[R-SIG-Mac] Problems with runtime linking of R-extension

[Keith O'Hara]

Try adding '/usr/local/lib' to DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH. If that doesn't fix the problem, try modifying the install name of libaf to include /usr/local/lib. Something like:

sudo install_name_tool -id /usr/local/lib/libaf.dylib /usr/local/lib/libaf.dylib

or

sudo install_name_tool -id /usr/local/lib/libaf.3.dylib /usr/local/lib/libaf.3.dylib

This has fixed runtime path issues for me in the past.

Keith


> On Feb 23, 2018, at 4:16 AM, Ralf Stubner <ralf.stubner at r-institute.com> wrote:
> 
> Hi all,
> 
> I am trying to port RcppArrayFire
> (https://github.com/RInstitute/rcpparrayfire) to Mac OS, but I am having
> some troubles with resolving linked libraries. I have tried to reduce
> the issue as much as possible, i.e. no Rcpp and no package structure. It
> seems to be MacOS specific since the same code works on Linux (as does
> RcppArrayFire). I also asked this on stackoverflow
> (https://stackoverflow.com/questions/48705490/runtime-linking-r-extension-on-macos),
> but that did not draw a lot of attention. Maybe someone on this list can
> shed some light on this:
> 
> When I install ArrayFire (http://arrayfire.com/) on MacOS using the
> binary installer, the libraries are installed in /usr/local/lib with an
> install name starting with @rpath:
> 
> $ otool -L /usr/local/lib/libaf.dylib /usr/local/lib/libaf.dylib:
> 	@rpath/libaf.3.dylib (compatibility version 3.0.0, current version 3.5.1)
> 	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
> 120.1.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1226.10.1)
> 
> I can compile, link and run simple examples, e.g.
> 
> #include <arrayfire.h>
> #include <stdio.h>
> 
> int main() {
>  unsigned int count;
>  at_get_backend_count(&count);
>  printf("backends: %d\n", count);
>  return 0;
> }
> 
> gives
> 
> $ /usr/local/clang4/bin/clang -laf -o minimal minimal.c
> $ otool -L minimal
> minimal:
> 	@rpath/libaf.3.dylib (compatibility version 3.0.0, current version 3.5.1)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1252.0.0)
> $ ./minimal
> backends: 2
> 
> 
> To do the same from R I use
> 
> #include <arrayfire.h>
> #include <Rinternals.h>
> SEXP count_backends() {
>  unsigned int count;
>  af_get_backend_count(&count);
>  Rprintf("backends: %d\n", count);
>  return R_NilValue;
> }
> 
> And compile it with
> 
> $ PKG_LIBS=-laf R CMD SHLIB minimal.c /usr/local/clang4/bin/clang
> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include   -fPIC  -Wall -g -O2  -c minimal.c -o minimal.o
> /usr/local/clang4/bin/clang -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib
> -o minimal.so minimal.o -laf -F/Library/Frameworks/R.framework/..
> -framework R -Wl,-framework -Wl,CoreFoundation
> $ otool -L minimal.so  minimal.so:
> 	minimal.so (compatibility version 0.0.0, current version 0.0.0)
> 	@rpath/libaf.3.dylib (compatibility version 3.0.0, current version 3.5.1)
> 	/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libR.dylib
> (compatibility version 3.4.0, current version 3.4.3)
> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1451.0.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1252.0.0)
> 
> If I then try to load the resulting library, I get this error message:
> 
> R> dyn.load("minimal.so")
> Error in dyn.load("minimal.so") :   unable to load shared object
> '/Users/ralf/Documents/af-simple/minimalR/minimal.so':
>  dlopen(/Users/ralf/Documents/af-simple/minimalR/minimal.so, 6):
> Library not loaded: @rpath/libaf.3.dylib
>  Referenced from: /Users/ralf/Documents/af-simple/minimalR/minimal.so
>  Reason: image not found
> Execution halted
> 
> 
> Both the binary and the R-extension library refer to the external
> library using the same install name, but for the R-extension this
> reference cannot be resolved. Why is this the case?
> 
> Thanks
> Ralf
> 
> PS: Used versions:
> * Mac OS High Siearra
> * R 3.4.3
> * clang 4.0.0 from https://cran.r-project.org/bin/macosx/tools/
> 
> -- 
> Ralf Stubner
> Senior Software Engineer / Trainer
> 
> R Institute GmbH
> Dortustraße 48
> 14467 Potsdam
> 
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> 
> Mail: ralf.stubner at r-institute.com
> 
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