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 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss