Hi Jim,
RDGeneral/export.h is generated when you run cmake; it is not part of
the distribution.
If you do a
mkdir build && cd build && cmake ..
in the RDKit root directory the file will be generated, then you may
copy it in your RDGeneral directory.
It is worth mentioning that the PGXS-style Makefile is currently
deprecated; you can build the PostgreSQL cartridge as part of a standard
CMake build by setting the relevant cmake variables, e.g.
-DRDK_BUILD_PGSQL=ON \
-DRDK_PGSQL_STATIC=ON \
-DPostgreSQL_ROOT=/usr/pgsql-12 \
-DPostgreSQL_INCLUDE_DIR=/usr/pgsql-12/include \
-DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-12/include/server \
-DPostgreSQL_LIBRARY_DIR=/usr/pgsql-12/lib \
However, if you prefer to use the PGXS-style Makefile, it should work
provided you generate RDGeneral/export.h by running cmake once and then
copy it to your own RDGeneral directory.
I hope the above helps, cheers
p.
On 29/03/2020 17:18, Finnerty, Jim via Rdkit-devel wrote:
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.cppbfp_gist.cbitstring.ccache.cCMakeLists.txt*DataStructs**Geometry*guc.clow_gist.cmol_op.crdkit--3.8.sqlrdkit_gist.crdkit_io.cREADMEsfp_op.c
bfp_gin.cbfp_op.cbitstring.hcache.h*data**expected**GraphMol*guc.hMakefile*RDGeneral*rdkit.control
rdkit.hrdkit.sql.inrxn_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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