mdelaurentis
commented
11 years ago Mani,
Thanks for your interest in RUM. Since the bottom line of the test output indicates that the tests passed ("Result: PASS"), everything should be ok. There are some tests that were skipped because they require an index to be installed, and there were some warning messages that were printed out, but all the tests that were run actually passed. I'll work on suppressing those warning messages to avoid any confusion in the future.
Thanks,
Mike
On Tue, Oct 16, 2012 at 5:24 PM, nmanik notifications@github.com wrote:
I read the publication and looking forward to using RUM! Thanks for building it and all your efforts to make it easier to use! When I installed it and ran "make test", I see results: pass but I also see some tests failing. Is this something to be worried about? Thanks! ~Mani
My linux version is Linux version 2.6.18-194.11.4.el5 ( mockbuild@x86-009.build.bos.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)) #1 https://github.com/PGFI/rum/issues/1 SMP Fri Sep 17 04:57:05 EDT 2010
Next "make test" output PERL_DL_NONLAZY=1 /misc1/usrlocal/bio_apps/perl-5.1.12/bin/perl "-MExtUtils::Command::MM" "-e" "testharness(0, 'blib/lib', 'blib/arch')" t/.t t/00-load.t .................... 1/1 # Testing RUM v2.0.3_01, Perl 5.012001, /misc1/usrlocal/bio_apps/perl-5.1.12/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 ..................... 1/29 "my" variable $conf masks earlier declaration in same scope at t/config.t line 139. t/config.t ..................... ok
t/count-reads-mapped.t ......... 1/2 Use of uninitialized value $_[0] in string eq at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.301/t/../lib/RUM/Common.pm line 208, <$[...]> line 3923. Use of uninitialized value $int in string at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.3_01/t/../lib/RUM/Common.pm line 210, <$*[...]> line 3923. t/count-reads-mapped.t ......... ok
t/coverage-map.t ............... ok
t/file_iterator.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-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 .. ok
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 ............... ok
t/pod.t ........................ ok
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-to-cov.t ................. ok
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 ............ 1/13 unlink0: /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.3_01/t/tmp/workflow-runner.9PwX9O is gone already at t/workflow-runner.t line 0 t/workflow-runner.t ............ ok
t/workflow.t ................... 1/8 Use of uninitialized value in concatenation (.) or string at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.3_01/t/../lib/RUM/Workflow.pm line 511. t/workflow.t ................... ok
t/workflows.t .................. skipped: Arabidopsis index needed All tests successful. Test Summary Report
t/boilerplate.t (Wstat: 0 Tests: 3 Failed: 0) TODO passed: 1, 3 Files=49, Tests=737, 37 wallclock secs ( 0.24 usr 0.08 sys + 14.42 cusr 1.85 csys = 16.59 CPU) Result: PASS
— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/142.
nmanik
I read the publication and looking forward to using RUM! Thanks for building it and all your efforts to make it easier to use! When I installed it and ran "make test", I see results: pass but I also see some tests failing. Is this something to be worried about? Thanks! ~Mani
My linux version is Linux version 2.6.18-194.11.4.el5 (mockbuild@x86-009.build.bos.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)) #1 SMP Fri Sep 17 04:57:05 EDT 2010
Next "make test" output PERL_DL_NONLAZY=1 /misc1/usrlocal/bio_apps/perl-5.1.12/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/00-load.t .................... 1/1 # Testing RUM v2.0.3_01, Perl 5.012001, /misc1/usrlocal/bioapps/perl-5.1.12/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 ..................... 1/29 "my" variable $conf masks earlier declaration in same scope at t/config.t line 139. t/config.t ..................... ok
t/count-reads-mapped.t ......... 1/2 Use of uninitialized value $[0] in string eq at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.301/t/../lib/RUM/Common.pm line 208, <$[...]> line 3923. Use of uninitialized value $int in string at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.301/t/../lib/RUM/Common.pm line 210, <$[...]> line 3923. t/count-reads-mapped.t ......... ok
t/coverage-map.t ............... ok
t/file_iterator.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-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 .. ok
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 ............... ok
t/pod.t ........................ ok
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-to-cov.t ................. ok
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 ............ 1/13 unlink0: /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.3_01/t/tmp/workflow-runner.9PwX9O is gone already at t/workflow-runner.t line 0 t/workflow-runner.t ............ ok
t/workflow.t ................... 1/8 Use of uninitialized value in concatenation (.) or string at /hpc3/sg/sg_data/users/narayananm/tools/RUM-Pipeline-v2.0.3_01/t/../lib/RUM/Workflow.pm line 511. t/workflow.t ................... ok
t/workflows.t .................. skipped: Arabidopsis index needed All tests successful.
Test Summary Report
t/boilerplate.t (Wstat: 0 Tests: 3 Failed: 0) TODO passed: 1, 3 Files=49, Tests=737, 37 wallclock secs ( 0.24 usr 0.08 sys + 14.42 cusr 1.85 csys = 16.59 CPU) Result: PASS