From bcc2e0ed2e0849f64de970877c75350ca96510af Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 7 Jun 2018 20:33:10 +0200
Subject: gnu: r-rcas: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
---
 gnu/packages/bioinformatics.scm | 42 ++++++++++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 17 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 828e965989..18b787b704 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8529,43 +8529,51 @@ (define-public r-bamsignals
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.3.4")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
+                "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)
-       ("r-testthat" ,r-testthat)
+     `(("r-testthat" ,r-testthat)
        ;; During vignette building knitr checks that "pandoc-citeproc"
        ;; is in the PATH.
        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
     (propagated-inputs
-     `(("r-data-table" ,r-data-table)
+     `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biomart" ,r-biomart)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-org-ce-eg-db" ,r-org-ce-eg-db)
-       ("r-org-dm-eg-db" ,r-org-dm-eg-db)
-       ("r-org-mm-eg-db" ,r-org-mm-eg-db)
+       ("r-biostrings" ,r-biostrings)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
        ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
        ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
        ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
-       ("r-topgo" ,r-topgo)
+       ("r-cowplot" ,r-cowplot)
+       ("r-data-table" ,r-data-table)
+       ("r-dbi" ,r-dbi)
        ("r-dt" ,r-dt)
+       ("r-genomation" ,r-genomation)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggseqlogo" ,r-ggseqlogo)
+       ("r-knitr" ,r-knitr)
+       ("r-motifrg" ,r-motifrg)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-org-ce-eg-db" ,r-org-ce-eg-db)
+       ("r-org-dm-eg-db" ,r-org-dm-eg-db)
+       ("r-org-mm-eg-db" ,r-org-mm-eg-db)
        ("r-pbapply" ,r-pbapply)
+       ("r-pheatmap" ,r-pheatmap)
        ("r-plotly" ,r-plotly)
        ("r-plotrix" ,r-plotrix)
-       ("r-motifrg" ,r-motifrg)
-       ("r-genomation" ,r-genomation)
-       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-proxy" ,r-proxy)
+       ("r-rsqlite" ,r-rsqlite)
        ("r-rtracklayer" ,r-rtracklayer)
-       ("r-rmarkdown" ,r-rmarkdown)))
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-topgo" ,r-topgo)))
     (synopsis "RNA-centric annotation system")
     (description
      "RCAS aims to be a standalone RNA-centric annotation system that provides
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