From 6d5a4dd0a7c808e1318a8c8da88def7196027f94 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 18 Nov 2020 16:06:22 +0100
Subject: [PATCH] gnu: r-mutationalpatterns: Update to 3.0.1.

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial,
r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove
r-reshape2 and r-summarizedexperiment.
---
 gnu/packages/bioinformatics.scm | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d098fffb6..b2625342b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8943,33 +8943,40 @@ (define-public rcas-web
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "2.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm"))))
+         "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
        ;; These two packages are suggested packages
        ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-genomicranges" ,r-genomicranges)
+       ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
        ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggalluvial" ,r-ggalluvial)
+       ("r-ggdendro" ,r-ggdendro)
        ("r-ggplot2" ,r-ggplot2)
        ("r-iranges" ,r-iranges)
+       ("r-magrittr" ,r-magrittr)
        ("r-nmf" ,r-nmf)
-       ("r-plyr" ,r-plyr)
        ("r-pracma" ,r-pracma)
-       ("r-reshape2" ,r-reshape2)
-       ("r-cowplot" ,r-cowplot)
-       ("r-ggdendro" ,r-ggdendro)
+       ("r-purrr" ,r-purrr)
        ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
        ("r-variantannotation" ,r-variantannotation)))
     (home-page "https://bioconductor.org/packages/MutationalPatterns/")
     (synopsis "Extract and visualize mutational patterns in genomic data")