On Jul 2, 2010, at 2:47 AM, Greg Landrum wrote: > I'm really excited to announce the most recent contribution from > Novartis to the RDKit: a cartridge for similarity searching in > PostgeSQL.
Thanks for doing this Greg, and thanks to the contributors from Novartis that you mentioned. Has anyone gotten it to compile on Mac OS X 10.6 where the postgres install was done through Mac Ports? Here's the installation location on my machine [gateway:Code/PgSQL/rdkit] dalke% locate postgres | grep '/postgres$' /opt/local/lib/postgresql83/bin/postgres ... > There's a README that gives some build/install instructions (it's > pretty easy), but I'll be adding additional information on the wiki on > pages linked from here: > http://code.google.com/p/rdkit/wiki/PostgresCartridge and when I do the suggested Copy the cartridge directory ($RDBASE/Code/PgSQL/rdkit) to the postgresql contrib directory I run into problems because I have no postgresql contrib directory. Looking around, there's Postgres extension system called PGXS which is meant for third-party extensions. In fact, it seems that building in contrib is a relatively rare task: (from http://justatheory.com/computers/databases/postgresql/no_more_use_pgxs.html ) "I find this annoying, because third-party extensions are almost never built from the contrib directory," I tried to put something together to get it working. This is as far as I got #========= MODULE_big = rdkit OBJS = rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o PG_CPPFLAGS = -I$(BOOSTHOME) -I${RDKIT}/Code -DRDKITVER='"001900"' PG_CONFIG = /opt/local/lib/postgresql83/bin/pg_config PGXS := $(shell $(PG_CONFIG) --pgxs) include $(PGXS) #============ I'm on the right track, it seems, but compilation failed with guc.c: In function ‘initRDKitGUC’: guc.c:84: warning: passing argument 8 of ‘DefineCustomRealVariable’ makes pointer from integer without a cast guc.c:84: error: too many arguments to function ‘DefineCustomRealVariable’ and at that point I decided I had had enough of working with Postgres and RDKit for the weekend. ;) BTW, that guc.c has a typo (twice due to copy and paste): "Moleculas with similarity lower than threshold are not similar should be "Molecules with similarity lower than threshold are not similar ("Moleculas" -> "Molecules") Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
