[BioC] Problem loading RdbiPgSQL

Seth Falcon sfalcon at fhcrc.org
Fri May 4 22:53:19 CEST 2007

Thomas Adams <Thomas.Adams at noaa.gov> writes:

> Seth,
> Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8
> installed and your grep command reveals that PQfsize is in the
> libpq-fe.h file located in /usr/include. In fact, when I install
> RdbiPgSQL from source, it's easy to see that the build process
> explicitly looks for the availability of libpq-fe.h.

That's good.  I expect RdbiPgSQL will work with 7.4.8 (not sure, but I
think your problem lies elsewhere).

> I do not have any control over what version of PostgreSQL we have
> installed, so migrating to version 8.1.4 (or whatever) is not possible
> at this time. Can anyone suggest an alternative way to install
> RdbiPgSQL that circumvents this problem? Is there a Linux binary
> available that I can install — will this even work?

Did you try via biocLite?  It might fail, but that failure might give
us some clues.

Can you look at the output of 

"ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so"

both from the command line where you successfully built/installed
RdbiPgSQL and from inside R using the system() command?

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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