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There is currently a bug (or feature?) in the current version of Yosemite (OS X 10.10) that messes with the passing of environmental variables to programs launched from Finder (as pointed out by Adam Maxwell). Notably, this means that PATH variables are not passed properly to R.app or RStudio.app. You may end up seeing errors such as the following:
Error in system("pdflatex", intern = TRUE) : error in running command sh: pdflatex: command not found Error in system("convert", intern = TRUE) : error in running command sh: convert: command not found
Until Apple releases a fix to this, the easy workaround is to launch the desired application from the command-line (terminal). For example to launch R, you can instead run
/Applications/R.app/Contents/MacOS/R
And for RStudio, you can run
/Applications/RStudio.app/Contents/MacOS/RStudio
Let’s hope Apple releases a fix soon.   UPDATE from RStudio:  ” We’ve fixed this on our end in the latest version of RStudio for OS X, available here: http://www.rstudio.com/products/rstudio/download/ Give it a try and let us know if it works for you. “