Added 'DB_File' requirement to some tests files that use it,
so they can be skipped if its missing (ContigSpectrum.t,
SeqFeature.t & transfac_pro.t)
Several LocalDB tests were failing for Windows' ActivePerl,
because ActivePerl were producing a ".index.pag" and ".index.dir"
files instead of a single ".index" file (like Strawberry Perl).
Also, ActivePerl were not deleting temporary files if their
tied-hash was not made undef after the untie on DESTROY,
and had to add several explicit DESTROY calls to test files.
Changed argument "requires_modules" to "require_module"
for SeqFeature.t and transfac_pro.t, since its only 1
Added 'Data::Stag' requirement to many tests files
that depend on it, so they can be skipped if its missing
BioFetch.t & SwissProt.t: Fixed some number of skipped tests
and cleaned format and indentation
RemoteBlast.t: Fixed several number of skipped tests,
increased significantly server waiting cycle (sleep + retries)
because server was taking much longer than current setting
to return results, and cleaned format and indentation
RandomFactory.t: Removed unused dependency "Math::Random",
which only appears in this file and not in any module.
A machine without the module installed still passed all tests.
Taxonomy.t: Added missing 'DB_File' requirement
RemoteBlast_rpsblast.t: Fixed a few number of skipped tests,
and cleaned format and indentation
Added some changes and bugfixes
Build.PL: Demoted 'DB_File' status from "required" to
"recommended", and added in "recommended" missing modules
that are requested by some test files (Bio::Phylo, XML::DOM
and XML::DOM::XPath). NOTE: The 3 modules added were
confirmed to be correctly installed by ActivePerl.
Bio/Root/Storable.pm: Explicitly closed some open filehandles
that were not stored, because they were causing random failures
on temporary file deletion in ActivePerl