Bio-MLST-Check v2.1.1706216 Perl 5 v5.38.2 amd64-freebsd
- Status
- Fail
- From
- Slaven Rezić
- Dist
-
Bio-MLST-Check v2.1.1706216
- Platform
- Perl 5 v5.38.2 amd64-freebsd
- Date
- 2023-12-25 11:22:22
- ID
- df41087c-a317-11ee-91f6-bc396e8775ea
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 5.38.2, created by CPAN-Reporter-1.2019.
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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/usr/perl5.38.2/bin/perl5.38.2" "-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 7.70
#
# === Build Requires ===
#
# Module Want Have
# ------------------- ---- ----
# ExtUtils::MakeMaker any 7.70
#
# === Test Requires ===
#
# Module Want Have
# ------------------- ---- --------
# Env::Path any 0.19
# ExtUtils::MakeMaker any 7.70
# File::Slurp any 9999.32
# File::Spec any 3.88
# File::Touch any 0.12
# HTTP::Status any 6.45
# IO::Scalar any 2.113
# String::Util any 1.34
# Test::Exception any 0.43
# Test::MockModule any 0.177.0
# Test::More any 1.302198
# Test::Most any 0.38
#
# === Test Recommends ===
#
# Module Want Have
# ---------- -------- --------
# CPAN::Meta 2.120900 2.150010
#
# === Runtime Requires ===
#
# Module Want Have
# ---------------------------- ---- ----------
# Bio::AlignIO any 1.7.8
# Bio::Perl any 1.7.4
# Bio::PrimarySeq any 1.7.8
# Bio::SeqIO any 1.7.8
# Bio::SimpleAlign any 1.7.8
# Cwd any 3.89
# Data::Dumper any 2.188
# Exporter any 5.77
# File::Basename any 2.86
# File::Copy any 2.41
# File::Path 2.06 2.18
# File::Temp any 0.2311
# File::Which any 1.27
# Getopt::Long any 2.57
# HTTP::Request any 6.45
# LWP::Simple any 6.72
# LWP::UserAgent any 6.72
# List::Util any 1.63
# Moose any 2.2206
# Moose::Role any 2.2206
# Moose::Util::TypeConstraints any 2.2206
# POSIX any 2.13
# Parallel::ForkManager any 2.02
# Regexp::Common any 2017060201
# Text::CSV any 2.04
# Try::Tiny any 0.31
# XML::LibXML any 2.0209
# lib any 0.65
# strict any 1.12
# warnings any 1.65
#
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(0xcc26da23a80)') 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(0xcc26da23a80)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0xcc26da23a80)') 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(0xcc26da23a80)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0xcc26da23a80)') 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(0xcc26da23a80)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0xcc26db0c4c8)') 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(0xcc26db0c4c8)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0xcc26db0c4c8)') 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(0xcc26db0c4c8)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0xcc26db0c4c8)') 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(0xcc26db0c4c8)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0xcc26d5db5a0)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xcc26d5db5a0)') 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(0xcc26db08168)', 'spreadsheet_genomic_rows', 'ARRAY(0xcc26c9232d0)', 'output_directory', '/home/cpansand/.cpan/build/2023122511/Bio-MLST-Check-2.1.1706216-0/iQzrQi59sX', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0xcc26d5db5a0)') called at t/CDC/Convert.t line 50
# 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
t/Download/Database_fails.t ....... ok
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(0x2bc94bb3d690)') 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(0x2bc94bb3d690)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2bc94bb3d690)') 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(0x2bc94bb3d690)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2bc94bb3d690)') 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(0x2bc94bb3d690)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x2bc94bb3d4b0)') 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(0x2bc94bb3d4b0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x2bc94bb3d4b0)') 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(0x2bc94bb3d4b0)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x2bc94bb3d4b0)') 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(0x2bc94bb3d4b0)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2bc94ba9c918)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2bc94ba9c918)') 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(0x2bc94b87dd20)', 'spreadsheet_genomic_rows', 'ARRAY(0x2bc94b882240)', 'output_directory', '/home/cpansand/.cpan/build/2023122511/Bio-MLST-Check-2.1.1706216-0/Zhg5m2uOxT', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2bc94ba9c918)') 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(0x2a529f9e27e0)') 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(0x2a529f9e27e0)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2a529f9e27e0)') 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(0x2a529f9e27e0)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2a529f9e27e0)') 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(0x2a529f9e27e0)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x2a529f964de0)') 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(0x2a529f964de0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x2a529f964de0)') 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(0x2a529f964de0)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x2a529f964de0)') 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(0x2a529f964de0)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2a529f9e2258)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2a529f9e2258)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') 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(0x2a529f033270)') 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(0x2a529f033270)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2a529f033270)') 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(0x2a529f033270)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2a529f033270)') 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(0x2a529f033270)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x2a529f964df8)') 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(0x2a529f964df8)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x2a529f964df8)') 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(0x2a529f964df8)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x2a529f964df8)') 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(0x2a529f964df8)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2a529f9e2318)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2a529f9e2318)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') 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(0x2a529dbbed20)', 'spreadsheet_genomic_rows', 'ARRAY(0x2a529dbbec78)', 'output_directory', '/home/cpansand/.cpan/build/2023122511/Bio-MLST-Check-2.1.1706216-0/OHjUkn3w8a', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2a529f9e2258)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') 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(0x2a529dbbeca8)', 'spreadsheet_genomic_rows', 'ARRAY(0x2a529dbbecf0)', 'output_directory', '/home/cpansand/.cpan/build/2023122511/Bio-MLST-Check-2.1.1706216-0/OHjUkn3w8a', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2a529f9e2318)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x2a529ec1d930)') 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"
'
#
# 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(0x17be2a0298e8)') 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(0x17be2a0298e8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x17be2a0298e8)') 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(0x17be2a0298e8)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x17be2a0298e8)') 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(0x17be2a0298e8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x17be2a0298e8)') 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(0x2839b057e450)') 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(0x2839b057e450)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2839b057e450)') 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(0x2839b057e450)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2839b057e450)') 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(0x2839b057e450)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x2839b057e450)') 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
t/Validate/Executable.t ........... ok
Test Summary Report
-------------------
t/Blast/BlastN.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Blast/Database.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/CDC/Convert.t (Wstat: 65280 (exited 255) Tests: 12 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Output/MultipleFastas.t (Wstat: 65280 (exited 255) Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Output/MultipleSpecies.t (Wstat: 512 (exited 2) Tests: 13 Failed: 2)
Failed tests: 6, 9
Non-zero exit status: 2
t/Output/SpreadsheetRow.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/requires_external.t (Wstat: 512 (exited 2) Tests: 2 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 2
t/SequenceTypes/CompareAlleles.t (Wstat: 65280 (exited 255) Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=21, Tests=194, 16 wallclock secs ( 0.09 usr 0.02 sys + 7.23 cusr 1.19 csys = 8.54 CPU)
Result: FAIL
Failed 8/21 test programs. 4/194 subtests failed.
*** Error code 255
Stop.
make: stopped in /home/cpansand/.cpan/build/2023122511/Bio-MLST-Check-2.1.1706216-0
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- ----------
Bio::AlignIO 0 1.7.8
Bio::Perl 0 1.7.4
Bio::PrimarySeq 0 1.7.8
Bio::SeqIO 0 1.7.8
Bio::SimpleAlign 0 1.7.8
Cwd 0 3.89
Data::Dumper 0 2.188
Exporter 0 5.77
File::Basename 0 2.86
File::Copy 0 2.41
File::Path 2.06 2.18
File::Temp 0 0.2311
File::Which 0 1.27
Getopt::Long 0 2.57
HTTP::Request 0 6.45
lib 0 0.65
List::Util 0 1.63
LWP::Simple 0 6.72
LWP::UserAgent 0 6.72
Moose 0 2.2206
Moose::Role 0 2.2206
Moose::Util::TypeConstraints 0 2.2206
Parallel::ForkManager 0 2.02
POSIX 0 2.13
Regexp::Common 0 2017060201
strict 0 1.12
Text::CSV 0 2.04
Try::Tiny 0 0.31
warnings 0 1.65
XML::LibXML 0 2.0209
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.70
File::Slurp 0 9999.32
File::Spec 0 3.88
File::Touch 0 0.12
HTTP::Status 0 6.45
IO::Scalar 0 2.113
String::Util 0 1.34
Test::Exception 0 0.43
Test::MockModule 0 0.177.0
Test::More 0 1.302198
Test::Most 0 0.38
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.70
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/freebsd14.0:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 95106
PERL5_CPAN_IS_RUNNING = 95106
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 76269,95106
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2023122510/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/local/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2023122510
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/perl5.38.2/bin/perl5.38.2
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.36
CPAN::Meta 2.150010
Cwd 3.89
ExtUtils::CBuilder 0.280238
ExtUtils::Command 7.70
ExtUtils::Install 2.22
ExtUtils::MakeMaker 7.70
ExtUtils::Manifest 1.75
ExtUtils::ParseXS 3.51
File::Spec 3.88
JSON 4.10
JSON::PP 4.16
Module::Build 0.4234
Module::Signature 0.88
Parse::CPAN::Meta 2.150010
Test2 1.302198
Test::Harness 3.48
Test::More 1.302198
YAML 1.30
YAML::Syck 1.34
version 0.9930
--
Summary of my perl5 (revision 5 version 38 subversion 2) configuration:
Platform:
osname=freebsd
osvers=14.0-stable
archname=amd64-freebsd
uname='freebsd cloud11.bbbike.org 14.0-stable freebsd 14.0-stable #0 stable14-8d42f85d9: wed dec 13 14:10:27 utc 2023 root@cloud11.bbbike.org:usrobjhomeprojectsfreebsd-srcamd64.amd64sysgeneric amd64 '
config_args='-ds -e -Dprefix=/usr/perl5.38.2 -Dcf_email=srezic@cpan.org -Doptimize=-O2 -pipe'
hint=recommended
useposix=true
d_sigaction=define
useithreads=undef
usemultiplicity=undef
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
Compiler:
cc='cc'
ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
optimize='-O2 -pipe'
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='FreeBSD Clang 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)'
gccosandvers=''
intsize=4
longsize=8
ptrsize=8
doublesize=8
byteorder=12345678
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=16
longdblkind=3
ivtype='long'
ivsize=8
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='cc'
ldflags ='-Wl,-E -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib /usr/lib/clang/16/lib
libs=-lpthread -lgdbm -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -ldl -lm -lcrypt -lutil -lc
libc=
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags=' '
cccdlflags='-DPIC -fPIC'
lddlflags='-shared -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_LONG_DOUBLE
HAS_STRTOLD
HAS_TIMES
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_SIPHASH13
PERL_HASH_USE_SBOX32
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_SAFE_PUTENV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
Built under freebsd
Compiled at Dec 13 2023 17:28:52
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="95106"
PERL5_CPAN_IS_RUNNING="95106"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="76269,95106"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2023122510/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/usr/perl5.38.2/lib/site_perl/5.38.2/amd64-freebsd
/usr/perl5.38.2/lib/site_perl/5.38.2
/usr/perl5.38.2/lib/5.38.2/amd64-freebsd
/usr/perl5.38.2/lib/5.38.2
.