[DRE-maint] Bug#890691: ruby-bio FTBFS with ruby 2.5

[Andreas Tille]

Hi,

I confirm that this bug persists also for the latest upstream version I
injected in Git[1] has the same issue.  I bet some Ruby programmer could
easily fix the cause:

./build/ruby-bio-1.5.1/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:154: warning: constant ::Fixnum is deprecated
/build/ruby-bio-1.5.1/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:154: warning: constant ::Fixnum is deprecated
................
...............................................................................
........................................................../build/ruby-bio-1.5.1/lib/bio/db/soft.rb:220: warning: constant ::Fixnum is deprecated
/build/ruby-bio-1.5.1/lib/bio/db/soft.rb:226: warning: constant ::Fixnum is deprecated
.....................
...............................................................................
.O
===============================================================================
Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)]
/build/ruby-bio-1.5.1/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability'
===============================================================================
O
===============================================================================
Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)]
/build/ruby-bio-1.5.1/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability'
===============================================================================
...............................................................................
........................................................E
===============================================================================
Error: test_na_seqstat(Bio::TestShellPluginSeq): ArgumentError: incomplete format specifier; use %% (double %) instead
/build/ruby-bio-1.5.1/lib/bio/shell/plugin/seq.rb:85:in `format'
/build/ruby-bio-1.5.1/lib/bio/shell/plugin/seq.rb:85:in `block in seqstat'
/build/ruby-bio-1.5.1/lib/bio/shell/plugin/seq.rb:84:in `each'
/build/ruby-bio-1.5.1/lib/bio/shell/plugin/seq.rb:84:in `seqstat'
/build/ruby-bio-1.5.1/test/unit/bio/shell/plugin/test_seq.rb:118:in `test_na_seqstat'


The error message looks pretty clear and should be no big deal but I simply
do not speak Ruby.

Kind regards

       Andreas.

[1] https://salsa.debian.org/ruby-team/ruby-bio

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