After further investigations, this:
>       t/Ontology/OntologyEngine.t .. 1/31 Undefined subroutine 
> &main::throws_ok called at t/Ontology/OntologyEngine.t line 117.
and friends looks to stem from Bio::Root::Test not reexporting
Test::Most submodules anymore.  I'm not entirely sure whether
the bug is in bioperl or Test::Most, but fixing the issue from
bioperl is manageable, by patching lib/Bio/Root/Test.pm:

-8<-------------------------------------------------------------
--- bioperl.orig/lib/Bio/Root/Test.pm
+++ bioperl/lib/Bio/Root/Test.pm
@@ -150,6 +150,12 @@
 
 our @EXPORT = (
     @Test::Most::EXPORT,
+    @Test::More::EXPORT,
+    @Test::Exception::EXPORT,
+    @Test::Warn::EXPORT,
+    @Test::Deep::EXPORT,
+    @Test::Diff::EXPORT,
+    @Test::Differences::EXPORT,
 
     #@Bio::Root::Test::Warn::EXPORT,
     # Test::Warn method wrappers
-8<-------------------------------------------------------------

I will proceed with the package upload tonight.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <[email protected]>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/3, please excuse my verbosity
   `-

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