jb_pl_test_output

#   Failed test 'bin/draw-basepair-track.pl compiled ok'
#   at tests/perl_tests/00.compile.t line 45.
# stdout: 
# stderr: Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
# Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
# Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
# Compilation failed in require at bin/draw-basepair-track.pl line 82.
# BEGIN failed--compilation aborted at bin/draw-basepair-track.pl line 82.
# Looks like you failed 1 test of 44.
tests/perl_tests/00.compile.t ..................... 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/44 subtests 
tests/perl_tests/add-json.pl.t .................... ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/tDho95noju
tests/perl_tests/bam-to-json.pl.t ................. ok
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/koENVNZ5dU
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/pnWxAFa2aL
tests/perl_tests/biodb-to-json.pl.t ............... ok
tests/perl_tests/conf_format.t .................... ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/rMNPgkI6H_
Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
Compilation failed in require at bin/draw-basepair-track.pl line 82.
BEGIN failed--compilation aborted at bin/draw-basepair-track.pl line 82.

#   Failed test 'script ran ok'
#   at tests/perl_tests/draw-basepair-track.pl.t line 32.

#   Failed test 'made some pngs'
#   at tests/perl_tests/draw-basepair-track.pl.t line 36.

#   Failed test 'made trackData'
#   at tests/perl_tests/draw-basepair-track.pl.t line 38.
No such file or directory reading /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/rMNPgkI6H_/tracks/foo/mahoney/trackData.json at tests/perl_tests/lib/FileSlurping.pm line 99.
# Tests were run but no plan was declared and done_testing() was not seen.
tests/perl_tests/draw-basepair-track.pl.t ......... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 3/3 subtests 
tests/perl_tests/fakefasta.t ...................... ok
tests/perl_tests/featurestream.t .................. ok

#   Failed test 'got the right number of classes'
#   at tests/perl_tests/flatfile-to-json.pl.t line 339.
#          got: '334'
#     expected: '5'
# [
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# ]

#   Failed test 'got the right number of classes'
#   at tests/perl_tests/flatfile-to-json.pl.t line 339.
#          got: '333'
#     expected: '5'
# [
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#       'Start',
#       'End',
#       'Strand',
#       'Source',
#       'Id',
#       'Seq_id',
#       'Subfeatures',
#       'Score',
#       'Name',
#       'Type'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Type',
#       'Name',
#       'Subfeatures',
#       'Score',
#       'Seq_id',
#       'Id',
#       'Source'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Type',
#       'Name',
#       'Subfeatures',
#       'Score',
#       'Id',
#       'Seq_id',
#       'Source'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Source',
#       'Seq_id',
#       'Id',
#       'Subfeatures',
#       'Score',
#       'Name',
#       'Type'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Name',
#       'Type',
#       'Subfeatures',
#       'Score',
#       'Seq_id',
#       'Id',
#       'Source'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Name',
#       'Type',
#       'Score',
#       'Subfeatures',
#       'Seq_id',
#       'Id',
#       'Source'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Subfeatures',
#       'Score',
#       'Type',
#       'Name',
#       'Source',
#       'Seq_id',
#       'Id'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Id',
#       'Seq_id',
#       'Source',
#       'Name',
#       'Type',
#       'Subfeatures',
#       'Score'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Type',
#       'Name',
#       'Score',
#       'Subfeatures',
#       'Seq_id',
#       'Id',
#       'Source'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Strand',
#       'Seq_id',
#       'Id',
#       'Source',
#       'Name',
#       'Type',
#       'Subfeatures',
#       'Score'
#     ],
#     'isArrayAttr' => {
#       'Subfeatures' => 1
#     }
#   },
#   {
#     'attributes' => [
#       'Start',
#       'End',
#       'Chunk'
#     ],
#     'isArrayAttr' => {
#       'Sublist' => 1
#     }
#   }
# ]

#   Failed test at tests/perl_tests/flatfile-to-json.pl.t line 386.
#     Structures begin differing at:
#          $got->{attributes}[3] = 'Score'
#     $expected->{attributes}[3] = 'Seq_id'
# {
#   'featureCount' => 20,
#   'formatVersion' => 1,
#   'histograms' => {
#     'meta' => [],
#     'stats' => []
#   },
#   'intervals' => {
#     'classes' => [
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Name',
#           'Seq_id'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Name',
#           'Seq_id',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Seq_id',
#           'Name'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Name',
#           'Seq_id'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Seq_id',
#           'Name'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Name',
#           'Seq_id',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Name',
#           'Seq_id'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Seq_id',
#           'Name'
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#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
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#           'End',
#           'Strand',
#           'Seq_id',
#           'Name',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Name',
#           'Seq_id'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Seq_id',
#           'Name',
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#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
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#           'Strand',
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#           'Name',
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#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
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#           'Name',
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#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Seq_id',
#           'Name',
#           'Score'
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#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Seq_id',
#           'Name',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Name',
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#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Seq_id',
#           'Name',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
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#           'Chunk'
#         ],
#         'isArrayAttr' => {
#           'Sublist' => 1
#         }
#       }
#     ],
#     'count' => 20,
#     'lazyClass' => 17,
#     'maxEnd' => 102906693,
#     'minStart' => 102746607,
#     'nclist' => [
#       [
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#         1,
#         '1',
#         'chr10_100010101',
#         'chr10'
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#       [
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#         102757063,
#         1,
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#         'chr10',
#         '1'
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#       [
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#       [
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#         'chr10_100023087'
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#       [
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#         102763900,
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#         '1'
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#       [
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#         102779028,
#         1,
#         '1',
#         'chr10',
#         'chr10_100042744'
#       ],
#       [
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#         102791548,
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#       [
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#       [
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#         1,
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#       [
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#         102821466,
#         1,
#         'chr10',
#         'chr10_100089212',
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#       [
#         9,
#         102821565,
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#         1,
#         '1',
#         'chr10_100090127',
#         'chr10'
#       ],
#       [
#         10,
#         102822305,
#         102822874,
#         1,
#         'chr10',
#         'chr10_100090866',
#         '1'
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#       [
#         11,
#         102825930,
#         102826474,
#         1,
#         '1',
#         'chr10_100094501',
#         'chr10'
#       ],
#       [
#         12,
#         102826938,
#         102827286,
#         1,
#         '1',
#         'chr10_100095501',
#         'chr10'
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#       [
#         13,
#         102827366,
#         102827778,
#         1,
#         'chr10',
#         'chr10_100095928',
#         '1'
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#       [
#         14,
#         102883063,
#         102883551,
#         1,
#         'chr10',
#         'chr10_100154436',
#         '1'
#       ],
#       [
#         15,
#         102891173,
#         102891794,
#         1,
#         '1',
#         'chr10_100162617',
#         'chr10'
#       ],
#       [
#         16,
#         102893599,
#         102894301,
#         1,
#         'chr10',
#         'chr10_100165069',
#         '1'
#       ],
#       [
#         9,
#         102905801,
#         102906693,
#         1,
#         '1',
#         'chr10_100177356',
#         'chr10'
#       ]
#     ],
#     'urlTemplate' => 'lf-{Chunk}.jsonz'
#   }
# }

#   Failed test at tests/perl_tests/flatfile-to-json.pl.t line 424.
#     Structures begin differing at:
#          $got->{attributes}[3] = 'Name'
#     $expected->{attributes}[3] = 'Source'
# {
#   'featureCount' => 7,
#   'formatVersion' => 1,
#   'histograms' => {
#     'meta' => [
#       {
#         'arrayParams' => {
#           'chunkSize' => 10000,
#           'length' => 3,
#           'urlTemplate' => 'hist-500-{Chunk}.jsonz'
#         },
#         'basesPerBin' => '500'
#       }
#     ],
#     'stats' => [
#       {
#         'basesPerBin' => '500',
#         'max' => 4,
#         'mean' => '2.33333333333333'
#       }
#     ]
#   },
#   'intervals' => {
#     'classes' => [
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Name',
#           'Type',
#           'Seq_id',
#           'Score',
#           'Source'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Score',
#           'Source',
#           'Name',
#           'Type',
#           'Seq_id'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Source',
#           'Score',
#           'Seq_id',
#           'Type',
#           'Name'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Source',
#           'Score',
#           'Seq_id',
#           'Type',
#           'Name'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Strand',
#           'Seq_id',
#           'Type',
#           'Name',
#           'Source',
#           'Score'
#         ],
#         'isArrayAttr' => {}
#       },
#       {
#         'attributes' => [
#           'Start',
#           'End',
#           'Chunk'
#         ],
#         'isArrayAttr' => {
#           'Sublist' => 1
#         }
#       }
#     ],
#     'count' => 7,
#     'lazyClass' => 5,
#     'maxEnd' => 1262,
#     'minStart' => 792,
#     'nclist' => [
#       [
#         0,
#         792,
#         842,
#         0,
#         'FakeName',
#         'micro_array_oligo',
#         'ctgA',
#         '41.32',
#         'zonk'
#       ],
#       [
#         1,
#         852,
#         902,
#         0,
#         '21.2',
#         'zonk',
#         'FakeName',
#         'micro_array_oligo',
#         'ctgA'
#       ],
#       [
#         2,
#         912,
#         962,
#         0,
#         'zonk',
#         '20.8',
#         'ctgA',
#         'micro_array_oligo',
#         'FakeName'
#       ],
#       [
#         3,
#         1032,
#         1082,
#         0,
#         'zonk',
#         '17.08',
#         'ctgA',
#         'micro_array_oligo',
#         'FakeName'
#       ],
#       [
#         0,
#         1092,
#         1142,
#         0,
#         'FakeName',
#         'micro_array_oligo',
#         'ctgA',
#         '9.76',
#         'zonk'
#       ],
#       [
#         4,
#         1152,
#         1202,
#         0,
#         'ctgA',
#         'micro_array_oligo',
#         'FakeName',
#         'zonk',
#         '3.81'
#       ],
#       [
#         2,
#         1212,
#         1262,
#         0,
#         'zonk',
#         '3.3',
#         'ctgA',
#         'micro_array_oligo',
#         'FakeName'
#       ]
#     ],
#     'urlTemplate' => 'lf-{Chunk}.jsonz'
#   }
# }
# Looks like you failed 4 tests of 37.
tests/perl_tests/flatfile-to-json.pl.t ............ 
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/37 subtests 
tests/perl_tests/genbank.t ........................ ok
tests/perl_tests/generate-names-incremental.pl.t .. ok

#   Failed test 'got right data from volvox test data run'
#   at tests/perl_tests/generate-names.pl.t line 39.
#     Structures begin differing at:
#          $got->{c00/f.json}{rs17883998}{exact}[0][1] = '12'
#     $expected->{c00/f.json}{rs17883998}{exact}[0][1] = '11'

#   Failed test 'same data after incremental run with --safeMode'
#   at tests/perl_tests/generate-names.pl.t line 58.
#     Structures begin differing at:
#          $got->{6bf/3.json}{rs112989936}{exact}[0][1] = '12'
#     $expected->{6bf/3.json}{rs112989936}{exact}[0][1] = '11'
# Looks like you failed 2 tests of 3.
tests/perl_tests/generate-names.pl.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/3 subtests 
tests/perl_tests/json.t ........................... ok
# loaded 2559 test features
tests/perl_tests/lazy_nclist.t .................... ok
tests/perl_tests/maker2jbrowse.t .................. ok
tests/perl_tests/nclist.t ......................... ok
WARNING: multiple reference sequences found named 'NC_001133', using only the first one.

#   Failed test 'see 12 uncompressed seq chunks'
#   at tests/perl_tests/prepare-refseqs.pl.t line 59.
#          got: '0'
#     expected: '12'
# []

#   Failed test 'see 12 uncompressed seq chunks'
#   at tests/perl_tests/prepare-refseqs.pl.t line 73.
#          got: '0'
#     expected: '12'
# []
WARNING: multiple reference sequences found named 'NC_001133', using only the first one.

#   Failed test 'see 3 COMPRESSED seq chunks'
#   at tests/perl_tests/prepare-refseqs.pl.t line 89.
#          got: '0'
#     expected: '3'
# /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/UtLONTroDH
# Looks like you failed 3 tests of 13.
tests/perl_tests/prepare-refseqs.pl.t ............. 
Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/13 subtests 
tests/perl_tests/remove-track.pl.t ................ ok
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/08n9Kk20KW
# Track nonExistentTrack not found in the UCSC track database (trackDb.txt.gz) file.  Is it a real UCSC track? at bin/ucsc-to-json.pl line 194.
# To format the jaxQtlAsIs track, you must have both files tests/data/hg19/database//jaxQtlAsIs.sql and tests/data/hg19/database//jaxQtlAsIs.txt.gz
tests/perl_tests/ucsc-to-json.pl.t ................ ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/mYJ1oU9krD
tests/perl_tests/wig-to-json.pl.t ................. ok

Test Summary Report
-------------------
tests/perl_tests/00.compile.t                   (Wstat: 256 Tests: 44 Failed: 1)
  Failed test:  19
  Non-zero exit status: 1
tests/perl_tests/draw-basepair-track.pl.t       (Wstat: 512 Tests: 3 Failed: 3)
  Failed tests:  1-3
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
tests/perl_tests/flatfile-to-json.pl.t          (Wstat: 1024 Tests: 37 Failed: 4)
  Failed tests:  30, 32, 35, 37
  Non-zero exit status: 4
tests/perl_tests/generate-names.pl.t            (Wstat: 512 Tests: 3 Failed: 2)
  Failed tests:  1-2
  Non-zero exit status: 2
tests/perl_tests/prepare-refseqs.pl.t           (Wstat: 768 Tests: 13 Failed: 3)
  Failed tests:  5, 7, 9
  Non-zero exit status: 3
Files=20, Tests=224, 15 wallclock secs ( 0.07 usr  0.03 sys + 12.41 cusr  1.59 csys = 14.10 CPU)
Result: FAIL