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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
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") |