[BioLib-dev] installation

[Pjotr Prins]

On Sat, Apr 25, 2009 at 06:52:25PM -0700, Joel Martin wrote:
> I wouldn't be installing into /usr though, for now I'm putting it into
> /scratch and if deploying it I'd put it into an nfs mounted directory
> that's shared across lots of machines and not in /usr
> 
>  the rpath for the libbiolib_*.so where I installed all seem correct like,
> 
> ldd /scratch/j_martin/biotrash/lib/libbiolib_staden_io_lib-0.0.4.so 
>         libz.so.1 => /usr/lib/libz.so.1 (0x00002b1f89a60000)
>         libc.so.6 => /lib/libc.so.6 (0x00002b1f89b76000)
>         /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

Good.

> the ones that are in the perl tree are missing rpaths,
> 
> ldd /jgi/tools/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/staden_io_lib.so
>         libbiolib_staden_io_lib-0.0.4.so => not found
>         libperl.so => not found
>         libz.so.1 => /usr/lib/libz.so.1 (0x00002ac2b898e000)
>         libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002ac2b8aa5000)
>         libm.so.6 => /lib/libm.so.6 (0x00002ac2b8ca3000)
>         libc.so.6 => /lib/libc.so.6 (0x00002ac2b8e25000)
>         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002ac2b9063000)
>         /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

What I see is that you need to tell the dynamic loader where to find
the shared libraries in a non-standard location to find

  /scratch/j_martin/biotrash/lib/libbiolib_staden_io_lib-0.0.4.so 

These libraries are 'system wide' libraries simply containing the
StadenIO binaries. These also link against Ruby etc. Perl does not
know about their non-standard location (Perl on OSX being the
exception). Try setting LD_LIBRARY_PATH.

> ** note, out of over 100 .so files in my perl install, these are the
> only one linked against
>    libperl.so

SWIG generated code makes Perl XS calls - I think they are in
libperl.

Pj.