Your message dated Sun, 22 Jul 2018 16:02:52 +0800
with message-id <20180722080251.GA20239@tx.local>
and subject line Re: ruby-bio FTBFS with ruby 2.5
has caused the Debian Bug report #890691,
regarding ruby-bio FTBFS with ruby 2.5
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
890691: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890691
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ruby-bio
Version: 1.5.0-2
Severity: serious
Tags: buster sid
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ruby-bio.html
...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Run tests for ruby2.5 from debian/ruby-tests.rb │
└──────────────────────────────────────────────────────────────────────────────┘
RUBYLIB=/build/1st/ruby-bio-1.5.0/debian/ruby-bio/usr/lib/ruby/vendor_ruby:.
GEM_PATH=debian/ruby-bio/usr/share/rubygems-integration/all:/var/lib/gems/2.5.0:/usr/lib/x86_64-linux-gnu/rubygems-integration/2.5.0:/usr/share/rubygems-integration/2.5.0:/usr/share/rubygems-integration/all
ruby2.5 debian/ruby-tests.rb
Loaded suite debian/ruby-tests
Started
...............................................................................
.................................................................../build/1st/ruby-bio-1.5.0/test/unit/bio/test_alignment.rb:631:
warning: constant ::Fixnum is deprecated
/build/1st/ruby-bio-1.5.0/test/unit/bio/test_alignment.rb:633: warning:
constant ::Fixnum is deprecated
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.............................................................../build/1st/ruby-bio-1.5.0/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:154:
warning: constant ::Fixnum is deprecated
/build/1st/ruby-bio-1.5.0/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:154:
warning: constant ::Fixnum is deprecated
................
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........................................................../build/1st/ruby-bio-1.5.0/lib/bio/db/soft.rb:220:
warning: constant ::Fixnum is deprecated
/build/1st/ruby-bio-1.5.0/lib/bio/db/soft.rb:226: warning: constant ::Fixnum is
deprecated
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...............................................................................
.O
===============================================================================
test randomly failing skipped
[test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)]
/build/1st/ruby-bio-1.5.0/test/unit/bio/sequence/test_common.rb:324:in
`test_randomize_equiprobability'
===============================================================================
O
===============================================================================
test randomly failing skipped
[test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)]
/build/1st/ruby-bio-1.5.0/test/unit/bio/sequence/test_common.rb:330:in
`test_randomize_with_hash_equiprobability'
===============================================================================
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........................................................E
===============================================================================
Error: test_na_seqstat(Bio::TestShellPluginSeq): ArgumentError: incomplete
format specifier; use %% (double %) instead
/build/1st/ruby-bio-1.5.0/lib/bio/shell/plugin/seq.rb:85:in `format'
/build/1st/ruby-bio-1.5.0/lib/bio/shell/plugin/seq.rb:85:in `block in seqstat'
/build/1st/ruby-bio-1.5.0/lib/bio/shell/plugin/seq.rb:84:in `each'
/build/1st/ruby-bio-1.5.0/lib/bio/shell/plugin/seq.rb:84:in `seqstat'
/build/1st/ruby-bio-1.5.0/test/unit/bio/shell/plugin/test_seq.rb:118:in
`test_na_seqstat'
115: $str << obj.to_s
116: end
117: end
=> 118: seqstat(naseq)
119: undef puts
120: alias puts puts_orig
121: assert_equal(output, $str)
===============================================================================
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Finished in 15.8237365 seconds.
------
3849 tests, 21478 assertions, 0 failures, 1 errors, 0 pendings, 2 omissions, 0
notifications
99.974% passed
------
243.24 tests/s, 1357.33 assertions/s
ERROR: Test "ruby2.5" failed. Exiting.
dh_auto_install: dh_ruby --install /build/1st/ruby-bio-1.5.0/debian/ruby-bio
returned exit code 1
make[1]: *** [debian/rules:32: override_dh_auto_install] Error 1
--- End Message ---
--- Begin Message ---
Version: 1.5.1-1
Hey Andreas,
* Andreas Tille <andr...@an3as.eu> [180716 18:11]:
> I'd love to fix this bug since this package is of relevance for Debian
> Med. It seems to boil down to
>
> Error: test_na_seqstat(Bio::TestShellPluginSeq): ArgumentError: incomplete
> format specifier; use %% (double %) instead
>
> which sounds pretty easy for somebody who speaks Ruby (which is not the
> case for me). Could anybody provide a patch (or just do a team upload
> of this package which I updated in Git to latest upstream since Mai)?
I've just applied a patch and uploaded the package.
There are some warnings that point to outdated symbols, so upstream
will need to work on updating the code a bit for 2.5+.
Thanks,
Chris
--- End Message ---
