summaryrefslogtreecommitdiff
path: root/gnu
diff options
context:
space:
mode:
authorzimoun <zimon.toutoune@gmail.com>2021-03-15 14:01:29 +0100
committerRicardo Wurmus <rekado@elephly.net>2021-03-15 14:05:22 +0100
commit852fa82d4ccd902dfd7b8e673d4d1f71fd69e89a (patch)
treee482fcbcb65bb9b1cd176f59081e602b2f0c38dd /gnu
parentd5576b6eb7808574dd519bf7591b4cf08ea6cb2c (diff)
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.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioconductor.scm49
-rw-r--r--gnu/packages/bioinformatics.scm49
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")