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.master
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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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;; 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-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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