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From: metabase:user:00e8548a-0e72-11e3-8ee3-df0a9c418065
Subject: FAIL Bio-MLST-Check-1.150910 v5.10.1 GNU/Linux
Date: 2015-04-11T04:05:55Z
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 5.10.1, created by CPAN-Reporter-1.2014.
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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/usr/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(0x2e71318)') 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(0x2e71318)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2e71318)') 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(0x2e71318)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2e71318)') 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(0x2e71318)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x2e714b0)') 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(0x2e714b0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x2e714b0)') 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(0x2e714b0)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x2e714b0)') 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(0x2e714b0)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2c9a9a8)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c9a9a8)') 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(0x2e27b78)', 'spreadsheet_genomic_rows', 'ARRAY(0x2e27ae8)', 'output_directory', '/root/.cpan/build/Bio-MLST-Check-1.150910-oRaddu/AfUatAbxd0', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c9a9a8)') 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(0x40e9f70)') 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(0x40e9f70)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x40e9f70)') 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(0x40e9f70)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x40e9f70)') 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(0x40e9f70)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x440e8f0)') 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(0x440e8f0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x440e8f0)') 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(0x440e8f0)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x440e8f0)') 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(0x440e8f0)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x43fc470)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x43fc470)') 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(0x3362478)', 'spreadsheet_genomic_rows', 'ARRAY(0x43fc4b8)', 'output_directory', '/root/.cpan/build/Bio-MLST-Check-1.150910-oRaddu/yOQqHjSH_w', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x43fc470)') 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(0x3401978)') 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(0x3401978)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x3401978)') 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(0x3401978)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x3401978)') 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(0x3401978)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x3490268)') 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(0x3490268)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x3490268)') 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(0x3490268)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x3490268)') 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(0x3490268)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2c23138)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c23138)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') 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(0x3402020)') 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(0x3402020)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x3402020)') 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(0x3402020)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x3402020)') 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(0x3402020)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x34900a0)') 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(0x34900a0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x34900a0)') 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(0x34900a0)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x34900a0)') 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(0x34900a0)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2c93860)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c93860)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') 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(0x310e1e0)', 'spreadsheet_genomic_rows', 'ARRAY(0x275a940)', 'output_directory', '/root/.cpan/build/Bio-MLST-Check-1.150910-oRaddu/RDzvlQEYhv', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c93860)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') 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(0x2c938f0)', 'spreadsheet_genomic_rows', 'ARRAY(0x2c8e040)', 'output_directory', '/root/.cpan/build/Bio-MLST-Check-1.150910-oRaddu/RDzvlQEYhv', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2c23138)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x29d1588)') 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(0x35e4868)') 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(0x35e4868)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x35e4868)') 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(0x35e4868)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x35e4868)') 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(0x35e4868)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x35e4868)') 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(0x25735d8)') 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(0x25735d8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x25735d8)') 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(0x25735d8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x25735d8)') 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(0x25735d8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x25735d8)') 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, 11 wallclock secs ( 0.06 usr 0.04 sys + 5.82 cusr 0.77 csys = 6.69 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 2.154
File::Basename 0 2.77
File::Copy 0 2.14
File::Path 2.06 2.09
File::Temp 0 0.2304
File::Which 0 1.16
Getopt::Long 0 2.45
lib 0 0.63
LWP::Simple 0 6.13
Moose 0 2.1403
Moose::Role 0 2.1403
Moose::Util::TypeConstraints 0 2.1403
Parallel::ForkManager 0 1.12
Regexp::Common 0 2013031301
Text::CSV 0 1.33
XML::LibXML 0 2.0118
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.04
File::Slurp 0 9999.19
strict 0 1.04
String::Util 0 1.24
Test::Most 0 0.34
warnings 0 1.06
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.04
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
PERL5LIB = /root/.cpan/build/String-Util-1.24-pKi8Zu/blib/arch:/root/.cpan/build/String-Util-1.24-pKi8Zu/blib/lib:/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/arch:/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/lib:/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/arch:/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/lib:/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/arch:/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/lib:/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/arch:/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/lib:/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/arch:/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/lib:/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/arch:/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/lib:/root/.cpan/build/Text-CSV-1.33-808sI7/blib/arch:/root/.cpan/build/Text-CSV-1.33-808sI7/blib/lib:/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/arch:/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 25594
PERL5_CPAN_IS_RUNNING = 25594
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 25592,25594
PERL_CR_SMOKER_CURRENT = Bio-MLST-Check-1.150910
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = linux
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 0 / 0
$GID = 0 0
$EGID = 0 0
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.10
CPAN::Meta 2.150001
Cwd 3.47
ExtUtils::CBuilder 0.280220
ExtUtils::Command 1.20
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.04
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.24
File::Spec 3.47
JSON 2.61
JSON::PP 2.27300
Module::Build 0.4211
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.35
Test::More 1.001014
YAML 1.14
YAML::Syck 1.29
version 0.9912
--
Summary of my perl5 (revision 5 version 10 subversion 1) configuration:
Platform:
osname=linux, osvers=2.6.32-220.el6.x86_64, archname=x86_64-linux-thread-multi
uname='linux c6b8.bsys.dev.centos.org 2.6.32-220.el6.x86_64 #1 smp tue dec 6 19:48:22 gmt 2011 x86_64 x86_64 x86_64 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DDEBUGGING=-g -Dversion=5.10.1 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5 -Dsitearch=/usr/local/lib64/perl5 -Dprivlib=/usr/share/perl5 -Darchlib=/usr/lib64/perl5 -Dvendorlib=/usr/share/perl5/vendor_perl -Dvendorarch=/usr/lib64/perl5/vendor_perl -Dinc_version_list=5.10.0 -Darchname=x86_64-linux-thread-multi -Dlibpth=/usr/local/lib64 /lib64 /usr/lib64 -Duseshrplib -Dusethreads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dusesitecustomize'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.4.7 20120313 (Red Hat 4.4.7-11)', 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='gcc', ldflags =' -fstack-protector'
libpth=/usr/local/lib64 /lib64 /usr/lib64
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version='2.12'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -Wl,-rpath,/usr/lib64/perl5/CORE'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
Built under linux
Compiled at Nov 12 2014 09:09:35
%ENV:
PERL5LIB="/root/.cpan/build/String-Util-1.24-pKi8Zu/blib/arch:/root/.cpan/build/String-Util-1.24-pKi8Zu/blib/lib:/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/arch:/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/lib:/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/arch:/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/lib:/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/arch:/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/lib:/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/arch:/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/lib:/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/arch:/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/lib:/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/arch:/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/lib:/root/.cpan/build/Text-CSV-1.33-808sI7/blib/arch:/root/.cpan/build/Text-CSV-1.33-808sI7/blib/lib:/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/arch:/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="25594"
PERL5_CPAN_IS_RUNNING="25594"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="25592,25594"
PERL_CR_SMOKER_CURRENT="Bio-MLST-Check-1.150910"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/root/.cpan/build/String-Util-1.24-pKi8Zu/blib/arch
/root/.cpan/build/String-Util-1.24-pKi8Zu/blib/lib
/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/arch
/root/.cpan/build/Number-Misc-1.2-UfSGiX/blib/lib
/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/arch
/root/.cpan/build/Env-Path-0.19-zyiQtF/blib/lib
/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/arch
/root/.cpan/build/File-Slurp-9999.19-bJv1gW/blib/lib
/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/arch
/root/.cpan/build/BioPerl-1.6.924-Kw4Wt8/blib/lib
/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/arch
/root/.cpan/build/Data-Stag-0.14-C8AJ70/blib/lib
/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/arch
/root/.cpan/build/Regexp-Common-2013031301-pVx6TP/blib/lib
/root/.cpan/build/Text-CSV-1.33-808sI7/blib/arch
/root/.cpan/build/Text-CSV-1.33-808sI7/blib/lib
/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/arch
/root/.cpan/build/Parallel-ForkManager-1.12-5S55Ox/blib/lib
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.