{"action":"created","issue":{"url":"https://api.github.com/repos/cancerit/cgpPindel/issues/46","repository_url":"https://api.github.com/repos/cancerit/cgpPindel","labels_url":"https://api.github.com/repos/cancerit/cgpPindel/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/cancerit/cgpPindel/issues/46/comments","events_url":"https://api.github.com/repos/cancerit/cgpPindel/issues/46/events","html_url":"https://github.com/cancerit/cgpPindel/issues/46","id":160372606,"number":46,"title":"Problem in compiling cgpPindel","user":{"login":"GKerdivel","id":19853994,"avatar_url":"https://avatars.githubusercontent.com/u/19853994?v=3","gravatar_id":"","url":"https://api.github.com/users/GKerdivel","html_url":"https://github.com/GKerdivel","followers_url":"https://api.github.com/users/GKerdivel/followers","following_url":"https://api.github.com/users/GKerdivel/following{/other_user}","gists_url":"https://api.github.com/users/GKerdivel/gists{/gist_id}","starred_url":"https://api.github.com/users/GKerdivel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GKerdivel/subscriptions","organizations_url":"https://api.github.com/users/GKerdivel/orgs","repos_url":"https://api.github.com/users/GKerdivel/repos","events_url":"https://api.github.com/users/GKerdivel/events{/privacy}","received_events_url":"https://api.github.com/users/GKerdivel/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2016-06-15T09:04:50Z","updated_at":"2016-06-16T12:25:55Z","closed_at":null,"body":"I am trying to install cgpPindel but it fails during installation\r\n\r\nHere is my error log: \r\n\r\n```\r\n...\r\n<== Installed dependencies for .. Finishing.\r\n done.\r\nInstalling cgpPindel ...Generating a Unix-style Makefile\r\nWriting Makefile for cgpPindel\r\nWriting MYMETA.yml and MYMETA.json\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/VcfConverter.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/InputGen.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/PindelPostProcessing/FilterRules.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/InputGen/Pair.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/InputGen/Read.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/Implement.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecordGenerator.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/InputGen/PairToPindel.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/PindelRecordParser.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/InputGen/SamHeader.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/PindelRecord.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/PindelPostProcessing/AbstractExe.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/PindelPostProcessing/VcfSoftFlagger.pm (unchanged)\r\nSkip blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecord.pm (unchanged)\r\ncp bin/pindel_merge_vcf_bam.pl blib/script/pindel_merge_vcf_bam.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel_merge_vcf_bam.pl\r\ncp bin/pindel_np_from_vcf.pl blib/script/pindel_np_from_vcf.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel_np_from_vcf.pl\r\ncp bin/pindel.pl blib/script/pindel.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel.pl\r\ncp bin/pindel_2_combined_vcf.pl blib/script/pindel_2_combined_vcf.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel_2_combined_vcf.pl\r\ncp bin/pindel_germ_bed.pl blib/script/pindel_germ_bed.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel_germ_bed.pl\r\ncp bin/FlagVcf.pl blib/script/FlagVcf.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/FlagVcf.pl\r\ncp bin/pindel_input_gen.pl blib/script/pindel_input_gen.pl\r\n/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pindel_input_gen.pl\r\nManifying blib/man1/FlagVcf.pl.1p\r\nManifying blib/man1/pindel.pl.1p\r\nManifying blib/man1/pindel_2_combined_vcf.pl.1p\r\nManifying blib/man1/pindel_germ_bed.pl.1p\r\nManifying blib/man1/pindel_input_gen.pl.1p\r\nManifying blib/man1/pindel_merge_vcf_bam.pl.1p\r\nManifying blib/man1/pindel_np_from_vcf.pl.1p\r\nManifying blib/man3/Sanger::CGP::Pindel::Implement.3pm\r\nManifying blib/man3/Sanger::CGP::Pindel::InputGen.3pm\r\nManifying blib/man3/Sanger::CGP::Pindel::InputGen::Pair.3pm\r\nManifying blib/man3/Sanger::CGP::Pindel::InputGen::SamHeader.3pm\r\nManifying blib/man3/Sanger::CGP::Pindel::OutputGen::CombinedRecordGenerator.3pm\r\nManifying blib/man3/Sanger::CGP::Pindel::OutputGen::PindelRecordParser.3pm\r\nManifying blib/man3/Sanger::CGP::PindelPostProcessing::VcfSoftFlagger.3pm\r\nPERL_DL_NONLAZY=1 /usr/bin/perl \"-MExtUtils::Command::MM\" \"-MTest::Harness\" \"-e\" \"undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')\" t/*.t\r\nt/1_pm_compile.t ...................... 1/? values on reference is experimental at /home/gwenneg/bin/cgpPindel-2.0.6/perl/blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecordGenerator.pm line 384.\r\nvalues on reference is experimental at /home/gwenneg/bin/cgpPindel-2.0.6/perl/blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecordGenerator.pm line 385.\r\nt/1_pm_compile.t ...................... ok    \r\nt/2_pl_compile.t ...................... 4/? \r\n#   Failed test 'Compilation check: /home/gwenneg/bin/cgpPindel-2.0.6/perl/t/../bin/pindel_germ_bed.pl'\r\n#   at t/2_pl_compile.t line 61.\r\n# Looks like you failed 1 test of 8.\r\nt/2_pl_compile.t ...................... Dubious, test returned 1 (wstat 256, 0x100)\r\nFailed 1/8 subtests \r\nt/inputGenRead.t ...................... ok   \r\nt/outputGenCombinedRecordGenerator.t .. 1/? values on reference is experimental at /home/gwenneg/bin/cgpPindel-2.0.6/perl/blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecordGenerator.pm line 384.\r\nvalues on reference is experimental at /home/gwenneg/bin/cgpPindel-2.0.6/perl/blib/lib/Sanger/CGP/Pindel/OutputGen/CombinedRecordGenerator.pm line 385.\r\nt/outputGenCombinedRecordGenerator.t .. ok   \r\nt/outputGenPindelRecordParser.t ....... ok   \r\nt/outputGenVcfConverter.t ............. ok   \r\nt/vcfPindelFlagger.t .................. ok    \r\n\r\nTest Summary Report\r\n-------------------\r\nt/2_pl_compile.t                    (Wstat: 256 Tests: 8 Failed: 1)\r\n  Failed test:  8\r\n  Non-zero exit status: 1\r\nFiles=7, Tests=83,  2 wallclock secs ( 0.04 usr  0.01 sys +  1.19 cusr  0.06 csys =  1.30 CPU)\r\nResult: FAIL\r\nFailed 1/7 test programs. 1/83 subtests failed.\r\nMakefile:966: recipe for target 'test_dynamic' failed\r\nmake: *** [test_dynamic] Error 255\r\n failed.  See setup.log file for error messages. cgpPindel install failed.\r\n    Please check INSTALL file for items that should be installed by a package manager\r\n\r\n```\r\n\r\nThanks for helping,\r\n\r\nRegards\r\n\r\nGwenneg Kerdivel"},"comment":{"url":"https://api.github.com/repos/cancerit/cgpPindel/issues/comments/226470168","html_url":"https://github.com/cancerit/cgpPindel/issues/46#issuecomment-226470168","issue_url":"https://api.github.com/repos/cancerit/cgpPindel/issues/46","id":226470168,"user":{"login":"GKerdivel","id":19853994,"avatar_url":"https://avatars.githubusercontent.com/u/19853994?v=3","gravatar_id":"","url":"https://api.github.com/users/GKerdivel","html_url":"https://github.com/GKerdivel","followers_url":"https://api.github.com/users/GKerdivel/followers","following_url":"https://api.github.com/users/GKerdivel/following{/other_user}","gists_url":"https://api.github.com/users/GKerdivel/gists{/gist_id}","starred_url":"https://api.github.com/users/GKerdivel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GKerdivel/subscriptions","organizations_url":"https://api.github.com/users/GKerdivel/orgs","repos_url":"https://api.github.com/users/GKerdivel/repos","events_url":"https://api.github.com/users/GKerdivel/events{/privacy}","received_events_url":"https://api.github.com/users/GKerdivel/received_events","type":"User","site_admin":false},"created_at":"2016-06-16T12:25:55Z","updated_at":"2016-06-16T12:25:55Z","body":"When I run\r\nperl -I /home/gwenneg/cgp/lib/perl5 -c bin/pindel_germ_bed.pl\r\nI obtain the following:\r\nkeys on reference is experimental at bin/pindel_germ_bed.pl line 74.\r\n\r\nThe file /home/gwenneg/cgp/lib/perl5/PCAP.pm exists"}}
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