[Bioc-devel] Different behavior under windows causing build failure and errors

[Sean Davis]

I have a question that is going to be ill-formed and lacking in detail (and
perhaps unanswerable here).  I have recently uploaded a package, GEOquery,
that works fine on my MacOS 10.4.3 system and appears to have no problems
building on other platforms, except Windows.  However, I do not have access
to a Windows build machine to even troubleshoot.  The Build check results on
windows as reported here:

http://www.bioconductor.org/checkResults/1.8/html/lemming/GEOquery.buildsrc.
html

The offending error seems to come up when a command like the following (and
Build fails because the vignette does this in one of the code blocks):

 getGEO('GSE462')

The function getGEO downloads a file from a url and then parses it.  With
other format files (GDS, GSM, GSE), the command seems to work fine.  Does
anyone have any ideas what might be up?  I would really like to troubleshoot
here, but I just can't think of a way to do so, as the error is clearly
windows-specific.  Have others faced similar problems with Windows behaving
quite differently, even when the package contains only R code?

Thanks,
Sean