[BioC] Problem loading RdbiPgSQL

[Seth Falcon]

Hi Thomas,

Thomas Adams <Thomas.Adams at noaa.gov> writes:
> Following your suggestion, I get:
>
> from a Linux prompt:
>
> ldd
> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so
>
> produces:
>
>        libc.so.6 => /lib/tls/libc.so.6 (0x00329000)
>        /lib/ld-linux.so.2 (0x00a17000)

This is quite strange and very different from what I get on one of our
Linux servers.

ldd RLIBS/2.5/RdbiPgSQL/libs/RdbiPgSQL.so 
        libpq.so.4 => /usr/lib64/libpq.so.4 (0x00002aaaaabd3000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x00002aaaaacf5000)
        libssl.so.0.9.7 => /usr/lib64/libssl.so.0.9.7 (0x00002aaaaaf20000)
        libcrypto.so.0.9.7 => /usr/lib64/libcrypto.so.0.9.7 (0x00002aaaab057000)
        libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00002aaaab28f000)
        libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002aaaab407000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00002aaaab541000)
        libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aaaab655000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00002aaaab76b000)
        /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab881000)
        libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00002aaaab984000)
        libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00002aaaabaa8000)
        libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00002aaaabbab000)

In particular, the fact that your .so file doesn't link to libpq.so
explains why you get the error message about PQfsize being missing.
So now you need to figure out why you are ending up with an
RdbiPgSQL.so that is not linked to libpq.

You said that you found the PostgreSQL include files in /usr/include.
Can you check that you also have libpq.so.* in /usr/lib?  If so, have
you tried:

R CMD INSTALL \
 --configure-args='--with-pgsql-libraries=/usr/lib --with-pgsql-libraries=/usr/include' \
 RdbiPgSQL_1.8.0.tar.gz

And capture all of the output in case this also does not work.

> within R:
>
>> system("ldd 
> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so")
>        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…

The only differences I see are the memory addresses and that is
expected.

> 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.

That's a good reason :-)


-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org