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From: metabase:user:30ae4450-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.14.3
Date: 2016-03-10T02:21:01Z
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_AssemblyImprovement-1.160490
on perl 5.14.3, created by CPAN-Reporter-1.2014.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from 'C:\strawberry5143\c\bin\dmake.exe test':
C:\strawberry5143\perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib\lib', 'blib\arch')" t/*.t t/Abacas/*.t t/AdapterRemoval/Trimmomatic/*.t t/Assemble/SGA/*.t t/Circlator/*.t t/DigitalNormalisation/Khmer/*.t t/FillGaps/*.t t/IvaQC/*.t t/Overall/*.t t/PrepareForSubmission/*.t t/PrimerRemoval/*.t t/Quiver/*.t t/Scaffold/*.t t/Util/*.t t/Validate/*.t
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\wypD_ZGz2r/contigs.fa_my_reference.fa.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/IO.pm:270
STACK: Bio::SeqIO::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:499
STACK: Bio::SeqIO::fasta::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio\SeqIO\fasta.pm:87
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:375
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:421
STACK: Bio::AssemblyImprovement::Abacas::DelimiterRole::_split_sequence_on_delimiter lib/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm:70
STACK: Bio::AssemblyImprovement::Abacas::Main::run lib/Bio/AssemblyImprovement/Abacas/Main.pm:73
STACK: Bio::AssemblyImprovement::Abacas::Iterative::_run_abacas lib/Bio/AssemblyImprovement/Abacas/Iterative.pm:74
STACK: Bio::AssemblyImprovement::Abacas::Iterative::run lib/Bio/AssemblyImprovement/Abacas/Iterative.pm:46
STACK: t/Abacas/Iterative.t:24
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
t/Abacas/Iterative.t ....................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\hvYDP10LuX/contigs.fa_my_reference.fa.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/IO.pm:270
STACK: Bio::SeqIO::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:499
STACK: Bio::SeqIO::fasta::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio\SeqIO\fasta.pm:87
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:375
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:421
STACK: Bio::AssemblyImprovement::Abacas::DelimiterRole::_split_sequence_on_delimiter lib/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm:70
STACK: Bio::AssemblyImprovement::Abacas::Main::run lib/Bio/AssemblyImprovement/Abacas/Main.pm:73
STACK: t/Abacas/Main.t:25
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
t/Abacas/Main.t .........................
Dubious, test returned 2 (wstat 512, 0x200)
All 4 subtests passed
"java" ¥ ï¥âáï ¢ãâ॥© ¨«¨ ¢¥è¥©
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Error running Trimmomatic with:
java -Xmx1000m -jar t/DummyTrimmomatic.jar PE -threads 1 t/data/trimmo_reads_1.fastq t/data/trimmo_reads_2.fastq trimmed.paired_1.fastq trimmed.unpaired_1.fastq trimmed.paired_2.fastq trimmed.unpaired_2.fastq ILLUMINACLIP:C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\t\data\trimmo_adapters.fasta:2:10:7:1 MINLEN:50 at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 45.
# Tests were run but no plan was declared and done_testing() was not seen.
t/AdapterRemoval/Trimmomatic/Main.t .....
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
_sga_preprocessed.fastq: No such file or directory at lib/Bio/AssemblyImprovement/Util/UnzipFileIfNeededRole.pm line 18.
# Tests were run but no plan was declared and done_testing() was not seen.
t/Assemble/SGA/IndexAndCorrectReads.t ...
Dubious, test returned 2 (wstat 512, 0x200)
All 1 subtests passed
C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\Qe6xWo3Mq2/_sga_preprocessed.fastq: No such file or directory at lib/Bio/AssemblyImprovement/Util/UnzipFileIfNeededRole.pm line 18.
cannot remove path when cwd is C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/Qe6xWo3Mq2 for C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\Qe6xWo3Mq2: at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
# Tests were run but no plan was declared and done_testing() was not seen.
t/Assemble/SGA/Main.t ...................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
# Failed test 'SGA preprocessed file exists in expected location'
# at t/Assemble/SGA/PreprocessReads.t line 52.
# Failed test 'SGA preprocessed file exists in expected location'
# at t/Assemble/SGA/PreprocessReads.t line 70.
# Looks like you failed 2 tests of 11.
t/Assemble/SGA/PreprocessReads.t ........
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/11 subtests
"C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_circlator_script" ¥ ï¥âáï ¢ãâ॥© ¨«¨ ¢¥è¥©
ª®¬ ¤®©, ¨á¯®«ï¥¬®© ¯à®£à ¬¬®© ¨«¨ ¯ ª¥âë¬ ä ©«®¬.
Failed to run circlator with C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_circlator_script all C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/contigs.fa C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/shuffled.fastq tmp_circularised at lib/Bio/AssemblyImprovement/Circlator/Main.pm line 49.
# Tests were run but no plan was declared and done_testing() was not seen.
t/Circlator/Main.t ......................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
gzip failed: input file 'C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/variable_length.fastq.keep' does not exist
# Tests were run but no plan was declared and done_testing() was not seen.
t/DigitalNormalisation/Khmer/Main.t .....
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\JwCccYH4lC\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\JwCccYH4lC: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\kQOR3YhyZG\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\kQOR3YhyZG: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\vRyJGWVVsZ\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\vRyJGWVVsZ: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
t/FillGaps/GapFillerConfig.t ............ ok
# Failed test 'gap filled file exists in expected location'
# at t/FillGaps/Iterative.t line 30.
# Failed test 'gap filled file exists in expected location'
# at t/FillGaps/Iterative.t line 47.
# Looks like you failed 2 tests of 12.
t/FillGaps/Iterative.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/12 subtests
"C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_iva_qc_script" ¥ ï¥âáï ¢ãâ॥© ¨«¨ ¢¥è¥©
ª®¬ ¤®©, ¨á¯®«ï¥¬®© ¯à®£à ¬¬®© ¨«¨ ¯ ª¥âë¬ ä ©«®¬.
Error running iva_qc with: C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_iva_qc_script -f C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/forward.fastq -r C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/reverse.fastq --ref_db C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/database C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/contigs.fa test_iva_qc
# Failed test 'test_iva_qc.stats.txt OK'
# at t/IvaQC/Main.t line 46.
# Failed test 'test_iva_qc.assembly_contigs_hit_ref.fasta OK'
# at t/IvaQC/Main.t line 46.
# Failed test 'test_iva_qc.assembly_vs_ref.coords OK'
# at t/IvaQC/Main.t line 46.
# Failed test 'test_iva_qc.assembly_v_ref.act.sh OK'
# at t/IvaQC/Main.t line 46.
# Failed test 'test_iva_qc.assembly_v_ref.blastn OK'
# at t/IvaQC/Main.t line 46.
# Looks like you failed 5 tests of 16.
t/IvaQC/Main.t ..........................
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/16 subtests
"grep" ¥ ï¥âáï ¢ãâ॥© ¨«¨ ¢¥è¥©
ª®¬ ¤®©, ¨á¯®«ï¥¬®© ¯à®£à ¬¬®© ¨«¨ ¯ ª¥âë¬ ä ©«®¬.
# No tests run!
t/Overall/CheckAllModulesCompile.t ...... skipped: (no reason given)
t/PrepareForSubmission/RenameContigs.t .. ok
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Looks like you failed 2 tests of 6.
t/PrimerRemoval/Main.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/6 subtests
No consensus.fasta file. Error running Quiver with:
C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_quiver_script.pl --threads 6 --memory 8 --no_bsub --reference C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/contigs.fa RS_Resequencing tmp_quiver C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/data/ at lib/Bio/AssemblyImprovement/Quiver/Main.pm line 57.
# Tests were run but no plan was declared and done_testing() was not seen.
t/Quiver/Main.t .........................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
# Failed test 'java in PATH'
# at t/requires_external.t line 8.
# Looks like you failed 1 test of 1.
t/requires_external.t ...................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests
t/Scaffold/Descaffold.t ................. ok
# Failed test 'Scaffolding file exists in expected location'
# at t/Scaffold/Iterative.t line 29.
# Failed test 'Scaffolding file exists in expected location'
# at t/Scaffold/Iterative.t line 44.
# Looks like you failed 2 tests of 12.
t/Scaffold/Iterative.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/12 subtests
t/Scaffold/PreprocessInputFiles.t ....... ok
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\zPPBKla9cV\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\zPPBKla9cV: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\4rCHZmF0Mg\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\4rCHZmF0Mg: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot unlink file for C:\DOCUME~1\c\LOCALS~1\Temp\OsDOEDJe53\_config_file: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\DOCUME~1\c\LOCALS~1\Temp\OsDOEDJe53: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
t/Scaffold/SSpaceConfig.t ............... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not write file 'C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/fasta_processor->output_filename_test.fa': Invalid argument
STACK: Error::throw
STACK: Bio::Root::Root::throw C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/Root/IO.pm:270
STACK: Bio::SeqIO::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:499
STACK: Bio::SeqIO::fasta::_initialize C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio\SeqIO\fasta.pm:87
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:375
STACK: Bio::SeqIO::new C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib/Bio/SeqIO.pm:421
STACK: Bio::AssemblyImprovement::Util::FastaTools::remove_small_contigs lib/Bio/AssemblyImprovement/Util/FastaTools.pm:30
STACK: t/Util/FastaTools.t:30
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
t/Util/FastaTools.t .....................
Dubious, test returned 22 (wstat 5632, 0x1600)
All 2 subtests passed
t/Util/FastqTools.t ..................... ok
# Failed test 'sort contigs'
# at t/Util/OrderContigsByLength.t line 30.
# Failed test at t/Util/OrderContigsByLength.t line 31.
# Could not open file C:\DOCUME~1\c\LOCALS~1\Temp\u8gCrP_K0d\contigs_needing_sorted.fa.sorted: No such file or directory
cannot unlink file for C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\qCfZYLhAWS\contigs_needing_sorted.temp.fa: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\qCfZYLhAWS: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
# Failed test 'sort contigs'
# at t/Util/OrderContigsByLength.t line 35.
# Failed test at t/Util/OrderContigsByLength.t line 36.
# Could not open file C:\DOCUME~1\c\LOCALS~1\Temp\u8gCrP_K0d\user_file_name.fa: No such file or directory
cannot unlink file for C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\W18V6rJQ71\contigs_needing_sorted.temp.fa: Permission denied at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
cannot remove directory for C:\strawberry5143\cpan\build\Bio_AssemblyImprovement-1.160490-qRcKOD\W18V6rJQ71: Directory not empty at C:/strawberry5143/perl/lib/File/Temp.pm line 2445.
# Looks like you failed 4 tests of 11.
t/Util/OrderContigsByLength.t ...........
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/11 subtests
C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_sspace_v2_script.pl does not exist. Using default: C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_sspace_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/does_not_exist.pl does not exist. Using default: C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
# Failed test at t/Validate/Executable.t line 39.
# got: 'C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_sspace_script.pl'
# expected: 'C:/strawberry5143/cpan/build/Bio_AssemblyImprovement-1.160490-qRcKOD/t/dummy_sspace_v2_script.pl'
# Looks like you failed 1 test of 4.
t/Validate/Executable.t .................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/4 subtests
Test Summary Report
-------------------
t/Abacas/Iterative.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Abacas/Main.t (Wstat: 512 Tests: 4 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/AdapterRemoval/Trimmomatic/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Assemble/SGA/IndexAndCorrectReads.t (Wstat: 512 Tests: 1 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Assemble/SGA/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Assemble/SGA/PreprocessReads.t (Wstat: 512 Tests: 11 Failed: 2)
Failed tests: 8, 11
Non-zero exit status: 2
t/Circlator/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/DigitalNormalisation/Khmer/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/FillGaps/Iterative.t (Wstat: 512 Tests: 12 Failed: 2)
Failed tests: 8, 12
Non-zero exit status: 2
t/IvaQC/Main.t (Wstat: 1280 Tests: 16 Failed: 5)
Failed tests: 3-7
Non-zero exit status: 5
t/Overall/CheckAllModulesCompile.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
t/PrimerRemoval/Main.t (Wstat: 512 Tests: 6 Failed: 2)
Failed tests: 5-6
Non-zero exit status: 2
t/Quiver/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/requires_external.t (Wstat: 256 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 1
t/Scaffold/Iterative.t (Wstat: 512 Tests: 12 Failed: 2)
Failed tests: 8, 12
Non-zero exit status: 2
t/Util/FastaTools.t (Wstat: 5632 Tests: 2 Failed: 0)
Non-zero exit status: 22
Parse errors: No plan found in TAP output
t/Util/OrderContigsByLength.t (Wstat: 1024 Tests: 11 Failed: 4)
Failed tests: 4-5, 8-9
Non-zero exit status: 4
t/Validate/Executable.t (Wstat: 256 Tests: 4 Failed: 1)
Failed test: 2
Non-zero exit status: 1
Files=24, Tests=163, 640 wallclock secs ( 0.06 usr + 0.12 sys = 0.18 CPU)
Result: FAIL
Failed 18/24 test programs. 19/163 subtests failed.
dmake.exe: Error code 129, while making 'test_dynamic'
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 0
Cwd 0 3.36
Env::Path 0 0.18
ExtUtils::MakeMaker 0 6.62
File::Basename 0 2.82
File::Copy 0 2.21
File::Path 2.07 2.08_01
File::Slurp 0 9999.19
File::Spec 0 3.33
File::Temp 0 0.22
File::Which 0 1.09
Getopt::Long 0 2.38
Getopt::Std 0 1.06
IO::Compress::Gzip 0 2.055
IO::Uncompress::Gunzip 0 2.055
lib 0 0.63
Moose 0 2.0604
Moose::Role 0 2.0604
POSIX 0 1.24
Statistics::Lite 0 3.62
strict 0 1.04
Switch 0 2.17
Test::File::Contents 0 0.20
Test::Most 0 0.31
warnings 0 1.12
build_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 6.62
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 6.62
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\WINDOWS\system32\cmd.exe
NUMBER_OF_PROCESSORS = 1
PATH = C:\IM\ImageMagick-6.8.2-Q16;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\strawberry5143\c\bin;C:\strawberry5143\perl\site\bin;C:\strawberry5143\perl\bin
PERL5LIB = C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/arch;C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib;C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/arch;C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/lib;C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/arch;C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 28320
PERL5_CPAN_IS_RUNNING = 28320
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1352,28320
PERL_CR_SMOKER_CURRENT = Bio_AssemblyImprovement-1.160490
PERL_CR_SMOKER_RUNONCE = 1
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PROCESSOR_IDENTIFIER = x86 Family 16 Model 5 Stepping 3, AuthenticAMD
TEMP = C:\DOCUME~1\c\LOCALS~1\Temp
TERM = dumb
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = C:\strawberry5143\perl\bin\perl.exe
$UID/$EUID = 0 / 0
$GID = 0
$EGID = 0
Win32::GetOSName = WinXP/.Net
Win32::GetOSVersion = Service Pack 3, 5, 1, 2600, 2, 3, 0, 256, 1
Win32::FsType = NTFS
Win32::IsAdminUser = 1
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.9800
CPAN::Meta 2.120921
Cwd 3.36
ExtUtils::CBuilder 0.280205
ExtUtils::Command 1.17
ExtUtils::Install 1.56
ExtUtils::MakeMaker 6.62
ExtUtils::Manifest 1.61
ExtUtils::ParseXS 3.15
File::Spec 3.33
JSON 2.53
JSON::PP 2.27200
Module::Build 0.4003
Module::Signature 0.68
Parse::CPAN::Meta 1.4404
Test::Harness 3.25
Test::More 0.98
YAML 0.84
YAML::Syck 1.22
version 0.9901
--
Summary of my perl5 (revision 5 version 14 subversion 3) configuration:
Platform:
osname=MSWin32, osvers=4.0, archname=MSWin32-x86-multi-thread
uname='Win32 strawberry-perl 5.14.3.1 #1 Wed Oct 17 22:51:55 2012 i386'
config_args='undef'
hint=recommended, useposix=true, d_sigaction=undef
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags =' -s -O2 -DWIN32 -DPERL_TEXTMODE_SCRIPTS -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -fno-strict-aliasing -mms-bitfields',
optimize='-s -O2',
cppflags='-DWIN32'
ccversion='', gccversion='4.6.3', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=undef, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='long long', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='g++', ldflags ='-s -L"C:\strawberry5143\perl\lib\CORE" -L"C:\strawberry5143\c\lib"'
libpth=C:\strawberry5143\c\lib C:\strawberry5143\c\i686-w64-mingw32\lib
libs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
perllibs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
libc=, so=dll, useshrplib=true, libperl=libperl514.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_win32.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-mdll -s -L"C:\strawberry5143\perl\lib\CORE" -L"C:\strawberry5143\c\lib"'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_IMPLICIT_SYS
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV PL_OP_SLAB_ALLOC
USE_ITHREADS USE_LARGE_FILES USE_PERLIO
USE_PERL_ATOF
Built under MSWin32
Compiled at Oct 17 2012 23:05:06
%ENV:
PERL5LIB="C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/arch;C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib;C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/arch;C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/lib;C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/arch;C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/lib"
PERL5_CPANPLUS_IS_RUNNING="28320"
PERL5_CPAN_IS_RUNNING="28320"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1352,28320"
PERL_CR_SMOKER_CURRENT="Bio_AssemblyImprovement-1.160490"
PERL_CR_SMOKER_RUNONCE="1"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/arch
C:\strawberry5143\cpan\build\BioPerl-1.6.924-rtJTD0/blib/lib
C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/arch
C:\strawberry5143\cpan\build\Switch-2.17-GlDZ60/blib/lib
C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/arch
C:\strawberry5143\cpan\build\Statistics-Lite-3.62-U3FobR/blib/lib
C:/strawberry5143/perl/site/lib
C:/strawberry5143/perl/vendor/lib
C:/strawberry5143/perl/lib
.