[BioC] Problem loading RdbiPgSQL

Thomas Adams Thomas.Adams at noaa.gov
Fri May 4 22:29:12 CEST 2007


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.

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?


Seth Falcon wrote:
> 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

Thomas E Adams
National Weather Service
Ohio River Forecast Center
1901 South State Route 134
Wilmington, OH 45177

EMAIL:	thomas.adams at noaa.gov

VOICE:	937-383-0528
FAX:	937-383-0033

More information about the Bioconductor mailing list