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[cjfields@Chriss-iMac bioperl-pipeline (v2)]$ make test
PERL_DL_NONLAZY=1 /Users/cjfields/perl5/perlbrew/perls/perl-5.20.1t/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Analysis.t ......... ok
t/BatchSubmission.t .. Job Scheduler not installed. Skipping test 1 to 4
t/BatchSubmission.t .. ok
t/BlastPipe.t ........ 1/12 Using a hash as a reference is deprecated at /Users/cjfields/bioperl/bioperl-pipeline/blib/lib/Bio/Pipeline/Manager.pm line 293.
t/BlastPipe.t ........ ok
t/Blat.t ............. ok
t/Cdna2Genome.t ...... 2/5 Using a hash as a reference is deprecated at /Users/cjfields/bioperl/bioperl-pipeline/blib/lib/Bio/Pipeline/Manager.pm line 293.
Problem running perl scripts/PipelineManager -dbhost localhost  -dbname _testdb_Chriss_iMac_local_377571 -xml xml/templates/cdna2genome_pipeline.xml  -schema sql/schema.sql -l -f -xf -verbose 0: Status 255 at t/BiopipeTestDB.pm line 357.
    BiopipeTestDB::run_pipeline(BiopipeTestDB=HASH(0x7fc541337ef0), "xml/templates/cdna2genome_pipeline.xml") called at t/Cdna2Genome.t line 52
t/Cdna2Genome.t ...... Dubious, test returned 2 (wstat 512, 0x200)
All 5 subtests passed
    (less 3 skipped subtests: 2 okay)
t/Feature_filter.t ... ok
t/Genewise.t ......... 1/15 GeneWise6 Matrix calculation: [1312000] Cells 99%
Information
    Name SINFRUP00000067802 is longer than allowed name block (15).
Truncating

# Test 5 got: "1046" (t/Genewise.t at line 62)
#   Expected: "865"
#  t/Genewise.t line 62 is:   ok($start, 865);#ok5
# Test 6 got: "1066" (t/Genewise.t at line 64)
#   Expected: "897"
#  t/Genewise.t line 64 is:   ok($end, 897);#ok6
# Test 8 got: "1046" (t/Genewise.t at line 70)
#   Expected: "865"
#  t/Genewise.t line 70 is:   ok($featpair->feature1->start,865);
# Test 9 got: "1066" (t/Genewise.t at line 71)
#   Expected: "897"
#  t/Genewise.t line 71 is:   ok($featpair->feature1->end,897);
# Test 11 got: <UNDEF> (t/Genewise.t at line 73)
#    Expected: "17.01"
#  t/Genewise.t line 73 is:   ok($featpair->feature1->score,17.01);
# Test 12 got: "1" (t/Genewise.t at line 74)
#    Expected: "120"
#  t/Genewise.t line 74 is:   ok($featpair->feature2->start,120);
# Test 13 got: "7" (t/Genewise.t at line 75)
#    Expected: "130"
#  t/Genewise.t line 75 is:   ok($featpair->feature2->end,130);
# Test 15 got: <UNDEF> (t/Genewise.t at line 77)
#    Expected: "17.01"
#  t/Genewise.t line 77 is:   ok($featpair->feature2->score,17.01);
t/Genewise.t ......... Failed 8/15 subtests
t/Genscan.t .......... Genscan program not found. Skipping tests 1 to 2.
t/Genscan.t .......... ok
t/Input.t ............ ok
t/Job.t .............. ok
t/JobAdaptor.t ....... ok
t/Output.t ........... ok
t/PhylipPipe.t ....... 1/8 Using a hash as a reference is deprecated at /Users/cjfields/bioperl/bioperl-pipeline/blib/lib/Bio/Pipeline/Manager.pm line 293.
Problem running perl scripts/PipelineManager -dbhost localhost  -dbname _testdb_Chriss_iMac_local_377781 -xml xml/templates/phylip_tree_pipeline.xml  -schema sql/schema.sql -l -f -xf -verbose 0: Status 255 at t/BiopipeTestDB.pm line 357.
    BiopipeTestDB::run_pipeline(BiopipeTestDB=HASH(0x7fb07424f1d0), "xml/templates/phylip_tree_pipeline.xml") called at t/PhylipPipe.t line 49
# Looks like you planned 8 tests but ran 1.
# Looks like your test exited with 2 just after 1.
t/PhylipPipe.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/8 subtests
t/Promoterwise.t ..... ok
t/Transformer.t ...... ok

Test Summary Report
-------------------
t/Cdna2Genome.t    (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/Genewise.t       (Wstat: 0 Tests: 15 Failed: 8)
  Failed tests:  5-6, 8-9, 11-13, 15
t/PhylipPipe.t     (Wstat: 512 Tests: 1 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 8 tests but ran 1.
Files=15, Tests=119, 13 wallclock secs ( 0.08 usr  0.04 sys +  3.23 cusr  0.54 csys =  3.89 CPU)
Result: FAIL
Failed 3/15 test programs. 8/119 subtests failed.
make: *** [test_dynamic] Error 255

[cjfields@Chriss-iMac bioperl-pipeline (v2)]$ prove -lr t/Cdna2Genome.t
t/Cdna2Genome.t .. 1/5 Problem running perl scripts/PipelineManager -dbhost localhost  -dbname _testdb_Chriss_iMac_local_391271 -xml xml/templates/cdna2genome_pipeline.xml  -schema sql/schema.sql -l -f -xf -verbose 0: Status 255 at t/BiopipeTestDB.pm line 357.
    BiopipeTestDB::run_pipeline(BiopipeTestDB=HASH(0x7fb57b752be8), "xml/templates/cdna2genome_pipeline.xml") called at t/Cdna2Genome.t line 52
t/Cdna2Genome.t .. Dubious, test returned 2 (wstat 512, 0x200)
All 5 subtests passed
    (less 3 skipped subtests: 2 okay)

Test Summary Report
-------------------
t/Cdna2Genome.t (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
Files=1, Tests=5,  1 wallclock secs ( 0.01 usr  0.00 sys +  0.35 cusr  0.06 csys =  0.42 CPU)
Result: FAIL

[cjfields@Chriss-iMac bioperl-pipeline (v2)]$ perl scripts/PipelineManager -dbhost localhost  -dbname _testdb_Chriss_iMac_local_391271 -xml xml/templates/cdna2genome_pipeline.xml  -schema sql/schema.sql -l -f -xf -verbose 1
Creating _testdb_Chriss_iMac_local_391271
Loading Schema...
Reading Data_setup xml   : xml/templates/cdna2genome_pipeline.xml
Doing DBAdaptor and IOHandler setup
Doing Transformers..
Doing Pipeline Flow Setup
Doing Analysis..
Doing Rules
Doing Job Setup...
Loading of pipeline completed
Removing Lock File...
Done
///////////////////////////////////////////////////////////
4 analysis found.
Running test and setup..

//////////// Analysis Test ////////////
Checking Analysis 1 DataMongerBio::Pipeline::Manager::test_analysis /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Manager.pm:223
Skipping test for DataMongerBio::Pipeline::Analysis::test_and_setup /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:235
 ok
Checking Analysis 2 BlastBio::Pipeline::Manager::test_analysis /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Manager.pm:223
Logic name Blast  already set.
unable to determine program versionBio::Pipeline::Analysis::set_program_version_if_needed /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:421
runnable already set to Bio::Pipeline::Runnable::BlastBio::Pipeline::Analysis::match_program_to_runnable /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:452
 ok
Checking Analysis 3 DataMongerBio::Pipeline::Manager::test_analysis /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Manager.pm:223
Skipping test for DataMongerBio::Pipeline::Analysis::test_and_setup /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:235
 ok
Checking Analysis 4 Sim4Bio::Pipeline::Manager::test_analysis /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Manager.pm:223
Logic name Sim4  already set.
unable to determine program versionBio::Pipeline::Analysis::set_program_version_if_needed /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:421
runnable already set to Bio::Pipeline::Runnable::Sim4Bio::Pipeline::Analysis::match_program_to_runnable /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Analysis.pm:452
 ok

Fetching Jobs...

Fetched 1 incomplete jobs
Running job: 1 | analysis: 1| /tmp//59/_testdb_Chriss_iMac_local_391271_DataMonger.1444424847.926.out /tmp//59/_testdb_Chriss_iMac_local_391271_DataMonger.1444424847.926.err

Fetched 1 completed jobs
Going to snooze for 3 seconds...
Waking up and run again!

Fetching Jobs...

Fetched 1 incomplete jobs
Running job: 2 | analysis: 2| /tmp//25/_testdb_Chriss_iMac_local_391271_Blast.1444424847.568.out /tmp//25/_testdb_Chriss_iMac_local_391271_Blast.1444424847.568.err

Fetched 1 completed jobs
Creating 1 jobs
Running job: 3 | analysis: 3| /tmp//63/_testdb_Chriss_iMac_local_391271_.job_3.DataMonger.1444424847.550.out /tmp//63/_testdb_Chriss_iMac_local_391271_.job_3.DataMonger.1444424847.550.err
Going to snooze for 3 seconds...
Waking up and run again!

Fetching Jobs...

Fetched 1 incomplete jobs
Running job: 4 | analysis: 4| /tmp//14/_testdb_Chriss_iMac_local_391271_Sim4.1444424847.636.out /tmp//14/_testdb_Chriss_iMac_local_391271_Sim4.1444424847.636.err

[cjfields@Chriss-iMac bioperl-pipeline (v2)]$ cat /tmp//14/_testdb_Chriss_iMac_local_391271_Sim4.1444424847.636.err
READING: Lost the will to live Error. Problems with runnableDB fetching input
[AnyDBM_File doesn't define an EXISTS method at /Users/cjfields/bioperl/bioperl-live/Bio/DB/IndexedBase.pm line 622.
]

------------- EXCEPTION -------------
MSG: Problems with runnableDB fetching input
[AnyDBM_File doesn't define an EXISTS method at /Users/cjfields/bioperl/bioperl-live/Bio/DB/IndexedBase.pm line 622.
]

STACK Bio::Pipeline::Job::_run_analysis /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Job.pm:371
STACK Bio::Pipeline::Job::run /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Job.pm:297
STACK Bio::Pipeline::Job::run_local /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Job.pm:316
STACK Bio::Pipeline::Manager::run /Users/cjfields/bioperl/bioperl-pipeline/lib/Bio/Pipeline/Manager.pm:344
STACK toplevel scripts/PipelineManager:161
-------------------------------------