[BioC] Problem loading RdbiPgSQL

Thomas Adams Thomas.Adams at noaa.gov
Fri May 4 23:31:14 CEST 2007


Following your suggestion, I get:

from a Linux prompt:

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


        libc.so.6 => /lib/tls/libc.so.6 (0x00329000)
        /lib/ld-linux.so.2 (0x00a17000)

within R:

 > system("ldd 
        libc.so.6 => /lib/tls/libc.so.6 (0x0022d000)
        /lib/ld-linux.so.2 (0x00a17000)

I'm guessing the "libc.so.6 =>…" line differences is suspicious…

As far as trying installing via biocLite? I'm avoiding this route for 
the following reason: The system I am using, where R is installed and 
where I need it to work along with our PostgreSQL database, is in an 
isolated network without, direct access to the internet. So, the install 
process would be more complicated than using the biocLite install 
script, since I would have to individually download each package, use a 
two-step process to ftp the packages through a firewall, and install 
them (maybe you can suggest a simple way of doing this) separately.

Also, it may be obvious, but I have to install R in a non-standard 
location due to our system restrictions.

Thanks again for your help…


Seth Falcon wrote:
> 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

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

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