[Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

[Finnerty, J. <jfi...@am...>]

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