gnu: Add r-bioccheck.

* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
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Roel Janssen 2016-10-20 09:51:28 +02:00
parent c645cef7da
commit 4644644ace
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@ -5936,6 +5936,54 @@ Bioconductor PDF and HTML documents. Package vignettes illustrate use and
functionality.") functionality.")
(license license:artistic2.0))) (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 (define-public r-getopt
(package (package
(name "r-getopt") (name "r-getopt")