[BioC] Problem loading RdbiPgSQL

Seth Falcon sfalcon at fhcrc.org
Fri May 4 05:32:53 CEST 2007

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

> I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have 
> successfully built and installed (independently) versions 1.8 and 1.10 
> of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. 
> However, when I attempt to load RdbiPgSQL, I get the following error:
>  > library(RdbiPgSQL)
> Loading required package: Rdbi
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>        unable to load shared library 
> '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so':
>  /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: 
> undefined symbol: PQfsize
> Error: package/namespace load failed for 'RdbiPgSQL'
> The library 
> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so 
> does exist.
> Any suggestions?

Did you try using biocLite?  Details in just about every other
post on this list and on the BioC website.  Anyhow, version 1.8.0 for
Rdbi and RdbiPgSQL are the ones to use with R 2.4.1.

What version of PostgreSQL are you using?  We have tested against
8.1.4.  If you have a different version, you might want to verify that
PQfsize is indeed gone.  I did:

pg_config --version
grep PQfsize `pg_config --includedir`/*.h

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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