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
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
And for RStudio, you can run
Let’s hope Apple releases a fix soon.