Hi, On Thu, Aug 8, 2013 at 1:42 PM, Tom Schoenemann <[email protected]> wrote: > Hello, > > I am trying to get a custom R package (from another group) to run on my > system. If I call it from the command line r, it works fine. If I call it > from R.app, it complains with: > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ANTsR/libs/libRantsRegistration.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ANTsR/libs/libRantsRegistration.so, > 6): Library not loaded: libitkdouble-conversion-4.5.1.dylib > Referenced from: > /Applications/image-processing/ANTsR/src/ANTS/ANTS-build/lib/libl_antsRegistration.dylib > Reason: image not found > Error: package or namespace load failed for ‘ANTsR’ > > (ANTsR is the package I'm trying to get working) > > I CAN get it to work by doing this on the command line first: > > export > DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib > > and then also opening the R.app from the command line: > > open /Applications/R.app/ > > However, I can't seem to get R.app to know about > export > DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib > unless I do it this way. > > So my questions are: > > 1) how can I get R.app to know about the DYLD_FALLBACK_LIBRARY_PATH? I tried > putting it into my .Renviron file, but it doesn't work (maybe the syntax is > supposed to be different?) > > 2) why does r on the command line know about dynamic libraries, but R.app > does not?? This seems like a bug, but maybe there is a good reason for it?
I believe this is due to the phenomenon explained here: http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x Look for the answer that starts with "Up to and including Lion" Also you'll find a link to a free preference pane you can install that lets you handle these things with a GUI (pref pane) -- I've never used it, but you can find it here: http://diaryproducts.net/EnvPane https://github.com/hschmidt/EnvPane You could also try to manually set the environment variable in your working R session, via: R> Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH="/Library/Frameworks/R.framework/Resources/lib") not sure if that'll work, but easy enough to try before. Still -- it's possible that DYLD vars won't work in this way. See this: http://support.apple.com/kb/TS4267 Sorry -- no concrete answers here, but hopefully these things will help you find a workable solution. -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
