On Mon, Apr 27, 2015 at 11:19 AM, Gianluca Sforna <[email protected]> wrote:
> On Mon, Apr 27, 2015 at 5:10 AM, Greg Landrum <[email protected]>
> 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.
>
There's certainly no reason why the java wrappers shouldn't work if they
are dynamically linked; I just tried it on my ubuntu box and they work
fine. I don't normally do it because it would make distributing the
wrappers for knime much more complex.
>
> >
> > 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 :)
>
I didn't see anything suspicious or odd in the build command.
Have you tried making sure that you are picking up the correct shared libs
by doing an ldd on libGraphMolWrap.so and confirming that it's using the
right libraries?
-greg
> 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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