Hi Andrew, On Sun, Jul 4, 2010 at 6:36 AM, Andrew Dalke <da...@dalkescientific.com> wrote: > 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?
I've built it on 10.5 using an install of postgres from source; so I guess that's a "no, but I did something like that." :-) > >> 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 ($RDBASE/Code/PgSQL/rdkit) to > the postgresql contrib directory > > I run into problems because I have no postgresql contrib directory. lovely; I guess this is because you didn't install from source. > Looking around, there's Postgres extension system called PGXS which > is meant for third-party extensions. In fact, it seems that building > in contrib is a relatively rare task: > > (from > http://justatheory.com/computers/databases/postgresql/no_more_use_pgxs.html ) > > > "I find this annoying, because third-party extensions are almost > never built from the contrib directory," > > > I tried to put something together to get it working. This is as > far as I got > > #========= > > MODULE_big = rdkit > OBJS = rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o > cache.o adapter.o > PG_CPPFLAGS = -I$(BOOSTHOME) -I${RDKIT}/Code -DRDKITVER='"001900"' > > > PG_CONFIG = /opt/local/lib/postgresql83/bin/pg_config > PGXS := $(shell $(PG_CONFIG) --pgxs) > include $(PGXS) > > > #============ Thanks for giving this a try and pointing to the blog post. I'll see if I can get the changes working on Linux so that I can lift the requirement that people have a postgres source installation. > 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") Thanks... that one I know I can fix. ;-) -greg ------------------------------------------------------------------------------ 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
