[BioLib-dev] Test Errors on Ubuntu

[Chris Fields]

Pjotr,

Just noticed an odd error on Ubuntu using the latest github; basically,
everything builds on Ubuntu just fine, but there appear to be odd issues
with shared libs.  This doesn't affect the example or emboss, but affyio
and (strangely) io_lib are affected.  

The library in question is libR.so; this pops up with failing tests for
affyio and io_lib with 'make test'.  Here are the relevant errors from
the test scripts (bootstrapping problem):

cjfields at pyrimidine:~/src/biolib/src/mappings/swig/perl/test$ perl
test_staden_io_lib.pl
Can't load '/usr/local/lib/perl/5.10.0/staden_io_lib.so' for module
staden_io_lib: libR.so: cannot open shared object file: No such file or
directory at /usr/lib/perl/5.10/DynaLoader.pm line 196.
 at /usr/local/lib/perl/5.10.0/biolib/staden_io_lib.pm line 10
Compilation failed in require at test_staden_io_lib.pl line 1.
BEGIN failed--compilation aborted at test_staden_io_lib.pl line 1.

cjfields at pyrimidine:~/src/biolib/src/mappings/swig/perl/test$ perl
test_affyio.pl
Can't load '/usr/local/lib/perl/5.10.0/affyio.so' for module affyio:
libR.so: cannot open shared object file: No such file or directory
at /usr/lib/perl/5.10/DynaLoader.pm line 196.
 at /usr/local/lib/perl/5.10.0/biolib/affyio.pm line 10
Compilation failed in require at test_affyio.pl line 4.
BEGIN failed--compilation aborted at test_affyio.pl line 4.

For some reason the absolute path is dropped.  I understand this
affecting affyio, but it's strange that io_lib is also affected.  OS X
doesn't seem to be affected, but 

I'll pass on the config and build output to you off-list, or I could put
it up on Issues on github if you would like.

chris