After installation, I've got a failure message from "make test"
in merge-gnu-and-tnu-and-cnu.t and rum-to-sam.t as below.
Would you please give me an advice for fixing this?
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-load.t ...................... 1/1 # Testing RUM v2.0.5_06, Perl 5.014002, /usr/bin/perl
t/00-load.t ...................... ok
t/bindeps.t ...................... ok
t/boilerplate.t .................. ok
t/cluster.t ...................... skipped: Test::MockObject Test::MockObject::Extends Arabidopsis index needed
t/common.t ....................... ok
t/config.t ....................... ok
t/count-reads-mapped.t ........... ok
t/coverage-map.t ................. ok
t/file_iterator.t ................ ok
t/get-inferred-internal-exons.t .. ok
t/get-nu-stats.t ................. ok
t/heap.t ......................... ok
t/indexing.t ..................... ok
t/junctions-to-bed.t ............. ok
t/limit-nu.t ..................... ok
t/make-gu-and-gnu.t .............. ok
t/make-rum-junctions-file.t ...... ok
t/make-tu-and-tnu.t .............. ok
t/make-unmapped-file.t ........... ok
t/manifest.t ..................... skipped: Author tests not required for installation
t/merge-bowtie-and-blat.t ........ ok
t/merge-chr-counts.t ............. ok
t/merge-gnu-and-tnu-and-cnu.t .... 1/1
Failed test at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
Looks like you failed 1 test of 1.
t/merge-gnu-and-tnu-and-cnu.t .... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests
t/merge-gu-and-tu.t .............. ok
t/merge-junctions.t .............. ok
t/merge-nu-stats.t ............... ok
t/merge-quants.t ................. ok
t/merge-sorted-rum-files.t ....... ok
t/parse-blat-out.t ............... ok
t/platform.t ..................... ok
t/pod-coverage.t ................. skipped: Test::Pod::Coverage 1.08 required for testing POD coverage
t/pod.t .......................... skipped: Test::Pod 1.22 required for testing POD
t/quant-map.t .................... ok
t/quantify-exons.t ............... ok
t/remove-dups.t .................. ok
t/repository.t ................... ok
t/rum-config-file.t .............. ok
t/rum-final-cleanup.t ............ ok
t/rum-to-cov.t ................... ok
t/rum-to-quantifications.t ....... ok
t/rum-to-sam.t ................... 1/10
Failed test 'u'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 2/10
Failed test 'u_nu'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 3/10
Failed test 'nu_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
Failed test 'u_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 5/10
Failed test 'nu'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 6/10
Failed test 'u_nu_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 7/10
Failed test 'suppress1'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 8/10
Failed test 'suppress2'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 9/10
Failed test 'suppress3'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 10/10 # Looks like you failed 9 tests of 10.
t/rum-to-sam.t ................... Dubious, test returned 9 (wstat 2304, 0x900)
Failed 9/10 subtests
t/runner-usage.t ................. skipped: Arabidopsis index needed
t/samio.t ........................ ok
t/sge.t .......................... ok
t/sort-by-location.t ............. ok
t/sort-rum-by-id.t ............... ok
t/sort-rum-by-location.t ......... ok
t/sort.t ......................... ok
t/standard-options.t ............. ok
t/state-machine.t ................ ok
t/subproc.t ...................... ok
t/workflow-runner.t .............. ok
t/workflow.t ..................... ok
t/workflows.t .................... skipped: Arabidopsis index needed
After installation, I've got a failure message from "make test" in merge-gnu-and-tnu-and-cnu.t and rum-to-sam.t as below. Would you please give me an advice for fixing this?
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/00-load.t ...................... 1/1 # Testing RUM v2.0.5_06, Perl 5.014002, /usr/bin/perl t/00-load.t ...................... ok
t/bindeps.t ...................... ok
t/boilerplate.t .................. ok
t/cluster.t ...................... skipped: Test::MockObject Test::MockObject::Extends Arabidopsis index needed t/common.t ....................... ok
t/config.t ....................... ok
t/count-reads-mapped.t ........... ok
t/coverage-map.t ................. ok
t/file_iterator.t ................ ok
t/get-inferred-internal-exons.t .. ok
t/get-nu-stats.t ................. ok
t/heap.t ......................... ok
t/indexing.t ..................... ok
t/junctions-to-bed.t ............. ok
t/limit-nu.t ..................... ok
t/make-gu-and-gnu.t .............. ok
t/make-rum-junctions-file.t ...... ok
t/make-tu-and-tnu.t .............. ok
t/make-unmapped-file.t ........... ok
t/manifest.t ..................... skipped: Author tests not required for installation t/merge-bowtie-and-blat.t ........ ok
t/merge-chr-counts.t ............. ok
t/merge-gnu-and-tnu-and-cnu.t .... 1/1
Failed test at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
Looks like you failed 1 test of 1.
t/merge-gnu-and-tnu-and-cnu.t .... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/1 subtests t/merge-gu-and-tu.t .............. ok
t/merge-junctions.t .............. ok
t/merge-nu-stats.t ............... ok
t/merge-quants.t ................. ok
t/merge-sorted-rum-files.t ....... ok
t/parse-blat-out.t ............... ok
t/platform.t ..................... ok
t/pod-coverage.t ................. skipped: Test::Pod::Coverage 1.08 required for testing POD coverage t/pod.t .......................... skipped: Test::Pod 1.22 required for testing POD t/quant-map.t .................... ok
t/quantify-exons.t ............... ok
t/remove-dups.t .................. ok
t/repository.t ................... ok
t/rum-config-file.t .............. ok
t/rum-final-cleanup.t ............ ok
t/rum-to-cov.t ................... ok
t/rum-to-quantifications.t ....... ok
t/rum-to-sam.t ................... 1/10
Failed test 'u'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 2/10
Failed test 'u_nu'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 3/10
Failed test 'nu_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
Failed test 'u_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 5/10
Failed test 'nu'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 6/10
Failed test 'u_nu_quals'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 7/10
Failed test 'suppress1'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 8/10
Failed test 'suppress2'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 9/10
Failed test 'suppress3'
at /home/heewlim/Programs/RUM/t/../lib/RUM/TestUtils.pm line 60.
t/rum-to-sam.t ................... 10/10 # Looks like you failed 9 tests of 10. t/rum-to-sam.t ................... Dubious, test returned 9 (wstat 2304, 0x900) Failed 9/10 subtests t/runner-usage.t ................. skipped: Arabidopsis index needed t/samio.t ........................ ok
t/sge.t .......................... ok
t/sort-by-location.t ............. ok
t/sort-rum-by-id.t ............... ok
t/sort-rum-by-location.t ......... ok
t/sort.t ......................... ok
t/standard-options.t ............. ok
t/state-machine.t ................ ok
t/subproc.t ...................... ok
t/workflow-runner.t .............. ok
t/workflow.t ..................... ok
t/workflows.t .................... skipped: Arabidopsis index needed
Test Summary Report
t/boilerplate.t (Wstat: 0 Tests: 3 Failed: 0) TODO passed: 1, 3 t/merge-gnu-and-tnu-and-cnu.t (Wstat: 256 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 1 t/rum-to-sam.t (Wstat: 2304 Tests: 10 Failed: 9) Failed tests: 1-9 Non-zero exit status: 9 Files=54, Tests=514, 18 wallclock secs ( 0.39 usr 0.07 sys + 14.67 cusr 0.84 csys = 15.97 CPU) Result: FAIL Failed 2/54 test programs. 10/514 subtests failed. make: *\ [test_dynamic] Error 255