Hi Paul, Simply copying the Code directory after building rdkit sounds problematic. Since the Code directory contains mainly C++ source code, copying it might not do anything useful.
The compilation error was because that the linker could not find the static libraries that are part of RDKit build result. It seems like your RDBASE points to /SW/python/lib/python2.6/site-packages/rdkit/. Just redefine your RDBASE - maybe just point to the root of the RDKit source tree - and make sure $RDBASE/lib is the directory that contains lots of .a and .so files such as libFileParsers_static.a. My understanding it that the cartridge is a fairly independent piece of RDKit. It's statically linked against the rest part of RDKit. Therefore, it is perfectly fine to point RDBASE to the original root directory of RDkit source tree even if it looks ugly. After the cartridge is built and installed, you could move the RDKit source tree around, change RDBASE value or even delete the whole source tree and the cartridge should still function. Regards, Eddie On Jul 6, 2011, at 2:31 AM, [email protected] wrote: > Dear all, > > I manually copied the Code directory after building rdkit into $RDBASE - > don't understand why it was not copied over... > > Running make > in $RDBASE/Code/PgSQL/rdkit > gives the following: > " > g++ -fomit-frame-pointer -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 > -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -Wall > -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement > -Wendif-labels -fno-strict-aliasing -fwrapv -fpic -shared rdkit_io.o > mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o > -L/SW/python/lib/python2.6/site-packages/rdkit//lib -L/usr/lib > -lFileParsers_static -lSmilesParse_static -lFingerprints_static > -lSubgraphs_static -lSubstructMatch_static -lDescriptors_static > -lPartialCharges_static -lGraphMol_static -lDataStructs_static > -lRDGeometryLib_static -lRDGeneral_static -o rdkit.so > /usr/lib/gcc/i586-suse-linux/4.5/../../../../i586-suse-linux/bin/ld: cannot > find -lFileParsers_static > collect2: ld returned 1 exit status > make: *** [rdkit.so] Error 1 > " > > > Cheers, > Paul > > This message and any attachment are confidential and may be privileged or > otherwise protected from disclosure. If you are not the intended recipient, > you must not copy this message or attachment or disclose the contents to > any other person. If you have received this transmission in error, please > notify the sender immediately and delete the message and any attachment > from your system. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not accept liability for any omissions or errors in this > message which may arise as a result of E-Mail-transmission or for damages > resulting from any unauthorized changes of the content of this message and > any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not guarantee that this message is free of viruses and does > not accept liability for any damages caused by any virus transmitted > therewith. > > Click http://disclaimer.merck.de to access the German, French, Spanish and > Portuguese versions of this disclaimer. > > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
