Your message dated Sun, 08 Sep 2013 12:18:09 +0000
with message-id <e1vidwp-0001ih...@franck.debian.org>
and subject line Bug#720776: fixed in bioperl 1.6.920-1
has caused the Debian Bug report #720776,
regarding bioperl: FTBFS with perl 5.18: test failures
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.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
720776: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=720776
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: bioperl
Version: 1.6.901-3
Severity: serious
Justification: transition imminent
User: debian-p...@lists.debian.org
Usertags: perl-5.18-transition
Tags: sid jessie
This package FTBFS with perl 5.18:
# Failed test at t/Assembly/ContigSpectrum.t line 311.
# got: '88.8076923076923'
# expected: '88.7692307692308'
# Failed test at Bio/Root/Test.pm line 435.
# got: '74.727'
# expected: '74.7486'
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not find sequence species1635|5973 in contig contig00001_6
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Assembly::Contig::get_seq_by_name Bio/Assembly/Contig.pm:1063
STACK: t/Assembly/ContigSpectrum.t:336
-----------------------------------------------------------
# Looks like you planned 236 tests but ran 215.
# Looks like you failed 2 tests of 215 run.
# Looks like your test exited with 255 just after 215.
t/Assembly/ContigSpectrum.t ..................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 23/236 subtests
...
# Failed test at t/Map/Map.t line 322.
# got: 'Bio::Map::Position=HASH(0xa6595ec)'
# expected: 'Bio::Map::Position=HASH(0xa6592b8)'
# Failed test at t/Map/Map.t line 323.
# got: 'Bio::Map::Position=HASH(0xa6592b8)'
# expected: 'Bio::Map::Position=HASH(0xa6595ec)'
# Failed test at t/Map/Map.t line 324.
# got: undef
# expected: 'Bio::Map::Position=HASH(0xa65a048)'
Can't call method "toString" on an undefined value at t/Map/Map.t line 325.
# Looks like you planned 267 tests but ran 134.
# Looks like you failed 3 tests of 134 run.
# Looks like your test exited with 255 just after 134.
t/Map/Map.t ..................................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 136/267 subtests
...
# Failed test at t/Ontology/IO/obo.t line 47.
# got: '2'
# expected: '5'
# Failed test at t/Ontology/IO/obo.t line 49.
# Failed test at t/Ontology/IO/obo.t line 51.
# Failed test at t/Ontology/IO/obo.t line 53.
# Failed test at t/Ontology/IO/obo.t line 55.
# Failed test at t/Ontology/IO/obo.t line 57.
# Failed test at t/Ontology/IO/obo.t line 61.
# got: '10'
# expected: '2'
# Failed test 'Got positively regulates predicate'
# at t/Ontology/IO/obo.t line 182.
# got: 'REGULATES'
# expected: 'POSITIVELY_REGULATES'
# Looks like you failed 8 tests of 92.
t/Ontology/IO/obo.t ..........................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/92 subtests
..
# Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm'
# at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/GuessSeqFormat.pm (233): Non-ASCII character seen before =encoding i
n 'K<E4>h<E4>ri,'. Assuming ISO8859-1
# Failed test 'POD test for Bio/Tools/Geneid.pm'
# at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/Geneid.pm (37): Non-ASCII character seen before =encoding in 'Guig
<F3>'. Assuming ISO8859-1
# Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm'
# at /usr/share/perl5/Test/Pod.pm line 186.
# Bio/Tools/Run/WrapperBase.pm (181): Non-ASCII character seen before =encoding
in 'NB:<CA>This'. Assuming ISO8859-1
# Failed test 'POD test for Bio/Tree/Statistics.pm'
# at /usr/share/perl5/Test/Pod.pm line 186.
Wide character in print at /usr/share/perl/5.18/Test/Builder.pm line 1759.
# Bio/Tree/Statistics.pm (214): Non-ASCII character seen before =encoding in
'defining'. Assuming UTF-8
# Failed test 'POD test for examples/biblio/biblio-eutils-example.pl'
# at /usr/share/perl5/Test/Pod.pm line 186.
# examples/biblio/biblio-eutils-example.pl (108): Non-ASCII character seen
before =encoding in '<LastName>Kub<ED>ckov<E1></LastName>'. Assuming ISO8859-1
# Looks like you failed 5 tests of 1011.
t/PodSyntax.t ................................
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/1011 subtests
..
Test Summary Report
-------------------
t/Assembly/ContigSpectrum.t (Wstat: 65280 Tests: 215 Failed: 2)
Failed tests: 203, 205
Non-zero exit status: 255
Parse errors: Bad plan. You planned 236 tests but ran 215.
t/Map/Map.t (Wstat: 65280 Tests: 134 Failed: 3)
Failed tests: 132-134
Non-zero exit status: 255
Parse errors: Bad plan. You planned 267 tests but ran 134.
t/Ontology/IO/obo.t (Wstat: 2048 Tests: 92 Failed: 8)
Failed tests: 14-20, 65
Non-zero exit status: 8
t/PodSyntax.t (Wstat: 1280 Tests: 1011 Failed: 5)
Failed tests: 197, 239, 307, 345, 964
Non-zero exit status: 5
Files=349, Tests=22424, 291 wallclock secs ( 3.27 usr 2.58 sys + 141.92 cusr
15.12 csys = 162.89 CPU)
Result: FAIL
Please ask debian-p...@lists.debian.org if you need help with preparing
or testing a change; if you have a suitable test i386 system you can
install perl 5.18 by adding experimental to your sources as well as the
repository at <http://people.debian.org/~dom/perl/test/perl-5.18.0/>
You can also find more about the perl 5.18 transition, which we hope
to start this week[1], at <http://bugs.debian.org/712615>.
Thanks for your work!
Cheers,
Dominic.
[1] apologies for the late appearance of this bug report; earlier
test coverage did not cover this package
--- End Message ---
--- Begin Message ---
Source: bioperl
Source-Version: 1.6.920-1
We believe that the bug you reported is fixed in the latest version of
bioperl, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 720...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated bioperl package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 08 Sep 2013 20:56:00 +0900
Source: bioperl
Binary: bioperl libbio-perl-perl
Architecture: source all
Version: 1.6.920-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Charles Plessy <ple...@debian.org>
Description:
bioperl - Perl tools for computational molecular biology
libbio-perl-perl - BioPerl core perl modules
Closes: 720776
Changes:
bioperl (1.6.920-1) unstable; urgency=low
.
* New upstream release (Closes: #720776)
* Adjusted Depends and Recommends (4 additions).
* Removed patch ‘fix_berkeleydb3_temp_file_creation’ applied upstream.
* Use canonical VCS URLs.
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Files:
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bioperl_1.6.920.orig.tar.gz
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bioperl_1.6.920-1.debian.tar.gz
1c660df940939a37c9387cb8a324fba5 415806 science optional
bioperl_1.6.920-1_all.deb
c64907b887d512a1259dfb715e81c039 4753598 perl optional
libbio-perl-perl_1.6.920-1_all.deb
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