134 lines
7 KiB
Text
134 lines
7 KiB
Text
perl-blead
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==========
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cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
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Work directory is /home/ryan/.cpanm/work/1493027855.8662
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You have make /usr/bin/make
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You have LWP 6.26
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You have /bin/tar: tar (GNU tar) 1.29
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Copyright (C) 2015 Free Software Foundation, Inc.
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License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
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This is free software: you are free to change and redistribute it.
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There is NO WARRANTY, to the extent permitted by law.
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Written by John Gilmore and Jay Fenlason.
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You have /usr/bin/unzip
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Searching NGS::Tools::BAMSurgeon () on cpanmetadb ...
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Unpacking NGS-Tools-BAMSurgeon-v1.0.0.tar.gz
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--> Working on NGS::Tools::BAMSurgeon
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Fetching http://www.cpan.org/authors/id/B/BO/BOUTROSLB/NGS-Tools-BAMSurgeon-v1.0.0.tar.gz ... OK
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NGS-Tools-BAMSurgeon-v1.0.0
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NGS-Tools-BAMSurgeon-v1.0.0/Build.PL
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NGS-Tools-BAMSurgeon-v1.0.0/META.yml
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NGS-Tools-BAMSurgeon-v1.0.0/MANIFEST
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NGS-Tools-BAMSurgeon-v1.0.0/META.json
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NGS-Tools-BAMSurgeon-v1.0.0/lib
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon.pm
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon/Helper.pm
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon/Somatic.pm
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon/Merge.pm
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NGS-Tools-BAMSurgeon-v1.0.0/lib/NGS/Tools/BAMSurgeon/Germline.pm
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NGS-Tools-BAMSurgeon-v1.0.0/bin
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NGS-Tools-BAMSurgeon-v1.0.0/bin/get_coverage.R
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NGS-Tools-BAMSurgeon-v1.0.0/bin/make_yaml_het.pl
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NGS-Tools-BAMSurgeon-v1.0.0/bin/bamsurgeon
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NGS-Tools-BAMSurgeon-v1.0.0/bin/generate_signature.pl
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NGS-Tools-BAMSurgeon-v1.0.0/bin/germline.pl
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NGS-Tools-BAMSurgeon-v1.0.0/share
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NGS-Tools-BAMSurgeon-v1.0.0/share/imputed_byref.csv
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NGS-Tools-BAMSurgeon-v1.0.0/share/config.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/replicationtime_mutationrate.csv
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NGS-Tools-BAMSurgeon-v1.0.0/share/germ_mut.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/somatic.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/signatures.txt
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NGS-Tools-BAMSurgeon-v1.0.0/share/cancer_sig_vary.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/template.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/cancer_mut_vary.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/share/cancer_sigmut.yaml
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NGS-Tools-BAMSurgeon-v1.0.0/t
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NGS-Tools-BAMSurgeon-v1.0.0/t/00-bamsurgeon.t
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Entering NGS-Tools-BAMSurgeon-v1.0.0
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Checking configure dependencies from META.json
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Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
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Checking if you have Module::Build 0.38 ... Yes (0.4222)
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Running Build.PL
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Configuring NGS-Tools-BAMSurgeon-v1.0.0 ... Created MYMETA.yml and MYMETA.json
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Creating new 'Build' script for 'NGS-Tools-BAMSurgeon' version 'v1.0.0'
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Checking dependencies from MYMETA.json ...
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Checking if you have Moose 0 ... Yes (2.2004)
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Checking if you have Cwd 0 ... Yes (3.62)
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Checking if you have Test::More 0 ... Yes (1.302078)
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Checking if you have File::Path 0 ... Yes (2.12)
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Checking if you have File::ShareDir 1.00 ... Yes (1.102)
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Checking if you have YAML 0 ... Yes (1.23)
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Checking if you have Pod::Usage 0 ... Yes (1.69)
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Checking if you have FindBin 0 ... Yes (1.51)
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Checking if you have List::MoreUtils 0 ... Yes (0.418)
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Checking if you have Params::Validate 0 ... Yes (1.26)
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Checking if you have HPCI 0 ... Yes (0.50)
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Checking if you have Data::Dumper 0 ... Yes (2.161)
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Checking if you have File::Copy 0 ... Yes (2.32)
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Checking if you have List::Util 0 ... Yes (1.47)
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Checking if you have Moose::Util 0 ... Yes (2.2004)
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Checking if you have File::Basename 0 ... Yes (2.85)
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Checking if you have Moose::Role 0 ... Yes (2.2004)
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OK
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Building and testing NGS-Tools-BAMSurgeon-v1.0.0 ... Building NGS-Tools-BAMSurgeon
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# Failed test 'use NGS::Tools::BAMSurgeon;'
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# at t/00-bamsurgeon.t line 17.
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# Tried to use 'NGS::Tools::BAMSurgeon'.
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# Error: You can only consume roles, BLSupport::Logging::Role is not a Moose role at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux/Moose/Exporter.pm line 419
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# Moose::with('BLSupport::Logging::Role') called at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 146
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# require NGS/Tools/BAMSurgeon.pm at t/00-bamsurgeon.t line 17
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# main::BEGIN at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 0
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# eval {...} at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 0
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# eval 'package main;
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# BEGIN { ${^WARNING_BITS} = $args[-1] if defined $args[-1] }
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# #line 17 t/00-bamsurgeon.t
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# use NGS::Tools::BAMSurgeon @{$args[0]};
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# 1;
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# ' at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Test/More.pm line 1031
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# Test::More::_eval('package main;^JBEGIN { ${^WARNING_BITS} = $args[-1] if defined $args[-1] }^J#line 17 t/00-bamsurgeon.t^Juse NGS::Tools::BAMSurgeon @{$args[0]};^J1;^J', 'ARRAY(0x55799ddd5e98)', 'UUUUUUUUUUUUUUUUU^A') called at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Test/More.pm line 1007
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# Test::More::use_ok('NGS::Tools::BAMSurgeon') called at t/00-bamsurgeon.t line 17
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# main::BEGIN at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 0
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# eval {...} at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 0
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# Compilation failed in require at t/00-bamsurgeon.t line 17.
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# BEGIN failed--compilation aborted at t/00-bamsurgeon.t line 17.
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Can't locate object method "_set_config_path" via package "NGS::Tools::BAMSurgeon" at /home/ryan/.cpanm/work/1493027855.8662/NGS-Tools-BAMSurgeon-v1.0.0/blib/lib/NGS/Tools/BAMSurgeon.pm line 380.
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# Tests were run but no plan was declared and done_testing() was not seen.
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# Looks like your test exited with 255 just after 1.
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t/00-bamsurgeon.t ..
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Dubious, test returned 255 (wstat 65280, 0xff00)
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Failed 1/1 subtests
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Test Summary Report
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-------------------
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t/00-bamsurgeon.t (Wstat: 65280 Tests: 1 Failed: 1)
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Failed test: 1
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Non-zero exit status: 255
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Parse errors: No plan found in TAP output
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Files=1, Tests=1, 1 wallclock secs ( 0.01 usr 0.00 sys + 0.18 cusr 0.00 csys = 0.19 CPU)
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Result: FAIL
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Failed 1/1 test programs. 1/1 subtests failed.
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! Installing NGS::Tools::BAMSurgeon failed. See /home/ryan/.cpanm/work/1493027855.8662/build.log for details. Retry with --force to force install it.
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FAIL
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Command [cpanm --reinstall --verbose NGS::Tools::BAMSurgeon] terminated with exit code 1 ($? = 256) under the following perl environment:
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Command terminated with non-zero status.
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Current perl:
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Name: perl-blead
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Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
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Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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Compiled at: Mar 30 2017 03:10:09
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perlbrew:
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version: 0.78
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ENV:
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PERLBREW_ROOT: /home/ryan/perl5/perlbrew
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PERLBREW_HOME: /home/ryan/.perlbrew
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PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
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