[BioC] Problem loading RdbiPgSQL

[Sean Davis]

Seth Falcon wrote:
> 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 if that doesn't work, I would suggest installing postgresql from 
source into your home directory (or some other directory to which you 
have access) and try the same (with appropriate lib and include 
directories (note that the above should have 
--with-pgsql-includes=/usr/include, I think).  We have not had trouble 
on either MacOS or linux with doing so.  There is no need to run or even 
set up the installed version of postgresql, just link to its libraries.  
The compatibility between various versions of postgresql is pretty 
remarkable, so hopefully any newer version of postgresql will work for you.

Sean