Re: [Rd] How to list package dependency on a Bioconductor package?

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Tue, 08 May 2012 12:52:27 -0400

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@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: āedgeRā
>>>>> 
>>>>> 
>>>>> 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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> 
> 
> -- 
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109

>
>

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