diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 49 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
2 files changed, 49 insertions, 49 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d02639a3..7c97e52312 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8452,6 +8452,55 @@ microarray data.") 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") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad3ae204e1..d8d64818d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,55 +7691,6 @@ including VCF header and contents in RDF and JSON.") (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") |