{"action":"opened","issue":{"url":"https://api.github.com/repos/itmat/rum/issues/184","labels_url":"https://api.github.com/repos/itmat/rum/issues/184/labels{/name}","comments_url":"https://api.github.com/repos/itmat/rum/issues/184/comments","events_url":"https://api.github.com/repos/itmat/rum/issues/184/events","html_url":"https://github.com/itmat/rum/issues/184","id":60270010,"number":184,"title":"Test failed: merge-gnu-and-tnu-and-cnu.t & rum-to-sam.t","user":{"login":"bellelavie","id":11378811,"avatar_url":"https://avatars.githubusercontent.com/u/11378811?v=3","gravatar_id":"","url":"https://api.github.com/users/bellelavie","html_url":"https://github.com/bellelavie","followers_url":"https://api.github.com/users/bellelavie/followers","following_url":"https://api.github.com/users/bellelavie/following{/other_user}","gists_url":"https://api.github.com/users/bellelavie/gists{/gist_id}","starred_url":"https://api.github.com/users/bellelavie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bellelavie/subscriptions","organizations_url":"https://api.github.com/users/bellelavie/orgs","repos_url":"https://api.github.com/users/bellelavie/repos","events_url":"https://api.github.com/users/bellelavie/events{/privacy}","received_events_url":"https://api.github.com/users/bellelavie/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-03-08T18:42:25Z","updated_at":"2015-03-08T18:42:25Z","closed_at":null,"body":"After installation, I've got a failure message from \"make test\"\r\nin merge-gnu-and-tnu-and-cnu.t and rum-to-sam.t as below.\r\nWould you please give me an advice for fixing this?\r\n\r\nPERL_DL_NONLAZY=1 /usr/bin/perl \"-MExtUtils::Command::MM\" \"-e\" \"test_harness(0, 'blib/lib', 'blib/arch')\" t/*.t\r\nt/00-load.t ...................... 1/1 # Testing RUM v2.0.5_06, Perl 5.014002, /usr/bin/perl\r\nt/00-load.t ...................... ok   \r\nt/bindeps.t ...................... ok   \r\nt/boilerplate.t .................. ok   \r\nt/cluster.t ...................... skipped: Test::MockObject Test::MockObject::Extends Arabidopsis index needed\r\nt/common.t ....................... ok     \r\nt/config.t ....................... ok     \r\nt/count-reads-mapped.t ........... ok   \r\nt/coverage-map.t ................. ok     \r\nt/file_iterator.t ................ ok   \r\nt/get-inferred-internal-exons.t .. ok   \r\nt/get-nu-stats.t ................. ok   \r\nt/heap.t ......................... ok   \r\nt/indexing.t ..................... ok     \r\nt/junctions-to-bed.t ............. ok     \r\nt/limit-nu.t ..................... ok   \r\nt/make-gu-and-gnu.t .............. ok   \r\nt/make-rum-junctions-file.t ...... ok   \r\nt/make-tu-and-tnu.t .............. ok   \r\nt/make-unmapped-file.t ........... ok   \r\nt/manifest.t ..................... skipped: Author tests not required for installation\r\nt/merge-bowtie-and-blat.t ........ ok   \r\nt/merge-chr-counts.t ............. ok   \r\nt/merge-gnu-and-tnu-and-cnu.t .... 1/1 \r\n#   Failed test at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\n# Looks like you failed 1 test of 1.\r\nt/merge-gnu-and-tnu-and-cnu.t .... Dubious, test returned 1 (wstat 256, 0x100)\r\nFailed 1/1 subtests \r\nt/merge-gu-and-tu.t .............. ok   \r\nt/merge-junctions.t .............. ok     \r\nt/merge-nu-stats.t ............... ok   \r\nt/merge-quants.t ................. ok   \r\nt/merge-sorted-rum-files.t ....... ok   \r\nt/parse-blat-out.t ............... ok   \r\nt/platform.t ..................... ok   \r\nt/pod-coverage.t ................. skipped: Test::Pod::Coverage 1.08 required for testing POD coverage\r\nt/pod.t .......................... skipped: Test::Pod 1.22 required for testing POD\r\nt/quant-map.t .................... ok    \r\nt/quantify-exons.t ............... ok   \r\nt/remove-dups.t .................. ok   \r\nt/repository.t ................... ok   \r\nt/rum-config-file.t .............. ok     \r\nt/rum-final-cleanup.t ............ ok   \r\nt/rum-to-cov.t ................... ok     \r\nt/rum-to-quantifications.t ....... ok     \r\nt/rum-to-sam.t ................... 1/10 \r\n#   Failed test 'u'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 2/10 \r\n#   Failed test 'u_nu'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 3/10 \r\n#   Failed test 'nu_quals'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\n\r\n#   Failed test 'u_quals'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 5/10 \r\n#   Failed test 'nu'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 6/10 \r\n#   Failed test 'u_nu_quals'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 7/10 \r\n#   Failed test 'suppress1'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 8/10 \r\n#   Failed test 'suppress2'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 9/10 \r\n#   Failed test 'suppress3'\r\n#   at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.\r\nt/rum-to-sam.t ................... 10/10 # Looks like you failed 9 tests of 10.\r\nt/rum-to-sam.t ................... Dubious, test returned 9 (wstat 2304, 0x900)\r\nFailed 9/10 subtests \r\nt/runner-usage.t ................. skipped: Arabidopsis index needed\r\nt/samio.t ........................ ok   \r\nt/sge.t .......................... ok     \r\nt/sort-by-location.t ............. ok   \r\nt/sort-rum-by-id.t ............... ok   \r\nt/sort-rum-by-location.t ......... ok   \r\nt/sort.t ......................... ok     \r\nt/standard-options.t ............. ok     \r\nt/state-machine.t ................ ok     \r\nt/subproc.t ...................... ok     \r\nt/workflow-runner.t .............. ok     \r\nt/workflow.t ..................... ok   \r\nt/workflows.t .................... skipped: Arabidopsis index needed\r\n\r\nTest Summary Report\r\n-------------------\r\nt/boilerplate.t                (Wstat: 0 Tests: 3 Failed: 0)\r\n  TODO passed:   1, 3\r\nt/merge-gnu-and-tnu-and-cnu.t  (Wstat: 256 Tests: 1 Failed: 1)\r\n  Failed test:  1\r\n  Non-zero exit status: 1\r\nt/rum-to-sam.t                 (Wstat: 2304 Tests: 10 Failed: 9)\r\n  Failed tests:  1-9\r\n  Non-zero exit status: 9\r\nFiles=54, Tests=514, 18 wallclock secs ( 0.39 usr  0.07 sys + 14.67 cusr  0.84 csys = 15.97 CPU)\r\nResult: FAIL\r\nFailed 2/54 test programs. 10/514 subtests failed.\r\nmake: *** [test_dynamic] Error 255\r\n"}}