[R] Why won't R CMD CHECK run configure?

[Alexander James Rickett]

I'm trying to get ready to submit a package to CRAN, but in order for the package to install on OS X, I need to temporarily set an environment variable.  I put this in the  'configure' script, and 'R CMD INSTALL MyPackage' works fine, but when I do 'R CMD CHECK MyPackage', and it tests installation, the configure script doesn't run and consequently the installation fails.  Should I be setting the variable another way?  It passes all the other checks, and it will install outside of check, so could I just submit it as is?

Thanks!