Bio-MLST-Check v2.1.1706216 Perl 5 v5.18.0 x86_64-linux-ld
- Status
- Fail
- From
- Andreas J. König (ANDK)
- Dist
-
Bio-MLST-Check v2.1.1706216
- Platform
- Perl 5 v5.18.0 x86_64-linux-ld
- Date
- 2017-12-02 20:39:45
- ID
- eecf9842-d7a0-11e7-84da-a8e0c4fe1824
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 5.18.0, 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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/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/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 7.30
#
# === Build Requires ===
#
# Module Want Have
# ------------------- ---- ----
# ExtUtils::MakeMaker any 7.30
#
# === Test Requires ===
#
# Module Want Have
# ------------------- ---- --------
# Env::Path any 0.19
# ExtUtils::MakeMaker any 7.30
# File::Slurp any 9999.19
# File::Spec any 3.62
# File::Touch any 0.11
# HTTP::Status any 6.13
# IO::Scalar any 2.111
# String::Util any 1.26
# Test::Exception any 0.43
# Test::MockModule any 0.13
# Test::More any 1.302118
# 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 3.62
# Data::Dumper any 2.161
# Exporter any 5.72
# File::Basename any 2.84
# File::Copy any 2.26
# File::Path 2.06 2.15
# File::Temp any 0.2304
# File::Which any 1.22
# Getopt::Long any 2.5
# HTTP::Request any 6.13
# LWP::Simple any 6.27
# LWP::UserAgent any 6.27
# List::Util any 1.49
# Moose any 2.2007
# Moose::Role any 2.2007
# Moose::Util::TypeConstraints any 2.2007
# POSIX any 1.32
# Parallel::ForkManager any 1.19
# Regexp::Common any 2017060201
# Text::CSV any 1.95
# Try::Tiny any 0.28
# XML::LibXML any 2.0129
# lib any 0.63
# strict any 1.07
# warnings any 1.18
#
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(0x5634820d3010)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x5634820d3010)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x5634820d3010)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x5634820d3010)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x5634820d3010)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x5634820d3010)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x5634820f7b90)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x5634820d3610)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x5634820d3610)') 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(0x5634820d2c50)', 'spreadsheet_genomic_rows', 'ARRAY(0x5634820d3640)', 'output_directory', '/tmp/loop_over_bdir-25695-NUVOoM/Bio-MLST-Check-2.1.1706216-0/4jtBIdmify', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x5634820d3610)') 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
Prototype mismatch: sub LWP::Simple::getstore ($$) vs none at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
t/Download/Database_fails.t ....... ok
Prototype mismatch: sub LWP::Simple::getstore ($$) vs none at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/Test/MockModule.pm line 154.
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(0x55964d272c58)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x55964d272c58)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55964d272c58)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55964d272c58)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55964d272c58)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55964d272c58)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55964b63de28)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x55964e16e1c8)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55964e16e1c8)') 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(0x55964e16e000)', 'spreadsheet_genomic_rows', 'ARRAY(0x55964e14ed30)', 'output_directory', '/tmp/loop_over_bdir-25695-NUVOoM/Bio-MLST-Check-2.1.1706216-0/sVjvVtnWJ2', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55964e16e1c8)') 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(0x55f1201637f8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x55f1201637f8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55f1201637f8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55f1201637f8)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55f1201637f8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55f1201637f8)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55f120163bd0)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x55f11d56de98)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55f11d56de98)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') 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(0x55f120164a80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x55f120164a80)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55f120164a80)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55f120164a80)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55f120164a80)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55f120164a80)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at reader Bio::MLST::ProcessFasta::_compare_alleles (defined at lib/Bio/MLST/ProcessFasta.pm line 25) line 7
Bio::MLST::ProcessFasta::_compare_alleles('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at reader Bio::MLST::ProcessFasta::_sequence_type_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 26) line 7
Bio::MLST::ProcessFasta::_sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at reader Bio::MLST::ProcessFasta::_spreadsheet_row_obj (defined at lib/Bio/MLST/ProcessFasta.pm line 27) line 7
Bio::MLST::ProcessFasta::_spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x55f120164e58)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x55f11f938320)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55f11f938320)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') 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(0x55f11f52ebd0)', 'spreadsheet_genomic_rows', 'ARRAY(0x55f11fd1dca8)', 'output_directory', '/tmp/loop_over_bdir-25695-NUVOoM/Bio-MLST-Check-2.1.1706216-0/Xac5wkLUu3', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55f11d56de98)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') 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(0x55f11ee5e0f8)', 'spreadsheet_genomic_rows', 'ARRAY(0x55f11f33db50)', 'output_directory', '/tmp/loop_over_bdir-25695-NUVOoM/Bio-MLST-Check-2.1.1706216-0/Xac5wkLUu3', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x55f11f938320)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x55f11f8c8dd8)') 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(0x55fcbac326d8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x55fcbac326d8)') 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(0x55acc5ec5c50)') called at reader Bio::MLST::CompareAlleles::_blast_db_location_obj (defined at lib/Bio/MLST/CompareAlleles.pm line 21) line 7
Bio::MLST::CompareAlleles::_blast_db_location_obj('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') called at reader Bio::MLST::CompareAlleles::_blast_db_location (defined at lib/Bio/MLST/CompareAlleles.pm line 22) line 7
Bio::MLST::CompareAlleles::_blast_db_location('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') called at reader Bio::MLST::CompareAlleles::matching_sequences (defined at lib/Bio/MLST/CompareAlleles.pm line 24) line 7
Bio::MLST::CompareAlleles::matching_sequences('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x55acc5ec5c50)') 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 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
Files=21, Tests=194, 37 wallclock secs ( 0.09 usr 0.10 sys + 8.06 cusr 1.47 csys = 9.72 CPU)
Result: FAIL
Failed 8/21 test programs. 4/194 subtests failed.
Makefile:1064: 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 1.007002
Bio::PrimarySeq 0 1.007002
Bio::SeqIO 0 0
Bio::SimpleAlign 0 0
Cwd 0 3.62
Data::Dumper 0 2.161
Exporter 0 5.72
File::Basename 0 2.84
File::Copy 0 2.26
File::Path 2.06 2.15
File::Temp 0 0.2304
File::Which 0 1.22
Getopt::Long 0 2.5
HTTP::Request 0 6.13
lib 0 0.63
List::Util 0 1.49
LWP::Simple 0 6.27
LWP::UserAgent 0 6.27
Moose 0 2.2007
Moose::Role 0 2.2007
Moose::Util::TypeConstraints 0 2.2007
Parallel::ForkManager 0 1.19
POSIX 0 1.32
Regexp::Common 0 2017060201
strict 0 1.07
Text::CSV 0 1.95
Try::Tiny 0 0.28
warnings 0 1.18
XML::LibXML 0 2.0129
build_requires:
Module Need Have
---------------------------- ---- ----------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.30
File::Slurp 0 9999.19
File::Spec 0 3.62
File::Touch 0 0.11
HTTP::Status 0 6.13
IO::Scalar 0 2.111
String::Util 0 1.26
Test::Exception 0 0.43
Test::MockModule 0 0.13
Test::More 0 1.302118
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------------- ---- ----------
ExtUtils::MakeMaker 0 7.30
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB = /tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/arch:/tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 25698
PERL5_CPAN_IS_RUNNING = 25698
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1821,25698
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.20
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280226
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.62
JSON 2.97000
JSON::PP 2.97000
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302118
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 18 subversion 0) configuration:
Derived from: a9acda3b5f74585852a57b51b724804ac586cb0b
Platform:
osname=linux, osvers=4.12.0-2-amd64, archname=x86_64-linux-ld
uname='linux k93msid 4.12.0-2-amd64 #1 smp debian 4.12.13-1 (2017-09-19) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c -Dmyhostname=k93msid -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dlibswanted=cl pthread socket inet nsl gdbm dbm malloc dl ld sun m crypt sec util c cposix posix ucb BSD gdbm_compat -Uuseithreads -Duselongdouble -DDEBUGGING=-g'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=define
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g',
cppflags='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='7.2.0', 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 /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.24.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.24'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND PERL_USE_DEVEL
USE_64_BIT_ALL USE_64_BIT_INT USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LONG_DOUBLE USE_PERLIO
USE_PERL_ATOF
Locally applied patches:
uncommitted-changes
Built under linux
Compiled at Oct 4 2017 06:24:09
%ENV:
PERL5LIB="/tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/arch:/tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="25698"
PERL5_CPAN_IS_RUNNING="25698"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1821,25698"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/arch
/tmp/loop_over_bdir-25695-NUVOoM/File-Touch-0.11-0/blib/lib
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0/x86_64-linux-ld
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/site_perl/5.18.0
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/5.18.0/x86_64-linux-ld
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.18.0/2d7c/lib/5.18.0
.