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From: metabase:user:30ae4450-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-MLST-Check-1.150910 v5.16.2 GNU/Linux
Date: 2015-04-08T15:51:44Z
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 5.16.2, created by CPAN-Reporter-1.2011_03.
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 "/home/c/perl5/perlbrew/perls/5.16.2i/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.
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.
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(0x84e9c50)') 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(0x84e9c50)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x84e9c50)') 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(0x84e9c50)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x84e9c50)') 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(0x84e9c50)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x84ea440)') 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(0x84ea440)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x84ea440)') 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(0x84ea440)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x84ea440)') 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(0x84ea440)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x9a1f048)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x9a1f048)') 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, <ACTUAL> line 2.
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x9a67db0)', 'spreadsheet_genomic_rows', 'ARRAY(0x84e9b50)', 'output_directory', '/home/c/.cpan/build/Bio-MLST-Check-1.150910-JIjKrz/ciTo4qHfOt', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x9a1f048)') called at t/CDC/Convert.t line 49
# Tests were run but no plan was declared and done_testing() was not seen.
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(0x9c743f0)') 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(0x9c743f0)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x9c743f0)') 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(0x9c743f0)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x9c743f0)') 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(0x9c743f0)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x9b46140)') 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(0x9b46140)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x9b46140)') 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(0x9b46140)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x9b46140)') 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(0x9b46140)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x9c7ecc0)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x9c7ecc0)') 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(0x9c7e940)', 'spreadsheet_genomic_rows', 'ARRAY(0x9c7ea50)', 'output_directory', '/home/c/.cpan/build/Bio-MLST-Check-1.150910-JIjKrz/ukxHZ4kLxh', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x9c7ecc0)') called at t/Output/MultipleFastas.t line 30
# Tests were run but no plan was declared and done_testing() was not seen.
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(0xaf9fed8)') 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(0xaf9fed8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0xaf9fed8)') 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(0xaf9fed8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0xaf9fed8)') 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(0xaf9fed8)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0xafba630)') 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(0xafba630)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0xafba630)') 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(0xafba630)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0xafba630)') 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(0xafba630)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0xada0bb8)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xada0bb8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') 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(0xaf8f998)') 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(0xaf8f998)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0xaf8f998)') 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(0xaf8f998)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0xaf8f998)') 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(0xaf8f998)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0xafba620)') 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(0xafba620)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0xafba620)') 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(0xafba620)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0xafba620)') 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(0xafba620)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0xacab520)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xacab520)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') 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(0xa9b56d0)', 'spreadsheet_genomic_rows', 'ARRAY(0xafa51d0)', 'output_directory', '/home/c/.cpan/build/Bio-MLST-Check-1.150910-JIjKrz/5VPNZnxKmW', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xada0bb8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') 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(0xa5a72a0)', 'spreadsheet_genomic_rows', 'ARRAY(0xa90adb8)', 'output_directory', '/home/c/.cpan/build/Bio-MLST-Check-1.150910-JIjKrz/5VPNZnxKmW', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xacab520)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0xa9e2950)') 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(0x85fe4b0)') 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(0x85fe4b0)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x85fe4b0)') 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(0x85fe4b0)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x85fe4b0)') 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(0x85fe4b0)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x85fe4b0)') called at t/Output/SpreadsheetRow.t line 20
# Tests were run but no plan was declared and done_testing() was not seen.
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(0x82a2500)') 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(0x82a2500)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x82a2500)') 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(0x82a2500)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x82a2500)') 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(0x82a2500)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x82a2500)') called at t/SequenceTypes/CompareAlleles.t line 17
# Tests were run but no plan was declared and done_testing() was not seen.
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, 10 wallclock secs ( 0.06 usr 0.13 sys + 7.44 cusr 0.96 csys = 8.59 CPU)
Result: FAIL
Failed 8/17 test programs. 4/163 subtests failed.
make: *** [test_dynamic] ÐÑибка 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 3.40
Data::Dumper 0 2.139
File::Basename 0 2.84
File::Copy 0 2.23
File::Path 2.06 2.08_01
File::Temp 0 0.2301
File::Which 0 1.09
Getopt::Long 0 2.38
lib 0 0.63
LWP::Simple 0 6.00
Moose 0 2.0802
Moose::Role 0 2.0802
Moose::Util::TypeConstraints 0 2.0802
Parallel::ForkManager 0 1.03
Regexp::Common 0 2011121001
Text::CSV 0 1.21
XML::LibXML 0 2.0018
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.18
ExtUtils::MakeMaker 0 7.04
File::Slurp 0 9999.19
strict 0 1.07
String::Util 0 1.21
Test::Most 0 0.31
warnings 0 1.13
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.04
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = ru_RU.utf8
PATH = /home/c/perl5/perlbrew/bin:/home/c/perl5/perlbrew/perls/5.16.2i/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB = /home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/arch:/home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 24402
PERL5_CPAN_IS_RUNNING = 24402
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 23009,24402
PERLBREW_MANPATH = /home/c/perl5/perlbrew/perls/5.16.2i/man
PERLBREW_PATH = /home/c/perl5/perlbrew/bin:/home/c/perl5/perlbrew/perls/5.16.2i/bin
PERLBREW_PERL = 5.16.2i
PERLBREW_ROOT = /home/c/perl5/perlbrew
PERLBREW_SKIP_INIT = 1
PERLBREW_VERSION = 0.58
PERL_CR_SMOKER_CURRENT = Bio-MLST-Check-1.150910
PERL_CR_SMOKER_RUNONCE = 1
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/c/perl5/perlbrew/perls/5.16.2i/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 24 25 27 29 30 44 46 108 109 115 1000 1001
$EGID = 1000 24 25 27 29 30 44 46 108 109 115 1000 1001
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.00
CPAN::Meta 2.120921
Cwd 3.40
ExtUtils::CBuilder 0.280206
ExtUtils::Command 1.17
ExtUtils::Install 1.58
ExtUtils::MakeMaker 7.04
ExtUtils::Manifest 1.65
ExtUtils::ParseXS 3.16
File::Spec 3.40
JSON 2.53
JSON::PP 2.27203
Module::Build 0.4005
Module::Signature 0.70
Parse::CPAN::Meta 1.4404
Test::Harness 3.30
Test::More 0.98
YAML 0.84
YAML::Syck 1.22
version 0.9901
--
Summary of my perl5 (revision 5 version 16 subversion 2) configuration:
Platform:
osname=linux, osvers=2.6.32-5-686, archname=i686-linux-thread-multi
uname='linux deb1 2.6.32-5-686 #1 smp sun sep 23 09:49:36 utc 2012 i686 gnulinux '
config_args='-de -Dprefix=/home/c/perl5/perlbrew/perls/5.16.2i -Dusethreads -Aeval:scriptdir=/home/c/perl5/perlbrew/perls/5.16.2i/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', 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',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.4.5', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/../lib /usr/lib/../lib /lib /usr/lib /usr/lib/i486-linux-gnu /usr/lib64
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.11.3.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.11.3'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV USE_ITHREADS
USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_PERLIO
USE_PERL_ATOF USE_REENTRANT_API
Built under linux
Compiled at Jan 26 2013 16:12:36
%ENV:
PERL5LIB="/home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/arch:/home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="24402"
PERL5_CPAN_IS_RUNNING="24402"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="23009,24402"
PERLBREW_MANPATH="/home/c/perl5/perlbrew/perls/5.16.2i/man"
PERLBREW_PATH="/home/c/perl5/perlbrew/bin:/home/c/perl5/perlbrew/perls/5.16.2i/bin"
PERLBREW_PERL="5.16.2i"
PERLBREW_ROOT="/home/c/perl5/perlbrew"
PERLBREW_SKIP_INIT="1"
PERLBREW_VERSION="0.58"
PERL_CR_SMOKER_CURRENT="Bio-MLST-Check-1.150910"
PERL_CR_SMOKER_RUNONCE="1"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/arch
/home/c/.cpan/build/BioPerl-1.6.924-_gZ6xG/blib/lib
/home/c/perl5/perlbrew/perls/5.16.2i/lib/site_perl/5.16.2/i686-linux-thread-multi
/home/c/perl5/perlbrew/perls/5.16.2i/lib/site_perl/5.16.2
/home/c/perl5/perlbrew/perls/5.16.2i/lib/5.16.2/i686-linux-thread-multi
/home/c/perl5/perlbrew/perls/5.16.2i/lib/5.16.2
.