How to list package dependency on a Bioconductor package?

Steven,

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

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How to list package dependency on a Bioconductor package?

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