Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.
List all used modules in META.yml requires
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.
Error: Atom.pm, Bond.pm, File.pm, File/Dumper.pm, File/Formula.pm, Mol.pm, Obj.pm
Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Chemistry::Bond, Chemistry::File, Chemistry::File::Formula, Chemistry::Obj
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
|Chemistry::Atom||Chemical atoms as objects in molecules||0.25||metacpan|
|Chemistry::Bond||Chemical bonds as objects in molecules||0.25||metacpan|
|Chemistry::File||Molecule file I/O base class||0.25||metacpan|
|Chemistry::File::Formula||Molecular formula reader/formatter||0.25||metacpan|
|Chemistry::Mol||Molecule object toolkit||0.25||metacpan|
|Chemistry::Obj||Abstract chemistry object||0.25||metacpan|