gnu: r-bioccheck: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
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					 2 changed files with 49 additions and 49 deletions
				
			
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					@ -8452,6 +8452,55 @@ microarray data.")
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monograph.")
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					monograph.")
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    (license license:artistic2.0)))
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					    (license license:artistic2.0)))
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					(define-public r-bioccheck
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					  (package
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					    (name "r-bioccheck")
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					    (version "1.26.0")
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					    (source (origin
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					              (method url-fetch)
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					              (uri (bioconductor-uri "BiocCheck" version))
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					              (sha256
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					               (base32
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					                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
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					    (properties
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					     `((upstream-name . "BiocCheck")))
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					    (build-system r-build-system)
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					    (arguments
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					     '(#:phases
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					       (modify-phases %standard-phases
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					         ;; This package can be used by calling BiocCheck(<package>) from
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					         ;; within R, or by running R CMD BiocCheck <package>.  This phase
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					         ;; makes sure the latter works.  For this to work, the BiocCheck
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					         ;; script must be somewhere on the PATH (not the R bin directory).
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					         (add-after 'install 'install-bioccheck-subcommand
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					           (lambda* (#:key outputs #:allow-other-keys)
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					             (let* ((out (assoc-ref outputs "out"))
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					                    (dest-dir (string-append out "/bin"))
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					                    (script-dir
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					                     (string-append out "/site-library/BiocCheck/script/")))
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					               (mkdir-p dest-dir)
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					               (symlink (string-append script-dir "/checkBadDeps.R")
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					                        (string-append dest-dir "/checkBadDeps.R"))
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					               (symlink (string-append script-dir "/BiocCheck")
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					                        (string-append dest-dir "/BiocCheck")))
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					             #t)))))
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					    (propagated-inputs
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					     `(("r-codetools" ,r-codetools)
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					       ("r-graph" ,r-graph)
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					       ("r-httr" ,r-httr)
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					       ("r-knitr" ,r-knitr)
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					       ("r-optparse" ,r-optparse)
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					       ("r-biocmanager" ,r-biocmanager)
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					       ("r-biocviews" ,r-biocviews)
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					       ("r-stringdist" ,r-stringdist)))
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					    (native-inputs
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					     `(("r-knitr" ,r-knitr)))
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					    (home-page "https://bioconductor.org/packages/BiocCheck")
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					    (synopsis "Executes Bioconductor-specific package checks")
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					    (description "This package contains tools to perform additional quality
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					checks on R packages that are to be submitted to the Bioconductor repository.")
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					    (license license:artistic2.0)))
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(define-public r-biocgraph
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					(define-public r-biocgraph
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  (package
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					  (package
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    (name "r-biocgraph")
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					    (name "r-biocgraph")
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					@ -7691,55 +7691,6 @@ including VCF header and contents in RDF and JSON.")
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    (home-page "https://github.com/vcflib/bio-vcf")
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					    (home-page "https://github.com/vcflib/bio-vcf")
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    (license license:expat)))
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					    (license license:expat)))
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(define-public r-bioccheck
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  (package
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    (name "r-bioccheck")
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    (version "1.26.0")
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    (source (origin
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              (method url-fetch)
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              (uri (bioconductor-uri "BiocCheck" version))
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              (sha256
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               (base32
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                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
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    (properties
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     `((upstream-name . "BiocCheck")))
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    (build-system r-build-system)
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    (arguments
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     '(#:phases
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       (modify-phases %standard-phases
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         ;; This package can be used by calling BiocCheck(<package>) from
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         ;; within R, or by running R CMD BiocCheck <package>.  This phase
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					 | 
				
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         ;; makes sure the latter works.  For this to work, the BiocCheck
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         ;; script must be somewhere on the PATH (not the R bin directory).
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					 | 
				
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         (add-after 'install 'install-bioccheck-subcommand
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           (lambda* (#:key outputs #:allow-other-keys)
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             (let* ((out (assoc-ref outputs "out"))
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                    (dest-dir (string-append out "/bin"))
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                    (script-dir
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                     (string-append out "/site-library/BiocCheck/script/")))
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               (mkdir-p dest-dir)
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               (symlink (string-append script-dir "/checkBadDeps.R")
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                        (string-append dest-dir "/checkBadDeps.R"))
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               (symlink (string-append script-dir "/BiocCheck")
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                        (string-append dest-dir "/BiocCheck")))
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             #t)))))
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    (propagated-inputs
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					 | 
				
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     `(("r-codetools" ,r-codetools)
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       ("r-graph" ,r-graph)
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					 | 
				
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       ("r-httr" ,r-httr)
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					 | 
				
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       ("r-knitr" ,r-knitr)
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					 | 
				
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       ("r-optparse" ,r-optparse)
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					 | 
				
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       ("r-biocmanager" ,r-biocmanager)
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					 | 
				
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       ("r-biocviews" ,r-biocviews)
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       ("r-stringdist" ,r-stringdist)))
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					 | 
				
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    (native-inputs
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     `(("r-knitr" ,r-knitr)))
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					 | 
				
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    (home-page "https://bioconductor.org/packages/BiocCheck")
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					 | 
				
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    (synopsis "Executes Bioconductor-specific package checks")
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					 | 
				
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    (description "This package contains tools to perform additional quality
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					 | 
				
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checks on R packages that are to be submitted to the Bioconductor repository.")
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    (license license:artistic2.0)))
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					 | 
				
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(define-public r-s4vectors
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					(define-public r-s4vectors
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  (package
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					  (package
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    (name "r-s4vectors")
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					    (name "r-s4vectors")
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