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 +++++-----
 gnu/packages/emacs.scm            |  2 +-
 gnu/packages/machine-learning.scm |  2 +-
 gnu/packages/python.scm           |  2 +-
 gnu/packages/statistics.scm       | 12 ++++++------
 guix/build-system/r.scm           |  2 +-
 6 files changed, 15 insertions(+), 15 deletions(-)

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)
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c6e62acb7a..18d25b743b 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2924,7 +2924,7 @@ E-Prime forbids the use of the \"to be\" form to strengthen your writing.")
                 (string-append "SHELL = " (which "sh")))))))))
     (inputs
      `(("emacs" ,emacs-minimal)
-       ("r" ,r)))
+       ("r-minimal" ,r-minimal)))
     (native-inputs
      `(("perl" ,perl)
        ("texinfo" ,texinfo)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 73c78744f8..5379893b76 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -402,7 +402,7 @@ sample proximities between pairs of cases.")
     (inputs
      `(("python" ,python)
        ("numpy" ,python-numpy)
-       ("r" ,r)
+       ("r-minimal" ,r-minimal)
        ("octave" ,octave)
        ("swig" ,swig)
        ("hdf5" ,hdf5)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ba3c7d4c36..6c91401e22 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4085,7 +4085,7 @@ operators such as union, intersection, and difference.")
      `(("readline" ,readline)
        ("icu4c" ,icu4c)
        ("pcre" ,pcre)
-       ("r" ,r)
+       ("r-minimal" ,r-minimal)
        ("r-survival" ,r-survival)))
     (native-inputs
      `(("zlib" ,zlib)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 656895273f..3a26e23053 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -103,9 +103,9 @@ be output in text, PostScript, PDF or HTML.")
 ;; Update this package together with the set of recommended packages: r-boot,
 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
-(define-public r
+(define-public r-minimal
   (package
-    (name "r")
+    (name "r-minimal")
     (version "3.3.3")
     (source (origin
               (method url-fetch)
@@ -538,14 +538,14 @@ definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
 curves, Cox models, and parametric accelerated failure time models.")
     (license license:lgpl2.0+)))
 
-(define-public r-with-recommended-packages
-  (package (inherit r)
-    (name "r-with-recommended-packages")
+(define-public r
+  (package (inherit r-minimal)
+    (name "r")
     (source #f)
     (build-system trivial-build-system)
     (arguments '(#:builder (mkdir %output)))
     (propagated-inputs
-     `(("r" ,r)
+     `(("r-minimal" ,r-minimal)
        ("r-boot" ,r-boot)
        ("r-class" ,r-class)
        ("r-cluster" ,r-cluster)
diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index e8269fdeb1..c649036210 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -62,7 +62,7 @@ release corresponding to NAME and VERSION."
   "Return the default R package."
   ;; Lazily resolve the binding to avoid a circular dependency.
   (let ((r-mod (resolve-interface '(gnu packages statistics))))
-    (module-ref r-mod 'r)))
+    (module-ref r-mod 'r-minimal)))
 
 (define* (lower name
                 #:key source inputs native-inputs outputs system target
-- 
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