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gnu: r-bioccheck: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
This commit is contained in:
zimoun 2021-03-15 14:01:29 +01:00 committed by Ricardo Wurmus
parent d5576b6eb7
commit 852fa82d4c
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GPG key ID: 197A5888235FACAC
2 changed files with 49 additions and 49 deletions
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49
gnu/packages/bioconductor.scm
View file

@ -8452,6 +8452,55 @@ (define-public r-bioccasestudies
monograph.")
(license license:artistic2.0)))
(define-public r-bioccheck
(package
(name "r-bioccheck")
(version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
"1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
(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)))))
(propagated-inputs
`(("r-codetools" ,r-codetools)
("r-graph" ,r-graph)
("r-httr" ,r-httr)
("r-knitr" ,r-knitr)
("r-optparse" ,r-optparse)
("r-biocmanager" ,r-biocmanager)
("r-biocviews" ,r-biocviews)
("r-stringdist" ,r-stringdist)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://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-biocgraph
(package
(name "r-biocgraph")

49
gnu/packages/bioinformatics.scm
View file

@ -7691,55 +7691,6 @@ (define-public bio-vcf
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
(define-public r-bioccheck
(package
(name "r-bioccheck")
(version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
"1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
(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)))))
(propagated-inputs
`(("r-codetools" ,r-codetools)
("r-graph" ,r-graph)
("r-httr" ,r-httr)
("r-knitr" ,r-knitr)
("r-optparse" ,r-optparse)
("r-biocmanager" ,r-biocmanager)
("r-biocviews" ,r-biocviews)
("r-stringdist" ,r-stringdist)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://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-s4vectors
(package
(name "r-s4vectors")