[BioC] pd.mapping 10Karray

[Seth Falcon]

Hi Marianne,

I'm not yet sure what is going on with pdInfoBuilder, but perhaps we
can sort it out...

"Marianne Tuefferd" <tuefferd at vjf.inserm.fr> writes:
>  > library("pdInfoBuilder")
>  > pkg <- new("AffySNPPDInfoPkgSeed",
> +            version = "0.0",
> +            email = "tuefferd at vjf.inserm.fr",
> +            biocViews = "AnnotationData",
> +            cdfFile = cdfFile,
> +            csvAnnoFile = csvAnno,
> +            csvSeqFile = csvSeq)
>  > makePdInfoPackage(pkg, destDir = ".")
> Creating package in ./pd.mapping10k.xba142
> Error in gsub(pattern, replacement, x, ignore.case, extended, fixed,
> useBytes) :
>     invalid argument
>  > traceback()
> 7: gsub(nm[i], symbolValues[[i]], res)
> 6: subsFileName(tmp[length(tmp)])
> 5: cpSubs(src, dest)
> 4: copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues,
>         recursive = TRUE)
> 3: createPackage(pkgname = pkgName, destinationDir = destDir, originDir
> = templateDir,
>         symbolValues = syms, quiet = quiet)
> 2: makePdInfoPackage(pkg, destDir = ".")
> 1: makePdInfoPackage(pkg, destDir = ".")

This is useful output.  Can you try two things?

1. Try setting options(error=recover) and then rerun the above
   example.  When the error occurs you will be put into the debugger
   and can select a frame to enter (numbered like the stack trace
   above).  Find the frame with the gsub call, and print out the value
   of nm[i], sumbolValues[[i]], res.  Since the error is telling us
   that one of these is not somehow valid

2. I notice that your locale setting is not "C" and I wonder if
   rerunning the example after setting Sys.setlocale(locale="C")
   changes anything.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/