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45608 commits

Author SHA1 Message Date
Mark H Weaver
96c158be1b
gnu: linux-libre: Update deblob scripts. 
* gnu/packages/linux.scm (deblob-scripts-4.19): Update to 4.19.90.
(deblob-scripts-4.14): Update to 4.14.159.
(deblob-scripts-5.3, deblob-scripts-4.9, deblob-scripts-4.4): Update version
numbers to 5.3.17, 4.9.206, and 4.4.206, respectively, although the scripts
themselves have not changed.
 2019-12-18 15:13:39 -05:00
Ricardo Wurmus
77e2de3654
gnu: Add r-biodist. 
* gnu/packages/bioconductor.scm (r-biodist): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
0156297f29
gnu: Add r-biocworkflowtools. 
* gnu/packages/bioconductor.scm (r-biocworkflowtools): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
43b66e3f7c
gnu: Add r-biocset. 
* gnu/packages/bioconductor.scm (r-biocset): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
4a18112dfb
gnu: Add r-biocpkgtools. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
4d12c1e335
gnu: Add r-biocor. 
* gnu/packages/bioconductor.scm (r-biocor): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
c2b36a0441
gnu: Add r-bioconcotk. 
* gnu/packages/bioconductor.scm (r-bioconcotk): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
0678479391
gnu: Add r-multiassayexperiment. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): New variable.
 2019-12-18 15:29:08 +01:00
Ricardo Wurmus
244270e6ae
gnu: Add r-experimenthub. 
* gnu/packages/bioconductor.scm (r-experimenthub): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
49f0860be0
gnu: Add r-biocgraph. 
* gnu/packages/bioconductor.scm (r-biocgraph): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
f180be2923
gnu: Add r-bioccasestudies. 
* gnu/packages/bioconductor.scm (r-bioccasestudies): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
21afe920f1
gnu: Add r-ebarrays. 
* gnu/packages/bioconductor.scm (r-ebarrays): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
f388834e11
gnu: Add r-reactomepa. 
* gnu/packages/bioconductor.scm (r-reactomepa): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
c373223e63
gnu: Add r-graphite. 
* gnu/packages/bioconductor.scm (r-graphite): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
3eacc8fa8f
gnu: Add r-influencer. 
* gnu/packages/cran.scm (r-influencer): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
ff1146b9b1
gnu: Add r-curatedtcgadata. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata): New variable.
 2019-12-18 15:29:07 +01:00
Ricardo Wurmus
6f15ea2415
gnu: Add r-reactome-db. 
* gnu/packages/bioconductor.scm (r-reactome-db): New variable.
 2019-12-18 15:29:07 +01:00
Efraim Flashner
7e9d6f0f3f
gnu: libmicrohttpd: Update to 0.9.69. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.69.
 2019-12-18 10:34:27 +02:00
Efraim Flashner
8fd6049403
gnu: cmst: Update to 2019.01.13. 
* gnu/packages/connman.scm (cmst): Update to 2019.01.13.
 2019-12-18 10:29:28 +02:00
Efraim Flashner
92fe25130c
gnu: python-ecdsa: Actually run the test suite. 
* gnu/packages/python-crypto.scm (python-ecdsa)[arguments]: Replace
'check phase.
[native-inputs]: Add python-pytest.
 2019-12-18 09:54:47 +02:00
Efraim Flashner
c57b8419f4
gnu: python-ecdsa: Update to 0.14.1. 
* gnu/packages/python-crypto.scm (python-ecdsa): Update to 0.14.1.
[inputs]: Move openssl ...
[native-inputs]: ... to here.
[propagated-inputs]: Add python-six.
 2019-12-18 09:53:48 +02:00
Mark H Weaver
ef6856ea72
gnu: linux-libre: Update to 5.3.17. 
* gnu/packages/linux.scm (linux-libre-5.3-version): Update to 5.3.17.
(linux-libre-5.3-pristine-source): Update hash.
 2019-12-17 17:24:23 -05:00
Mark H Weaver
a15adacb52
gnu: linux-libre@4.19: Update to 4.19.90. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.90.
(linux-libre-4.19-pristine-source): Update hash.
 2019-12-17 17:23:42 -05:00
Mark H Weaver
0bb64e1796
gnu: linux-libre@4.14: Update to 4.14.159. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.159.
(linux-libre-4.14-pristine-source): Update hash.
 2019-12-17 17:22:36 -05:00
Ricardo Wurmus
29fd736a66
gnu: Add r-biobroom. 
* gnu/packages/bioconductor.scm (r-biobroom): New variable.
 2019-12-17 20:02:18 +01:00
Ricardo Wurmus
48bcbef07a
gnu: Add r-bioassayr. 
* gnu/packages/bioconductor.scm (r-bioassayr): New variable.
 2019-12-17 20:02:18 +01:00
Ricardo Wurmus
991554fc92
gnu: Add r-chemminer. 
* gnu/packages/bioconductor.scm (r-chemminer): New variable.
 2019-12-17 20:02:18 +01:00
Ricardo Wurmus
d38775b13f
gnu: Add r-bigpint. 
* gnu/packages/bioconductor.scm (r-bigpint): New variable.
 2019-12-17 20:02:18 +01:00
Ricardo Wurmus
820373dbc8
gnu: Add r-bigmemoryextras. 
* gnu/packages/bioconductor.scm (r-bigmemoryextras): New variable.
 2019-12-17 20:02:18 +01:00
Ricardo Wurmus
6ca6f8663b
gnu: Add r-biggr. 
* gnu/packages/bioconductor.scm (r-biggr): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
5aef09bd0e
gnu: Add r-hyperdraw. 
* gnu/packages/bioconductor.scm (r-hyperdraw): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
75a8bb3185
gnu: Add r-hypergraph. 
* gnu/packages/bioconductor.scm (r-hypergraph): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
e823337c6e
gnu: Add r-rsbml. 
* gnu/packages/bioconductor.scm (r-rsbml): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
40fe63ad8a
gnu: Add r-bifet. 
* gnu/packages/bioconductor.scm (r-bifet): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
de9374b73c
gnu: Add r-bicare. 
* gnu/packages/bioconductor.scm (r-bicare): New variable.
 2019-12-17 20:02:17 +01:00
Ricardo Wurmus
6bd50acf41
gnu: Add r-bhc. 
* gnu/packages/bioconductor.scm (r-bhc): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
75eb1149f3
gnu: Add r-bgx. 
* gnu/packages/bioconductor.scm (r-bgx): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
d11d6feafa
gnu: Add r-bgmix. 
* gnu/packages/bioconductor.scm (r-bgmix): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
1028bf0a05
gnu: Add r-rsvg. 
* gnu/packages/cran.scm (r-rsvg): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
59d485e118
gnu: Add r-shinycssloaders. 
* gnu/packages/cran.scm (r-shinycssloaders): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
96afb6c683
gnu: Add r-lim. 
* gnu/packages/cran.scm (r-lim): New variable.
 2019-12-17 20:02:16 +01:00
Ricardo Wurmus
c686e53afe
gnu: Add r-diagram. 
* gnu/packages/cran.scm (r-diagram): New variable.
 2019-12-17 20:02:15 +01:00
Ricardo Wurmus
5828dd030b
gnu: Add r-poibin. 
* gnu/packages/cran.scm (r-poibin): New variable.
 2019-12-17 20:02:15 +01:00
Ricardo Wurmus
595036d9f9
gnu: Add libsbml. 
* gnu/packages/bioinformatics.scm (libsbml): New variable.
 2019-12-17 20:02:11 +01:00
Jethro Cao
328dd9b7c2
gnu: Add love-nuklear. 
* gnu/packages/game-development.scm (love-nuklear): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-12-17 17:41:28 +01:00
Guillaume Le Vaillant
2963ae8e4a
gnu: txr: Update to 229. 
* gnu/packages/lisp.scm (txr): Update to 229.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-12-17 17:41:28 +01:00
Konrad Hinsen
a7c75b8dbf
gnu: gfortran: change to a hidden package 
* gnu/packages/gcc.scm (gfortran-4.8, gfortran-4.9)
(gfortran-5, gfortran-6, gfortran-7, gfortran-8)
(gfortran-9): Wrap in 'hidden-package'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-12-17 17:41:28 +01:00
Ludovic Courtès
3e313792aa
gnu: python-elasticsearch: Update to 7.1.0. 
* gnu/packages/python-web.scm (python-elasticsearch): Update to 7.1.0.
 2019-12-17 17:41:27 +01:00
Ricardo Wurmus
aaa74ee57d
gnu: r-pracma: Update to 2.2.9. 
* gnu/packages/cran.scm (r-pracma): Update to 2.2.9.
 2019-12-17 14:58:33 +01:00
Ricardo Wurmus
5722022f88
gnu: r-repr: Update to 1.0.2. 
* gnu/packages/cran.scm (r-repr): Update to 1.0.2.
 2019-12-17 14:58:33 +01:00
Ricardo Wurmus
cd0e2815d5
gnu: r-ggeffects: Update to 0.14.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.14.0.
[propagated-inputs]: Remove r-dplyr and r-rlang.
 2019-12-17 14:58:33 +01:00
Ricardo Wurmus
f6e75823bd
gnu: r-dvmisc: Update to 1.1.4. 
* gnu/packages/cran.scm (r-dvmisc): Update to 1.1.4.
[propagated-inputs]: Add r-tab; remove r-purrr.
 2019-12-17 14:58:33 +01:00
Ricardo Wurmus
6e963260ae
gnu: r-ttr: Update to 0.23-6. 
* gnu/packages/cran.scm (r-ttr): Update to 0.23-6.
 2019-12-17 14:58:33 +01:00
Ricardo Wurmus
4d6ccb0000
gnu: r-argparser: Update to 0.6. 
* gnu/packages/cran.scm (r-argparser): Update to 0.6.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
f87c672789
gnu: r-ordinal: Update to 2019.12-10. 
* gnu/packages/cran.scm (r-ordinal): Update to 2019.12-10.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
f98480a975
gnu: r-seurat: Update to 3.1.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
8a51ddce25
gnu: r-bh: Update to 1.72.0-1. 
* gnu/packages/statistics.scm (r-bh): Update to 1.72.0-1.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
3b21f5814c
gnu: Add r-tab. 
* gnu/packages/cran.scm (r-tab): New variable.
 2019-12-17 14:58:32 +01:00
Ricardo Wurmus
5ba865a73f
gnu: Add r-gee. 
* gnu/packages/cran.scm (r-gee): New variable.
 2019-12-17 14:58:32 +01:00
Efraim Flashner
5a0beca3aa
gnu: shotwell: Clean-up inputs. 
* gnu/packages/gnome.scm (shotwell)[arguments]: Add phase to skip
gtk-update-icon-cache.
[inputs]: Sort alphabetically. Move glib:bin ...
[native-inputs]: ... to here. Remove desktop-file-utils, gtk+:bin.
 2019-12-17 10:23:02 +02:00
Efraim Flashner
914c8cdf07
gnu: dia: Fix version number. 
This commit is actually after to 0.97.3 release.

* gnu/packages/gnome.scm (dia)[version]: Use git-version.
[source]: Update to new source uri. Use git-file-name.
 2019-12-17 09:57:21 +02:00
Efraim Flashner
4b3e91de2d
gnu: dia: Don't override bootstrap phase. 
* gnu/packages/gnome.scm (dia)[arguments]: Remove custom 'run-autogen
phgase. Add phase before 'bootstrap to not run configure.
 2019-12-17 09:51:48 +02:00
Efraim Flashner
a315afa35b
gnu: dia: Fix-up inputs. 
* gnu/packages/gnome.scm (dia)[inputs]: Sort alphabetically. Move
glib:bin ...
[native-inputs]: ... to here. Sort alphabetically.
 2019-12-17 09:50:37 +02:00
Efraim Flashner
80a06e6206
gnu: libidl: Hard-code name in source uri. 
* gnu/packages/gnome.scm (libidl)[source]: Hard-code name.
 2019-12-17 09:37:34 +02:00
Efraim Flashner
ef2c55bbcf
gnu: libidl: Set upstream name. 
* gnu/packages/gnome.scm (libidl)[properties]: New field.
 2019-12-17 09:37:34 +02:00
Efraim Flashner
fb9399e93f
gnu: brasero: Update home-page. 
* gnu/packages/gnome.scm (brasero)[home-page]: Use new home-page.
 2019-12-17 09:37:34 +02:00
Efraim Flashner
ba549e17fa
gnu: brasero: Fix-up inputs. 
* gnu/packages/gnome.scm (brasero)[inputs]: Move itstool ...
[native-inputs]: ... to here.
 2019-12-17 09:37:34 +02:00
Efraim Flashner
d1df755435
gnu: brasero: Hard-code name in source uri. 
* gnu/packages/gnome.scm (brasero)[source]: Hard-code name.
 2019-12-17 09:37:22 +02:00
Efraim Flashner
ca825070e4
gnu: pinfo: Use a source file name. 
* gnu/packages/texinfo.scm (pinfo)[source]: Add 'file-name'.
 2019-12-17 09:17:27 +02:00
Vagrant Cascadian
e5c32a3afa
gnu: electron-cash: Use substitute-keyword-arguments from electrum. 
* gnu/packages/finance (electron-cash)[arguments]: Use
  substitute-keyword-arguments to re-use arguments from electrum.
 2019-12-16 15:26:07 -08:00
Vagrant Cascadian
d08c3e51ab
gnu: electron-cash: Update to 4.0.12. 
* gnu/packages/finanace (electron-cash): Update to 4.0.12.
  [source] switch to git.
  [inputs] Add libsecp256k1.
  [arguments] Add phase patching to use libsecp256k1 from inputs.
 2019-12-16 14:35:16 -08:00
Vagrant Cascadian
b9676a4bbb
gnu: libsecp256k1: Update to 20191213. 
* gnu/packages/crypto (libsecp256k1): Update to 20191213.
 2019-12-16 14:35:12 -08:00
Ricardo Wurmus
94f9c0cdc4
gnu: python-gffutils: Update description. 
* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.
 2019-12-16 23:32:55 +01:00
Mădălin Ionel Patrașcu
cfd83f3282
gnu: Add python-gffutils. 
* gnu/packages/bioinformatics.scm (python-gffutils): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-16 23:27:00 +01:00
Ricardo Wurmus
b7716f1b39
gnu: Remove python2-dask. 
This package can no longer be built with Python 2.

* gnu/packages/python-xyz.scm (python2-dask): Remove variable.
 2019-12-16 23:22:12 +01:00
Ricardo Wurmus
86c7ca07aa
gnu: python-dask: Update to 2.9.0. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2.9.0.
[arguments]: Adjust phase to disable broken tests.
[propagated-inputs]: Add python-fsspec and python-packaging.
 2019-12-16 23:22:12 +01:00
Ricardo Wurmus
c70a019137
gnu: Add python-fsspec. 
* gnu/packages/python-xyz.scm (python-fsspec): New variable.
 2019-12-16 23:22:12 +01:00
Mădălin Ionel Patrașcu
4ade2dd9d2
gnu: python-pyfaidx: Update to 0.5.7. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
 2019-12-16 23:22:12 +01:00
Christopher Baines
27d083433a
gnu: guix-data-service: Update to 0.0.1-8.a019a5e. 
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-8.a019a5e.
 2019-12-16 21:00:46 +00:00
Brett Gilio
1171c4b3c0
Revert "gnu: ccls: Configure using -isystem for header files." 
This reverts commit 2c82d4ad10.
 2019-12-16 14:05:17 -06:00
Brett Gilio
792c3db553
Revert "gnu: ccls: Adjust indentation" 
This reverts commit 3c80b07a0b.
 2019-12-16 14:04:59 -06:00
Mădălin Ionel Patrașcu
db6bd842aa
gnu: Add python-argh. 
* gnu/packages/python-xyz.scm (python-argh): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-16 17:30:33 +01:00
Mădălin Ionel Patrașcu
dbcef44a0b
gnu: Add python-iocapture. 
* gnu/packages/python-xyz.scm (python-iocapture): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-12-16 17:27:03 +01:00
Jan Nieuwenhuizen
d0a26d0be9
gnu: gash: Update to 0.2.0. 
* gnu/packages/shells.scm (gash): Update to 0.2.0.
 2019-12-16 17:06:07 +01:00
Mathieu Othacehe
46429444d6
gnu: psmisc: Fix cross-compilation. 
* gnu/packages/linux.scm (psmisc)[arguments]: Pass
ac_cv_func_malloc_0_nonnull=yes and ac_cv_func_realloc_0_nonnull=yes options
that are required when cross-compiling.
 2019-12-16 16:45:34 +01:00
Mathieu Othacehe
88ca4029a6
gnu: iw: Fix cross-compilation. 
* gnu/packages/linux.scm (iw)[arguments]: Set PKG_CONFIG and CC variables
correctly for cross-compilation.
 2019-12-16 16:19:39 +01:00
Ricardo Wurmus
c6a7fe7937
gnu: yoshimi: Update to 1.6.1. 
* gnu/packages/music.scm (yoshimi): Update to 1.6.1.
 2019-12-16 15:43:31 +01:00
Pierre Neidhardt
709f839c20
gnu: emacs-helm-fish-completion: Update to 0.2. 
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.2.
 2019-12-16 15:35:40 +01:00
Mathieu Othacehe
8c4c5bf86a
Revert "gnu: info-reader: Fix cross-compilation." 
This reverts commit 614a1e3fa2.
This is broken on master with the following error:

output (`/gnu/store/6rnhfi8zrdajbahbq9ii8bpj7mwfcjba-info-reader-6.6') is not
allowed to refer to path
`/gnu/store/ziinjmbnq004866mwjrczsk12wf35qb8-perl-5.30.0' build of
/gnu/store/nnfvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv failed View
build log at
'/var/log/guix/drvs/nn/fvr10713khxp1bkbpwi5wxbj8cm4wb-info-reader-6.6.drv.bz2'.
 2019-12-16 15:08:08 +01:00
Efraim Flashner
d0ef3a0048
gnu: libreoffice: Update to 6.3.4.2. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.3.4.2.
 2019-12-16 14:13:16 +02:00
Ricardo Wurmus
223236f6c2
gnu: guile-studio: Update to 0.0.2. 
* gnu/packages/guile-xyz.scm (guile-studio): Update to 0.0.2.
[arguments]: Only include emacs inputs in INPUTS make flag.
 2019-12-16 08:04:18 +01:00
Brett Gilio
3c80b07a0b
gnu: ccls: Adjust indentation 
* gnu/packages/cpp.scm (ccls): Adjust indentation.
 2019-12-16 00:10:14 -06:00
Brett Gilio
2c82d4ad10
gnu: ccls: Configure using -isystem for header files. 
* gnu/packages/cpp.scm (ccls): Configure using -isystem for header files.
[arguments]: Use GCC as a build input for preprocessing and searching GCC
subdirectories, this provides better support for header file completion on
runtime.
[inputs]: Add ncurses for command-line support. Remove LLVM, it is not needed.
[native-inputs]: Move rapidjson from inputs to native-inputs, add GCC.
 2019-12-16 00:06:05 -06:00
Alexandros Theodotou
90ee17cdac
gnu: Add python-sphinx-intl 
* gnu/packages/sphinx.scm (python-sphinx-intl): New variable.

Signed-off-by: Brett Gilio <brettg@posteo.net>
 2019-12-15 22:53:50 -06:00
Nicolas Goaziou
00386d3430
gnu: Add emacs-eww-lnum. 
* gnu/packages/emacs-xyz.scm (emacs-eww-lnum): New variable.
 2019-12-15 23:33:06 +01:00
Ricardo Wurmus
e703f6d8ef
gnu: Add pinfo. 
* gnu/packages/texinfo.scm (pinfo): New variable.
 2019-12-15 23:12:56 +01:00
Ricardo Wurmus
34982a4622
gnu: r-quantreg: Update to 5.54. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.54.
 2019-12-15 23:12:04 +01:00
Ricardo Wurmus
155d48f6c6
gnu: r-glmnet: Update to 3.0-2. 
* gnu/packages/statistics.scm (r-glmnet): Update to 3.0-2.
 2019-12-15 23:12:04 +01:00
Ricardo Wurmus
468fb90fdd
gnu: r-sparsem: Update to 1.78. 
* gnu/packages/statistics.scm (r-sparsem): Update to 1.78.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
 2019-12-15 23:12:04 +01:00
Ricardo Wurmus
804e0682bf
gnu: r-segmented: Update to 1.1-0. 
* gnu/packages/statistics.scm (r-segmented): Update to 1.1-0.
 2019-12-15 23:12:04 +01:00