[BioC] Problem loading RdbiPgSQL

Herve Pages hpages at fhcrc.org
Tue May 8 20:35:56 CEST 2007

Hi Thomas,

Why don't you show us the output of the compilation process? When you run R CMD check on the
RdbiPgSQL source tarball that you used for installation, it creates an RdbiPgSQL.Rcheck folder
with an 00install.out file inside. You could compare this 00install.out file with the output
produced by our build system here

  (scroll down to the RdbiPgSQL.Rcheck/00install.out section)

In particular pay attention to this line

  gcc -std=gnu99 -shared -L/usr/local/lib64 -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -lpq ...

For most R installations there will be no "-L/home/biocbuild/bbs-2.0-bioc/R/lib -lR" part
like we have but this is OK (this only shows up if R itself has been initially configured
with --enable-R-shlib at built time).
Anyway, given that your resulting RdbiPgSQL.so file is not linked against the libpq
library, I suspect something is going wrong with the above 'gcc -shared ...' command.

Let's do some basic checking:

  1) On a RPM-based system like yours (Red Hat), you must have the following RPMs installed:
     Check with 'rpm -qa | grep -i postgres' and send us the output if you have some

  2) You should be able to compile and run this "hello world" program:

       #include <stdio.h>
       int main() {
         printf("hello world\n");
         return 0;

     Put this in test.c and compile with:

       gcc test.c -lpq

     You should be able to run it with ./a.out
     Now the -lpq option is not required here but it allows us to check that this executable
     has been properly linked to the libpq library (even if the test.c code doesn't use it).
     Check the links with

       hpages at wellington:~> ldd a.out
         linux-gate.so.1 =>  (0xffffe000)
         libpq.so.3 => /usr/lib/libpq.so.3 (0x40030000)
         libc.so.6 => /lib/tls/libc.so.6 (0x4004c000)
         libssl.so.0.9.7 => /usr/lib/libssl.so.0.9.7 (0x40162000)
         libcrypto.so.0.9.7 => /usr/lib/libcrypto.so.0.9.7 (0x40192000)
         libkrb5.so.17 => /usr/lib/libkrb5.so.17 (0x40283000)
         libcrypt.so.1 => /lib/libcrypt.so.1 (0x402be000)
         libresolv.so.2 => /lib/libresolv.so.2 (0x402f0000)
         libnsl.so.1 => /lib/libnsl.so.1 (0x40304000)
         libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4031a000)
         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
         libdl.so.2 => /lib/libdl.so.2 (0x4032c000)
         libasn1.so.6 => /usr/lib/libasn1.so.6 (0x40330000)
         libroken.so.16 => /usr/lib/libroken.so.16 (0x40357000)
         libcom_err.so.2 => /lib/libcom_err.so.2 (0x40368000)
         libdb-4.2.so => /usr/lib/tls/libdb-4.2.so (0x4036b000)

     Yes there are a lot! But the most important is having this line

         libpq.so.3 => ...

     If you don't have this or if you were not able to compile test.c in the first place
     with an error like

       hpages at wellington:~> gcc test.c -lpq
       /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse-linux/bin/ld: cannot find -lpq
       collect2: ld returned 1 exit status

     then look at the 'gcc -shared ...' command in your RdbiPgSQL.Rcheck/00install.out file,
     look for the first -L option (could be -L/usr/lib, or -L/usr/local/lib,
     or -L/usr/local/lib64, etc...), make sure that there is a libpq.so.* file (or symlink)
     in the folder specified in this -L option and try to compile test.c again with this -L option
     i.e. with something like 'gcc test.c -L/usr/local/lib -lpq' (use _your_ -L option).
     It's important to put the -L option _before_ -lpq

     If this doesn't work or if you end up with an a.out executable that is not properly
     linked to libpq.so.3 (the trailing number 3 could be different for you)
     then you have a PostgreSQL or gcc installation/configuration problem and you will
     need to ask your local system administrator for help.


Thomas Adams wrote:
> Seth,
> 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)
> 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…
> 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…
> Tom
> 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

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