TakeV/guix
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity
62227 commits 102 branches 35 tags 561 MiB
Commit graph

62227 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus f85794edb8
gnu: r-rtracklayer: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.48.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 58613ca1e5
gnu: r-genomicalignments: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.24.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus 87c98cf701
gnu: r-summarizedexperiment: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 46e103a1b5
gnu: r-delayedarray: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.0.
[propagated-inputs]: Remove r-biocparallel.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 1f9c87a442
gnu: r-rsamtools: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.4.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus d3491d4dad
gnu: r-biostrings: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm ( r-biostrings): Update to 2.56.0.
[propagated-inputs]: Add r-crayon.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus cb486f16da
gnu: r-biocparallel: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus e87e6cc89d
gnu: r-biomart: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 920224771f
gnu: r-annotationdbi: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 7d91e3bed4
gnu: r-biobase: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 087a97f8df
gnu: r-genomicranges: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus e0d40fa275
gnu: r-xvector: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 49c766d0bb
gnu: r-limma: Update to 3.44.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus cdd83b2e22
gnu: r-variantannotation: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus c14d59d9ad
gnu: r-edger: Update to 3.30.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus 506735eea6
gnu: r-genomeinfodb: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 8a38b676da
gnu: r-iranges: Update to 2.22.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus f189f536be
gnu: r-s4vectors: Update to 0.26.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 9f416be83d
gnu: r-biocstyle: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 5de96ae98b
gnu: r-grohmm: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus bb18d11d85
gnu: r-systempiper: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 681cca95b3
gnu: r-shortread: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 3d2899dab5
gnu: r-gostats: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus be414286bc
gnu: r-category: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus a8613ff861
gnu: r-gseabase: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus 7d8b96e24b
gnu: r-rbgl: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 397568dbca
gnu: r-annotationforge: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus db5addba2c
gnu: r-dexseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 3d7de4ed82
gnu: r-deseq2: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 5fdea056c9
gnu: r-genefilter: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus c85e5ac0df
gnu: r-rgraphviz: Update to 2.32.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 2226a2a8de
gnu: r-preprocesscore: Update to 1.50.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 67a289e5bd
gnu: Add r-dot. 
* gnu/packages/cran.scm (r-dot): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 06ceac32e6
gnu: Add r-v8. 
* gnu/packages/cran.scm (r-v8): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus e6aacef67e
gnu: Add r-scatterpie. 
* gnu/packages/cran.scm (r-scatterpie): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 45f54b418b
gnu: Add r-gprofiler2. 
* gnu/packages/cran.scm (r-gprofiler2): New variable.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus f9311eaa7c
gnu: node: Build shared library. 
* gnu/packages/node.scm (node)[arguments]: Build shared library.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus 8e518d4802
guix: Update to Bioconductor 3.11. 
* guix/build-system/r.scm (bioconductor-uri): Use new URL.
* guix/import/cran.scm (%bioconductor-version): Update to 3.11.
 2020-06-13 01:19:38 +02:00
Ricardo Wurmus a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
 2020-06-13 01:19:38 +02:00
Christopher Baines db6290af7c
lint: check-patch-file-names: Use origin-actual-file-name. 
This avoids crashes for the patch-file-names checker where a <origin> is used
for a patch, but without a value for the file-name field. This is currently
the case with the bash package.

* guix/lint.scm (check-patch-file-names): Change origin-file-name to
origin-actual-file-name.
 2020-06-12 22:26:47 +01:00
Ludovic Courtès 29e4d3ea06
gnu: guile-sqlite3: Update to 0.1.1. 
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.1.
[source]: Remove 'patches', 'modules', and 'snippet'.
* gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2020-06-12 18:56:11 +02:00
Ludovic Courtès 52c529ff20
git-authenticate: Disallow SHA1 (and MD5) signatures. 
* guix/git-authenticate.scm (commit-signing-key): Add
 #:disallowed-hash-algorithms and honor it.
(authenticate-commit)[recent-commit?]: New variable.
Pass #:disallowed-hash-algorithms to 'commit-signing-key'.
* tests/git-authenticate.scm ("signed commits, SHA1 signature"): New test.
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 7def5056b6
gnu: Add liblogging. 
* gnu/packages/c.scm (liblogging): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:11 +02:00
Katherine Cox-Buday 0aee6e51b4
gnu: Add libfastjson. 
* gnu/packages/c.scm (libfastjson): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Katherine Cox-Buday 70a49ef76b
gnu: Add libestr. 
* gnu/packages/c.scm (libestr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Ryan Desfosses 3bec7a356a
gnu: Add emacs-shell-pop. 
* gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-12 18:56:10 +02:00
Efraim Flashner 205a0ecd5b
download: Add more apache mirrors. 
* guix/download.scm (%mirrors): Add more apache mirrors.
 2020-06-12 18:28:51 +03:00
Efraim Flashner 9a01efa262
gnu: Fix apache mirror URIs. 
* gnu/packages/web.scm (serf)[source]: Remove redundant part of URI.
* gnu/packages/java.scm (ant-bootstrap, java-commons-httpclient,
java-jakarta-oro)[source]: Same.
* gnu/packages/maven.scm (maven-shared-utils, maven-plugin-annotations,
maven-wagon-provider-api, maven-artifact)[source]: Same.
 2020-06-12 18:23:27 +03:00