"In order to standardize your PATH setting in R, you can set it in your .Renviron file "
Doesn't work for my issue, as I noted below. The methods I listed, on the other hand, do work. Am I missing something from FAQ 12.18 from your link? Also, does anyone have any specific reasons to fear setting DYLD_FALLBACK_LIBRARY_PATH as I have? I'm asking because I don't have the experience that you all do. -Tom On Aug 9, 2013, at 7:55 PM, Simon Urbanek <[email protected]> wrote: > On Aug 9, 2013, at 5:40 PM, Tom Schoenemann wrote: > >> You may not have read the whole thread. >> > > I did but apparently you didn't read my answer -- just for clarification > 12.18 is from > http://r.research.att.com/man/RMacOSX-FAQ.html > in 3.0 release FAQ it is under number 10.13 (unfortunately someone broke the > numbering recently). > > Cheers, > S > > >> On Aug 8, 2013, at 5:18 PM, Tom Schoenemann <[email protected]> wrote: >> >> >>> My .Renviron looks like this: >>> >>> DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib >>> >>> When I restart R.app, it does seem to have this set: >>> >>>> Sys.getenv() >>> DYLD_FALLBACK_LIBRARY_PATH >>> "/Library/Frameworks/R.framework/Resources/lib" >>> >>> However, the package that needs to know this is still complaining that it >>> can't find the dynamic libraries it needs. >> >> The reason seems to be: >> >> On Aug 9, 2013, at 3:10 AM, Prof Brian Ripley <[email protected]> wrote: >> >>> It is not 'R.app doesn't respect DYLD_FALLBACK_LIBRARY_PATH': R.app knows >>> nothing about it. Rather, it is dyld which I would expect to read its >>> environment variables only when the process is launched (and as Steve >>> Lianoglou has pointed out, which plists are read before dyld is initialized >>> for a process has changed over time). >> >> >> Regarding why this package requires DYLD_FALLBACK_LIBRARY_PATH to be set to >> work via GUI is something that I don't understand myself, but will certainly >> pass on your comments to the package maintainers. >> >> Regarding the dangers some of you see of using DYLD_FALLBACK_LIBRARY_PATH in >> this way, can anyone elaborate in a way that a package user like myself can >> appreciate? How exactly could it wreck my system? Given that this package >> is extremely useful to my research, I'm willing to chance it if it only >> means odd messages in the terminal. If my disk gets wiped, I might be more >> concerned. >> >> Thanks for any help you can provide to enlighten me more (this has been very >> enlightening so far). >> >> -Tom >> >> On Aug 9, 2013, at 5:12 PM, Simon Urbanek <[email protected]> >> wrote: >> >>> Sorry for coming in late - I was traveling - otherwise I'd hope to stop >>> this madness earlier :) >>> >>> Any reason why R for Mac FAQ 12.18 (and the proposed solutions) would not >>> apply here? >>> >>> I also agree that DYLD_FALLBACK_LIBRARY_PATH should not be messed with and >>> that the proper solution is to fix the libtk*dylib which has bad ID and >>> thus gets linked incorrectly (missing path). >>> >>> Cheers, >>> Simon >>> >>> >>> On Aug 8, 2013, at 4:42 PM, Tom Schoenemann 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? >>>> >>>> Thanks for any suggestions, >>>> >>>> -Tom >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>> >> >> >> > _________________________________________________ P. Thomas Schoenemann Associate Professor Department of Anthropology Cognitive Science Program Indiana University Bloomington, IN 47405 Phone: 812-855-8800 E-mail: [email protected] Open Research Scan Archive (ORSA) Co-Director Consulting Scholar Museum of Archaeology and Anthropology University of Pennsylvania http://www.indiana.edu/~brainevo [[alternative HTML version deleted]]
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