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authorRoel Janssen <roel@gnu.org>2016-10-20 09:51:28 +0200
committerRoel Janssen <roel@gnu.org>2016-10-20 09:53:02 +0200
commit4644644ace2ab64a07c075fe587c29abd3bb376a (patch)
tree1ef87d61cb194e7c32f024895aed5a2a9f47da4f
parentc645cef7da813ca305a9adeab08f34e925e560cc (diff)
downloadpatches-4644644ace2ab64a07c075fe587c29abd3bb376a.tar
patches-4644644ace2ab64a07c075fe587c29abd3bb376a.tar.gz
gnu: Add r-bioccheck.
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm48
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3fe7b5f3ae..d0b8056179 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5936,6 +5936,54 @@ Bioconductor PDF and HTML documents. Package vignettes illustrate use and
functionality.")
(license license:artistic2.0)))
+(define-public r-bioccheck
+ (package
+ (name "r-bioccheck")
+ (version "1.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocCheck" version))
+ (sha256
+ (base32
+ "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack"))))
+ (properties
+ `((upstream-name . "BiocCheck")))
+ (build-system r-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ ;; This package can be used by calling BiocCheck(<package>) from
+ ;; within R, or by running R CMD BiocCheck <package>. This phase
+ ;; makes sure the latter works. For this to work, the BiocCheck
+ ;; script must be somewhere on the PATH (not the R bin directory).
+ (add-after 'install 'install-bioccheck-subcommand
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (dest-dir (string-append out "/bin"))
+ (script-dir
+ (string-append out "/site-library/BiocCheck/script/")))
+ (mkdir-p dest-dir)
+ (symlink (string-append script-dir "/checkBadDeps.R")
+ (string-append dest-dir "/checkBadDeps.R"))
+ (symlink (string-append script-dir "/BiocCheck")
+ (string-append dest-dir "/BiocCheck")))
+ #t)))))
+ (native-inputs
+ `(("which" ,which)))
+ (propagated-inputs
+ `(("r-graph" ,r-graph)
+ ("r-knitr" ,r-knitr)
+ ("r-httr" ,r-httr)
+ ("r-optparse" ,r-optparse)
+ ("r-devtools" ,r-devtools)
+ ("r-biocinstaller" ,r-biocinstaller)
+ ("r-biocviews" ,r-biocviews)))
+ (home-page "http://bioconductor.org/packages/BiocCheck")
+ (synopsis "Executes Bioconductor-specific package checks")
+ (description "This package contains tools to perform additional quality
+checks on R packages that are to be submitted to the Bioconductor repository.")
+ (license license:artistic2.0)))
+
(define-public r-getopt
(package
(name "r-getopt")