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32904 Commits

Author SHA1 Message Date
Ricardo Wurmus 9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3b8c884285
gnu: r-rbgl: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus ffe16ef33c
gnu: r-dexseq: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus f7e95c50b8
gnu: r-deseq2: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus feb561f721
gnu: r-scran: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus fd7301676e
gnu: r-sjplot: Update to 2.6.2. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.6.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus e45f4a4dab
gnu: r-sjmisc: Update to 2.7.7. 
* gnu/packages/cran.scm (r-sjmisc): Update to 2.7.7.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 5e8282a4a0
gnu: r-rmpi: Update to 0.6-9. 
* gnu/packages/cran.scm (r-rmpi): Update to 0.6-9.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 80c4e75b87
gnu: r-seqminer: Update to 7.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3bc0667f3c
gnu: r-bookdown: Update to 0.9. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus c3e5b456be
gnu: r-protviz: Update to 0.4.0. 
* gnu/packages/cran.scm (r-protviz): Update to 0.4.0.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 209e504bb1
gnu: r-ontologyindex: Update to 2.5. 
* gnu/packages/cran.scm (r-ontologyindex): Update to 2.5.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus e041740289
gnu: r-chemometricswithr: Update to 0.1.13. 
* gnu/packages/cran.scm (r-chemometricswithr): Update to 0.1.13.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 9ad5f4ba19
gnu: r-grimport: Update to 0.9-1.1. 
* gnu/packages/cran.scm (r-grimport): Update to 0.9-1.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 16d296bbd1
gnu: r-shades: Update to 1.3.1. 
* gnu/packages/cran.scm (r-shades): Update to 1.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 6eab52e0dd
gnu: r-ggeffects: Update to 0.8.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.8.0.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus de7631b278
gnu: r-slam: Update to 0.1-44. 
* gnu/packages/cran.scm (r-slam): Update to 0.1-44.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 2652e2534f
gnu: r-refgenome: Update to 1.7.3.1. 
* gnu/packages/cran.scm (r-refgenome): Update to 1.7.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f0867a0e8b
gnu: r-findpython: Update to 1.0.4. 
* gnu/packages/cran.scm (r-findpython): Update to 1.0.4.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 12502bf4e8
gnu: r-prediction: Update to 0.3.6.1. 
* gnu/packages/cran.scm (r-prediction): Update to 0.3.6.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus fbd263cd4a
gnu: r-abn: Update to 1.3. 
* gnu/packages/cran.scm (r-abn): Update to 1.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1b1444012b
gnu: r-sjstats: Update to 0.17.3. 
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 9df469a1d4
gnu: r-emmeans: Update to 1.3.1. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1afe56444e
gnu: r-glmmtmb: Update to 0.2.3. 
* gnu/packages/cran.scm (r-glmmtmb): Update to 0.2.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1417d5f1d5
gnu: r-rio: Update to 0.5.16. 
* gnu/packages/cran.scm (r-rio): Update to 0.5.16.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 962304c31c
gnu: r-arules: Update to 1.6-2. 
* gnu/packages/cran.scm (r-arules): Update to 1.6-2.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f2fc34f241
gnu: r-fnn: Update to 1.1.2.2. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.2.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f0fe1a5a45
gnu: r-shinyace: Update to 0.3.3. 
* gnu/packages/cran.scm (r-shinyace): Update to 0.3.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 5f1f11049f
gnu: r-cubature: Update to 2.0.3. 
* gnu/packages/cran.scm (r-cubature): Update to 2.0.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 7abb15f2bb
gnu: r-tseries: Update to 0.10-46. 
* gnu/packages/cran.scm (r-tseries): Update to 0.10-46.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 9d83132757
gnu: r-statnet-common: Update to 4.2.0. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.2.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 7e9e9c9c46
gnu: r-tinytex: Update to 0.10. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.10.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus fc00a1f0fc
gnu: r-pillar: Update to 1.3.1. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.1.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 111516f9d6
gnu: r-gclus: Update to 1.3.2. 
* gnu/packages/cran.scm (r-gclus): Update to 1.3.2.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus ed46a05c75
gnu: r-laeken: Update to 0.5.0. 
* gnu/packages/cran.scm (r-laeken): Update to 0.5.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus fc74de42da
gnu: r-ddalpha: Update to 1.3.8. 
* gnu/packages/cran.scm (r-ddalpha): Update to 1.3.8.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 221b3b164d
gnu: r-rmysql: Update to 0.10.16. 
* gnu/packages/cran.scm (r-rmysql): Update to 0.10.16.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 1c6d199ee8
gnu: r-mitml: Update to 0.3-7. 
* gnu/packages/cran.scm (r-mitml): Update to 0.3-7.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 5703991841
gnu: r-recipes: Add missing input. 
* gnu/packages/cran.scm (r-recipes)[propagated-inputs]: Add r-withr.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 77f97229c9
gnu: r-dimred: Add missing input. 
* gnu/packages/cran.scm (r-dimred)[propagated-inputs]: Add r-magrittr.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 8f88701491
gnu: r-lava: Update to 1.6.4. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.4.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 397dba01c6
gnu: r-powerlaw: Update to 0.70.2. 
* gnu/packages/cran.scm (r-powerlaw): Update to 0.70.2.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 72c4987506
gnu: r-circlize: Update to 0.4.5. 
* gnu/packages/cran.scm (r-circlize): Update to 0.4.5.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 422dea1774
gnu: r-ps: Update to 1.3.0. 
* gnu/packages/cran.scm (r-ps): Update to 1.3.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus dcf89cc0cf
gnu: r-haven: Update to 2.0.0. 
* gnu/packages/cran.scm (r-haven): Update to 2.0.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 69aad34ae0
gnu: r-feather: Update to 0.3.2. 
* gnu/packages/cran.scm (r-feather): Update to 0.3.2.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 1add168ab5
gnu: r-htmltable: Update to 1.13.1. 
* gnu/packages/cran.scm (r-htmltable): Update to 1.13.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 37349c717e
gnu: r-httpuv: Update to 1.4.5.1. 
* gnu/packages/cran.scm (r-httpuv): Update to 1.4.5.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 0c025a7f79
gnu: r-clipr: Update to 0.5.0. 
* gnu/packages/cran.scm (r-clipr): Update to 0.5.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 2e4fc4ac62
gnu: r-caret: Update to 6.0-81. 
* gnu/packages/statistics.scm (r-caret): Update to 6.0-81.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus aa72d7f7f5
gnu: r-quantreg: Update to 5.38. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.38.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 9b7df80b9b
gnu: r-rcppeigen: Update to 0.3.3.5.0. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.5.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus bcc17f7f11
gnu: r-rrcov: Update to 1.4-7. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.4-7.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 70ee5ab137
gnu: r-cowplot: Update to 0.9.4. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.9.4.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 7213ef07c6
gnu: r-rann: Update to 2.6.1. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 2c8594d963
gnu: r-sfsmisc: Update to 1.1-3. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-3.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 54ebdf6f74
gnu: r-rmarkdown: Update to 1.11. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.11.
[propagated-inputs]: Remove r-rprojroot.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus fb45934202
gnu: r-rstudioapi: Update to 0.9.0. 
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.9.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 8f49d99a84
gnu: r-git2r: Update to 0.24.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.24.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus c12e429348
gnu: r-httr: Update to 1.4.0. 
* gnu/packages/statistics.scm (r-httr): Update to 1.4.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 02c89c5812
gnu: r-commonmark: Update to 1.7. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.7.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus fe8c44502b
gnu: r-checkmate: Update to 1.9.0. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca4861c602
gnu: r-backports: Update to 1.1.3. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 23347dc353
gnu: r-dbplyr: Update to 1.3.0. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.3.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus f12ed3664d
gnu: r-tibble: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-tibble): Update to 2.0.0.
[propagated-inputs]: Add r-fansi and r-pkgconfig.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus c668a95861
gnu: r-rlang: Update to 0.3.1. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.3.1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 495866a9d7
gnu: r-knitr: Update to 1.21. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.21.
[propagated-inputs]: Add r-xfun.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus bf3aded0cf
gnu: r-markdown: Update to 0.9. 
* gnu/packages/statistics.scm (r-markdown): Update to 0.9.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus eae93bd3f2
gnu: r-bh: Update to 1.69.0-1. 
* gnu/packages/statistics.scm (r-bh): Update to 1.69.0-1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b6e27673e6
gnu: r-pheatmap: Update to 1.0.12. 
* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.12.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca2bc7e037
gnu: r-mgcv: Update to 1.8-26. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-26.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 60f1bce09f
gnu: r-codetools: Update to 0.2-16. 
* gnu/packages/statistics.scm (r-codetools): Update to 0.2-16.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 3dbd87f504
gnu: r-class: Update to 7.3-15. 
* gnu/packages/statistics.scm (r-class): Update to 7.3-15.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 35cf4874cc
gnu: r-survival: Update to 2.43-3. 
* gnu/packages/statistics.scm (r-survival): Update to 2.43-3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 11a36548d9
gnu: r-argparse: Update to 2.0.0. 
* gnu/packages/cran.scm (r-argparse): Update to 2.0.0.
[propagated-inputs]: Add r-r6; remove r-proto.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 527c605598
gnu: r-callr: Update to 3.1.1. 
* gnu/packages/cran.scm (r-callr): Update to 3.1.1.
[propagated-inputs]: Remove r-base64enc.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b140569e18
gnu: r-readxl: Update to 1.2.0. 
* gnu/packages/cran.scm (r-readxl): Update to 1.2.0.
[propagated-inputs]: Add r-progress.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0aad198e2b
gnu: r-pracma: Update to 2.2.2. 
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 44c69a536e
gnu: r-rcpparmadillo: Update to 0.9.200.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0e87bf0177
gnu: r-processx: Update to 3.2.1. 
* gnu/packages/cran.scm (r-processx): Update to 3.2.1.
[propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 2766d3436a
gnu: r-sjlabelled: Update to 1.0.16. 
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16.
[propagated-inputs]: Remove r-tibble and r-tidyselect.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 813d9c51e3
gnu: r-broom: Update to 0.5.1. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.1.
[propagated-inputs]: Add r-generics.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 25c67ecfc6
gnu: Add r-generics. 
* gnu/packages/cran.scm (r-generics): New variable.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 646e1ef059
gnu: r-curl: Update to 3.3. 
* gnu/packages/cran.scm (r-curl): Update to 3.3.
[inputs]: Add zlib.
[native-inputs]: Add pkg-config.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus ef91530362
gnu: r-readr: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-readr): Update to 1.3.1.
[propagated-inputs]: Add r-clipr and r-crayon.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 48102ce123
gnu: r-mvabund: Update to 4.0.1. 
* gnu/packages/cran.scm (r-mvabund): Update to 4.0.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 04a18a81ae
gnu: r-writexl: Update to 1.1. 
* gnu/packages/cran.scm (r-writexl): Update to 1.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus a2315c6702
gnu: r-jsonlite: Update to 1.6. 
* gnu/packages/cran.scm (r-jsonlite): Update to 1.6.
 2019-01-12 23:35:11 +01:00
Kei Kebreau ea600ff709
gnu: python-pillow: Update homepage. 
* gnu/packages/python.scm (python-pillow)[homepage]: Update URL.
 2019-01-12 16:39:26 -05:00
Kei Kebreau acbf312573
gnu: python-pillow: Update to 5.4.0 
* gnu/packages/python.scm (python-pillow): Update to 5.4.0.
[arguments]: Add 'patch-ldconfig' phase.
 2019-01-12 16:38:36 -05:00
Ricardo Wurmus 146c6b62bf
gnu: Sort package modules in (gnu packages guile). 
* gnu/packages/guile.scm: Sort list of gnu/packages modules.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 7d8baff97b
gnu: impressive: Update to 0.12.0. 
* gnu/packages/pdf.scm (impressive): Update to 0.12.0.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 24155bf40d
gnu: Move Java compression packages to new module. 
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
 2019-01-12 12:14:28 +01:00
guy fleury iteriteka 1704367719
gnu: Add Bochs. 
* gnu/packages/virtualization.scm (bochs): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-01-11 17:09:20 -05:00
Leo Famulari 81c64748ba
gnu: Stellarium: Update to 0.18.3. 
* gnu/packages/astronomy.scm (stellarium): Update to 0.18.3.
[arguments]: Skip a broken test.
 2019-01-11 17:07:55 -05:00
Pierre Neidhardt 1ac0c1b899
gnu: opendht: Make argon2 a propagated input so that its .pc is found. 
* gnu/packages/networking.scm (opendht)[inputs]: Remove argon2.
[propagated-inputs]: Add it here.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt e0fa641380
gnu: opendht: Use jsoncpp and restbed. 
* gnu/packages/crypto.scm (opendht): Move definition to networking.scm.
* gnu/packages/networking.scm (opendht)[inputs]: Add jsoncpp and restbed.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt 362fba83dd
gnu: Add restbed. 
* gnu/packages/networking.scm (restbed): New variable.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt 50e1843b3a
gnu: libupnp: Update to 1.6.25. 
* gnu/packages/upnp.scm (libupnp): Update to 1.6.25.
 2019-01-11 19:48:00 +01:00
Hartmut Goebel 46b082f97f
gnu: kinit: Use KDEINIT5_LIBRARY_PATH to search for dynlibs. 
Using LIBRARY_PATH was introduced in
16b8aff85b, but is wrong since
this variable is used by the compiler (gcc) at link time.

* gnu/packages/patches/kinit-kdeinit-libpath.patch: Change
  LIBRARY_PATH to KDEINIT5_LIBRARY_PATH.
* gnu/packages/kde-frameworks.scm (kinit)[native-search-paths]:
  New field.
 2019-01-11 16:35:52 +01:00