From simon.urbanek at r-project.org  Tue May  8 17:44:02 2012
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 8 May 2012 11:44:02 -0400
Subject: [Rd] How to list package dependency on a Bioconductor package?
In-Reply-To: <CAMe5z5m=6=hdN8Ne4+p3XquTRYFZZAHWQovHjkgZKmV2oYzaiA@mail.gmail.com>
References: <CAMe5z5nqAOk7hWXZ8ePs8XsPv=cSk8zO1vrm3doDZA4k+buhFQ@mail.gmail.com>
	<4F02F7BF.4040606@statistik.tu-dortmund.de>
	<CAMe5z5m=6=hdN8Ne4+p3XquTRYFZZAHWQovHjkgZKmV2oYzaiA@mail.gmail.com>
Message-ID: <02FFE7E8-4543-4368-9028-BA04EB893322@r-project.org>

Steven,

On May 7, 2012, at 1:24 PM, Steven Lund wrote:

> I recently submit a package called QuasiSeq.  The package source and
> Windows binary worked fine, but the MacOS X binary failed. The bottom of
> the CRAN page for QuasiSeq shows
> 
> Downloads:
>  Package source:     QuasiSeq_1.0-1.tar.gz
>  MacOS X binary:     not available, see check log.
>  Windows binary:     QuasiSeq-1.0-1.zip
>  Reference manual:  QuasiSeq.pdf
> 
> 
> The log for the MacOS X binary shows
>   - using R version 2.15.0 (2012-03-30)
>   - using platform: i386-apple-darwin9.8.0 (32-bit)
>   -  using session charset: ASCII
>   -  checking for file 'QuasiSeq/DESCRIPTION' ... OK
>   -  this is package 'QuasiSeq' version '1.0-1'
>   -  checking package namespace information ... OK
>   -  checking package dependencies ... ERROR
>           Package required but not available: 'edgeR'
> 
>           See the information on DESCRIPTION files in the chapter
> 'Creating R
>           packages' of the 'Writing R Extensions' manual.
>   -  elapsed time (check, wall clock): 0:01
> 
> Is there a simple remedy to the problems caused by the dependency on edgeR,
> or would you advise that I put a work-around into my source code using
> 'require' so I can list edgeR under Suggests instead of Depends or Includes?
> 

Well, if your package doesn't depend on it, it should certainly not be in Depends. But that is a design decision (depending on packages outside CRAN is somewhat tricky because in general you cannot guarantee availability, but it is legal ;)).

If you need any additional non-CRAN dependencies on Mac OS X, they can be installed if there are working self-sufficient binaries, you just need to tell me.

Cheers,
Simon


> 
> On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
> <ligges at statistik.tu-dortmund.de>wrote:
> 
>> 
>> 
>> On 03.01.2012 00:16, Steven Lund wrote:
>> 
>>> I know others have asked similar questions to the R developers, but I
>>> could not find the solution to this question.  Please forgive me if I
>>> have missed a crucial point in a previous post.
>>> 
>>> I would like to submit a package to CRAN that depends on the
>>> bioconductor package "edgeR".  Listing "edgeR" under the Depends or
>>> Imports lines in the DESCRIPTION file for my package causes an error
>>> when running the `R CMD check' command on my package's 'tar.gz' file:
>>> 
>>> * checking package dependencies ... ERROR
>>> Package required but not available: ?edgeR?
>>> 
>>> 
>>> Is there documentation or an example anywhere of how to handle
>>> dependencies on Bioconductor packages when creating a package for
>>> CRAN?
>>> 
>> 
>> 
>> Same as for CRAN packages. The CRAN check farm will automatically install
>> the dependency from BioConductor if available for the corresponding
>> platform / R version.
>> 
>> Uwe Ligges
>> 
>> 
>> 
>> 
>> 
>>> Thank you!
>>> 
>>> -Steve
>>> 
>>> ______________________________**________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel>
>>> 
>> 
> 
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> 
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[Rd] How to list package dependency on a Bioconductor package?
Simon Urbanek