R.app is a process. R is a shell script that launches a process. Both
inherit the environment they are launched from, but it is usually
different from the GUI and from a terminal.
It is regarded as a security hole to allow a running process to change
the settings of its dynamic loader (dyld on OS X), so I would not expect
that setting such environment variables from within R.app (including
from reading .Renviron) to affect dyld. So if it did for Marc, I am
surprised and would expect that hole to be plugged in due course.
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).
This is not really the best way to extend the library search path. In
this case, for one package, the simplest way is to use -rpath when the
package was installed (and I believe you can set or edit the runpath
after the .so is made with install_name_tool).
On 08/08/2013 22:00, Marc Schwartz wrote:
On Aug 8, 2013, at 3:42 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?
Thanks for any suggestions,
-Tom
In general, OSX GUI based apps do not inherit the shell environment. This is
the case with Emacs on OSX for example.
What is the syntax that you used in .Renviron? It should be along the lines of:
DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
Note, do not use 'export' before the above. I just tried it here and it worked.
Take a look at ?Startup for more details.
Regards,
Marc Schwartz
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Brian D. Ripley, [email protected]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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