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Author SHA1 Message Date
Ricardo Wurmus e21b668e52
gnu: r-rversions: Update to 2.0.1. 
* gnu/packages/statistics.scm (r-rversions): Update to 2.0.1.
 2019-12-04 09:39:43 +01:00
Ricardo Wurmus 14ebd6f762
gnu: r-survival: Update to 3.1-8. 
* gnu/packages/statistics.scm (r-survival): Update to 3.1-8.
 2019-12-04 09:39:36 +01:00
Ricardo Wurmus 41728d234b
gnu: r-all: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-all)[source]: Use bioconductor-uri.
 2019-12-04 09:36:34 +01:00
Ricardo Wurmus 545e67ac03
gnu: r-hsmmsinglecell: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-hsmmsinglecell)[source]: Use
bioconductor-uri.
 2019-12-04 09:36:15 +01:00
Ricardo Wurmus b86f77469b
gnu: r-arrmdata: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-arrmdata)[source]: Use bioconductor-uri.
 2019-12-04 09:35:59 +01:00
Ricardo Wurmus ced61edf5d
gnu: r-abadata: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-abadata)[source]: Use bioconductor-uri.
 2019-12-04 09:35:44 +01:00
Ricardo Wurmus eed2766a45
gnu: r-do-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-do-db)[source]: Use bioconductor-uri.
 2019-12-04 09:35:26 +01:00
Ricardo Wurmus 25f567a85a
gnu: r-illuminahumanmethylationepicmanifest: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest)[source]:
Use bioconductor-uri.
 2019-12-04 09:35:08 +01:00
Ricardo Wurmus 6aca4054e0
gnu: r-fdb-infiniummethylation-hg19: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19)[source]: Use
bioconductor-uri.
 2019-12-04 09:34:47 +01:00
Ricardo Wurmus c271d99025
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:34:13 +01:00
Ricardo Wurmus 1afdf41b49
gnu: r-txdb-mmusculus-ucsc-mm9-knowngene: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene)[source]:
Use bioconductor-uri.
 2019-12-04 09:33:54 +01:00
Ricardo Wurmus d78db08862
gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene)[source]:
Use bioconductor-uri.
 2019-12-04 09:33:35 +01:00
Ricardo Wurmus f2580a1385
gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:33:09 +01:00
Ricardo Wurmus 717d7cda9d
gnu: r-genelendatabase: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-genelendatabase)[source]: Use
bioconductor-uri.
 2019-12-04 09:32:48 +01:00
Ricardo Wurmus e7a8cf2e6e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:32:22 +01:00
Ricardo Wurmus 411be88bf3
gnu: r-org-mm-eg-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-org-mm-eg-db)[source]: Use
bioconductor-uri.
 2019-12-04 09:32:03 +01:00
Ricardo Wurmus f53becc6d8
gnu: r-org-hs-eg-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-org-hs-eg-db)[source]: Use
bioconductor-uri.
 2019-12-04 09:31:46 +01:00
Ricardo Wurmus 7bb65a2227
gnu: r-org-dr-eg-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-org-dr-eg-db)[source]: Use
bioconductor-uri.
 2019-12-04 09:31:19 +01:00
Ricardo Wurmus b0dfc79b0d
gnu: r-org-dm-eg-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-org-dm-eg-db)[source]: Use
bioconductor-uri.
 2019-12-04 09:30:58 +01:00
Ricardo Wurmus 1c05e637a4
gnu: r-org-ce-eg-db: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-org-ce-eg-db)[source]: Use
bioconductor-uri.
 2019-12-04 09:30:35 +01:00
Ricardo Wurmus f83404bc5b
gnu: r-bsgenome-mmusculus-ucsc-mm10: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:29:56 +01:00
Ricardo Wurmus 51dc4a2d70
gnu: r-bsgenome-mmusculus-ucsc-mm9-masked: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked)[source]:
Use bioconductor-uri.
 2019-12-04 09:29:26 +01:00
Ricardo Wurmus 21f6dae73d
gnu: r-bsgenome-mmusculus-ucsc-mm9: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:28:54 +01:00
Ricardo Wurmus a47646bd05
gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked)[source]:
Use bioconductor-uri.
 2019-12-04 09:28:34 +01:00
Ricardo Wurmus 88e7c7db59
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:28:04 +01:00
Ricardo Wurmus bf05ece1a2
gnu: r-bsgenome-dmelanogaster-ucsc-dm3-masked: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked)[source]:
Use bioconductor-uri.
 2019-12-04 09:27:15 +01:00
Ricardo Wurmus 87073b7ecb
gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
 2019-12-04 09:26:22 +01:00
Ricardo Wurmus 149f351f38
gnu: r-bsgenome-dmelanogaster-ucsc-dm6: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm6)[source]:
Use bioconductor-uri.
[arguments]: Permit substitution.
 2019-12-04 09:25:10 +01:00
Ricardo Wurmus 6998ecba74
gnu: r-bsgenome-celegans-ucsc-ce10: Use bioconductor-uri. 
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10)[source]: Use
bioconductor-uri.
[arguments]: Permit substitution.
 2019-12-04 09:24:09 +01:00
Brett Gilio 19e67f8216
gnu: emacs-olivetti: Update to 1.8.1. 
* gnu/packages/emacs-xyz.scm (emacs-olivetti): Update to 1.8.1.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-04 09:00:38 +01:00
Brett Gilio d6445fa690
gnu: emacs-irony-mode: Update to 1.4.0. 
* gnu/packages/emacs-xyz.scm (emacs-irony-mode): Update to 1.4.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-04 09:00:31 +01:00
Brett Gilio 362e5f9408
gnu: emacs-elisp-demos: Update to 2019.12.01. 
* gnu/packages/emacs-xyz.scm (emacs-elisp-demos): Update to 2019.12.01.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-04 09:00:22 +01:00
Brett Gilio 17f88b9c01
gnu: emacs-doom-modeline: Update to 2.8.0. 
* gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 2.8.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-04 08:59:43 +01:00
Ricardo Wurmus 312ec128af
gnu: python-pandas: Move to (gnu packages python-science). 
* gnu/packages/python-xyz.scm (python-pandas, python2-pandas): Move from
here...
* gnu/packages/python-science.scm (python-pandas, python2-pandas): ...to here.
* gnu/packages/benchmark.scm, gnu/packages/databases.scm,
gnu/packages/graph.scm, gnu/packages/parallel.scm,
gnu/packages/serialization.scm: Import (gnu packages python-science).
 2019-12-04 08:56:36 +01:00
Eric Bavier dc3e62a494
gnu: handbrake: Upgrade to 1.3.0. 
* gnu/packages/patches/handbrake-opt-in-nvenc.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/video.scm (handbrake)[source]: Upgrade to 1.3.0.  Remove
patch.
[native-inputs]: Remove cmake and curl.
[inputs]: Add dav1d and numactl.
[arguments]: Add "--disable-nvenc" to configure flags in place of patch.
Adjust "bootstrap" phase in response to upstream changes.
Add "patch-SHELL" and "relax-reqs" phases.
 2019-12-03 22:20:22 -06:00
Tobias Geerinckx-Rice 32c06affca
guix-install.sh: Use a deterministic umask. 
Users with strict umasks (e.g. 0077) would end up with an unreadable
/gnu (mode 0700) and no way to run guix.

Reported by A. <@aaap:matrix.org> on #guix.

* etc/guix-install.sh (main): Set umask before installing anything.
 2019-12-04 03:59:04 +01:00
Andreas Enge 4c16ffd383
gnu: tcc: Add search paths and drop the wrapper. 
* gnu/packages/c.scm (tcc): Add native search paths.
(tcc-wrapper): Remove variable.
 2019-12-03 22:18:08 +01:00
Tobias Geerinckx-Rice 1b6c5e8039
gnu: cmocka: Update to 1.1.5. 
* gnu/packages/check.scm (cmocka): Update to 1.1.5.
 2019-12-03 21:50:04 +01:00
Tobias Geerinckx-Rice efa45291b7
gnu: girara: Update to 0.3.3. 
* gnu/packages/gtk.scm (girara): Update to 0.3.3.
 2019-12-03 21:50:04 +01:00
Tobias Geerinckx-Rice 741b505307
gnu: libcdio: Update to 2.1.0. 
* gnu/packages/cdrom.scm (libcdio): Update to 2.1.0.
 2019-12-03 21:50:04 +01:00
Tobias Geerinckx-Rice a344a1af07
gnu: libcdio-paranoia: Update to 10.2+2.0.0. 
* gnu/packages/cdrom.scm (libcdio-paranoia): Update to 10.2+2.0.0.
 2019-12-03 21:50:03 +01:00
Tobias Geerinckx-Rice 6b9ec7b0ef
gnu: libburn: Update to 1.5.2. 
* gnu/packages/cdrom.scm (libburn): Update to 1.5.2.
 2019-12-03 21:50:03 +01:00
Ricardo Wurmus dfe11a489b
gnu: r-rsqlite: Update to 2.1.3. 
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.1.3.
 2019-12-03 14:54:20 +01:00
Ricardo Wurmus 64d576e514
gnu: r-roxygen2: Update to 7.0.2. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.0.2.
 2019-12-03 14:54:13 +01:00
Ricardo Wurmus 3fff4de729
gnu: r-testthat: Update to 2.3.1. 
* gnu/packages/statistics.scm (r-testthat): Update to 2.3.1.
 2019-12-03 14:54:06 +01:00
Ricardo Wurmus 6a7ac0a829
gnu: r-rspectra: Update to 0.16-0. 
* gnu/packages/cran.scm (r-rspectra): Update to 0.16-0.
 2019-12-03 14:53:59 +01:00
Ricardo Wurmus 8aab9b98cf
gnu: r-sjplot: Update to 2.8.1. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.8.1.
 2019-12-03 14:53:50 +01:00
Ricardo Wurmus de5092bab0
gnu: r-bayesplot: Update to 1.7.1. 
* gnu/packages/cran.scm (r-bayesplot): Update to 1.7.1.
 2019-12-03 14:53:42 +01:00
Ricardo Wurmus 27c2a6a160
gnu: r-maptools: Update to 0.9-9. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-9.
 2019-12-03 14:53:30 +01:00
Ricardo Wurmus a477a5c357
gnu: r-network: Update to 1.16.0. 
* gnu/packages/cran.scm (r-network): Update to 1.16.0.
 2019-12-03 14:53:22 +01:00