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From: metabase:user:30f4dfbe-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-MLST-Check-1.150910 v5.14.3 Mac OS X
Date: 2015-04-01T21:59:55Z
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Andrew Page,
This is a computer-generated report for Bio-MLST-Check-1.150910
on perl 5.14.3, created by CPAN-Reporter-1.2011.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/sw/bin/make test':
PERL_DL_NONLAZY=1 /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Blast/*.t t/CDC/*.t t/Download/*.t t/Input/*.t t/Output/*.t t/Overall/*.t t/SequenceTypes/*.t t/Settings/*.t
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 52
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa') called at t/Blast/BlastN.t line 14
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 1.
t/Blast/BlastN.t ....................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 1 subtests passed
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 52
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa') called at t/Blast/Database.t line 12
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 1.
t/Blast/Database.t ..................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 1 subtests passed
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/Streptococcus_pyogenes_emmST_contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7fce9e831848)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7fce9c745a80)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x7fce9e83af88)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7fce9e83af88)') called at t/CDC/Convert.t line 49
Attribute (header) does not pass the type constraint because: Validation failed for 'ArrayRef' with value undef at constructor Bio::MLST::Spreadsheet::File::new (defined at lib/Bio/MLST/Spreadsheet/File.pm line 48) line 34
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x7fce9e83ae68)', 'spreadsheet_genomic_rows', 'ARRAY(0x7fce9e83a808)', 'output_directory', '/Users/hornenj/.cpan/build/Bio-MLST-Check-1.150910-9X4gJ8/EuK2wn7EPa', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7fce9e83af88)') called at t/CDC/Convert.t line 49
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 13.
t/CDC/Convert.t .....................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 13 subtests passed
t/Download/Database.t ............... ok
t/Download/Databases.t .............. ok
t/Input/NormaliseFasta.t ............ ok
t/Output/Databases.t ................ ok
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f9c8cbaff80)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f9c8e800cb8)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x7f9c8c0121b0)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f9c8c0121b0)') called at t/Output/MultipleFastas.t line 30
Attribute (header) does not pass the type constraint because: Validation failed for 'ArrayRef' with value undef at constructor Bio::MLST::Spreadsheet::File::new (defined at lib/Bio/MLST/Spreadsheet/File.pm line 48) line 34
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x7f9c8cd5b570)', 'spreadsheet_genomic_rows', 'ARRAY(0x7f9c8c8b72d8)', 'output_directory', '/Users/hornenj/.cpan/build/Bio-MLST-Check-1.150910-9X4gJ8/Yuulxs_lD8', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f9c8c0121b0)') called at t/Output/MultipleFastas.t line 30
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 2.
t/Output/MultipleFastas.t ...........
Dubious, test returned 255 (wstat 65280, 0xff00)
All 2 subtests passed
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f90a4092618)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a40c9aa8)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x7f90a5d8da48)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f90a5d8da48)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at t/Output/MultipleSpecies.t line 28
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f90a4074280)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7f90a392aac0)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x7f90a5cfcb48)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f90a5cfcb48)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at t/Output/MultipleSpecies.t line 28
Attribute (header) does not pass the type constraint because: Validation failed for 'ArrayRef' with value undef at constructor Bio::MLST::Spreadsheet::File::new (defined at lib/Bio/MLST/Spreadsheet/File.pm line 48) line 34
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x7f90a5bb5298)', 'spreadsheet_genomic_rows', 'ARRAY(0x7f90a6834408)', 'output_directory', '/Users/hornenj/.cpan/build/Bio-MLST-Check-1.150910-9X4gJ8/EsaWlI6aCT', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f90a5d8da48)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at t/Output/MultipleSpecies.t line 28
Attribute (header) does not pass the type constraint because: Validation failed for 'ArrayRef' with value undef at constructor Bio::MLST::Spreadsheet::File::new (defined at lib/Bio/MLST/Spreadsheet/File.pm line 48) line 34
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x7f90a5c0afe0)', 'spreadsheet_genomic_rows', 'ARRAY(0x7f90a4078750)', 'output_directory', '/Users/hornenj/.cpan/build/Bio-MLST-Check-1.150910-9X4gJ8/EsaWlI6aCT', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x7f90a5cfcb48)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7f90a5c26960)') called at t/Output/MultipleSpecies.t line 28
readline() on closed filehandle $fh_in at lib/Bio/MLST/CheckMultipleSpecies.pm line 159.
readline() on closed filehandle $fh_in at lib/Bio/MLST/CheckMultipleSpecies.pm line 159.
readline() on closed filehandle $fh_in at lib/Bio/MLST/CheckMultipleSpecies.pm line 159.
readline() on closed filehandle $fh_in at lib/Bio/MLST/CheckMultipleSpecies.pm line 159.
# Failed test 'results content matches expected content'
# at t/Output/MultipleSpecies.t line 79.
# Structures begin differing at:
# $got->[0] = 'E.coli "matched 1 of 1 files"
'
# $expected->[0] = '"No matches found"
'
# Failed test 'results content matches expected content'
# at t/Output/MultipleSpecies.t line 79.
# Structures begin differing at:
# $got->[0] = 'E.coli "matched 1 of 1 files"
'
# $expected->[0] = '"No matches found"
'
# Looks like you failed 2 tests of 13.
t/Output/MultipleSpecies.t ..........
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/13 subtests
t/Output/OutputFasta.t .............. ok
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x7ff1a3812060)') called at t/Output/SpreadsheetRow.t line 20
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 1.
t/Output/SpreadsheetRow.t ...........
Dubious, test returned 255 (wstat 65280, 0xff00)
All 1 subtests passed
t/Overall/CheckAllModulesCompile.t .. ok
# Failed test 'blastn in PATH'
# at t/requires_external.t line 8.
# Failed test 'makeblastdb in PATH'
# at t/requires_external.t line 8.
# Looks like you failed 2 tests of 2.
t/requires_external.t ...............
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/2 subtests
Attribute (exec) does not pass the type constraint because: Validation failed for 'Bio::MLST::Executable' with value "makeblastdb" at constructor Bio::MLST::Blast::Database::new (defined at lib/Bio/MLST/Blast/Database.pm line 32) line 45
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa', 'exec', 'makeblastdb') called at lib/Bio/MLST/CompareAlleles.pm line 42
Bio::MLST::CompareAlleles::_build__blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x7f91890120d8)') called at t/SequenceTypes/CompareAlleles.t line 17
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 2.
t/SequenceTypes/CompareAlleles.t ....
Dubious, test returned 255 (wstat 65280, 0xff00)
All 2 subtests passed
t/SequenceTypes/SearchForFiles.t .... ok
t/SequenceTypes/SequenceType.t ...... ok
t/Settings/DatabaseSettings.t ....... ok
Test Summary Report
-------------------
t/Blast/BlastN.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Blast/Database.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/CDC/Convert.t (Wstat: 65280 Tests: 13 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Output/MultipleFastas.t (Wstat: 65280 Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Output/MultipleSpecies.t (Wstat: 512 Tests: 13 Failed: 2)
Failed tests: 6, 9
Non-zero exit status: 2
t/Output/SpreadsheetRow.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/requires_external.t (Wstat: 512 Tests: 2 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 2
t/SequenceTypes/CompareAlleles.t (Wstat: 65280 Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=17, Tests=163, 8 wallclock secs ( 0.04 usr 0.02 sys + 3.43 cusr 0.76 csys = 4.25 CPU)
Result: FAIL
Failed 8/17 test programs. 4/163 subtests failed.
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- ----------
Bio::AlignIO 0 0
Bio::Perl 0 0
Bio::PrimarySeq 0 0
Bio::SeqIO 0 0
Bio::SimpleAlign 0 0
Cwd 0 3.47
Data::Dumper 0 2.151
File::Basename 0 2.82
File::Copy 0 2.21
File::Path 2.06 2.09
File::Temp 0 0.2304
File::Which 0 1.09
Getopt::Long 0 2.42
lib 0 0.63
LWP::Simple 0 6.00
Moose 0 2.1213
Moose::Role 0 2.1213
Moose::Util::TypeConstraints 0 2.1213
Parallel::ForkManager 0 1.12
Regexp::Common 0 2013031301
Text::CSV 0 1.32
XML::LibXML 0 2.0116
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 6.98
File::Slurp 0 9999.19
strict 0 1.04
String::Util 0 1.24
Test::Most 0 0.34
warnings 0 1.12
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 6.98
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LC_ALL = POSIX
LD_LIBRARY_PATH = :/net/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb/mac/release/x86_64/lib
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin:/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.2/bin:/Users/hornenj/bin:/sw/lib/perl5/ExtUtils:/sw/bin:/am/ncbiapdata/bin:/usr/bin:/bin:/usr/X11R6/bin:/netopt/ncbi_tools/bin:/usr/local/ncbi/blast/bin:/net/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb/mac/release/x86_64/bin
PERL5LIB = /Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/arch:/Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/lib:/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/arch:/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/lib:/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/lib:/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/arch:/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 8530
PERL5_CPAN_IS_RUNNING = 8530
PERL5_MINISMOKEBOX = 0.58
PERLBREW_BASHRC_VERSION = 0.73
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_LIB =
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin
PERLBREW_PERL = perl-5.14.3
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_VERSION = 0.73
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT =
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm-256color
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/
VERSIONER_PERL_PREFER_32_BIT = no
VERSIONER_PERL_VERSION = 5.18
ac_cv_path_INTLTOOL_PERL = /usr/bin/perl
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin/perl
$UID/$EUID = 12481 / 12481
$GID = 14 14 5344 527 241
$EGID = 14 14 5344 527 241
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.10
CPAN::Meta 2.142690
Cwd 3.47
ExtUtils::CBuilder 0.280216
ExtUtils::Command 1.18
ExtUtils::Install 1.68
ExtUtils::MakeMaker 6.98
ExtUtils::Manifest 1.65
ExtUtils::ParseXS 3.24
File::Spec 3.47
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4210
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.33
Test::More 1.001014
YAML 1.01
YAML::Syck 1.29
version 0.9908
--
Summary of my perl5 (revision 5 version 14 subversion 3) configuration:
Platform:
osname=darwin, osvers=12.2.1, archname=darwin-2level
uname='darwin ncbimac2008.ncbi.nlm.nih.gov 12.2.1 darwin kernel version 12.2.1: thu oct 18 12:13:47 pdt 2012; root:xnu-2050.20.9~1release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fno-common -DPERL_DARWIN -fno-strict-aliasing -pipe -fstack-protector',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -fno-strict-aliasing -pipe -fstack-protector'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.24)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector'
libpth=/usr/lib
libs=-ldbm -ldl -lm -lutil -lc
perllibs=-ldl -lm -lutil -lc
libc=, so=dylib, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
Built under darwin
Compiled at Mar 4 2013 17:42:44
%ENV:
PERL5LIB="/Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/arch:/Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/lib:/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/arch:/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/lib:/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/lib:/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/arch:/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="8530"
PERL5_CPAN_IS_RUNNING="8530"
PERL5_MINISMOKEBOX="0.58"
PERLBREW_BASHRC_VERSION="0.73"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_LIB=""
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin"
PERLBREW_PERL="perl-5.14.3"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_VERSION="0.73"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT=""
PERL_MM_USE_DEFAULT="1"
@INC:
/Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/arch
/Users/hornenj/.cpan/build/String-Util-1.24-VqJHeu/blib/lib
/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/arch
/Users/hornenj/.cpan/build/Number-Misc-1.2-dwGNCB/blib/lib
/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/arch
/Users/hornenj/.cpan/build/Env-Path-0.19-8QG6B6/blib/lib
/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/arch
/Users/hornenj/.cpan/build/BioPerl-1.6.924-yUYrR7/blib/lib
/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/arch
/Users/hornenj/.cpan/build/Data-Stag-0.14-mKkEzX/blib/lib
/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/arch
/Users/hornenj/.cpan/build/Parallel-ForkManager-1.12-wyIYN5/blib/lib
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3/darwin-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3/darwin-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3
.