From simon.urbanek at r-project.org  Tue May  8 18:52:27 2012
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 8 May 2012 12:52:27 -0400
Subject: [Rd] How to list package dependency on a Bioconductor package?
In-Reply-To: <4FA94224.8060908@fhcrc.org>
References: <CAMe5z5nqAOk7hWXZ8ePs8XsPv=cSk8zO1vrm3doDZA4k+buhFQ@mail.gmail.com>
	<4F02F7BF.4040606@statistik.tu-dortmund.de>
	<CAMe5z5m=6=hdN8Ne4+p3XquTRYFZZAHWQovHjkgZKmV2oYzaiA@mail.gmail.com>
	<02FFE7E8-4543-4368-9028-BA04EB893322@r-project.org>
	<4FA94224.8060908@fhcrc.org>
Message-ID: <16E942D4-07FC-4B05-8C08-DE72C31518CA@r-project.org>


On May 8, 2012, at 11:56 AM, Martin Morgan wrote:

> On 5/8/2012 8:44 AM, Simon Urbanek wrote:
>> 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.
> 
> We're talking about a Bioconductor package here; the Mac binaries are available for R-2-15 http://bioconductor.org/packages/release/bioc/html/edgeR.html in the usual way; the Windows binaries are apparently discovered by the CRAN build system, so it sounds like CRAN's Mac builds are mis-configured, or Bioconductor's binary builds are inadequate?
> 

Neither, nor. 


>> 
>> 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>
>>>>> 
>>> 	[[alternative HTML version deleted]]
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 
> -- 
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> 



[Rd] How to list package dependency on a Bioconductor package?
Simon Urbanek