On Tue, Apr 28, 2015 at 5:59 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > 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.
Tried running the tests or a minimal example? > > 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? > It seems correct: $ ldd Code/JavaWrappers/gmwrapper/libGraphMolWrap.so linux-vdso.so.1 => (0x00007ffce97c4000) libRDInchiLib.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libRDInchiLib.so.1 (0x00007fa53fc8d000) libinchi.so.1 => /lib64/libinchi.so.1 (0x00007fa53f987000) libFileParsers.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libFileParsers.so.1 (0x00007fa53f6c2000) libSmilesParse.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libSmilesParse.so.1 (0x00007fa53f46d000) libDepictor.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libDepictor.so.1 (0x00007fa53f238000) libSubstructMatch.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libSubstructMatch.so.1 (0x00007fa53f023000) libChemReactions.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libChemReactions.so.1 (0x00007fa53edd8000) libFingerprints.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libFingerprints.so.1 (0x00007fa53eba2000) libChemTransforms.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libChemTransforms.so.1 (0x00007fa53e96c000) libSubgraphs.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libSubgraphs.so.1 (0x00007fa53e756000) libGraphMol.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libGraphMol.so.1 (0x00007fa53e43d000) libDataStructs.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libDataStructs.so.1 (0x00007fa53e15c000) libDescriptors.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libDescriptors.so.1 (0x00007fa53df2b000) libPartialCharges.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libPartialCharges.so.1 (0x00007fa53dd15000) libMolTransforms.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libMolTransforms.so.1 (0x00007fa53db01000) libDistGeomHelpers.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libDistGeomHelpers.so.1 (0x00007fa53d8d6000) libDistGeometry.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libDistGeometry.so.1 (0x00007fa53d6b3000) libForceFieldHelpers.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libForceFieldHelpers.so.1 (0x00007fa53d473000) libForceField.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libForceField.so.1 (0x00007fa53d1b5000) libEigenSolvers.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libEigenSolvers.so.1 (0x00007fa53cfac000) libOptimizer.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libOptimizer.so.1 (0x00007fa53cdaa000) libMolAlign.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libMolAlign.so.1 (0x00007fa53cb73000) libAlignment.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libAlignment.so.1 (0x00007fa53c968000) libSimDivPickers.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libSimDivPickers.so.1 (0x00007fa53c75f000) libRDGeometryLib.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libRDGeometryLib.so.1 (0x00007fa53c53d000) libRDGeneral.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libRDGeneral.so.1 (0x00007fa53c317000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fa53c0fb000) libhc.so.1 => /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib/libhc.so.1 (0x00007fa53bef8000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fa53bbe8000) libm.so.6 => /lib64/libm.so.6 (0x00007fa53b8e0000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fa53b6c9000) libc.so.6 => /lib64/libc.so.6 (0x00007fa53b30b000) /lib64/ld-linux-x86-64.so.2 (0x00007fa54039d000) However, I found that if you run java with the -cp option (as we do in tests) then the CLASSPATH env variable is ignored. I think this can be the reason why I have missing symbols. I hope to find a way to workaround this. -- 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
