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?
Martin
Cheers,
Simon
On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
<lig...@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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@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
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
