Ricardo Wurmus writes:
> Roel Janssen <r...@gnu.org> writes:
>
>> * gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
>> ---
>> gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
>> 1 file changed, 29 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm
>> b/gnu/packages/bioinformatics.scm
>> index 902d1d2..00a4161 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -5426,6 +5426,35 @@ like automatically generated help option and usage,
>> support for default
>> values, positional argument support, etc.")
>>
>> (license license:gpl2+)))
>>
>> +(define-public r-bioccheck
>> + (package
>> + (name "r-bioccheck")
>> + (version "1.8.2")
>> + (source (origin
>> + (method url-fetch)
>> + (uri (bioconductor-uri "BiocCheck" version))
>> + (sha256
>> + (base32
>> + "0bvkhxmr25nb0gkncifbc3x48i5zgls3737g3xais6jx16wd4q35"))))
>> + (properties
>> + `((upstream-name . "BiocCheck")))
>> + (build-system r-build-system)
>> + (inputs
>> + `(("which" ,which)))
>
> Is this a native input?
Ah, yes it is.
>> + (propagated-inputs
>> + `(("r-graph" ,r-graph)
>> + ("r-knitr" ,r-knitr)
>> + ("r-httr" ,r-httr)
>> + ("r-optparse" ,r-optparse)
>> + ("r-devtools" ,r-devtools)
>> + ("r-biocinstaller" ,r-biocinstaller)
>> + ("r-biocviews" ,r-biocviews)))
>> + (home-page "http://bioconductor.org/packages/BiocCheck";)
>> + (synopsis "Executes Bioconductor-specific package checks")
>> + (description "This package executes Bioconductor-specific
>> +package checks.")
>
> Well… okay. :) It would be nice if it was a little more specific.
>
> Maybe:
>
> This package contains tools to perform quality checks on R packages
> that are to be submitted to the Bioconductor repository.
>
> WDYT?
I used your description, but added "additional" to it. I also added a
custom build phase to make "R CMD BiocCheck" work.
Here's the new patch:
>From 1d9248098fc507876d77cddc890ea906aef7b83d Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@gnu.org>
Date: Wed, 19 Oct 2016 16:43:04 +0200
Subject: [PATCH] gnu: Add r-bioccheck.
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3fe7b5f..d21781f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5936,6 +5936,54 @@ Bioconductor PDF and HTML documents. Package vignettes
illustrate use and
functionality.")
(license license:artistic2.0)))
+(define-public r-bioccheck
+ (package
+ (name "r-bioccheck")
+ (version "1.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocCheck" version))
+ (sha256
+ (base32
+ "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack"))))
+ (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 _
+ (let ((dest-dir (string-append %output "/bin"))
+ (script-dir
+ (string-append %output "/site-library/BiocCheck/script/")))
+ (mkdir-p dest-dir)
+ (zero? (system* "ln" "--symbolic"
+ (string-append script-dir "/checkBadDeps.R")
+ (string-append dest-dir "/checkBadDeps.R")))
+ (zero? (system* "ln" "--symbolic"
+ (string-append script-dir "/BiocCheck")
+ (string-append dest-dir "/BiocCheck")))))))))
+ (native-inputs
+ `(("which" ,which)))
+ (propagated-inputs
+ `(("r-graph" ,r-graph)
+ ("r-knitr" ,r-knitr)
+ ("r-httr" ,r-httr)
+ ("r-optparse" ,r-optparse)
+ ("r-devtools" ,r-devtools)
+ ("r-biocinstaller" ,r-biocinstaller)
+ ("r-biocviews" ,r-biocviews)))
+ (home-page "http://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-getopt
(package
(name "r-getopt")
--
2.10.0
