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Author SHA1 Message Date
Ricardo Wurmus 4431dd3a4e
gnu: r-vgam: Update to 1.0-4. 
* gnu/packages/statistics.scm (r-vgam): Update to 1.0-4.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus 41692b2963
gnu: r-mclust: Update to 5.3. 
* gnu/packages/statistics.scm (r-mclust): Update to 5.3.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus 60869fb2f8
gnu: r-flexmix: Update to 2.3-14. 
* gnu/packages/statistics.scm (r-flexmix): Update to 2.3-14.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus 62d3afc3d6
gnu: r-fastica: Update to 1.2-1. 
* gnu/packages/statistics.scm (r-fastica): Update to 1.2-1.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus df03b6f90c
gnu: r-cowplot: Update to 0.8.0. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.8.0.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus d58faa7f44
gnu: r-rann: Update to 2.5.1. 
* gnu/packages/statistics.scm (r-rann): Update to 2.5.1.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus a8c2706de2
gnu: r-statmod: Update to 1.4.30. 
* gnu/packages/statistics.scm (r-statmod): Update to 1.4.30.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus 80d1185076
gnu: r-gdata: Update to 2.18.0. 
* gnu/packages/statistics.scm (r-gdata): Update to 2.18.0.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus 2c75199c56
gnu: r-sfsmisc: Update to 1.1-1. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-1.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus 1d256438c8
gnu: r-googlesheets: Update to 0.2.2. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.2.2.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus 9b9fef0eaf
gnu: r-tidyr: Update to 0.6.3. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.3.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus e1cd25bc78
gnu: r-glmnet: Update to 2.0-10. 
* gnu/packages/statistics.scm (r-glmnet): Update to 2.0-10.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus 1c576cbadb
gnu: r-irlba: Update to 2.2.1. 
* gnu/packages/statistics.scm (r-irlba): Update to 2.2.1.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus 81c057ced9
gnu: r-sparsem: Update to 1.77. 
* gnu/packages/statistics.scm (r-sparsem): Update to 1.77.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus 127b926bc1
gnu: r-segmented: Update to 0.5-2.1. 
* gnu/packages/statistics.scm (r-segmented): Update to 0.5-2.1.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus fe9917284f
gnu: r-xml: Update to 3.98-1.9. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.9.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus cc8ba9b69c
gnu: r-rmarkdown: Update to 1.6. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.6.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus 7c172eacfa
gnu: r-rcpparmadillo: Update to 0.7.900.2.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.900.2.0.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus 1c41d51743
gnu: r-plotrix: Update to 3.6-5. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-5.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus 76040b8561
gnu: r-readr: Update to 1.1.1. 
* gnu/packages/statistics.scm (r-readr): Update to 1.1.1.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus d8048a1212
gnu: r-withr: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-withr): Update to 2.0.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus f212bf84ab
gnu: r-git2r: Update to 0.19.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.19.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus 58e1ce86ab
gnu: r-checkmate: Update to 1.8.3. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.8.3.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus 63f934e672
gnu: r-backports: Update to 1.1.0. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus c832d326a1
gnu: r-formula: Update to 1.2-2. 
* gnu/packages/statistics.scm (r-formula): Update to 1.2-2.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus f05c6275b7
gnu: r-r6: Update to 2.2.2. 
* gnu/packages/statistics.scm (r-r6): Update to 2.2.2.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus b07c8c0156
gnu: r-knitr: Update to 1.16. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.16.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus 6dc86e8dfc
gnu: r-formatr: Update to 1.5. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.5.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus 12cd797541
gnu: r-evaluate: Update to 0.10.1. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.10.1.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus d5ce380711
gnu: r-dbi: Update to 0.7. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.7.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus 831858a7d3
gnu: r-bit64: Update to 0.9-7. 
* gnu/packages/statistics.scm (r-bit64): Update to 0.9-7.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus 6fb21ed2a3
gnu: r-mgcv: Update to 1.8-18. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-18.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus dbeda1b4a0
gnu: r-matrix: Update to 1.2-10. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-10.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus 74b037df64
gnu: r-foreign: Update to 0.8-69. 
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-69.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus af1eeabe89
gnu: r-boot: Update to 1.3-20. 
* gnu/packages/statistics.scm (r-boot): Update to 1.3-20.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus e584b9fc1b
gnu: r-curl: Update to 2.8.1. 
* gnu/packages/web.scm (r-curl): Update to 2.8.1.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus 53deffe5e9
gnu: r-htmlwidgets: Update to 0.9. 
* gnu/packages/web.scm (r-htmlwidgets): Update to 0.9.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus 850151058d
gnu: r-htmltools: Update to 0.3.6. 
* gnu/packages/web.scm (r-htmltools): Update to 0.3.6.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus a1e54db2ac
gnu: r-servr: Update to 0.6. 
* gnu/packages/web.scm (r-servr): Update to 0.6.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus 9fe794f0f7
gnu: r-jsonlite: Update to 1.5. 
* gnu/packages/web.scm (r-jsonlite): Update to 1.5.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus 2d81bc16a9
gnu: r-httpuv: Update to 1.3.5. 
* gnu/packages/web.scm (r-httpuv): Update to 1.3.5.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus 0f2eee0d96
gnu: r-pracma: Update to 2.0.7. 
* gnu/packages/maths.scm (r-pracma): Update to 2.0.7.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus 64c6712d03
gnu: r-knitrbootstrap: Update to 1.0.1. 
* gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.1.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus c628b8418a
gnu: r-ranger: Update to 0.8.0. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.8.0.
[propagated-inputs]: Add r-matrix and r-rcppeigen.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus cc9a778ecc
gnu: r-hmisc: Update to 4.0-3. 
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-3.
[propagated-inputs]: Remove r-base64.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus f9b3760636
gnu: r-plotly: Update to 4.7.1. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.7.1.
[propagated-inputs]: Add r-crosstalk, r-data-table, r-htmltools, and
r-rcolorbrewer.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus d59050823e
gnu: r-igraph: Update to 1.1.2. 
* gnu/packages/statistics.scm (r-igraph): Update to 1.1.2.
[propagated-inputs]: Remove r-nmf; add r-matrix and r-pkgconfig.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus 7b3688150b
gnu: r-purrr: Update to 0.2.2.2. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.2.2.
[propagated-inputs]: Remove r-bh and r-dplyr; add r-tibble.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus 5fc74f24bf
gnu: r-devtools: Update to 1.13.3. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.3.
[propagated-inputs]: Remove r-curl, r-digest, r-evaluate, r-roxygen2, and
r-rversions.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus aad948a0ea
gnu: r-tibble: Update to 1.3.3. 
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.3.
[propagated-inputs]: Remove r-lazyeval, add r-rlang.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus a40b2c2129
gnu: r-dplyr: Update to 0.7.2. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.2.
[propagated-inputs]: Remove r-lazyeval, r-dbi; add r-rlang, r-plogr, r-glue,
r-pkgconfig, r-bindrcpp.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus 4bb0b4cc0a
gnu: Add r-bindrcpp. 
* gnu/packages/cran.scm (r-bindrcpp): New variable.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus eed58a0886
gnu: Add r-bindr. 
* gnu/packages/cran.scm (r-bindr): New variable.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus a8cba9dd11
gnu: r-rcpp: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-rcpp): Move from here...
* gnu/packages/cran.scm (r-rcpp): ...to here.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus 736332c79c
gnu: r-rcpp: Update to 0.12.12. 
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.12.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus 847b457253
gnu: r-plogr: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-plogr): Move from here...
* gnu/packages/cran.scm (r-plogr): ...to here.
 2017-08-03 17:53:41 +02:00
Ricardo Wurmus 5bee6bf409
gnu: Add r-glue. 
* gnu/packages/cran.scm (r-glue): New variable.
 2017-08-03 17:53:41 +02:00
Danny Milosavljevic dd4b7476ec
gnu: Add grub-hybrid. 
* gnu/packages/bootloaders.scm (grub-hybrid): New variable.
 2017-08-03 16:35:34 +02:00
Ben Woodcroft 75e6639f36
gnu: htseq: Use PyPI URI. 
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
 2017-08-03 21:08:13 +10:00
Ben Woodcroft 92971d68ac
gnu: htseq: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
 2017-08-03 21:02:30 +10:00
Efraim Flashner a8ead6f91b
gnu: vc: Limit to x86_64 and i686. 
* gnu/packages/maths.scm (vc)[supported-systems]: New field.
 2017-08-03 13:34:18 +03:00
Manolis Ragkousis 5638d71502
gnu: openscenegraph: Add 'Release' configure flag. 
* gnu/packages/graphics.scm (openscenegraph)[arguments]: Add "-DCMAKE_BUILD_TYPE=Release".
 2017-08-03 10:35:31 +03:00
Eric Bavier 68a29ab8d0
gnu: Add LeoCAD. 
* gnu/packages/lego.scm (leocad): New variable.
 2017-08-03 00:33:02 -05:00
Tobias Geerinckx-Rice 5d8312f1c6
gnu: youtube-dl: Update to 2017.07.30.1. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.07.30.1.
 2017-08-03 05:31:24 +02:00
Tobias Geerinckx-Rice 6862c72373
gnu: tor: Update to 0.3.0.10. 
* gnu/packages/tor.scm (tor): Update to 0.3.0.10.
 2017-08-03 01:56:22 +02:00
Ludovic Courtès 49962b15a1
activation: Make sure /etc exists. 
Fixes <http://bugs.gnu.org/27146>.
Reported by ng0 <ng0@pragmatique.xyz>.

* gnu/build/activation.scm (activate-etc): Add call to 'mkdir-p'.
 2017-08-03 00:35:59 +02:00
Efraim Flashner edd08fb7ac
gnu: glibc@2.22: Fix security issues. 
Fixes CVE-2015-{5180,7547}, CVE-2016-{3075,3706,4429}.

* gnu/packages/base.scm (glibc@2.22)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2015-7547.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-02 21:51:35 +03:00
Efraim Flashner a0ae64a334
gnu: glibc@2.23: Fix CVE-2015-5180, CVE-2016-{3075,3706,4429}. 
* gnu/packages/base.scm (glibc@2.23)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2016-3075.patch,
gnu/packages/patches/glibc-CVE-2016-3706.patch,
gnu/packages/patches/glibc-CVE-2016-4429.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.
 2017-08-02 21:51:33 +03:00
Efraim Flashner 575e5e4e51
gnu: glibc@2.24: Fix CVE-2015-5180. 
* gnu/packages/base.scm (glibc@2.24)[source]: Add patch.
* gnu/packages/patches/glibc-CVE-2015-5180.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-02 21:51:31 +03:00
Leo Famulari 2c5cf84430
gnu: python2-conda: Fix build by building with enum34. 
* gnu/packages/package-management.scm (python2-conda): Use 'python2-variant'.
[native-inputs]: Add python2-enum34.
 2017-08-02 14:39:33 -04:00
Manolis Ragkousis 9ef5940ce4
gnu: calibre: Add python2-msgpack as an input. 
* gnu/packages/ebook.scm (calibre)[inputs]: Add python2-msgpack.
 2017-08-02 20:20:12 +03:00
Efraim Flashner 721d7a6912
gnu: gcc@4.7: Don't built on aarch64. 
* gnu/packages/gcc.scm (gcc@4.7, gcc@4.8, gcc@4.9)[supported-systems]:
New field.
 2017-08-02 19:14:26 +03:00
Leo Famulari 696f1d0fb1
gnu: libpng-apng: Be sure to apply the APNG patch. 
* gnu/packages/image.scm (libpng-apng)[arguments]: Check the return status of
the patching procedures.
 2017-08-02 11:17:57 -04:00
ng0 e0958c2df8
gnu: libpng-apng: Update to 1.6.28. 
Fixes <https://bugs.gnu.org/27556>.

* gnu/packages/image.scm (libpng-apng): Update to 1.6.28.
Remove inherit of 'libpng'.
[version]: Use own version, remove 'package-version libpng'.
[source]: Don't inherit the source of libpng.
[arguments]: Update hash of libpng-apng source.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-08-02 11:10:31 -04:00
Thomas Danckaert 33485fa913
gnu: eyed3: Update to 0.8, build with python3. 
* gnu/packages/mp3.scm (eyed3): [source] Update to 0.8.
[arguments]: Disable tests; don't use python-2.
[propagated-inputs]: Add python-six and python-grako.
[native-inputs]: Remove.
 2017-08-02 14:08:33 +02:00
Thomas Danckaert a70b03d413
gnu: Add python-grako 
* gnu/packages/python.scm (python-grako): New variable.
 2017-08-02 14:08:33 +02:00
Thomas Danckaert 0abf526420
gnu: hdf4: Update to 4.12.13. 
* gnu/packages/maths.scm (hdf4): Update to 4.12.13.
 2017-08-02 14:08:24 +02:00
Tobias Geerinckx-Rice ced2d2b7ca
gnu: libvirt: Update to 3.6.0. 
* gnu/packages/virtualization.scm (libvirt): Update to 3.6.0.
 2017-08-02 07:15:21 +02:00
Tobias Geerinckx-Rice 2e508b6dc0
gnu: libvirt: Use HTTPS. 
* gnu/packages/virtualization.scm (libvirt)[source, home-page]: Use HTTPS.
 2017-08-02 07:15:21 +02:00
Roel Janssen 2f06dc0435
gnu: Add r-rlang. 
* gnu/packages/statistics.scm (r-rlang): New variable.
 2017-08-02 00:57:39 +02:00
Roel Janssen f1915a5dd0
gnu: r-deseq2: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
 2017-08-02 00:33:23 +02:00
Roel Janssen fd215c2978
gnu: r-annotationforge: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
 2017-08-02 00:33:07 +02:00
Roel Janssen bd4a0bab5f
gnu: r-category: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
 2017-08-02 00:32:46 +02:00
Roel Janssen 0ff478344b
gnu: r-biocstyle: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
 2017-08-02 00:32:31 +02:00
Roel Janssen 9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
 2017-08-02 00:32:11 +02:00
Roel Janssen 3ec25eb2a8
gnu: r-iranges: Update to 2.10.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
 2017-08-02 00:31:46 +02:00
Roel Janssen 6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
 2017-08-02 00:31:28 +02:00
Roel Janssen 48f5d283b2
gnu: r-variantannotation: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
 2017-08-02 00:31:08 +02:00
Roel Janssen 1b4738e23c
gnu: r-limma: Update to 3.32.5. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
 2017-08-02 00:30:49 +02:00
Roel Janssen 1898a7832f
gnu: r-biobase: Update to 2.36.2. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
 2017-08-02 00:30:27 +02:00
Roel Janssen 62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
 2017-08-02 00:28:32 +02:00
Roel Janssen 0c6494a1db
gnu: r-biomart: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
 2017-08-02 00:28:16 +02:00
Roel Janssen 1ff74d074e
gnu: r-biocparallel: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
 2017-08-02 00:27:57 +02:00
Roel Janssen 5077bc3e2e
gnu: r-biostrings: Update to 2.44.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
 2017-08-02 00:27:35 +02:00
Roel Janssen adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
 2017-08-02 00:27:16 +02:00
Roel Janssen f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
 2017-08-02 00:26:55 +02:00
Roel Janssen 26760c80cd
gnu: r-genomicalignments: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
 2017-08-02 00:26:33 +02:00
Roel Janssen 15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
 2017-08-02 00:26:00 +02:00
Roel Janssen 8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
 2017-08-02 00:25:26 +02:00
Roel Janssen 9eb2714625
gnu: r-copywriter: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
 2017-08-02 00:25:00 +02:00
Roel Janssen bfa0d1e773
gnu: r-sva: Update to 3.24.4. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
 2017-08-02 00:24:27 +02:00
Roel Janssen 8060a61798
gnu: r-rsqlite: Update to 2.0. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.0.
 2017-08-02 00:23:16 +02:00
Roel Janssen 796237a9a4
gnu: Add r-blob. 
* gnu/packages/statistics.scm (r-blob): New variable.
 2017-08-02 00:22:33 +02:00
Roel Janssen aa184803f8
gnu: Add r-pkgconfig. 
* gnu/packages/statistics.scm (r-pkgconfig): New variable.
 2017-08-02 00:21:40 +02:00
Marius Bakke fc8f0631b4
gnu: re2: Update to 2017-08-01. 
* gnu/packages/regex.scm (re2): Update to 2017-08-01.
 2017-08-01 23:37:20 +02:00
Marius Bakke 1926fd2baa
gnu: maim: Update to 5.4.66. 
* gnu/packages/xdisorg.scm (maim): Update to 5.4.66.
 2017-08-01 23:35:31 +02:00
Marius Bakke 7d960db1e3
gnu: slop: Update to 7.3.48. 
* gnu/packages/xdisorg.scm (slop): Update to 7.3.48.
 2017-08-01 23:35:03 +02:00
Marius Bakke b73e49f595
gnu: git: Update to 2.13.4. 
* gnu/packages/version-control.scm (git): Update to 2.13.4.
 2017-08-01 23:34:41 +02:00
Roel Janssen 14fce399cc
gnu: r-foreign: Update hash after upstream tarball change. 
* gnu/packages/statistics.scm (r-foreign):  Update hash.  The only difference
  in the tarball is the metadata.  The contents are identical.
 2017-08-01 23:07:58 +02:00
Roel Janssen cdf124c607
gnu: r-foreign: Remove duplicate recipe. 
* gnu/packages/statistics.scm (r-foreign): Remove duplicate recipe.
 2017-08-01 23:06:02 +02:00
Leo Famulari d0386db493
gnu: rapidjson: Update to 1.1.0. 
* gnu/packages/web.scm (rapidjson): Update to 1.1.0.
[source]: Remove snippet.
 2017-08-01 14:42:44 -04:00
ng0 f2e1271809
gnu: Add pidentd. 
* gnu/packages/networking.scm (pidentd): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2017-08-01 20:57:51 +03:00
Kei Kebreau 89c9445aa2
gnu: hyperrogue: Update to 10.0e. 
* gnu/packages/games.scm (hyperrogue): Update to 10.0e.
[arguments]: Adjust accordingly.
 2017-08-01 12:14:54 -04:00
Efraim Flashner d931a4bbeb
gnu: metabat: Limit to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
 2017-08-01 17:28:35 +03:00
Kyle Meyer 4bfdf034e2
gnu: Add emacs-yasnippet-snippets. 
* gnu/packages/emacs.scm (emacs-yasnippet-snippets): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-08-01 15:33:07 +02:00
Kyle Meyer 1f0d47059d
gnu: emacs-yasnippet: Upgrade to 0.12.0. 
* gnu/packages/emacs.scm (emacs-yasnippet): Upgrade to 0.12.0.
[source]: Remove an uninstalled directory from yas-snippet-dirs.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-08-01 15:32:59 +02:00
Ludovic Courtès 04b6d6f7f7
gnu: guile-ssh: Update to 0.11.2. 
* gnu/packages/ssh.scm (guile-ssh): Update to 0.11.2.
[source]: Remove 'patches', 'modules', and 'snippet'.
* gnu/packages/patches/guile-ssh-channel-finalization.patch,
gnu/packages/patches/guile-ssh-double-free.patch,
gnu/packages/patches/guile-ssh-rexec-bug.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2017-08-01 15:32:07 +02:00
Adonay Felipe Nogueira 12235a124f
gnu: artanis: Unbundled guile-json and version according to documentation. 
* gnu/packages/guile.scm (artanis): Unbundled guile-json and version
according to documentation.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-08-01 15:32:07 +02:00
Muriithi Frederick Muriuki 269504a797
gnu: python-pbr-minimal: Update to 3.0.1 
* gnu/packages/python.scm (python-pbr-minimal): Update to 3.0.1
[source]: Update hash and remove patch.
* gnu/packages/patches/python-pbr-fix-man-page-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2017-08-01 15:21:52 +03:00
Leo Famulari 3d0fbd3c2f
gnu: libgit2: Enable SHA-1 collision detection. 
* gnu/packages/version-control.scm (libgit2)[arguments]: Enable '-DUSE_SHA1DC'
in #:configure-flags.
 2017-08-01 01:02:53 -04:00
Ben Woodcroft befb2c0e6e
gnu: ruby-bio-commandeer: Update to 0.2.0. 
* gnu/packages/ruby.scm (ruby-bio-commandeer): Update to 0.2.0.
 2017-08-01 14:09:07 +10:00
Ludovic Courtès e1ecc8908e
gnu: libmicrohttpd: Update to 0.9.55. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.55.
[arguments]: Add 'add-missing-LDFLAGS' phase.
 2017-07-31 22:51:34 +02:00
Ludovic Courtès a6b5af0cff
gnu: xf86-video-intel: Update snapshot. 
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2100efa.
Introduce 'revision' variable.
 2017-07-31 22:10:34 +02:00
Ludovic Courtès f0732ee485
gnu: guile-bytestructures: Install .go files to lib/guile/X.Y. 
* gnu/packages/guile.scm (guile-bytestructures)[arguments]: Install .go
files to OBJECT-DIR, defined as OUT/lib/guile/X.Y/site-ccache.
 2017-07-31 17:36:24 +02:00
ng0 54727850c3
gnu: tor: Remove '--enable-expensive-hardening' option. 
* gnu/packages/tor.scm (tor)[arguments]: Remove '--enable-expensive-hardening' option.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-07-31 17:06:45 +02:00
Peter Mikkelsen ee217402f7
gnu: erlang: Update to 20.0. 
* gnu/packages/erlang.scm (erlang): Update to 20.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-07-31 17:02:36 +02:00
Ludovic Courtès c27e02bf6b
gnu: network-manager: Add dependency on Newt. 
Suggested by Mark H Weaver.

* gnu/packages/gnome.scm (network-manager)[inputs]: Add NEWT.
 2017-07-31 15:23:06 +02:00
Ludovic Courtès 44b0faee6b
gnu: guile-git: Skip faulty tests on non-x86_64. 
Reported by Mark H Weaver.

* gnu/packages/guile.scm (guile-git)[arguments]: Add 'skip-tests' phase
unless on x86_64-linux.
 2017-07-31 15:23:06 +02:00
Ludovic Courtès 8ecba89b77
gnu: libgit2: Add "debug" output. 
* gnu/packages/version-control.scm (libgit2)[outputs]: New field.
 2017-07-31 15:23:06 +02:00
Ludovic Courtès 58dce7bfb5
gnu: libgit2: Update to 0.26.0. 
* gnu/packages/version-control.scm (libgit2): Update to 0.26.0.  Remove
"libgit2-use-after-free.patch".
* gnu/packages/patches/libgit2-use-after-free.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-07-31 15:23:05 +02:00
Efraim Flashner 6ce8fe4cd0
gnu: efl: Add wayland support. 
* gnu/packages/enlightenment.scm (efl)[inputs]: Add wayland-protocols.
Move mesa ...
[propagated-inputs]: ... to here. Add libinput, libxkbcommon, wayland.
[arguments]: Add flags to enable wayland, elput and drm.
 2017-07-31 15:16:23 +03:00
Efraim Flashner 0d3ecf77ba
gnu: gst-plugins-good: Update disable-failing-tests phase. 
* gnu/packages/gstreamer.scm (gst-plugins-good)[arguments]: Change the
list of tests to disable during 'disable-failing-tests phase.
 2017-07-31 15:16:21 +03:00
Leo Famulari 57f57a7bbf
services: ntp: Use the NTP pool via the 'guix' zone. 
* gnu/services/networking.scm (%ntp-servers): Use *.guix.pool.ntp.org.
 2017-07-30 20:21:36 -04:00
Ludovic Courtès 706448b193
gnu: automake: Add 1.15.1. 
* gnu/packages/autotools.scm (automake/latest): New variable.
 2017-07-30 22:31:10 +02:00
Ludovic Courtès c91171627b
gnu: guix: Search .go files of dependencies in lib/guile/. 
* gnu/packages/package-management.scm (guix)[arguments]: Add (srfi
srfi-26) to #:modules.  Introduce 'gopath', distinct from 'path'.
 2017-07-30 21:36:18 +02:00
Ludovic Courtès 1c0ee79d4d
gnu: guix: Update snapshot. 
* gnu/packages/package-management.scm (guix): Update to 228a398.
 2017-07-30 17:58:04 +02:00
Ludovic Courtès 1398a43816
services: openssh: Extensions provide extra authorized keys. 
* gnu/services/ssh.scm (extend-openssh-authorized-keys): New procedure.
(openssh-service-type)[compose, extend]: New fields.
* doc/guix.texi (Networking Services): Document the extension.
 2017-07-30 16:23:19 +02:00
Ludovic Courtès 4892eb7c6a
services: openssh: Add 'authorized-keys' field. 
* gnu/services/ssh.scm (<openssh-configuration>)[authorized-keys]: New
field.
(authorized-key-directory): New procedure.
(openssh-config-file): Honor 'authorized-keys'.
(openssh-activation): Use 'with-imported-modules'.  Make /etc/ssh
755.  Create /etc/ssh/authorized_keys.d.
* doc/guix.texi (Networking Services): Document it.
 2017-07-30 16:23:19 +02:00
Ludovic Courtès 75bddb13eb
services: cuirass: Set 'GIT_SSL_CAINFO' and 'GIT_EXEC_PATH'. 
Reported by Ricardo Wurmus.

* gnu/services/cuirass.scm (cuirass-shepherd-service): Pass
 #:environment-variables.
 2017-07-30 16:23:19 +02:00
Marius Bakke c918773a03
gnu: ffmpeg: Update to 3.3.3. 
* gnu/packages/video.scm (ffmpeg): Update to 3.3.3.
 2017-07-30 12:49:38 +02:00
Christopher Baines fa65e84aab
gnu: qemu: Build with support for Linux AIO 
Add libaio as an input, such that QEMU is built with support for Asynchronous
I/O (AIO).

* gnu/packages/virtualization.scm (qemu)[inputs]: Uncomment libaio.
 2017-07-30 09:56:00 +01:00
Christopher Baines 119fdd0d0e
services: Add memcached. 
* gnu/services/databases.scm (memcached-service-type, %memcached-accounts):
  New variables.
  (<memcached-configuration>): New record type.
  (memcached-service-type): New procedures.
* gnu/tests/databases.scm: New file.
* doc/guix.texi (Database Services): Document the new memcached service.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add entry for tests/databases.scm.
 2017-07-30 09:08:30 +01:00
Christopher Baines 686144e986
gnu: Add memcached. 
* gnu/packages/databases.scm (memcached): New variable.
 2017-07-30 09:06:52 +01:00
宋文武 c00c90ca37
gnu: retroarch: Update to 1.6.3. 
* gnu/packages/games.scm (retroarch): Update to 1.6.3.
 2017-07-30 15:15:34 +08:00
Theodoros Foradis 85cdab64c6
gnu: yosys: Add dependency on z3. 
* gnu/packages/fpga.scm (yosys): Add z3 to propagated-inputs.
 2017-07-29 23:03:47 +02:00
Theodoros Foradis 313844d9dc
gnu: Add z3. 
* gnu/packages/maths.scm (z3): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-07-29 23:03:47 +02:00
Peter Mikkelsen a4078acf4a
gnu: erlang: Fix man-pages search path of 'erl -man'. 
* gnu/packages/patches/erlang-man-path.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/erlang.scm (erlang)[source]: Use it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-07-29 23:03:47 +02:00
Oleg Pykhalov 53ac6977ac
gnu: tome4: Clean up snippet. 
* gnu/packages/games.scm (tome4)[source](snippet): Use a single
'substitute*' call instead of 'for-each'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-07-29 23:03:47 +02:00
Marius Bakke baa6b77789
gnu: vim: Update to 8.0.0808. 
* gnu/packages/vim.scm (vim): Update to 8.0.0808.
[arguments]: Remove obsolete 'make-bit-reproducable' phase.
(vim-full): Update to 8.0.0808.
[arguments]: Remove 'drop-failing-tests' phase.
 2017-07-29 23:01:17 +02:00
Kyle Meyer 24b115dff5
gnu: emacs: Check GUIX_ENVIRONMENT when autoloading packages. 
Check the environment profile so that we autoload packages that are given as
arguments to "guix environment" but are not in the system or user profile.
Note that the union of Emacs packages in the system, user, and environment
profiles will be autoloaded even when --pure was passed to "guix environment",
because it's not clear how to detect that --pure was given.

* gnu/packages/aux-files/emacs/guix-emacs.el (guix-emacs-autoload-packages):
Add Emacs packages from GUIX_ENVIRONMENT profile.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2017-07-29 23:19:17 +03:00