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 >>> <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
