Hello RDKit developers. I’m trying to make the RDKit extension available for
use in AWS Aurora PostgreSQL. Usually the way we integrate new extensions is
with a PGXS-style Makefile, and with all of the C or C++ sourcefiles, .config,
PGXS-style Makefile, .sql, and /sql files in one directory.
I copied the following files into a separate build directory (on Linux):
adapter.cpp bfp_gist.c bitstring.c cache.c CMakeLists.txt DataStructs
Geometry guc.c low_gist.c mol_op.c rdkit--3.8.sql rdkit_gist.c
rdkit_io.c README sfp_op.c
bfp_gin.c bfp_op.c bitstring.h cache.h data expected
GraphMol guc.h Makefile RDGeneral rdkit.control rdkit.h
rdkit.sql.in rxn_op.c sql
where /Geometry, /GraphMol, /RDGeneral, and /DataStructs are rsync’d from the
source directories under /Code, rdkit—3.8.sql is generated, and Makefile
replaces what CMake would have generated with a simpler PGXS-style Makefile:
MODULE_big = rdkit
OBJS = adapter.o bfp_gin.o bfp_gist.o bfp_op.o bitstring.o cache.o guc.o
low_gist.o mol_op.o rdkit_gist.o rdkit_io.o rxn_op.o sfp_op.o
EXTENSION = rdkit
DATA = rdkit--3.8.sql
REGRESS = bfpgin bfpgist-91 btree fpgist fps molgist props rdkit-91 reaction
sfpgist slfpgist
PG_CONFIG = pg_config
PGXS := $(shell $(PG_CONFIG) --pgxs)
include $(PGXS)
When I attempt to ‘make’ with this definition and with these files, I get:
In file included from adapter.cpp:32:0:
./GraphMol/RDKitBase.h:17:30: fatal error: RDGeneral/export.h: No such file or
directory
#include <RDGeneral/export.h>
and this is true: export.h isn’t in /RDGeneral, but it is included from
<GraphMol/RDKitBase.h>, at adapter.cpp line 32.
Where can I find export.h, and why isn’t it in RDGeneral/export.h?
Once I get past this issue, is there some reason why building RDKit in this way
won’t work?
Are the list of source files above complete for building the RDKit extension,
if you don’t need Python wrapper support?
Thank you,
/Jim
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