Bio-Roary v3.11.0 Perl 5 v5.22.3 cygwin-thread-multi
- Status
- Fail
- From
- David Solimano
- Dist
-
Bio-Roary v3.11.0
- Platform
- Perl 5 v5.22.3 cygwin-thread-multi
- Date
- 2017-10-21 08:40:23
- ID
- d01afcaa-f947-1014-9e73-37bb94f39f87
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-Roary-3.11.0
on perl 5.22.3, 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 'make test':
PERL_DL_NONLAZY=1 "/usr/bin/perl.exe" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/Roary/*.t t/Bio/Roary/CommandLine/*.t t/Bio/Roary/External/*.t t/Bio/Roary/Output/*.t t/Bio/Roary/QC/*.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
# ------------------- ---- --------
# Data::Dumper any 2.158
# Env::Path any 0.19
# ExtUtils::MakeMaker any 7.24
# File::Spec any 3.62
# Test::Files any 0.14
# Test::More any 1.302075
# Test::Most any 0.35
# Test::Output any 1.031
#
# === Test Recommends ===
#
# Module Want Have
# ---------- -------- --------
# CPAN::Meta 2.120900 2.150010
#
# === Runtime Requires ===
#
# Module Want Have
# ------------------- ---- -------
# Array::Utils any 0.5
# Bio::Perl any undef
# Bio::SeqIO any undef
# Bio::Tools::GFF any undef
# Bio::TreeIO any undef
# Cwd any 3.62
# Digest::MD5::File any 0.08
# Exception::Class any 1.42
# File::Basename any 2.85
# File::Copy any 2.30
# File::Find::Rule any 0.34
# File::Grep any 0.02
# File::Path any 2.12
# File::Slurper any 0.009
# File::Spec any 3.62
# File::Temp any 0.2304
# File::Which any 1.21
# FindBin any 1.51
# Getopt::Long any 2.49
# Graph any 0.9704
# Graph::Writer::Dot any 2.09
# List::Util any 1.47
# Log::Log4perl any 1.49
# Moose any 2.2004
# Moose::Role any 2.2004
# POSIX any 1.53_01
# PerlIO::utf8_strict any 0.006
# Text::CSV any 1.91
# strict any 1.09
# warnings any 1.34
#
t/00-report-prereqs.t ................................... ok
# Failed test 'blastp in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'makeblastdb in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mcl in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mcxdeblast in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'bedtools in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'prank in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'parallel in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mafft in PATH'
# at t/00_requires_external.t line 19.
# Looks like you failed 8 tests of 8.
t/00_requires_external.t ................................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
t/author-00-compile.t ................................... skipped: these tests are for testing by the author
t/author-pod-syntax.t ................................... skipped: these tests are for testing by the author
t/Bio/Roary/AccessoryBinaryFasta.t ...................... ok
Cant open file: _accessory_clusters.clstr# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 2.
t/Bio/Roary/AccessoryClustering.t .......................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
t/Bio/Roary/AnalyseGroups.t ............................. ok
t/Bio/Roary/AnnotateGroups.t ............................ ok
t/Bio/Roary/AssemblyStatistics.t ........................ ok
t/Bio/Roary/ChunkFastaFile.t ............................ ok
t/Bio/Roary/CombinedProteome.t .......................... ok
# Failed test 'Actual output file exists example_annotation.gff.proteome.faa -t 1 t/data/example_annotation.gff'
# at t/lib/TestHelper.pm line 139.
# Failed test 'Actual and expected output match for '-t 1 t/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 148.
# example_annotation.gff.proteome.faa absent
# Failed test 'Actual output file exists example_annotation.gff.proteome.faa t/data/example_annotation.gff'
# at t/lib/TestHelper.pm line 139.
# Failed test 'Actual and expected output match for 't/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 148.
# example_annotation.gff.proteome.faa absent
# Looks like you failed 4 tests of 7.
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ........
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/7 subtests
t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t .. ok
t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_1.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_2.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_3.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_1.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_2.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_3.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_1.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_2.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_3.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_1.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_2.gff.proteome.faa: No such file or directory
grep: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/jf4Hb2B_tK/query_3.gff.proteome.faa: No such file or directory
# Failed test 'Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.gff -t t/data/query_2.gff,t/data/query_3.gff''
# at t/lib/TestHelper.pm line 38.
# Structures begin differing at:
# $got->[1] = Does not exist
# $expected->[1] = ARRAY(0x603d122d0)
# Looks like you failed 1 test of 37.
t/Bio/Roary/CommandLine/QueryRoary.t ....................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/37 subtests
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/FM5qbC63VE/genbank1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/FM5qbC63VE/genbank2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/FM5qbC63VE/genbank3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff'
# at /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/t/lib/TestHelper.pm line 249.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 3.
t/Bio/Roary/CommandLine/Roary.t .........................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/3 subtests
t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ............ ok
t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ............. ok
t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ....... ok
t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t .... ok
t/Bio/Roary/ContigsToGeneIDsFromGFF.t ................... ok
t/Bio/Roary/EmblGroups.t ................................ ok
t/Bio/Roary/External/Blastp.t ........................... ok
t/Bio/Roary/External/Cdhit.t ............................ ok
# Failed test 'Check for parallel'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'parallel' in your $PATH
#
# doesn't match:
# (?^:Looking for 'parallel' - found )
# as expected
# Failed test 'Check for blastp'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'blastp' in your $PATH
#
# doesn't match:
# (?^:Looking for 'blastp' - found )
# as expected
# Failed test 'Check for makeblastdb'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'makeblastdb' in your $PATH
#
# doesn't match:
# (?^:Looking for 'makeblastdb' - found )
# as expected
# Failed test 'Check for mcl'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'mcl' in your $PATH
#
# doesn't match:
# (?^:Looking for 'mcl' - found )
# as expected
# Failed test 'Check for bedtools'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'bedtools' in your $PATH
#
# doesn't match:
# (?^:Looking for 'bedtools' - found )
# as expected
# Failed test 'Check for prank'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 Optional tool 'prank' not found in your $PATH
#
# doesn't match:
# (?^:Looking for 'prank' - found )
# as expected
# Failed test 'Check for mafft'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/10/21 04:33:26 ERROR: Can't find required 'mafft' in your $PATH
#
# doesn't match:
# (?^:Looking for 'mafft' - found )
# as expected
# Looks like you failed 7 tests of 13.
t/Bio/Roary/External/CheckTools.t .......................
Dubious, test returned 7 (wstat 1792, 0x700)
Failed 7/13 subtests
sh: mafft: command not found
# Failed test 'output for mafft matches'
# at t/Bio/Roary/External/Mafft.t line 39.
# +---+-----+---+-----------------------------------------------------------------------------+
# | |Got | |Expected |
# | Ln| | Ln| |
# +---+-----+---+-----------------------------------------------------------------------------+
# | | * 1|>1111#5_04506 *
# | | * 2|------------------------------------------------------------ *
# | | * 3|------------------------------------------------------------ *
# | | * 4|------------------------------------------------------------ *
# | | * 5|------------------------------------------------------------ *
# | | * 6|------------------------------------------------------------ *
# | | * 7|------------------------------------------------------------ *
# | | * 8|------------------------------------------------------------ *
# | | * 9|---------atggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 10|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 11|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 12|>1234_8#75_04759 *
# | | * 13|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 14|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 15|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 16|ctggattctttccggcgggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 17|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 18|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 19|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 20|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 21|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 22|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 23|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1_02853 *
# | | * 24|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 25|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 26|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 27|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 28|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 29|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 30|ttaatgttttcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 31|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 32|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 33|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 34|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_SL1344_v2_02736 *
# | | * 35|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 36|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 37|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 38|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 39|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 40|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 41|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 42|gatttacgtatggcaatcaccttacgggagctggatggcctgagctgtgaagagatagcg *
# | | * 43|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 44|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 45|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580_v1_02783 *
# | | * 46|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 47|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 48|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 49|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 50|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 51|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 52|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 53|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 54|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 55|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 56|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2_v1_02741 *
# | | * 57|atgagcgagcagttaacggac---gtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 58|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 59|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 60|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 61|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 62|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 63|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 64|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 65|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 66|attgataataaagttcaaccgcttatcaggcgttga *
# +---+-----+---+-----------------------------------------------------------------------------+
# Looks like you failed 1 test of 6.
t/Bio/Roary/External/Mafft.t ............................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/6 subtests
t/Bio/Roary/External/Makeblastdb.t ...................... ok
2017/10/21 04:34:02 Cannot find the mcxdeblast executable, please ensure its in your PATH
# Tests were run but no plan was declared and done_testing() was not seen.
t/Bio/Roary/External/Mcl.t ..............................
Dubious, test returned 254 (wstat 65024, 0xfe00)
All 5 subtests passed
# Failed test 'output file exists'
# at t/Bio/Roary/External/Prank.t line 33.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 't/data/prank_input.fa.aln': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::SortFasta::_input_seqio /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/blib/lib/Bio/Roary/SortFasta.pm:27
STACK: Bio::Roary::SortFasta::sort_fasta /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/blib/lib/Bio/Roary/SortFasta.pm:68
STACK: t/Bio/Roary/External/Prank.t:38
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 5.
t/Bio/Roary/External/Prank.t ............................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/5 subtests
t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t ........... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/z0Qi9iZxWx/example_annotation.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/z0Qi9iZxWx/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome 1 as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 30.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/z0Qi9iZxWx/example_annotation.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/TNeNjLFE85/example_annotation_no_fasta_line.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/TNeNjLFE85/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome 1 as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 44.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/TNeNjLFE85/example_annotation_2.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank1.gff.proteome.faa absent
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank2.gff.proteome.faa absent
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank3.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/LwW51kASUY/genbank3.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_1.gff.proteome.faa absent
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_2.gff.proteome.faa absent
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_3.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/EZ1Sq9_cZk/query_3.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 112.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_1.gff.proteome.faa absent
# Failed test 'content of proteome /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 112.
# /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/cn66WMKbmR/annotation_2.gff.proteome.faa absent
# Looks like you failed 10 tests of 20.
t/Bio/Roary/ExtractProteomeFromGFFs.t ...................
Dubious, test returned 10 (wstat 2560, 0xa00)
Failed 10/20 subtests
t/Bio/Roary/FilterFullClusters.t ........................ ok
t/Bio/Roary/GeneNamesFromGFF.t .......................... ok
t/Bio/Roary/GroupLabels.t ............................... ok
t/Bio/Roary/GroupStatistics.t ........................... ok
t/Bio/Roary/InflateClusters.t ........................... ok
t/Bio/Roary/OrderGenes.t ................................ ok
t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t ... ok
t/Bio/Roary/Output/DifferenceBetweenSets.t .............. ok
t/Bio/Roary/Output/GroupsMultifastaProtein.t ............ ok
t/Bio/Roary/Output/GroupsMultifastas.t .................. ok
Attribute (fasta_file) does not pass the type constraint because: Validation failed for 'Str' with value undef at reader Bio::Roary::Output::GroupsMultifastaNucleotide::fasta_file (defined at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 29) line 15
Bio::Roary::Output::GroupsMultifastaNucleotide::fasta_file('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x602185908)') called at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 43
Bio::Roary::Output::GroupsMultifastaNucleotide::_build__input_seqio('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x602185908)') called at reader Bio::Roary::Output::GroupsMultifastaNucleotide::_input_seqio (defined at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 30) line 8
Bio::Roary::Output::GroupsMultifastaNucleotide::_input_seqio('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x602185908)') called at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 53
Bio::Roary::Output::GroupsMultifastaNucleotide::populate_files('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x602185908)') called at lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm line 65
Bio::Roary::Output::GroupsMultifastasNucleotide::create_files('Bio::Roary::Output::GroupsMultifastasNucleotide=HASH(0x6021ae3d8)') called at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 40
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 127 just after 3.
t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ........
Dubious, test returned 127 (wstat 32512, 0x7f00)
All 3 subtests passed
t/Bio/Roary/Output/NumberOfGroups.t ..................... ok
t/Bio/Roary/Output/QueryGroups.t ........................ ok
t/Bio/Roary/ParallelAllAgainstAllBlast.t ................ ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/tVhMMmlTiN/example_annotation.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/tVhMMmlTiN/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /home/solimanod/.cpan/build/Bio-Roary-3.11.0-otGllp/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
t/Bio/Roary/PrepareInputFiles.t ......................... ok
t/Bio/Roary/PresenceAbsenceMatrix.t ..................... ok
t/Bio/Roary/QC/Report.t ................................. ok
2017/10/21 04:39:14 Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix, new GFF in the fixed_input_files directory: t/data/reformat_input_gffs/query_2.gff
2017/10/21 04:39:14 Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix, new GFF in the fixed_input_files directory: t/data/reformat_input_gffs/query_2.gff
t/Bio/Roary/ReformatInputGFFs.t ......................... ok
t/Bio/Roary/ReorderSpreadsheet.t ........................ ok
t/Bio/Roary/SampleOrder.t ............................... ok
t/Bio/Roary/SequenceLengths.t ........................... ok
t/Bio/Roary/SortFasta.t ................................. ok
t/Bio/Roary/SplitGroups.t ............................... ok
t/Bio/Roary/UniqueGenesPerSample.t ...................... ok
Test Summary Report
-------------------
t/00_requires_external.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/Bio/Roary/AccessoryClustering.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t (Wstat: 1024 Tests: 7 Failed: 4)
Failed tests: 4-7
Non-zero exit status: 4
t/Bio/Roary/CommandLine/QueryRoary.t (Wstat: 256 Tests: 37 Failed: 1)
Failed test: 27
Non-zero exit status: 1
t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 3 Failed: 1)
Failed test: 3
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/External/CheckTools.t (Wstat: 1792 Tests: 13 Failed: 7)
Failed tests: 3-9
Non-zero exit status: 7
t/Bio/Roary/External/Mafft.t (Wstat: 256 Tests: 6 Failed: 1)
Failed test: 6
Non-zero exit status: 1
t/Bio/Roary/External/Mcl.t (Wstat: 65024 Tests: 5 Failed: 0)
Non-zero exit status: 254
Parse errors: No plan found in TAP output
t/Bio/Roary/External/Prank.t (Wstat: 512 Tests: 5 Failed: 1)
Failed test: 5
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/ExtractProteomeFromGFFs.t (Wstat: 2560 Tests: 20 Failed: 10)
Failed tests: 4, 6, 9-11, 14-16, 19-20
Non-zero exit status: 10
t/Bio/Roary/Output/GroupsMultifastasNucleotide.t (Wstat: 32512 Tests: 3 Failed: 0)
Non-zero exit status: 127
Parse errors: No plan found in TAP output
Files=55, Tests=676, 717 wallclock secs ( 0.67 usr 0.86 sys + 143.70 cusr 483.92 csys = 629.15 CPU)
Result: FAIL
Failed 11/55 test programs. 33/676 subtests failed.
make: *** [Makefile:1398: test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------- -------- --------
Array::Utils 0 0.5
Bio::Perl 0 1.007002
Bio::SeqIO 0 0
Bio::Tools::GFF 0 1.007002
Bio::TreeIO 0 0
Cwd 0 3.62
Digest::MD5::File 0 0.08
Exception::Class 0 1.42
File::Basename 0 2.85
File::Copy 0 2.30
File::Find::Rule 0 0.34
File::Grep 0 0.02
File::Path 0 2.12
File::Slurper 0 0.009
File::Spec 0 3.62
File::Temp 0 0.2304
File::Which 0 1.21
FindBin 0 1.51
Getopt::Long 0 2.49
Graph 0 0.9704
Graph::Writer::Dot 0 2.09
List::Util 0 1.47
Log::Log4perl 0 1.49
Moose 0 2.2004
Moose::Role 0 2.2004
PerlIO::utf8_strict 0 0.006
POSIX 0 1.53_01
strict 0 1.09
Text::CSV 0 1.91
warnings 0 1.34
build_requires:
Module Need Have
------------------- -------- --------
Data::Dumper 0 2.158
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.24
File::Spec 0 3.62
Test::Files 0 0.14
Test::More 0 1.302075
Test::Most 0 0.35
Test::Output 0 1.031
configure_requires:
Module Need Have
------------------- -------- --------
ExtUtils::MakeMaker 0 7.24
opt_build_requires:
Module Need Have
------------------- -------- --------
CPAN::Meta 2.120900 2.150010
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\Windows\system32\cmd.exe
INCLUDE = C:\Program Files\IBM\WebSphere MQ\tools\c\include;C:\Program Files\IBM\WebSphere MQ\tools\cplus\include
LANG = en_US.UTF-8
LIB = C:\Program Files\IBM\WebSphere MQ\tools\lib64;C:\Program Files\IBM\WebSphere MQ\tools\lib
NUMBER_OF_PROCESSORS = 2
PATH = /usr/local/bin:/usr/bin:/cygdrive/c/ProgramData/Oracle/Java/javapath:/cygdrive/c/Program Files/IBM/WebSphere MQ/java/lib:/cygdrive/c/Program Files/IBM/WebSphere MQ/java/lib64:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/IBM/WebSphere MQ/bin64:/cygdrive/c/Program Files/IBM/WebSphere MQ/bin:/cygdrive/c/Program Files/IBM/WebSphere MQ/tools/c/samples/bin:/cygdrive/c/RV/BIN:/cygdrive/c/Strawberry/c/bin:/cygdrive/c/Strawberry/perl/site/bin:/cygdrive/c/Strawberry/perl/bin:/usr/lib/lapack
PERL5LIB = /home/solimanod/.cpan/build/Test-Files-0.14-ALth43/blib/arch:/home/solimanod/.cpan/build/Test-Files-0.14-ALth43/blib/lib:/home/solimanod/.cpan/build/Array-Utils-0.5-i9RQ40/blib/arch:/home/solimanod/.cpan/build/Array-Utils-0.5-i9RQ40/blib/lib:/home/solimanod/.cpan/build/File-Grep-0.02-anQwFZ/blib/arch:/home/solimanod/.cpan/build/File-Grep-0.02-anQwFZ/blib/lib:/home/solimanod/.cpan/build/Graph-ReadWrite-2.09-QXifnt/blib/arch:/home/solimanod/.cpan/build/Graph-ReadWrite-2.09-QXifnt/blib/lib:/home/solimanod/.cpan/build/Parse-Yapp-1.21-Vbm7PJ/blib/arch:/home/solimanod/.cpan/build/Parse-Yapp-1.21-Vbm7PJ/blib/lib:/home/solimanod/.cpan/build/PostScript-0.06-poEUJ8/blib/arch:/home/solimanod/.cpan/build/PostScript-0.06-poEUJ8/blib/lib:/home/solimanod/.cpan/build/Math-Random-0.72-nzTqCY/blib/arch:/home/solimanod/.cpan/build/Math-Random-0.72-nzTqCY/blib/lib:/home/solimanod/.cpan/build/PDF-API2-2.033-pQ9X7o/blib/arch:/home/solimanod/.cpan/build/PDF-API2-2.033-pQ9X7o/blib/lib:/home/solimanod/.cpan/build/Test-Memory-Cycle-1.06-C9Jgvg/blib/arch:/home/solimanod/.cpan/build/Test-Memory-Cycle-1.06-C9Jgvg/blib/lib:/home/solimanod/.cpan/build/Devel-Cycle-1.12-0icWFX/blib/arch:/home/solimanod/.cpan/build/Devel-Cycle-1.12-0icWFX/blib/lib:/home/solimanod/.cpan/build/XML-XML2JSON-0.06-pZEfLQ/blib/arch:/home/solimanod/.cpan/build/XML-XML2JSON-0.06-pZEfLQ/blib/lib:/home/solimanod/.cpan/build/YAML-Syck-1.30-Z1RyRF/blib/arch:/home/solimanod/.cpan/build/YAML-Syck-1.30-Z1RyRF/blib/lib:/home/solimanod/.cpan/build/Devel-Leak-0.03-TQoD_g/blib/arch:/home/solimanod/.cpan/build/Devel-Leak-0.03-TQoD_g/blib/lib:/home/solimanod/.cpan/build/Math-CDF-0.1-NLCSVj/blib/arch:/home/solimanod/.cpan/build/Math-CDF-0.1-NLCSVj/blib/lib:/home/solimanod/.cpan/build/SWF-Builder-0.16-4erzwB/blib/arch:/home/solimanod/.cpan/build/SWF-Builder-0.16-4erzwB/blib/lib:/home/solimanod/.cpan/build/SWF-File-0.42-mRDrBK/blib/arch:/home/solimanod/.cpan/build/SWF-File-0.42-mRDrBK/blib/lib:/home/solimanod/.cpan/build/Data-TemporaryBag-0.09-SDQjEO/blib/arch:/home/solimanod/.cpan/build/Data-TemporaryBag-0.09-SDQjEO/blib/lib:/home/solimanod/.cpan/build/Bio-Phylo-0.58-on85gC/blib/arch:/home/solimanod/.cpan/build/Bio-Phylo-0.58-on85gC/blib/lib:/home/solimanod/.cpan/build/SVG-Graph-0.02-1IynWw/blib/arch:/home/solimanod/.cpan/build/SVG-Graph-0.02-1IynWw/blib/lib:/home/solimanod/.cpan/build/Tree-DAG_Node-1.29-rBtgpK/blib/arch:/home/solimanod/.cpan/build/Tree-DAG_Node-1.29-rBtgpK/blib/lib:/home/solimanod/.cpan/build/Math-Spline-0.02-e9xKKJ/blib/arch:/home/solimanod/.cpan/build/Math-Spline-0.02-e9xKKJ/blib/lib:/home/solimanod/.cpan/build/Math-Derivative-1.01-X5Bp9m/blib/arch:/home/solimanod/.cpan/build/Math-Derivative-1.01-X5Bp9m/blib/lib:/home/solimanod/.cpan/build/Math-Utils-1.11-Q4XqO6/blib/arch:/home/solimanod/.cpan/build/Math-Utils-1.11-Q4XqO6/blib/lib:/home/solimanod/.cpan/build/Statistics-Descriptive-3.0612-f0Z5UT/blib/arch:/home/solimanod/.cpan/build/Statistics-Descriptive-3.0612-f0Z5UT/blib/lib:/home/solimanod/.cpan/build/Convert-Binary-C-0.78-v8Uh1M/blib/arch:/home/solimanod/.cpan/build/Convert-Binary-C-0.78-v8Uh1M/blib/lib:/home/solimanod/.cpan/build/SVG-2.78-X4Ynrr/blib/arch:/home/solimanod/.cpan/build/SVG-2.78-X4Ynrr/blib/lib:/home/solimanod/.cpan/build/XML-DOM-XPath-0.14-aQCHMx/blib/arch:/home/solimanod/.cpan/build/XML-DOM-XPath-0.14-aQCHMx/blib/lib:/home/solimanod/.cpan/build/XML-XPathEngine-0.14-Ha5GJ4/blib/arch:/home/solimanod/.cpan/build/XML-XPathEngine-0.14-Ha5GJ4/blib/lib:/home/solimanod/.cpan/build/XML-SAX-Writer-0.57-JPhjKA/blib/arch:/home/solimanod/.cpan/build/XML-SAX-Writer-0.57-JPhjKA/blib/lib:/home/solimanod/.cpan/build/XML-Filter-BufferText-1.01-0lzfNy/blib/arch:/home/solimanod/.cpan/build/XML-Filter-BufferText-1.01-0lzfNy/blib/lib:/home/solimanod/.cpan/build/Array-Compare-v3.0.0-U2lb0U/blib/arch:/home/solimanod/.cpan/build/Array-Compare-v3.0.0-U2lb0U/blib/lib:/home/solimanod/.cpan/build/Hash-FieldHash-0.15-yPZzaB/blib/arch:/home/solimanod/.cpan/build/Hash-FieldHash-0.15-yPZzaB/blib/lib:/home/solimanod/.cpan/build/Type-Tie-0.009-nZjK0q/blib/arch:/home/solimanod/.cpan/build/Type-Tie-0.009-nZjK0q/blib/lib:/home/solimanod/.cpan/build/Ref-Util-XS-0.116-rYj3NI/blib/arch:/home/solimanod/.cpan/build/Ref-Util-XS-0.116-rYj3NI/blib/lib:/home/solimanod/.cpan/build/Type-Tiny-XS-0.012-T6ygyZ/blib/arch:/home/solimanod/.cpan/build/Type-Tiny-XS-0.012-T6ygyZ/blib/lib:/home/solimanod/.cpan/build/Regexp-Util-0.003-mfPJPY/blib/arch:/home/solimanod/.cpan/build/Regexp-Util-0.003-mfPJPY/blib/lib:/home/solimanod/.cpan/build/Type-Tiny-1.002001-JeJOcs/blib/arch:/home/solimanod/.cpan/build/Type-Tiny-1.002001-JeJOcs/blib/lib:/home/solimanod/.cpan/build/Spreadsheet-ParseExcel-0.65-7HetYT/blib/arch:/home/solimanod/.cpan/build/Spreadsheet-ParseExcel-0.65-7HetYT/blib/lib:/home/solimanod/.cpan/build/Digest-Perl-MD5-1.9-lOgMnQ/blib/arch:/home/solimanod/.cpan/build/Digest-Perl-MD5-1.9-lOgMnQ/blib/lib:/home/solimanod/.cpan/build/Crypt-RC4-2.02-zWiXJG/blib/arch:/home/solimanod/.cpan/build/Crypt-RC4-2.02-zWiXJG/blib/lib:/home/solimanod/.cpan/build/OLE-Storage_Lite-0.19-AGuzIL/blib/arch:/home/solimanod/.cpan/build/OLE-Storage_Lite-0.19-AGuzIL/blib/lib:/home/solimanod/.cpan/build/Inline-C-0.78-Z008nC/blib/arch:/home/solimanod/.cpan/build/Inline-C-0.78-Z008nC/blib/lib:/home/solimanod/.cpan/build/Pegex-0.64-6ERUgh/blib/arch:/home/solimanod/.cpan/build/Pegex-0.64-6ERUgh/blib/lib:/home/solimanod/.cpan/build/XML-Twig-3.52-J7llyN/blib/arch:/home/solimanod/.cpan/build/XML-Twig-3.52-J7llyN/blib/lib:/home/solimanod/.cpan/build/Graph-0.9704-P6iyyJ/blib/arch:/home/solimanod/.cpan/build/Graph-0.9704-P6iyyJ/blib/lib:/home/solimanod/.cpan/build/Sort-Naturally-1.03-zqVGTO/blib/arch:/home/solimanod/.cpan/build/Sort-Naturally-1.03-zqVGTO/blib/lib:/home/solimanod/.cpan/build/Algorithm-Munkres-0.08-AW86KP/blib/arch:/home/solimanod/.cpan/build/Algorithm-Munkres-0.08-AW86KP/blib/lib:/home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/arch:/home/solimanod/.cpan/build/BioPerl-1.007002-9652aP/blib/lib:/home/solimanod/.cpan/build/Data-Stag-0.14-MebJmi/blib/arch:/home/solimanod/.cpan/build/Data-Stag-0.14-MebJmi/blib/lib:/home/solimanod/.cpan/build/Test-Most-0.35-sEeo0e/blib/arch:/home/solimanod/.cpan/build/Test-Most-0.35-sEeo0e/blib/lib:/home/solimanod/.cpan/build/Digest-MD5-File-0.08-SKnHEs/blib/arch:/home/solimanod/.cpan/build/Digest-MD5-File-0.08-SKnHEs/blib/lib:/home/solimanod/.cpan/build/Test-Output-1.031-pBlIGu/blib/arch:/home/solimanod/.cpan/build/Test-Output-1.031-pBlIGu/blib/lib:/home/solimanod/.cpan/build/Env-Path-0.19-_LNv1K/blib/arch:/home/solimanod/.cpan/build/Env-Path-0.19-_LNv1K/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 11592
PERL5_CPAN_IS_RUNNING = 11592
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 8780,11592
PERL_CR_SMOKER_CURRENT = Bio-Roary-3.11.0
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PROCESSOR_IDENTIFIER = Intel64 Family 6 Model 37 Stepping 1, GenuineIntel
SHELL = /bin/bash
TEMP = /tmp
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 1222856 / 1222856
$GID = 1049089 1049089 197609 545 14 4 11 15 4095 66048 1394915 1395145 1231332 1391115 1389702 1110237 1391333 1389528 1389547 1395231 1389592 1230946 1390011 1320982 1389527 1391107 1395210 1291971 1389747 1291952 1321739 1391014 1110272 1100291 1389439 1222766 1222819 1222732 1114690 1231058 1275974 1292197 1222743 1222741 1389953 1233131 1052870 1050371 1049701 1049741 1049748 1049779 1049783 1058315 1051691 1049994 1050059 1052837 1235940 1054462 1291964 1291449 1388773 1291954 1291893 1276307 1292037 1158631 1292385 1291940 1054217 1389585 1292046 1231333 1222696 1291966 1291957 1063805 1289842 1388864 1388423 1291953 1276165 1049735 1053718 1058356 1236080 1236107 401408
$EGID = 1049089 1049089 197609 545 14 4 11 15 4095 66048 1394915 1395145 1231332 1391115 1389702 1110237 1391333 1389528 1389547 1395231 1389592 1230946 1390011 1320982 1389527 1391107 1395210 1291971 1389747 1291952 1321739 1391014 1110272 1100291 1389439 1222766 1222819 1222732 1114690 1231058 1275974 1292197 1222743 1222741 1389953 1233131 1052870 1050371 1049701 1049741 1049748 1049779 1049783 1058315 1051691 1049994 1050059 1052837 1235940 1054462 1291964 1291449 1388773 1291954 1291893 1276307 1292037 1158631 1292385 1291940 1054217 1389585 1292046 1231333 1222696 1291966 1291957 1063805 1289842 1388864 1388423 1291953 1276165 1049735 1053718 1058356 1236080 1236107 401408
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.11_01
CPAN::Meta 2.150010
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
JSON 2.90
JSON::PP 2.27400
Module::Build 0.4222
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302075
YAML 1.23
YAML::Syck 1.30
version 0.9917
--
Summary of my perl5 (revision 5 version 22 subversion 3) configuration:
Platform:
osname=cygwin, osvers=2.6.1(0.30553), archname=cygwin-thread-multi
uname='cygwin_nt-6.3 cygwin 2.6.1(0.30553) 2016-12-16 11:55 x86_64 cygwin '
config_args='-des -Dprefix=/usr -Dmksymlinks -Darchname=x86_64-cygwin-threads -Dlibperl=cygperl5_22.dll -Dcc=gcc -Dld=g++ -Accflags=-ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/build=/usr/src/debug/perl-5.22.3-1 -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/src/perl-5.22.3=/usr/src/debug/perl-5.22.3-1 -fwrapv'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags ='-DPERL_USE_SAFE_PUTENV -D_GNU_SOURCE -U__STRICT_ANSI__ -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/build=/usr/src/debug/perl-5.22.3-1 -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/src/perl-5.22.3=/usr/src/debug/perl-5.22.3-1 -fwrapv -fno-strict-aliasing -fstack-protector-strong -D_FORTIFY_SOURCE=2',
optimize='-O3',
cppflags='-DPERL_USE_SAFE_PUTENV -D_GNU_SOURCE -U__STRICT_ANSI__ -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/build=/usr/src/debug/perl-5.22.3-1 -fdebug-prefix-map=/mnt/share/maint/perl.x86_64/src/perl-5.22.3=/usr/src/debug/perl-5.22.3-1 -fwrapv -fno-strict-aliasing -fstack-protector-strong'
ccversion='', gccversion='5.4.0', 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='g++', ldflags =' -Wl,--enable-auto-import -Wl,--export-all-symbols -Wl,--enable-auto-image-base -fstack-protector-strong'
libpth=/usr/lib
libs=-lpthread -lgdbm -ldb -ldl -lcrypt -lgdbm_compat
perllibs=-lpthread -ldl -lcrypt
libc=/usr/lib/libcygwin.a, so=dll, useshrplib=true, libperl=cygperl5_22.dll
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' --shared -Wl,--enable-auto-import -Wl,--export-all-symbols -Wl,--enable-auto-image-base -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_NEW_COPY_ON_WRITE
PERL_PRESERVE_IVUV PERL_USE_SAFE_PUTENV
USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS
USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME
USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
Built under cygwin
Compiled at Jan 15 2017 13:11:06
%ENV:
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PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="11592"
PERL5_CPAN_IS_RUNNING="11592"
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PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
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