On Mon, Apr 27, 2015 at 5:10 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> This is an unusual one. The SWIG wrappers do not do dynamic linking on
> linux, so it's not connected to LD_LIBRARY_PATH (the usual first guess).

Ah sorry, I forgot to mention I can not use static linking in RPM land
due to official packaging guidelines; hence, I am applying a couple
patches you can see here:
https://github.com/giallu/rdkit/commits/swig_packaging

to allow dynamic linking. I guess that makes it sort of "unsupported"
config. Nonetheless, I'd appreciate any idea to find a solution.


>
> What is the output you get if you remove the file:
> /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so
> and then build just the wrapper again with:
> VERBOSE=1 make GraphMolWrap
>
> I'm curious to see what the final link command looks like.

This is easy, I have the full verbose buid log :)

Linking CXX shared module libGraphMolWrap.so
cd 
/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/Code/JavaWrappers/gmwrapper
&& /usr/bin/cmake -E cmake_link_script
CMakeFiles/GraphMolWrap.dir/link.txt --verbose=1
/usr/lib64/ccache/c++  -fPIC -O2 -g -pipe -Wall
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -DNDEBUG
-Wl,-z,relro  -shared -Wl,-soname,libGraphMolWrap.so -o
libGraphMolWrap.so
CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o
../../../lib/libRDInchiLib.so.1.2015.03.1pre -linchi
../../../lib/libFileParsers.so.1.2015.03.1pre
../../../lib/libSmilesParse.so.1.2015.03.1pre
../../../lib/libDepictor.so.1.2015.03.1pre
../../../lib/libSubstructMatch.so.1.2015.03.1pre
../../../lib/libChemReactions.so.1.2015.03.1pre
../../../lib/libFingerprints.so.1.2015.03.1pre
../../../lib/libChemTransforms.so.1.2015.03.1pre
../../../lib/libSubgraphs.so.1.2015.03.1pre
../../../lib/libGraphMol.so.1.2015.03.1pre
../../../lib/libDataStructs.so.1.2015.03.1pre
../../../lib/libDescriptors.so.1.2015.03.1pre
../../../lib/libPartialCharges.so.1.2015.03.1pre
../../../lib/libMolTransforms.so.1.2015.03.1pre
../../../lib/libDistGeomHelpers.so.1.2015.03.1pre
../../../lib/libDistGeometry.so.1.2015.03.1pre
../../../lib/libForceFieldHelpers.so.1.2015.03.1pre
../../../lib/libForceField.so.1.2015.03.1pre
../../../lib/libEigenSolvers.so.1.2015.03.1pre
../../../lib/libOptimizer.so.1.2015.03.1pre
../../../lib/libMolAlign.so.1.2015.03.1pre
../../../lib/libAlignment.so.1.2015.03.1pre
../../../lib/libSimDivPickers.so.1.2015.03.1pre
../../../lib/libRDGeometryLib.so.1.2015.03.1pre
../../../lib/libRDGeneral.so.1.2015.03.1pre -lpthread -linchi
../../../lib/libDepictor.so.1.2015.03.1pre
../../../lib/libFileParsers.so.1.2015.03.1pre
../../../lib/libSubgraphs.so.1.2015.03.1pre
../../../lib/libSmilesParse.so.1.2015.03.1pre
../../../lib/libSubstructMatch.so.1.2015.03.1pre
../../../lib/libMolTransforms.so.1.2015.03.1pre
../../../lib/libGraphMol.so.1.2015.03.1pre -lpthread
../../../lib/libEigenSolvers.so.1.2015.03.1pre
../../../lib/libRDGeometryLib.so.1.2015.03.1pre
../../../lib/libDataStructs.so.1.2015.03.1pre
../../../lib/libRDGeneral.so.1.2015.03.1pre
../../../lib/libhc.so.1.2015.03.1pre
-Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib:



-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

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