bioperl / Bio-DB-NCBIHelper

BioPerl modules for accessing data from NCBI
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t/Query-Genbank.t fails #10

Open eserte opened 1 week ago

eserte commented 1 week ago

On some of my smoker systems the test suite fails like this:

#   Failed test at t/Query-Genbank.t line 42.
Use of uninitialized value $val in addition (+) at /usr/perl5.40.0/lib/site_perl/5.40.0/Test/Builder.pm line 798.
#     undef
#         >
#     '0'

#   Failed test at t/Query-Genbank.t line 44.
#     '0'
#         >
#     '0'

#   Failed test at t/Query-Genbank.t line 45.
#          got: '0'
#     expected: undef

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Error from Genbank: Pubmed 2.0 search API: URL not defined
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/cpansand/.cpan/build/2024093019/BioPerl-1.7.8-0/blib/lib/Bio/Root/Root.pm:449
STACK: Bio::DB::Query::GenBank::_parse_response /home/cpansand/.cpan/build/2024093019/Bio-DB-NCBIHelper-1.7.8-0/blib/lib/Bio/DB/Query/GenBank.pm:333
STACK: Bio::DB::Query::WebQuery::_run_query /home/cpansand/.cpan/build/2024093019/BioPerl-1.7.8-0/blib/lib/Bio/DB/Query/WebQuery.pm:349
STACK: Bio::DB::Query::GenBank::count /home/cpansand/.cpan/build/2024093019/Bio-DB-NCBIHelper-1.7.8-0/blib/lib/Bio/DB/Query/GenBank.pm:291
STACK: t/Query-Genbank.t:67
-----------------------------------------------------------

#   Failed test at t/Query-Genbank.t line 67.
Use of uninitialized value $val in addition (+) at /usr/perl5.40.0/lib/site_perl/5.40.0/Test/Builder.pm line 798.
#     undef
#         >
#     '0'

#   Failed test at t/Query-Genbank.t line 69.
#     '0'
#         >
#     '0'

#   Failed test at t/Query-Genbank.t line 70.
#          got: '0'
#     expected: undef
# Looks like you planned 18 tests but ran 21.
# Looks like you failed 6 tests of 21 run.
t/Query-Genbank.t ...... 
Dubious, test returned 6 (wstat 1536, 0x600)
Failed 3/18 subtests 
    (less 18 skipped subtests: -3 okay)
...
Test Summary Report
-------------------
t/Query-Genbank.t    (Wstat: 1536 (exited 6) Tests: 32 Failed: 17)
  Failed tests:  4-6, 13-17, 17-18, 18-19, 19-20, 20-21
                21
  Non-zero exit status: 6
  Parse errors: Tests out of sequence.  Found (8) but expected (9)
                Tests out of sequence.  Found (9) but expected (10)
                Tests out of sequence.  Found (9) but expected (11)
                Tests out of sequence.  Found (10) but expected (12)
                Tests out of sequence.  Found (10) but expected (13)
Displayed the first 5 of 25 TAP syntax errors.
...