/packages/backup.scm (duplicity): Update to 0.7.18.1.
[arguments]: Remove upstreamed '--ignore-mdc-error' kluge.
Rename 'patch-source' phase to 'use-store-file-names'.
 2018-08-30 03:51:00 +02:00
Kei Kebreau 99e0fb24fb
gnu: audacity: Fix GtkFileChooserDialog. 
* gnu/packages/audio.scm (audacity)[arguments]: Add 'wrap-program' phase to fix
GtkFileChooserDialog.
[inputs]: Rename "gtk" to "gtk+".
 2018-08-29 20:56:35 -04:00
Oleg Pykhalov 8490a8346b
services: Add ddclient service. 
* gnu/services/dns.scm (ddclient-configuration, ddclient-service-type): New
variables.
(uglify-field-name, serialize-field, serialize-boolean, serialize-integer,
serialize-string, serialize-list, serialize-extra-options,
ddclient-activation, ddclient-shepherd-service,
generate-ddclient-documentation): New procedures.
* doc/guix.texi (DNS Services): Document it.
 2018-08-30 01:19:47 +03:00
Ludovic Courtès 4db7a9dc66
linux-modules: Raise an error when a kernel module cannot be found. 
Previously we'd get an unhelpful backtrace like this:

  In gnu/build/linux-modules.scm:
     184:47  4 (recursive-module-dependencies _ #:lookup-module _)
      98:14  3 (module-dependencies _)
      85:18  2 (modinfo-section-contents _)
  In ice-9/ports.scm:
     439:11  1 (call-with-input-file #f #<procedure get-bytevector-al?> ?)
  In unknown file:
	     0 (open-file #f "r" #:encoding #f #:guess-encoding #f)

  ERROR: In procedure open-file:
  Wrong type (expecting string): #f
  builder for `/gnu/store/…-linux-modules.drv' failed with exit code 1

* gnu/build/linux-modules.scm (find-module-file): When MODULE cannot be
found, raise an error instead of returning #f.  This is more useful to
the user.
 2018-08-29 23:32:01 +02:00
Ludovic Courtès d258c79144
tests: Warn about test module load failures. 
Reported by Clément Lassieur <clement@lassieur.org>
and Leo Famulari <leo@famulari.name> at
<https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32545#11>.

* gnu/tests.scm (test-modules): Pass #:warn to 'scheme-modules'.
 2018-08-29 23:32:01 +02:00
Christopher Lemmer Webber caf8a003b3
gnu: emacs-racket-mode: Update to commit 92c3348. 
* gnu/packages/emacs.scm (emacs-racket-mode): Update to commit 92c3348.
 2018-08-29 15:52:20 -04:00
Vagrant Cascadian b4c698c8c9
gnu: python-trezor: Update to 0.10.2. 
* gnu/packages/finance.scm (python-trezor): Update to 0.10.2.
[arguments]: Replace check with tests that do not require hardware device.
[propagated-inputs]: Add python-click, python-libusb1, python-pyblake2 and
python-typing.
[native-inputs]: Add python-mock and python-pytest.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:52:56 -04:00
pimi 4f9355c360
gnu: Add gffcompare. 
gnu/packages/bioinformatics.scm (gffcompare): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:13:49 -04:00
pimi 9e21f2170e
gnu: Add r-abcoptim. 
gnu/packages/cran.scm (r-abcoptim): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:13:46 -04:00
Danny Milosavljevic 15c56e8273
gnu: Add solaar. 
* gnu/packages/admin.scm (solaar): New variable.
 2018-08-29 17:18:30 +02:00
Danny Milosavljevic ac94ccb9b4
gnu: Add python-pyudev. 
* gnu/packages/admin.scm (python-pyudev): New variable.
 2018-08-29 17:18:28 +02:00
Ricardo Wurmus c7fe888b42
gnu: Add python-scanpy. 
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus 22b770ce00
gnu: Add python-anndata. 
* gnu/packages/python.scm (python-anndata): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus d8b8eb3ff5
gnu: Add python-numba. 
* gnu/packages/python.scm (python-numba): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus 8892cac329
gnu: Add python-llvmlite. 
* gnu/packages/llvm.scm (python-llvmlite): New variable.
 2018-08-29 17:06:13 +02:00
Marius Bakke 9e17757ff5
Revert "gnu: snappy: Optimise." 
This causes too many rebuilds for the master branch.

This reverts commit f96ed06805.
 2018-08-29 16:58:54 +02:00
Ricardo Wurmus 9587544b44
gnu: Add ghc 8.4.3. 
* gnu/packages/haskell.scm (ghc-8): Rename this...
(ghc-8.0): ...to this.
(ghc): Point at ghc-8.0.
(ghc-8): New variable for GHC 8.4.3.

Co-authored-by: Timothy Samplet <samplet@ngyro.com>
 2018-08-29 16:56:35 +02:00
Ricardo Wurmus 59b55def00
gnu: Add r-infotheo. 
* gnu/packages/cran.scm (r-infotheo): New variable.
 2018-08-29 13:11:17 +02:00
Tobias Geerinckx-Rice acf18cb190
gnu: capstone: Use HTTPS home page. 
* gnu/packages/engineering.scm (capstone)[home-page]: Use HTTPS.
 2018-08-28 22:46:38 +02:00
Tobias Geerinckx-Rice 2c3d30ef51
gnu: r-plotrix: Update to 3.7-3. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-3.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice f882d7c7c5
gnu: python-apipkg: Update home page. 
* gnu/packages/python.scm (python-apipkg)[home-page]: Update.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice e29bb27d88
gnu: r-pracma: Update to 2.1.5. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.5.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice 7bbdd943e7
gnu: claws-mail: Update to 3.17.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.17.1.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice 4fca5a44f6
gnu: libntlm: Update to 1.5. 
* gnu/packages/gsasl.scm (libntlm): Update to 1.5.
[source]: Use HTTPS.
 2018-08-28 22:31:00 +02:00
Tobias Geerinckx-Rice f96ed06805
gnu: snappy: Optimise. 
* gnu/packages/compression.scm (snappy)[source]: Build with ‘-O2’.
* gnu/package/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-08-28 22:30:59 +02:00
Efraim Flashner dc8675afa7
gnu: Add urlscan. 
* gnu/packages/mail.scm (urlscan): New variable.
 2018-08-28 22:48:32 +03:00
Efraim Flashner 967de7c5b0
gnu: Add ephoto. 
* gnu/packages/enlightenment.scm (ephoto): New variable.
 2018-08-28 22:45:55 +03:00
Vagrant Cascadian 84fbb4b223
gnu: electron-cash: Update to 3.3.1. 
* gnu/packages/finance.scm (electron-cash): Update to 3.3.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-28 15:30:13 -04:00
Leo Famulari 8a5a1eff42
gnu: dropbear: Fix CVE-2018-15599. 
* gnu/packages/patches/dropbear-CVE-2018-15599.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ssh.scm (dropbear)[source]: Use it.
 2018-08-28 14:44:11 -04:00
Ludovic Courtès 6772ed1e07
services: openssh: Add 'log-level' field. 
* gnu/services/ssh.scm (<openssh-configuration>)[log-level]: New field.
(openssh-config-file): Honor it.
* doc/guix.texi (Networking Services): Document it.
 2018-08-28 12:35:02 +02:00
Ludovic Courtès 1ae29e3f5a
gnu: dico: Update to 2.6. 
* gnu/packages/dico.scm (dico): Update to 2.6.
[inputs]: Switch to GUILE-2.2.
 2018-08-28 12:35:02 +02:00
Ison111 d2434b6966
gnu: Add SpaceFM. 
* gnu/packages/lxde.scm (spacefm): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-28 12:35:02 +02:00
Alex Kost 40f7ebac66
gnu: Add emacs-build-farm. 
* gnu/packages/emacs.scm (emacs-build-farm): New variable.
 2018-08-28 12:23:52 +03:00
Alex Kost 8b1f8f64c8
gnu: openmw: Update to 0.44.0. 
* gnu/packages/game-development.scm (openmw): Update to 0.44.0.
 2018-08-28 12:23:52 +03:00
Chris Marusich 3bcb305b98
services: tor: Make it easier to use UNIX sockets. 
* doc/guix.texi (Networking Services): Document it, and mention that
tor-service is deprecated.
* gnu/services/networking.scm (<tor-configuration>) <socks-socket-type>:
New field.
(tor-configuration->torrc): When socks-socket-type is 'unix, set
SocksPort to UNIX domain socket /var/run/tor/socks-sock and set
UnixSocksGroupWritable to 1.
* gnu/tests/networking.scm (%tor-os/unix-socks-socket): Instead of using
a custom config file, just set socks-socket-type to 'unix.
 2018-08-28 00:25:05 -07:00
Chris Marusich b0f951e4f0
tests: tor: Add more test cases. 
* gnu/tests/networking.scm (%tor-os/unix-socks-socket): New variable.
(run-tor-test) <os/unix-socks-socket, marionette/unix-socks-socket>
<socket-directory>: New variables.
<"tor is alive">: Move common code from this test case...
<tor-is-alive?>: ...into this new procedure.
<"tor is listening", "tor is alive, even when using a SOCKS socket">
<"tor is listening, even when using a SOCKS socket">: New test cases.
 2018-08-28 00:19:58 -07:00
Chris Marusich cb29343940
marionette: Add wait-for-unix-socket. 
* gnu/build/marionette.scm (wait-for-unix-socket): New variable.
 2018-08-28 00:19:58 -07:00
Chris Marusich 4dd53a83b5
marionette: Add support for QEMU's "quit" command. 
* gnu/build/marionette.scm (marionette-control): Don't wait for the
monitor prompt when the command was "quit".
 2018-08-28 00:14:25 -07:00
Chris Marusich d973915e48
services: tor: Rename activation procedure. 
* gnu/services/networking.scm: Rename the procedure
tor-hidden-service-activation to tor-activation.
 2018-08-28 00:14:24 -07:00
Chris Marusich 5dfd80e1c5
services: tor: Add a system test. 
* gnu/services/networking.scm (tor-configuration->torrc): Set PidFile to
/var/run/tor/tor.pid in the base torrc configuration.
(tor-shepherd-service) <start>: Call make-forkexec-constructor/container with
a new #:pid-file argument to tell Shepherd where to find the PID file.  Add a
a new <file-system-mapping> to its existing #:mappings argument to share
/var/run/tor with the the container.
(tor-hidden-services-activation): Update docstring.  Create /var/run/tor and
set its permissions so only the tor user can access it.
* gnu/tests/networking.scm (%test-tor, %tor-os): New variables.
(run-tor-test): New procedure.
 2018-08-28 00:14:24 -07:00
Marius Bakke 526ce41930
gnu: GRUB: Check for errors from efibootmgr. 
* gnu/packages/patches/grub-check-error-efibootmgr.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bootloaders.scm (grub)[source](patches): New field.
 2018-08-28 01:19:28 +02:00
Marius Bakke 2987b2e0d2
gnu: seabios: Update source URI. 
* gnu/packages/firmware.scm (seabios)[source](uri): Download from seabios.org.
 2018-08-28 01:19:28 +02:00
Marius Bakke eb87b634a7
gnu: slang: Update to 2.3.2. 
* gnu/packages/slang.scm (slang): Update to 2.3.2.
 2018-08-28 01:19:28 +02:00
Marius Bakke 3c3c3d1d92
gnu: emacs-async: Download using git. 
The MELPA tarball hash changed.  Prevent this problem in the future
by downloading a git checkout.

* gnu/packages/emacs.scm (emacs-async)[home-page]: Update to actual.
[source]: Use GIT-FETCH.
 2018-08-28 01:19:28 +02:00
Leo Famulari 0de33cb364
gnu: feh: Enable EXIF support. 
* gnu/packages/image-viewers.scm (feh)[arguments]: Enable EXIF support.
(inputs): Add libexif.
 2018-08-27 17:04:57 -04:00
Leo Famulari f2d2dc70fc
gnu: libexif: Update home-page URL. 
* gnu/packages/photo.scm (libexif)[home-page]: Update URL.
 2018-08-27 17:04:57 -04:00
Leo Famulari 6635a3cc7f
gnu: python-pygit2: Update to 0.26.4. 
* gnu/packages/python.scm (python-pygit2, python2-pygit2): Update to 0.26.4.
[source]: Remove 'python-pygit2-disable-network-tests.patch'.
* gnu/packages/patches/python-pygit2-disable-network-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-08-27 15:13:46 -04:00
Clément Lassieur a30cbd5dfb
gnu: cuirass: Update to 8d40c49. 
* gnu/packages/ci.scm (cuirass): Update to 8d40c49.
 2018-08-27 16:12:56 +02:00
Pierre Neidhardt 4715f92ef0
Update email for Pierre Neidhardt. 
* .mailmap: Add name and email for Pierre Neidhardt.
* gnu/packages/c.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/disk.scm, gnu/packages/emacs.scm, gnu/packages/freedesktop.scm,
gnu/packages/golang.scm, gnu/packages/image.scm, gnu/packages/music.scm,
gnu/packages/networking.scm, gnu/packages/password-utils.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/textutils.scm, gnu/packages/video.scm, gnu/packages/xdisorg.scm:
Update email for Pierre Neidhardt.
 2018-08-27 14:46:26 +02:00
Rutger Helling 2aeee872a6
gnu: weston: Update to 5.0.0. 
* gnu/packages/freedesktop.scm (weston): Update to 5.0.0.
 2018-08-27 10:11:30 +02:00
Ludovic Courtès 1ca54999db
gnu: Add Lepton-EDA. 
* gnu/packages/engineering.scm (lepton-eda): New variable.
 2018-08-27 01:13:23 +02:00
Ludovic Courtès 69502b5eb4
gnu: Add guile-aa-tree. 
* gnu/packages/guile.scm (guile-aa-tree): New variable.
 2018-08-27 01:13:23 +02:00
Christopher Lemmer Webber 6948fa0875
gnu: emacs-racket-mode: Update to commit add0190. 
* gnu/packages/emacs.scm (emacs-racket-mode): Update to commit add0190.
 2018-08-26 07:02:04 -04:00
Arun Isaac 2cad58ca6f
gnu: ghc-scientific: Update to 0.3.6.2. 
* gnu/packages/haskell.scm (ghc-scientific): Update to 0.3.6.2.
[inputs]: Move ghc-tasty ...
[native-inputs]: ... to here.
 2018-08-26 11:48:22 +05:30
Arun Isaac 7550f4b0ef
gnu: ghc-integer-logarithms: Update to 1.0.2.1. 
* gnu/packages/haskell.scm (ghc-integer-logarithms): Update to 1.0.2.1.
[inputs]: Move ghc-quickcheck, ghc-smallcheck, ghc-tasty, ghc-tasty-hunit,
ghc-tasty-quickcheck, ghc-tasty-smallcheck ...
[native-inputs]: ... to here.
[home-page]: Update URI.
 2018-08-26 11:37:25 +05:30
Arun Isaac b625f3a5fb
gnu: ghc-smallcheck: Update to 1.1.5. 
* gnu/packages/haskell.scm (ghc-smallcheck): Update to 1.1.5.
 2018-08-26 11:33:48 +05:30
Arun Isaac 3c30054290
gnu: ghc-optparse-applicative: Update to 0.14.2.0. 
* gnu/packages/haskell.scm (ghc-optparse-applicative): Update to 0.14.2.0.
[arguments]: Enable tests.
 2018-08-26 11:27:00 +05:30
Mark H Weaver cfb15a5163
gnu: linux-libre: Update to 4.18.5. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.5.
(%linux-libre-hash): Update hash.
 2018-08-26 00:38:41 -04:00
Mark H Weaver fabe2c7354
gnu: linux-libre@4.14: Update to 4.14.67. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.67.
(%linux-libre-4.14-hash): Update hash.
 2018-08-26 00:36:42 -04:00
Mark H Weaver 8d55adfa67
gnu: linux-libre@4.9: Update to 4.9.124. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.124.
 2018-08-26 00:36:11 -04:00
Mark H Weaver 032712f621
gnu: linux-libre@4.4: Update to 4.4.152. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.152.
 2018-08-26 00:35:30 -04:00
Ludovic Courtès 64daf2177f
gnu: emacs-recent-addresses: Switch to a branch that works with Helm. 
* gnu/packages/emacs.scm (emacs-recent-addresses)[source]: Change URL
and update to afbbfdc.
 2018-08-26 01:47:41 +02:00
Kyle Meyer bff861ece5
gnu: Add emacs-git-annex. 
* gnu/packages/emacs.scm (emacs-git-annex): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-26 01:47:40 +02:00
Kyle Meyer 8a9e0b6ebf
gnu: emacs-recent-addresses: Add missing words to description. 
* gnu/packages/emacs.scm (emacs-recent-addresses)[description]: Add missing
words.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-08-26 01:47:40 +02:00
Kei Kebreau 7d01ee66d4
gnu: Add avogadro. 
* gnu/packages/chemistry.scm (avogadro): New variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2018-08-25 17:05:30 -04:00
Marius Bakke 94e9d750a2
gnu: libx11: Replace with 1.6.6 [security fixes]. 
This fixes CVE-2018-14599, CVE-2018-14600, and CVE-2018-14598.

* gnu/packages/xorg.scm (libx11)[replacement]: New field.
(libx11-1.6.6): New public variable.
 2018-08-25 16:32:06 +02:00
宋文武 7789bf9531
gnu: dante: Disable preloading to make 'sockd' work. 
* gnu/packages/networking.scm (dante)[arguments]: Pass '--disable-preload'
to #:configure-flags.
 2018-08-25 16:40:21 +08:00
Leo Famulari 36a8d5cdf4
gnu: OpenSSH: Update to 7.8p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.8p1.
[source]: Remove 'openssh-CVE-2018-15473.patch'.
* gnu/packages/patches/openssh-CVE-2018-15473.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-08-24 17:04:58 -04:00
Ludovic Courtès c1352b4bad
gnu: font-gnu-unifont: Update to 11.0.02. 
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 11.0.02.
[arguments]: Adjust code to install 'unifont.info.gz' in 'install'
phase.
 2018-08-24 17:54:10 +02:00
Ludovic Courtès bf0bb925ea
gnu: gdb: Update to 8.1.1. 
* gnu/packages/gdb.scm (gdb): Update to 8.1.1.
 2018-08-24 17:50:52 +02:00
Ricardo Wurmus 079cdd9c15
gnu: Add find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): New variable.
 2018-08-24 11:20:19 +02:00
Tobias Geerinckx-Rice 4a3cf8929f
gnu: r-catools: Update to 1.17.1.1. 
* gnu/packages/statistics.scm (r-catools): Update to 1.17.1.1.
 2018-08-24 04:25:50 +02:00
Tobias Geerinckx-Rice 0e5d66abf6
gnu: keepassxc: Update to 2.3.4. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.4.
[arguments]: Remove obsolete ‘patch-sources’ phase.
 2018-08-24 04:25:50 +02:00
Tobias Geerinckx-Rice a7b14a1b39
gnu: capstone: Update to 3.0.5. 
* gnu/packages/engineering.scm (capstone): Update to 3.0.5.
[arguments]: Set cstool's LDFLAGS in the environment instead of
SUBSTITUTE*ing the Makefile.
 2018-08-24 03:04:56 +02:00
Tobias Geerinckx-Rice 77c027b98b
gnu: r-trimcluster: Update to 0.1-2.1. 
* gnu/packages/statistics.scm (r-trimcluster): Update to 0.1-2.1.
 2018-08-24 02:30:43 +02:00
Tobias Geerinckx-Rice 6d83cd1f9a
gnu: r-synchronicity: Update to 1.3.5. 
* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.5.
 2018-08-24 02:30:42 +02:00
Tobias Geerinckx-Rice 6a9a50fd2f
gnu: guile-lib: Update to 0.2.6.1. 
* gnu/packages/guile.scm (guile-lib): Update to 0.2.6.1.
[source]: Remove obsolete snippet.
 2018-08-24 02:30:42 +02:00
Tobias Geerinckx-Rice a0a7e42500
gnu: tuxguitar: Update to 1.5.2. 
* gnu/packages/music.scm (tuxguitar): Update to 1.5.2.
[source]: Remove obsolete snippet.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice 38146797e6
gnu: libgig: Update to 4.1.0. 
* gnu/packages/music.scm (libgig): Update to 4.1.0.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice f6181921e5
gnu: denemo: Use INVOKE. 
* gnu/packages/music.scm (denemo)[arguments]: Substitute INVOKE for
SYSTEM*.
 2018-08-24 02:30:41 +02:00
Tobias Geerinckx-Rice fbde7b08e5
gnu: ncmpc: Update to 0.29. 
* gnu/packages/mpd.scm (ncmpc): Update to 0.29.
[build-system]: Switch to Meson.
[arguments]: Find ncurses.h.
[native-inputs]: Add gettext.
 2018-08-24 02:30:41 +02:00
Ludovic Courtès 0b4e5f7e5b
gnu: parallel: Update to 20180822. 
* gnu/packages/parallel.scm (parallel): Update to 20180822.
 2018-08-24 00:40:09 +02:00
Ludovic Courtès 444488fc1b
gnu: boost: Move 1.59.0 definition to boost.scm. 
Fixes a regression introduced in commit
7cbf06d8c2 where the top-level code of
these two modules would depend on each other, leading to "boost: unbound
variable" kind of errors in some circumstances.

* gnu/packages/databases.scm (boost-for-mysql): Move to...
* gnu/packages/boost.scm (boost-for-mysql): ... here.  Make public and
add 'properties' field.
 2018-08-24 00:36:04 +02:00
Tobias Geerinckx-Rice d32da49c76
gnu: r-devtools: Update to 1.13.6. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.6.
 2018-08-23 23:11:52 +02:00
Tobias Geerinckx-Rice c95f9f09a7
gnu: drumkv1: Update to 0.9.2. 
* gnu/packages/music.scm (drumkv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 69b4d24871
gnu: synthv1: Update to 0.9.2. 
* gnu/packages/music.scm (synthv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 29618d6722
gnu: samplv1: Update to 0.9.2. 
* gnu/packages/music.scm (samplv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 2c59066f6a
gnu: padthv1: Update to 0.9.2. 
* gnu/packages/music.scm (padthv1): Update to 0.9.2.
 2018-08-23 23:01:56 +02:00
Tobias Geerinckx-Rice 9459216aa1
gnu: Update home pages for the V1 synth family. 
* gnu/packages/music.scm (synthv1, drumkv1, samplv1, padthv1)
[home-page]: Update & use HTTPS.
 2018-08-23 23:01:55 +02:00
pimi 16b0e8da48
gnu: Add r-a3. 
gnu/packages/cran.scm (r-a3): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 881cc61c1b
gnu: Add r-manipulatewidget. 
gnu/packages/cran.scm (r-manipulatewidget): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 87b576aa8b
gnu: Add r-slam. 
gnu/packages/cran.scm (r-slam): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi c994418b8c
gnu: Add r-abcanalysis. 
gnu/packages/cran.scm (r-abcanalysis): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
pimi 67cf070239
gnu: Add r-miniui. 
gnu/packages/web.scm (r-miniui): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-23 16:26:40 -04:00
Tobias Geerinckx-Rice 694765e1d6
gnu: qjackctl: Update to 0.5.3. 
* gnu/packages/audio.scm (qjackctl): Update to 0.5.3.
 2018-08-23 17:16:42 +02:00
Tobias Geerinckx-Rice 97353dfb69
gnu: byobu: Update home page. 
* gnu/packages/screen.scm (byobu)[home-page]: Update & use HTTPS.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice 9e29921162
gnu: byobu: Update to 5.127. 
* gnu/packages/screen.scm (byobu): Update to 5.127.
* gnu/packages/patches/byobu-writable-status.patch: Adjust context
accordingly.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice f868276b8a
gnu: wine-staging-patchset-data: Don't use unstable archive. 
* gnu/packages/wine.scm (wine-staging-patchset-data)[source]:
Use GIT-FETCH and GIT-FILE-NAME.
[native-inputs]: Remove unzip.
[arguments]: Adjust and refactor accordingly.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice 574e2ee8ea
gnu: yubico-piv-tool: Update to 1.6.1. 
* gnu/packages/security-token.scm (yubico-piv-tool): Update to 1.6.1.
 2018-08-23 17:16:41 +02:00
Tobias Geerinckx-Rice fa5511b6e9
gnu: r-car: Update to 3.0-1. 
* gnu/packages/statistics.scm (r-car): Update to 3.0-1.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 39bb1cc77a
gnu: r-digest: Update to 0.6.16. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.16.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice ed61c44895
gnu: r-dplyr: Update to 0.7.6. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.6.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 51dbad04c5
gnu: r-rcpp: Update to 0.12.18. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.18.
 2018-08-23 17:16:40 +02:00
Tobias Geerinckx-Rice 02489a6646
gnu: duplicity: Update to 0.7.18. 
* gnu/packages/backup.scm (duplicity): Update to 0.7.18.
 2018-08-23 17:16:39 +02:00
Arun Isaac 72816ebed2
gnu: darcs: Update to 2.14.1. 
* gnu/packages/version-control.scm (darcs): Update to 2.14.1.
[arguments]: Add patch-sh phase. Enable tests.
 2018-08-23 15:51:43 +05:30
Arun Isaac d3c7e70858
gnu: ghc-zlib: Update to 0.6.2. 
* gnu/packages/haskell.scm (ghc-zlib): Update to 0.6.2.
 2018-08-23 14:43:48 +05:30
Arun Isaac cdccdec1f2
gnu: ghc-quickcheck-instances: Update to 0.3.18. 
* gnu/packages/haskell-check.scm (ghc-quickcheck-instances): Update to 0.3.18.
[arguments]: Allow building with newer base-compat.
 2018-08-23 14:37:57 +05:30
Arun Isaac f797a0e987
gnu: ghc-graphviz: Update to 2999.20.0.2. 
* gnu/packages/haskell.scm (ghc-graphviz): Update to 2999.20.0.2.
[native-inputs]: Add ghc-hspec, graphviz and hspec-discover.
 2018-08-23 13:21:23 +05:30