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

[Paolo T. <pao...@gm...>]

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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