view release on metacpan or  search on metacpan

deobfuscator/Deobfuscator/lib/Deobfuscator.pm  view on Meta::CPAN

=over

=item C<< error: couldn't eval $module >>

A package couldn't be loaded (eval'd), which would prevent us from determining
what its methods are.

=item C<< error: couldn't open $filename >>

One of the Berkeley databases couldn't be opened. Possible causes are:
deob_index.pl wasn't run and so the databases weren't created, or the database
files aren't in the correct place.

=item C<< error: couldn't close database >>

One of the Berkeley databases couldn't be closed. This might just be a
transient filesystem error.

=back

=item C<< error: couldn't load [module] >>

The BioPerl modules aren't in the Perl lib (PERL5LIB) and so can't be searched
(the Deobfuscator uses I<Class::Inspector> for this. Check that the value of
your PERL5LIB includes BioPerl's modules. If need be, you can set a use lub directive
at the beginning of deob_interface.cgi.

=back


=head1 CONFIGURATION AND ENVIRONMENT

This software requires:

=over

=item A working installation of the Berkeley DB

The Berkeley DB comes standard with most UNIX distributions, so you may
already have it installed. See L<http://www.sleepycat.com> for more information.

=item BioPerl

Deobfuscator.pm recursively navigates a directory of BioPerl modules. Note
that the BioPerl module directory need not be "installed"; any old location
will do. See L<http://www.bioperl.org> for the latest version.

=back


=head1 DEPENDENCIES

L<version>, L<Class::Inspector>, L<DB_File>


=head1 INCOMPATIBILITIES

None reported.


=head1 BUGS AND LIMITATIONS

In the current implementation, Deobfuscator does not show internal or private
methods (i.e. those whose name begins with an underscore). This is simply an
option in the Class::Inspector->methods call, and so could be presented as an
option to the user (patches welcome).

No bugs have been reported.


=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                       - General discussion
  http://bioperl.org/Support.html   - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  http://bugzilla.bioperl.org/


=head1 SEE ALSO

L<deob_index.pl>


=head1 AUTHOR

Dave Messina C<< <dave-pause@davemessina.net> >>


=head1 CONTRIBUTORS

=over

=item Laura Kavanaugh

=item David Curiel

=back


=head1 ACKNOWLEDGMENTS

This software was developed originally at the Cold Spring Harbor Laboratory's
Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David
Curiel, who provided much-needed guidance and assistance on this project.


=head1 LICENSE AND COPYRIGHT

Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved.