[R-sig-Fedora] Problem running R from within a script

[Joshua Kramer]

Thanks for the help Tom!

>> /usr/bin/R CMD BATCH --no-restore --no-save '--args $taxFile $taxFile.taxonomy' batchMakeTax.R batchMakeTax.log
>
> I'm just guessing here, but those ' ' single quotes don't seem to make
> sense. Try dropping them (or moving them to just be around '$taxFile
> $taxFile.taxonomy').

The problem is this.  When I drop the quotes alltogether, R considers the 
$taxFile to be the R input file, not a parameter.  When I put quotes 
around the '$taxFile $taxFile.taxonomy', it picks them up correctly but 
takes them literally, IE expects the $taxFile to have a quote as the first 
character of its filename.

Thanks,
-Josh

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