From 2d7c4ae3ee83841ef827a160b0d23c1d10d2570d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 17 Mar 2017 09:42:22 +0100
Subject: gnu: r: Rename to r-minimal.

* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
---
 gnu/packages/bioinformatics.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bd3c97b721..ccde01b119 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -478,7 +478,7 @@ BED, GFF/GTF, VCF.")
     (inputs
      `(("bedtools" ,bedtools-2.18)
        ("samtools" ,samtools-0.1)
-       ("r" ,r)
+       ("r-minimal" ,r-minimal)
        ("r-foreach" ,r-foreach)
        ("r-xnomial" ,r-xnomial)
        ("r-domc" ,r-domc)
@@ -1728,7 +1728,7 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
        ("python2-scipy" ,python2-scipy)
        ("python2-matplotlib" ,python2-matplotlib)))
     (propagated-inputs
-     `(("r" ,r)
+     `(("r-minimal" ,r-minimal)
        ("libsvm" ,libsvm)
        ("randomjungle" ,randomjungle)))
     (native-inputs
@@ -4004,7 +4004,7 @@ partial genes, and identifies translation initiation sites.")
        ("grep" ,grep)
        ("sed" ,sed)
        ("gawk" ,gawk)
-       ("r" ,r)
+       ("r-minimal" ,r-minimal)
        ("r-ggplot2" ,r-ggplot2)
        ("coreutils" ,coreutils)))
     (home-page "http://sanger-pathogens.github.io/Roary")
@@ -4119,7 +4119,7 @@ phylogenies.")
     (inputs
      `(("boost" ,boost)
        ("ncurses" ,ncurses)
-       ("r" ,r)
+       ("r-minimal" ,r-minimal)
        ("perl" ,perl)
        ("samtools" ,samtools-0.1)
        ("zlib" ,zlib)))
@@ -7636,7 +7636,7 @@ library implementing most of the pipeline's features.")
                  `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
              #t)))))
     (inputs
-     `(("r" ,r)
+     `(("r-minimal" ,r-minimal)
        ("r-rcas" ,r-rcas)
        ("guile-next" ,guile-next)
        ("guile-json" ,guile2.2-json)
-- 
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