On Jan 30, 2012, at 12:06 PM, Guillaume Meurice wrote: > Dear all, > > > I can't figure out how R.app is getting my environment variable $PATH. >
Try R for Mac FAQ 12.19. > Launching R via a terminal perfectly get my $PATH variable : > >> Sys.getenv()[["PATH"]] > [1] > "/Users/meurice/Documents/Developement/eclipseWorkSpace/ibp/genomics/utils/bash/:.:/usr/texbin/:/usr/local/texlive/2011/bin/x86_64-darwin:/opt/local/bin:/opt/local/sbin:/Users/meurice/Documents/Application/BioinfoTools/bowtie2-2.0.0-beta3:/Users/meurice/Documents/Developement/eclipseWorkSpace/ibp/genomics/utils/bash/:.:/usr/texbin/:/usr/local/texlive/2011/bin/x86_64-darwin:/opt/local/bin:/opt/local/sbin:/Users/meurice/Documents/Applications/BioinfoTools/bowtie2-2.0.0-beta3:/Users/meurice/Documents/Developement/eclipseWorkSpace/ibp/genomics/utils/bash/:.:/usr/texbin/:/usr/local/texlive/2011/bin/x86_64-darwin:/opt/local/bin:/opt/local/sbin:/Users/meurice/Documents/Tools/bowtie2-2.0.0-beta3:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin" > > > But when I'm launching R with R.app (or R studio), the $PATH I get from > Sys.getenv() has nothing to do with my current and real $PATH : > >> Sys.getenv()[["PATH"]] > [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" > > > I've managed to set up the $PATH directory through the use of .Renviron, but > I would really like R.app to read my $PATH from > my .bash_profil, which is not the case. > R.app is not a shell - and neither is R - so they simply use the environment you setup. .bash_* fines are only used by bash, so unless you start bash they have no meaning. R.app inherits the environment from the launch services which don't read your profile - again, it's not a shell. See Apple's QA in how to change the environments for apps: http://developer.apple.com/library/mac/#qa/qa1067/_index.html Cheers, Simon > > Thanks by advance for any help. > -- > GM > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] snowfall_1.84 snow_0.3-8 > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
