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From: metabase:user:322078bc-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-MLST-Check-2.1.1706216 v5.14.0 Debian GNU/kFreeBSD
Date: 2017-03-05T22:21:10Z
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 AJPAGE,
This is a computer-generated error report created automatically by
CPANPLUS, version 0.9162. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
TEST RESULTS:
Below is the error stack from stage 'make test':
PERL_DL_NONLAZY=1 "/home/cpan/pit/thr/perl-5.14.0/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 7.24
#
# === 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 3.62
# 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 1.302075
# 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 2.130_02
# Exporter any 5.64_03
# File::Basename any 2.82
# File::Copy any 2.21
# File::Path 2.06 2.12
# File::Temp any 0.2304
# File::Which any 1.21
# Getopt::Long any 2.38
# HTTP::Request any 6.11
# LWP::Simple any 6.22
# LWP::UserAgent any 6.22
# List::Util any 1.47
# Moose any 2.2004
# Moose::Role any 2.2004
# Moose::Util::TypeConstraints any 2.2004
# POSIX any 1.24
# Parallel::ForkManager any 1.19
# Regexp::Common any 2016060801
# Text::CSV any 1.91
# Try::Tiny any 0.28
# XML::LibXML any 2.0128
# lib any 0.63
# strict any 1.04
# warnings any 1.12
#
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(0x2f323a8)') 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(0x2f323a8)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2f323a8)') 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(0x2f323a8)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2f323a8)') 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(0x2f323a8)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x2f87cc0)') 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(0x2f87cc0)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x2f87cc0)') 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(0x2f87cc0)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x2f87cc0)') 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(0x2f87cc0)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2f7b1d8)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2f7b1d8)') 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(0x2f7aa58)', 'spreadsheet_genomic_rows', 'ARRAY(0x2615b00)', 'output_directory', '/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/YrZ9IEYkDV', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2f7b1d8)') 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 ($$) vs none at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
t/Download/Database_fails.t ....... ok
Prototype mismatch: sub LWP::Simple::getstore ($$) vs none at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success ($) vs none at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::getstore: none vs ($$) at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib/Test/MockModule.pm line 135.
Prototype mismatch: sub LWP::Simple::is_success: none vs ($) at /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/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(0x1000040)') 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(0x1000040)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x1000040)') 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(0x1000040)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x1000040)') 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(0x1000040)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7b3b40)') 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(0x7b3b40)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7b3b40)') 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(0x7b3b40)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7b3b40)') 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(0x7b3b40)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x2e48780)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2e48780)') 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(0x2e35400)', 'spreadsheet_genomic_rows', 'ARRAY(0x2e48618)', 'output_directory', '/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/bluKaibX13', 'spreadsheet_basename', 'mlst_results') called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x2e48780)') 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(0x2ea2838)') 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(0x2ea2838)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2ea2838)') 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(0x2ea2838)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2ea2838)') 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(0x2ea2838)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7b1020)') 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(0x7b1020)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7b1020)') 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(0x7b1020)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7b1020)') 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(0x7b1020)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x20937a0)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x20937a0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') 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(0x2ea3950)') 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(0x2ea3950)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x2ea3950)') 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(0x2ea3950)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x2ea3950)') 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(0x2ea3950)') called at lib/Bio/MLST/ProcessFasta.pm line 52
Bio::MLST::ProcessFasta::_build__compare_alleles('Bio::MLST::ProcessFasta=HASH(0x7b2308)') 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(0x7b2308)') called at lib/Bio/MLST/ProcessFasta.pm line 67
Bio::MLST::ProcessFasta::_build__sequence_type_obj('Bio::MLST::ProcessFasta=HASH(0x7b2308)') 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(0x7b2308)') called at lib/Bio/MLST/ProcessFasta.pm line 78
Bio::MLST::ProcessFasta::_build__spreadsheet_row_obj('Bio::MLST::ProcessFasta=HASH(0x7b2308)') 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(0x7b2308)') called at lib/Bio/MLST/Check.pm line 83
Bio::MLST::Check::_generate_spreadsheet_rows('Bio::MLST::Check=HASH(0x25f2b10)') called at lib/Bio/MLST/Check.pm line 105
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x25f2b10)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') 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(0x2b89d50)', 'spreadsheet_genomic_rows', 'ARRAY(0x21d6780)', 'output_directory', '/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/IY2tF9_gJM', 'spreadsheet_basename', 0001) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x20937a0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') 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(0x2b18198)', 'spreadsheet_genomic_rows', 'ARRAY(0x26886d0)', 'output_directory', '/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/IY2tF9_gJM', 'spreadsheet_basename', 0002) called at lib/Bio/MLST/Check.pm line 108
Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x25f2b10)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 115
Bio::MLST::CheckMultipleSpecies::_run_mlst_for_species_list('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') called at lib/Bio/MLST/CheckMultipleSpecies.pm line 232
Bio::MLST::CheckMultipleSpecies::create_result_files('Bio::MLST::CheckMultipleSpecies=HASH(0x7a14c0)') 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(0x28b7250)') 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(0x28b7250)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x28b7250)') 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(0x28b7250)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x28b7250)') 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(0x28b7250)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x28b7250)') 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(0x7a1340)') 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(0x7a1340)') called at lib/Bio/MLST/CompareAlleles.pm line 36
Bio::MLST::CompareAlleles::_build__blast_db_location('Bio::MLST::CompareAlleles=HASH(0x7a1340)') 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(0x7a1340)') called at lib/Bio/MLST/CompareAlleles.pm line 115
Bio::MLST::CompareAlleles::_build_matching_sequences('Bio::MLST::CompareAlleles=HASH(0x7a1340)') 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(0x7a1340)') called at lib/Bio/MLST/CompareAlleles.pm line 61
Bio::MLST::CompareAlleles::found_sequence_names('Bio::MLST::CompareAlleles=HASH(0x7a1340)') 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, 20 wallclock secs ( 0.08 usr 0.08 sys + 5.25 cusr 10.05 csys = 15.47 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:
Here is a list of prerequisites you specified and versions we
managed to load:
Module Name Have Want
Bio::AlignIO 0 0
Bio::Perl 0 0
Bio::PrimarySeq 0 0
Bio::SeqIO 0 0
Bio::SimpleAlign 0 0
Cwd 3.62 0
Data::Dumper 2.130_02 0
Env::Path 0.19 0
Exporter 5.64_03 0
ExtUtils::MakeMaker 7.24 0
File::Basename 2.82 0
File::Copy 2.21 0
File::Path 2.12 2.06
File::Slurp 9999.19 0
File::Spec 3.62 0
File::Temp 0.2304 0
File::Touch 0.11 0
File::Which 1.21 0
Getopt::Long 2.38 0
HTTP::Request 6.11 0
HTTP::Status 6.11 0
IO::Scalar 2.111 0
LWP::Simple 6.22 0
LWP::UserAgent 6.22 0
List::Util 1.47 0
Moose 2.2004 0
Moose::Role 2.2004 0
Moose::Util::TypeConstraints 2.2004 0
POSIX 1.24 0
Parallel::ForkManager 1.19 0
Regexp::Common 2016060801 0
String::Util 1.26 0
Test::Exception 0.43 0
Test::MockModule 0.11 0
Test::More 1.302075 0
Test::Most 0.35 0
Text::CSV 1.91 0
Try::Tiny 0.28 0
XML::LibXML 2.0128 0
lib 0.63 0
strict 1.04 0
warnings 1.12 0
Perl module toolchain versions installed:
Module Name Have
CPANPLUS 0.9162
CPANPLUS::Dist::Build 0.80
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
Module::Build 0.4220
Pod::Parser 1.37
Pod::Simple 3.16
Test2 1.302075
Test::Harness 3.36
Test::More 1.302075
version 0.9917
******************************** NOTE ********************************
The comments above are created mechanically, possibly without manual
checking by the sender. As there are many people performing automatic
tests on each upload to CPAN, it is likely that you will receive
identical messages about the same problem.
If you believe that the message is mistaken, please reply to the first
one with correction and/or additional informations, and do not take
it personally. We appreciate your patience. :)
**********************************************************************
Additional comments:
This report was machine-generated by CPANPLUS::Dist::YACSmoke 0.98.
Powered by minismokebox version 0.58
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_GB.UTF-8
LANGUAGE = en_GB:en
NONINTERACTIVE_TESTING = 1
PATH = /home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/nUfl3eYwf7/Moose-2.2004/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/1VrliuRunK/Package-Stash-0.37/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/cHM4TZca4K/libwww-perl-6.22/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/i2WqKjKcNl/Env-Path-0.19/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/5vRE9K4qcW/BioPerl-1.007001/blib/script:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/_6vvzzFxfd/Data-Stag-0.14/blib/script:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB = 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.cpanplus/5.14.0/build/6ApaZo3USL/Sub-Exporter-Progressive-0.001013/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/6ApaZo3USL/Sub-Exporter-Progressive-0.001013/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/eioG0bVjia/Devel-GlobalDestruction-0.14/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/eioG0bVjia/Devel-GlobalDestruction-0.14/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/EdGTVUmk2c/MRO-Compat-0.12/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/EdGTVUmk2c/MRO-Compat-0.12/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/uLYNwAonPa/Sub-Identify-0.12/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/uLYNwAonPa/Sub-Identify-0.12/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/0aVrbFqHOU/Devel-OverloadInfo-0.004/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/0aVrbFqHOU/Devel-OverloadInfo-0.004/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/gZyNYEkuv5/Eval-Closure-0.14/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/gZyNYEkuv5/Eval-Closure-0.14/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/blph7qYnUS/Scalar-List-Utils-1.47/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/blph7qYnUS/Scalar-List-Utils-1.47/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/SBJgFA4SW_/Module-Runtime-Conflicts-0.003/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/SBJgFA4SW_/Module-Runtime-Conflicts-0.003/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/dZd7dHpr4w/Sub-Name-0.21/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/dZd7dHpr4w/Sub-Name-0.21/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/PDLZlKLk_S/Test-Warnings-0.026/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/PDLZlKLk_S/Test-Warnings-0.026/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/NADWuIVY95/Package-DeprecationManager-0.17/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/NADWuIVY95/Package-DeprecationManager-0.17/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/oawpluJ3DR/Sub-Exporter-0.987/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/oawpluJ3DR/Sub-Exporter-0.987/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/v2iELlJUyQ/File-pushd-1.014/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/v2iELlJUyQ/File-pushd-1.014/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/puUNefMn8a/Test-Needs-0.002005/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/puUNefMn8a/Test-Needs-0.002005/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/iUxFyw4zIj/Devel-Hide-0.0009/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/iUxFyw4zIj/Devel-Hide-0.0009/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/i5YmAkNiJR/Variable-Magic-0.61/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/i5YmAkNiJR/Variable-Magic-0.61/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/KneiTdPZuM/B-Hooks-EndOfScope-0.21/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/KneiTdPZuM/B-Hooks-EndOfScope-0.21/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/7qn7IXIFTk/namespace-clean-0.27/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/7qn7IXIFTk/namespace-clean-0.27/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/ntkV0ZLfoS/Test-CleanNamespaces-0.22/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/ntkV0ZLfoS/Test-CleanNamespaces-0.22/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/nUfl3eYwf7/Moose-2.2004/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/nUfl3eYwf7/Moose-2.2004/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/82uADMVm5Y/Parallel-ForkManager-1.19/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/82uADMVm5Y/Parallel-ForkManager-1.19/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/Ln1aUGD6Bf/Regexp-Common-2016060801/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/Ln1aUGD6Bf/Regexp-Common-2016060801/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/60pu75NJjg/Number-Misc-1.2/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/60pu75NJjg/Number-Misc-1.2/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/x5WFVfSMy0/Test-Toolbox-0.4/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/x5WFVfSMy0/Test-Toolbox-0.4/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/Vc_gfvLpt_/String-Util-1.26/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/Vc_gfvLpt_/String-Util-1.26/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/LBClIRKwWp/SUPER-1.20141117/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/LBClIRKwWp/SUPER-1.20141117/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/y41tg_qqJk/Test-MockModule-0.11/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/wdS66fKlcA/Text-CSV-1.91/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/wdS66fKlcA/Text-CSV-1.91/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/a5NKLfNo8u/XML-NamespaceSupport-1.11/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/a5NKLfNo8u/XML-NamespaceSupport-1.11/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/wom1buXAd_/XML-SAX-Base-1.08/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/wom1buXAd_/XML-SAX-Base-1.08/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l1ROfkMDS_/XML-SAX-0.99/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l1ROfkMDS_/XML-SAX-0.99/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/g7Q811d9fD/XML-LibXML-2.0128/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/g7Q811d9fD/XML-LibXML-2.0128/blib/arch:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/blib/lib:/home/cpan/pit/thr/conf/perl-5.14.0/.cpanplus/5.14.0/build/l2GumWHydq/Bio-MLST-Check-2.1.1706216/blib/arch
PERL5_CPANPLUS_IS_RUNNING = 83935
PERL5_CPANPLUS_IS_VERSION = 0.9162
PERL5_MINISMOKEBOX = 0.58
PERL5_YACSMOKE_BASE = /home/cpan/pit/thr/conf/perl-5.14.0
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /home/cpan/pit/thr/perl-5.14.0/bin/perl
UID: $< = 1001
EUID: $> = 1001
GID: $( = 1001 1001
EGID: $) = 1001 1001
-------------------------------
--
Summary of my perl5 (revision 5 version 14 subversion 0) configuration:
Platform:
osname=gnukfreebsd, osvers=10.1-0-amd64, archname=x86_64-gnukfreebsd-thread-multi
uname='gnukfreebsd kondor 10.1-0-amd64 #0 wed, 16 mar 2016 23:16:33 +0000 x86_64 amd64 qemu virtual cpu version 2.0.0 gnukfreebsd '
config_args='-des -Dprefix=/home/cpan/pit/thr/perl-5.14.0 -Dusethreads'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.9.2', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-kfreebsd-gnu /lib/../lib /usr/lib/x86_64-kfreebsd-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -lgdbm -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/usr/lib/x86_64-kfreebsd-gnu/libc.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.19'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fpic', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.42
Built under gnukfreebsd
Compiled at May 7 2016 03:38:00
%ENV:
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PERL5_CPANPLUS_IS_RUNNING="83935"
PERL5_CPANPLUS_IS_VERSION="0.9162"
PERL5_MINISMOKEBOX="0.58"
PERL5_YACSMOKE_BASE="/home/cpan/pit/thr/conf/perl-5.14.0"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
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