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Re: [PATCH 7/7] gnu: Add r-bioccheck.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH 7/7] gnu: Add r-bioccheck. |
Date: |
Wed, 19 Oct 2016 19:09:14 +0200 |
User-agent: |
mu4e 0.9.16; emacs 25.1.1 |
Roel Janssen <address@hidden> writes:
> Ricardo Wurmus writes:
>
>> Roel Janssen <address@hidden> 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 <address@hidden>
> 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/")))
We usually prefer to do this
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
… out …)))
instead of using the magical “%output”.
> + (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")))))))))
Would it work to use “install-file” here (or to use Guile’s “symlink
oldpath newpath”) instead of shelling out?
~~ Ricardo