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From: metabase:user:320bfe00-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-MLST-Check-1.150910 v5.20.2 GNU/Linux
Date: 2015-04-01T13:17:41Z
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 5.20.2, created by CPAN-Reporter-1.2013.
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/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/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(0x3b5d2c8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x3b5d2c8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x3b5d2c8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x3b5d2c8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x3b5d2c8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x3b5d2c8)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 8
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 8
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 8
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x3b5d4f0)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x3b51e90)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x3b51e90)') 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(0x3b4d670)', 'spreadsheet_genomic_rows', 'ARRAY(0x3b51da0)', 'output_directory', '/tmp/loop_over_bdir-1359-LUUvs1/Bio-MLST-Check-1.150910-M8ut4b/GqqcyRlCI_', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x3b51e90)') 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(0x4514288)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x4514288)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x4514288)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x4514288)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x4514288)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x4514288)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 8
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 8
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 8
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x3b47378)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x4049a00)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x4049a00)') 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(0x448c710)', 'spreadsheet_genomic_rows', 'ARRAY(0x155ab60)', 'output_directory', '/tmp/loop_over_bdir-1359-LUUvs1/Bio-MLST-Check-1.150910-M8ut4b/i9T1bh2EEU', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x4049a00)') 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(0x389da80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x389da80)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x389da80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x389da80)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x389da80)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x389da80)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 8
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 8
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 8
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x389df18)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2de2318)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2de2318)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') 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(0x389d948)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x389d948)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x389d948)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x389d948)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x389d948)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x389d948)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 8
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 8
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at lib/Bio/MLST/ProcessFasta.pm line 77
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 8
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x380f8f8)') called at lib/Bio/MLST/Check.pm line 82
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2760830)') called at lib/Bio/MLST/Check.pm line 104
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2760830)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') 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(0x37120f0)', 'spreadsheet_genomic_rows', 'ARRAY(0x24c8bc0)', 'output_directory', '/tmp/loop_over_bdir-1359-LUUvs1/Bio-MLST-Check-1.150910-M8ut4b/ZvnwMwYS95', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2760830)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') 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(0x2aabf60)', 'spreadsheet_genomic_rows', 'ARRAY(0x33bdf10)', 'output_directory', '/tmp/loop_over_bdir-1359-LUUvs1/Bio-MLST-Check-1.150910-M8ut4b/ZvnwMwYS95', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 107
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2de2318)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x374bbe8)') 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(0x23f3ae8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x23f3ae8)') 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(0xf40ae8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 8
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 8
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 110
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 8
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0xf40ae8)') 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, 24 wallclock secs ( 0.05 usr 0.12 sys + 9.68 cusr 1.83 csys = 11.68 CPU)
Result: FAIL
Failed 8/17 test programs. 4/163 subtests failed.
Makefile:947: recipe for target 'test_dynamic' 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 3.48_01
Data::Dumper 0 2.154
File::Basename 0 2.85
File::Copy 0 2.30
File::Path 2.06 2.09
File::Temp 0 0.2304
File::Which 0 1.15
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 7.05_19
File::Slurp 0 9999.19
strict 0 1.08
String::Util 0 1.24
Test::Most 0 0.34
warnings 0 1.23
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.05_19
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LANGUAGE = en_US:en
PATH = /home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 1361
PERL5_CPAN_IS_RUNNING = 1361
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- ------------
CPAN 2.10
CPAN::Meta 2.150001
Cwd 3.48_01
ExtUtils::CBuilder 0.280220
ExtUtils::Command 7.05_19
ExtUtils::Install 1.67
ExtUtils::MakeMaker 7.05_19
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.24
File::Spec 3.48_01
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4211
Module::Signature 0.73
Parse::CPAN::Meta 1.4414
Test::Harness 3.35
Test::More 1.301001_100
YAML 1.14
YAML::Syck 1.29
version 0.9912
--
Summary of my perl5 (revision 5 version 20 subversion 2) configuration:
Commit id: c05ce579b6dae0f955ff8922469d49f95f4bf6fd
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux-thread-multi-ld
uname='linux k83 3.16.0-4-amd64 #1 smp debian 3.16.7-ckt7-1 (2015-03-01) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a -Dmyhostname=k83 -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Duseithreads -Duselongdouble'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=define
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -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 -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.9.2', 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='long double', nvsize=16, Off_t='off_t', lseeksize=8
alignbytes=16, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=libc-2.19.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.19'
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_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
PERL_USE_DEVEL USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LONG_DOUBLE USE_PERLIO
USE_PERL_ATOF USE_REENTRANT_API
Built under linux
Compiled at Mar 14 2015 20:37:19
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="1361"
PERL5_CPAN_IS_RUNNING="1361"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/lib/site_perl/5.20.2/x86_64-linux-thread-multi-ld
/home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/lib/site_perl/5.20.2
/home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/lib/5.20.2/x86_64-linux-thread-multi-ld
/home/sand/src/perl/repoperls/installed-perls/perl/v5.20.2/7e7a/lib/5.20.2
.