[BioC] GEOquery error

[Sean Davis]

Hi, Royce.

On Thu, May 1, 2014 at 4:46 PM, Royce W. Fletcher <royce at rwfletcher.com> wrote:
> getGEO seems to look for the gpl90.soft file in a random location; failing
> to find the file it then goes on to report an error.
>
> >From KnitHTML:
>
> geoq <- getGEO("GSE9514")
> ## Found 1 file(s)
> ## GSE9514_series_matrix.txt.gz
> ## File stored at:
> ## C:\DOCUME~1\ROYCEW~1.FLE\LOCALS~1\Temp\RtmpYNLMIX/GPL90.soft
> ## Error: only 0's may be mixed with negative subscripts
>
> The file C:\DOCUME~1\ROYCEW~1.FLE\LOCALS~1\Temp\RtmpYNLMIX  does not exist
> on my system.

This was a temporary directory created by R.  As soon as the R session
terminates, the directory is removed.  In any case, I don't think this
is the cause of the error, but thanks for thinking about the problem.

Sean