Hi Hans, On Tue, Mar 20, 2012 at 11:53 PM, Hans De Winter <hansdewin...@skynet.be> wrote: > > 1) I'm working on a Mac OS X 10.7 and I just installed (with the invaluable > help Eddie Cao) RDKIT using HomeBrew. Installation is OK and the Python > bindings work.
Excellent. > 2) I installed PostgreSQL 9.1.3, also with HomeBrew. Installation seems to > be OK as the creation of a DB works, just like starting the SQL-interpreter. Glad that's also easy. > 3) Now I want to build the PostgreSQL cartridge to RDKIT: > > Environment variables: > >> echo $BOOSTHOME > /usr/local/Cellar/boost/1.49.0 >> echo $RDBASE > /usr/local/share/RDKit >> echo $LD_LIBRARY_PATH > /usr/local/share/RDKit/lib: >> echo $DYLD_LIBRARY_PATH > /usr/local/share/RDKit/lib: > > Installation: > >> cd /usr/local/share/RDKit/Code/PgSQL/rdkit >> ls > ./ adapter.cpp expected/ rdkit.control rdkit_gist.c sql/ > ../ bfp_op.c guc.c rdkit.h rdkit_io.c uninstall_rdkit.sql > Makefile cache.c low_gist.c rdkit.sql.in rdkit_op.c > README data/ mol_op.c rdkit.sql91.in sfp_op.c >> make > p rdkit.sql91.in rdkit--3.1.sql > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o rdkit_io.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o mol_op.o mol_op.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o bfp_op.o bfp_op.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o sfp_op.o sfp_op.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o rdkit_gist.o rdkit_gist.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o low_gist.o low_gist.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o guc.o guc.c > /usr/bin/llvm-gcc -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -fPIC -c -o cache.o cache.c > llvm-g++ -Os -w -pipe -march=core2 -msse4 > -I/usr/local/Cellar/ossp-uuid/1.6.2/include -Wall -Wpointer-arith > -Wendif-labels -Wformat-security -fno-strict-aliasing -fwrapv > -Wno-deprecated -Wno-unused-function -I/usr/local/Cellar/boost/1.49.0 > -I/usr/local/share/RDKit/Code -DRDKITVER='"004000"' > -I/usr/local/Cellar/boost/1.49.0 -I/usr/local/share/RDKit/Code > -DRDKITVER='"004000"' -I. -I. > -I/usr/local/Cellar/postgresql/9.1.3/include/server > -I/usr/local/Cellar/postgresql/9.1.3/include/internal > -I/usr/local/Cellar/readline/6.2.2/include -I/usr/include/libxml2 > -I/usr/include/libxml2 -c -o adapter.o adapter.cpp > llvm-g++ -Os -w -pipe -march=core2 -msse4 > -I/usr/local/Cellar/ossp-uuid/1.6.2/include -Wall -Wmissing-prototypes > -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels > -Wformat-security -fno-strict-aliasing -fwrapv -bundle -multiply_defined > suppress -o rdkit.so 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/usr/local/Cellar/postgresql/9.1.3/lib > -L/usr/local/Cellar/readline/6.2.2/lib > -L/usr/local/Cellar/ossp-uuid/1.6.2/lib -Wl,-dead_strip_dylibs > -L/usr/local/share/RDKit/lib -lFileParsers_static -lSmilesParse_static > -lFingerprints_static -lSubgraphs_static -lSubstructMatch_static > -lDescriptors_static -lPartialCharges_static -lGraphMol_static > -lDataStructs_static -lRDGeometryLib_static -lRDGeneral_static > -bundle_loader /usr/local/Cellar/postgresql/9.1.3/bin/postgres > ld: library not found for -lFileParsers_static > collect2: ld returned 1 exit status > make: *** [rdkit.so] Error 1 > > Any advice on the cause of this latter load error? Are the > 'FileParsers_static' ever build when installing through HomeBrew? They are not (to make the builds go faster). But it's easy to work around. If you edit /usr/local/share/RDKit/Code/PgSQL/rdkit/Makefile and change STATIC_LINK=1 to STATIC_LINK=0 on line 3, the build and link should work. Best, -greg ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
