Back
From: metabase:user:30ae4450-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-MLST-Check-2.1.1706216 v5.25.8
Date: 2017-03-04T10:20:56Z
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-2.1.1706216
on perl 5.25.8, created by CPAN-Reporter-1.2018.
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 'C:\STRAWB~1\c\bin\dmake.exe test':
"C:\Strawberry258\perl\bin\perl.exe" "-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/SequenceTypes/*.t t/Settings/*.t t/Validate/*.t
#
# Versions for all modules listed in MYMETA.json (including optional ones):
#
# === Configure Requires ===
#
# Module Want Have
# ------------------- ---- ----
# ExtUtils::MakeMaker any 7.24
#
# === Build Requires ===
#
# Module Want Have
# ------------------- ---- ----
# ExtUtils::MakeMaker any 7.24
#
# === Test Requires ===
#
# Module Want Have
# ------------------- ---- --------
# Env::Path any 0.19
# ExtUtils::MakeMaker any 7.24
# File::Slurp any 9999.19
# File::Spec any 3.66
# File::Touch any 0.11
# HTTP::Status any 6.11
# IO::Scalar any 2.111
# String::Util any 1.26
# Test::Exception any 0.43
# Test::MockModule any 0.11
# Test::More any 1.302073
# Test::Most any 0.35
#
# === Test Recommends ===
#
# Module Want Have
# ---------- -------- --------
# CPAN::Meta 2.120900 2.150010
#
# === Runtime Requires ===
#
# Module Want Have
# ---------------------------- ---- ----------
# Bio::AlignIO any undef
# Bio::Perl any undef
# Bio::PrimarySeq any undef
# Bio::SeqIO any undef
# Bio::SimpleAlign any undef
# Cwd any 3.66
# Data::Dumper any 2.166
# Exporter any 5.72
# File::Basename any 2.85
# File::Copy any 2.32
# File::Path 2.06 2.12_01
# File::Temp any 0.2304
# File::Which any 1.21
# Getopt::Long any 2.49
# HTTP::Request any 6.11
# LWP::Simple any 6.15
# LWP::UserAgent any 6.15
# List::Util any 1.47
# Moose any 2.1807
# Moose::Role any 2.1807
# Moose::Util::TypeConstraints any 2.1807
# POSIX any 1.76
# Parallel::ForkManager any 1.19
# Regexp::Common any 2016060801
# Text::CSV any 1.33
# Try::Tiny any 0.27
# XML::LibXML any 2.0128
# lib any 0.63
# strict any 1.11
# warnings any 1.37
#
t/00-report-prereqs.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 52
Bio::MLST::Blast::Database::new('Bio::MLST::Blast::Database', 'fasta_file', 't/data/contigs.fa') called at t\Blast\BlastN.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 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 13
# 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(0x360666c)') 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(0x360666c)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x360666c)') 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(0x360666c)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x360666c)') 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(0x360666c)') called at lib\Bio\MLST\ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x36068bc)') 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(0x36068bc)') called at lib\Bio\MLST\ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x36068bc)') 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(0x36068bc)') called at lib\Bio\MLST\ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x36068bc)') 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(0x36068bc)') called at lib\Bio\MLST\Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x3099174)') called at lib\Bio\MLST\Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x3099174)') called at t\CDC\Convert.t line 50
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 44) line 39
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x267d3dc)', 'spreadsheet_genomic_rows', 'ARRAY(0x267d74c)', 'output_directory', 'C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\9j13GJGR9i', 'spreadsheet_basename', 'mlst_results') called at lib\Bio\MLST\Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x267d44c)') called at t\CDC\Convert.t line 50
cannot unlink file for C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\qO6dJ2EAlC\Streptococcus_pyogenes_emmST\profiles\Streptococcus_pyogenes_emmST.txt: Permission denied at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
cannot remove directory for C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\qO6dJ2EAlC\Streptococcus_pyogenes_emmST\profiles: Directory not empty at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
cannot remove directory for C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\qO6dJ2EAlC\Streptococcus_pyogenes_emmST: Directory not empty at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
cannot remove directory for C:/STRAWB~1/cpan/build/Bio-MLST-Check-2.1.1706216-0/qO6dJ2EAlC: Directory not empty at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 12.
t/CDC/Convert.t ...................
Dubious, test returned 255 (wstat 65280, 0xff00)
All 12 subtests passed
t/Download/Database.t ............. ok
Prototype mismatch: sub LWP::Simple::getstore ($$) vs none at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
t/Download/Database_fails.t ....... ok
Prototype mismatch: sub LWP::Simple::getstore ($$) vs none at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at C:/Strawberry258/perl/vendor/lib/Test/MockModule.pm line 135.
t/Download/Database_succeeds.t .... ok
t/Download/Databases.t ............ ok
t/FilterAlleles.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(0x34a0944)') 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(0x34a0944)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x34a0944)') 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(0x34a0944)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x34a0944)') 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(0x34a0944)') called at lib\Bio\MLST\ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x26b7464)') 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(0x26b7464)') called at lib\Bio\MLST\ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x26b7464)') 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(0x26b7464)') called at lib\Bio\MLST\ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x26b7464)') 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(0x26b7464)') called at lib\Bio\MLST\Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2e1fd2c)') called at lib\Bio\MLST\Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2e1fd2c)') called at t\Output\MultipleFastas.t line 32
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 44) line 39
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x99c10c)', 'spreadsheet_genomic_rows', 'ARRAY(0x99bf9c)', 'output_directory', 'C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\nv9vdO3Bx5', 'spreadsheet_basename', 'mlst_results') called at lib\Bio\MLST\Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x99bedc)') called at t\Output\MultipleFastas.t line 32
# 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(0x46f6924)') 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(0x46f6924)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x46f6924)') 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(0x46f6924)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x46f6924)') 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(0x46f6924)') called at lib\Bio\MLST\ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x47420a4)') 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(0x47420a4)') called at lib\Bio\MLST\ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x47420a4)') 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(0x47420a4)') called at lib\Bio\MLST\ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x47420a4)') 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(0x47420a4)') called at lib\Bio\MLST\Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x5626fdc)') called at lib\Bio\MLST\Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x5626fdc)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x5626abc)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x5626abc)') 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(0x5970d24)') 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(0x5970d24)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x5970d24)') 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(0x5970d24)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x5970d24)') 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(0x5970d24)') called at lib\Bio\MLST\ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x46dab8c)') 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(0x46dab8c)') called at lib\Bio\MLST\ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x46dab8c)') 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(0x46dab8c)') called at lib\Bio\MLST\ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x46dab8c)') 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(0x46dab8c)') called at lib\Bio\MLST\Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x419a3cc)') called at lib\Bio\MLST\Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x419a3cc)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x4199ebc)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x4199ebc)') 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 44) line 39
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x34d7274)', 'spreadsheet_genomic_rows', 'ARRAY(0x34d7294)', 'output_directory', 'C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\NN6uULVkNu', 'spreadsheet_basename', 0001) called at lib\Bio\MLST\Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x34d7164)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x2854a84)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x2854a84)') 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 44) line 39
Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x4588484)', 'spreadsheet_genomic_rows', 'ARRAY(0x45884a4)', 'output_directory', 'C:\STRAWB~1\cpan\build\Bio-MLST-Check-2.1.1706216-0\NN6uULVkNu', 'spreadsheet_basename', 0002) called at lib\Bio\MLST\Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x4588374)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x3562394)') called at lib\Bio\MLST\CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x3562394)') 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 74.
#
# 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 74.
#
# Structures begin differing at:
# $got->[0] = '"E.coli" "matched 1 of 1 files"'
# $expected->[0] = '"No matches found"
'
#
cannot unlink file for C:\DOCUME~1\a\LOCALS~1\Temp\DDAO77Lp0s\multi_mlst_results.genomic.csv: Permission denied at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
cannot remove directory for C:/DOCUME~1/a/LOCALS~1/Temp/DDAO77Lp0s: Directory not empty at C:/Strawberry258/perl/lib/File/Temp.pm line 1616.
# 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(0x3f8eec)') 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(0x3f8eec)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x3f8eec)') 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(0x3f8eec)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x3f8eec)') 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(0x3f8eec)') called at lib\Bio\MLST\CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x3f8eec)') called at t\Output\SpreadsheetRow.t line 22
# 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
# 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(0x99be1c)') 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(0x99be1c)') called at lib\Bio\MLST\CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x99be1c)') 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(0x99be1c)') called at lib\Bio\MLST\CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x99be1c)') 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(0x99be1c)') called at lib\Bio\MLST\CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x99be1c)') called at t\SequenceTypes\CompareAlleles.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 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
Could not find executable 'C:/STRAWB~1/cpan/build/Bio-MLST-Check-2.1.1706216-0/t/data/fake_executables/executable.sh', attempting to use defaults
Could not find any usable default executables in ''
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 7.
t/Validate/Executable.t ...........
Dubious, test returned 2 (wstat 512, 0x200)
All 7 subtests passed
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: 12 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
t/Validate/Executable.t (Wstat: 512 Tests: 7 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
Files=21, Tests=181, 46 wallclock secs ( 0.10 usr + 0.22 sys = 0.32 CPU)
Result: FAIL
Failed 9/21 test programs. 4/181 subtests failed.
dmake.exe: Error code 130, while making 'test_dynamic'
------------------------------
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 3.66
Data::Dumper 0 2.166
Exporter 0 5.72
File::Basename 0 2.85
File::Copy 0 2.32
File::Path 2.06 2.12_01
File::Temp 0 0.2304
File::Which 0 1.21
Getopt::Long 0 2.49
HTTP::Request 0 6.11
lib 0 0.63
List::Util 0 1.47
LWP::Simple 0 6.15
LWP::UserAgent 0 6.15
Moose 0 2.1807
Moose::Role 0 2.1807
Moose::Util::TypeConstraints 0 2.1807
Parallel::ForkManager 0 1.19
POSIX 0 1.76
Regexp::Common 0 2016060801
strict 0 1.11
Text::CSV 0 1.33
Try::Tiny 0 0.27
warnings 0 1.37
XML::LibXML 0 2.0128
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.24
File::Slurp 0 9999.19
File::Spec 0 3.66
File::Touch 0 0.11
HTTP::Status 0 6.11
IO::Scalar 0 2.111
String::Util 0 1.26
Test::Exception 0 0.43
Test::MockModule 0 0.11
Test::More 0 1.302073
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.24
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\WINDOWS\system32\cmd.exe
NUMBER_OF_PROCESSORS = 1
PATH = C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Git\cmd;C:\Strawberry258\c\bin;C:\Strawberry258\perl\site\bin;C:\Strawberry258\perl\bin
PERL5LIB = C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/arch;C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/lib;C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/arch;C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/lib;C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/arch;C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 3780
PERL5_CPAN_IS_RUNNING = 3780
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1612,3780
PERL_CR_SMOKER_CURRENT = Bio-MLST-Check-2.1.1706216
PERL_CR_SMOKER_RUNONCE = 1
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_HASH_SEED = 0x11111111
PERL_MM_USE_DEFAULT = 1
PROCESSOR_IDENTIFIER = x86 Family 16 Model 5 Stepping 3, AuthenticAMD
TEMP = C:\DOCUME~1\a\LOCALS~1\Temp
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = C:\Strawberry258\perl\bin\perl.exe
$UID/$EUID = 0 / 0
$GID = 0
$EGID = 0
Win32::GetOSName = WinXP/.Net
Win32::GetOSVersion = Service Pack 3, 5, 1, 2600, 2, 3, 0, 256, 1
Win32::FsType = NTFS
Win32::IsAdminUser = 1
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.14_01
CPAN::Meta 2.150010
Cwd 3.66
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.33
File::Spec 3.66
JSON 2.90
JSON::PP 2.27400_02
Module::Build 0.4220
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.36_01
Test::More 1.302073
YAML 1.21
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 25 subversion 8) configuration:
Platform:
osname=MSWin32
osvers=4.0
archname=MSWin32-x86-multi-thread
uname='Win32 strawberry-perl 5.25.8.1-beta1 #1 Thu Dec 29 20:16:24 2016 i386'
config_args='undef'
hint=recommended
useposix=true
d_sigaction=undef
useithreads=define
usemultiplicity=define
use64bitint=undef
use64bitall=undef
uselongdouble=undef
usemymalloc=n
bincompat5005=undef
Compiler:
cc='gcc'
ccflags =' -s -O2 -DWIN32 -DPERL_TEXTMODE_SCRIPTS -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -fwrapv -fno-strict-aliasing -mms-bitfields'
optimize='-s -O2'
cppflags='-DWIN32'
ccversion=''
gccversion='4.9.2'
gccosandvers=''
intsize=4
longsize=4
ptrsize=4
doublesize=8
byteorder=1234
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=12
longdblkind=3
ivtype='long'
ivsize=4
nvtype='double'
nvsize=8
Off_t='long long'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='g++'
ldflags ='-s -L"C:\STRAWB~1\perl\lib\CORE" -L"C:\STRAWB~1\c\lib"'
libpth=C:\STRAWB~1\c\lib C:\STRAWB~1\c\i686-w64-mingw32\lib C:\STRAWB~1\c\lib\gcc\i686-w64-mingw32\4.9.2
libs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
perllibs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
libc=
so=dll
useshrplib=true
libperl=libperl525.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_win32.xs
dlext=xs.dll
d_dlsymun=undef
ccdlflags=' '
cccdlflags=' '
lddlflags='-mdll -s -L"C:\STRAWB~1\perl\lib\CORE" -L"C:\STRAWB~1\c\lib"'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
HAVE_INTERP_INTERN
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT
PERL_IMPLICIT_SYS
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
Built under MSWin32
Compiled at Dec 29 2016 20:25:17
%ENV:
PERL5LIB="C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/arch;C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/lib;C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/arch;C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/lib;C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/arch;C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/lib"
PERL5_CPANPLUS_IS_RUNNING="3780"
PERL5_CPAN_IS_RUNNING="3780"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1612,3780"
PERL_CR_SMOKER_CURRENT="Bio-MLST-Check-2.1.1706216"
PERL_CR_SMOKER_RUNONCE="1"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_HASH_SEED="0x11111111"
PERL_MM_USE_DEFAULT="1"
@INC:
C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/arch
C:\STRAWB~1\cpan\build\String-Util-1.26-0/blib/lib
C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/arch
C:\STRAWB~1\cpan\build\Test-Toolbox-0.4-0/blib/lib
C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/arch
C:\STRAWB~1\cpan\build\Number-Misc-1.2-0/blib/lib
C:/Strawberry258/perl/site/lib
C:/Strawberry258/perl/vendor/lib
C:/Strawberry258/perl/lib
.