[R-SIG-Mac] R.app doesn't respect DYLD_FALLBACK_LIBRARY_PATH

[Marc Schwartz]

Hi all,

Just for clarification, I only set the variable in ~/.Renviron to be sure that it was picked up by R.app, in case Tom had not used the correct syntax. I did not actually install the package under discussion from the source at GitHub, so I cannot confirm that the approach resolved the issue that Tom is reporting. Tom's report would suggest that it does not.

Berend's reply would seem to support the notion that this is a problem in the way in which the package ends up being built, so would lead one down the path, I believe, of a bug in the package, perhaps in its make related files vis-a-vis the included C++ code. Thus a report to the package author would seem to be in order.

With respect to Kasper's reply, there are potential issues in resetting or unsetting DYLD_FALLBACK_LIBRARY_PATH or DYLD_LIBRARY_PATH in that there are other applications that can depend upon their value and if altered, can break those applications. So the caution is warranted.

If Tom is on Mountain Lion, the message:

  "dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/login) is setuid or setgid"

may be related to a known bug in Mountain Lion (OS X 10.8) that occurs when running sudo in a terminal session. It has been widely reported, with various attempts at resolution, including things like creating shell wrappers for sudo, but no definitive solution that lacks side effects has been put forth. Apple appears to know about the bug, since reports would suggest that it has been resolved in beta releases of Mavericks (OS X 10.9), but no official fix is yet pending for Mountain Lion. Perhaps a future update to Mountain Lion might include the fix if the Mavericks solution is stable.

If Tom is not on Mountain Lion, then the problem may yet be related in terms of the underlying etiology in setting DYLD_FALLBACK_LIBRARY_PATH, which brings Kasper's note of caution into consideration.

Regards,

Marc


On Aug 9, 2013, at 2:10 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

> 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 <toms at indiana.edu> 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
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac