Hi,
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.
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.
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?
Thx,
Hans
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