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By: a guest on Aug 3rd, 2012  |  syntax: None  |  size: 9.41 KB  |  hits: 11  |  expires: Never
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  1. jmoon@OLL-STEINLAB02:/var/www/jbrowse$ prove -lr t
  2. t/00.compile.t .............. ok    
  3. t/FastaDatabase.t ........... ok  
  4. t/bam-to-json.pl.t .......... # using temp dir /tmp/fAqCPTUjzu
  5. t/bam-to-json.pl.t .......... ok  
  6. t/biodb-to-json.pl.t ........ # writing output to /tmp/dXFIi_YjZH
  7. Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  8. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  9. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  10. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  11. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  12. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  13. Compilation failed in require at (eval 42) line 2.
  14.  at bin/biodb-to-json.pl line 121
  15. Could not open database: Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  16. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  17. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  18. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  19. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  20. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  21. Compilation failed in require at (eval 42) line 2.
  22.  at bin/biodb-to-json.pl line 121
  23. t/biodb-to-json.pl.t ........ 1/?
  24. #   Failed test 'biodb-to-json.pl ran ok'
  25. #   at t/biodb-to-json.pl.t line 23.
  26.  
  27. #   Failed test 'got right histogram output'
  28. #   at t/biodb-to-json.pl.t line 26.
  29. #     Structures begin differing at:
  30. #          $got = undef
  31. #     $expected = ARRAY(0x2406248)
  32. # undef
  33.  
  34. #   Failed test 'made right trackList.json'
  35. #   at t/biodb-to-json.pl.t line 29.
  36. #     Structures begin differing at:
  37. #          $got->{tracks}[1] = Does not exist
  38. #     $expected->{tracks}[1] = HASH(0x2406740)
  39. # {
  40. #   'formatVersion' => 1,
  41. #   'tracks' => [
  42. #     {
  43. #       'config' => {
  44. #         'chunkSize' => 20000,
  45. #         'urlTemplate' => 'seq/{refseq}/'
  46. #       },
  47. #       'key' => 'DNA',
  48. #       'label' => 'DNA',
  49. #       'type' => 'SequenceTrack'
  50. #     }
  51. #   ]
  52. # }
  53.  
  54. #   Failed test 'got the right names output'
  55. #   at t/biodb-to-json.pl.t line 244.
  56. #     Structures begin differing at:
  57. #          $got = undef
  58. #     $expected = ARRAY(0x2406650)
  59. # undef
  60. # Looks like you failed 4 tests of 6.
  61. t/biodb-to-json.pl.t ........ Dubious, test returned 4 (wstat 1024, 0x400)
  62. Failed 4/6 subtests
  63. t/draw-basepair-track.pl.t .. # using temp dir /tmp/yRw1da6Q_U
  64. t/draw-basepair-track.pl.t .. 1/? # using temp dir /tmp/_SVvWCZRrI
  65. t/draw-basepair-track.pl.t .. ok    
  66. t/fakefasta.t ............... ok  
  67. t/flatfile-to-json.pl.t ..... # using temp dir /tmp/ju7fJDdkkg
  68. t/flatfile-to-json.pl.t ..... ok  
  69. t/lazy_nclist.t ............. 1/? # loaded 2559 test features
  70. t/lazy_nclist.t ............. ok  
  71. t/nclist.t .................. ok  
  72. t/prepare-refseqs.pl.t ...... 1/?
  73. #   Failed test 'script succeeded for nonexistent ref'
  74. #   at t/prepare-refseqs.pl.t line 24.
  75.  
  76. #   Failed test 'warning message looks right'
  77. #   at t/prepare-refseqs.pl.t line 25.
  78. #                   'Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  79. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  80. # Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  81. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  82. # Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  83. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  84. # Compilation failed in require at (eval 55) line 2.
  85. #  at bin/prepare-refseqs.pl line 130
  86. # Could not open database: Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  87. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  88. # Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  89. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  90. # Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  91. # BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  92. # Compilation failed in require at (eval 55) line 2.
  93. #  at bin/prepare-refseqs.pl line 130
  94. # '
  95. #     doesn't match '(?^i:DOES NOT EXIST.+not found)'
  96. t/prepare-refseqs.pl.t ...... 3/? Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  97. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  98. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  99. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  100. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  101. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  102. Compilation failed in require at (eval 55) line 2.
  103.  at bin/prepare-refseqs.pl line 130
  104. Could not open database: Can't locate DB_File.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /var/www/jbrowse/lib /home/jmoon/perl5/lib/perl5/x86_64-linux /home/jmoon/perl5/lib/perl5 /usr/local/lib/perl5/site_perl/5.14.2/x86_64-linux /usr/local/lib/perl5/site_perl/5.14.2 /usr/local/lib/perl5/5.14.2/x86_64-linux /usr/local/lib/perl5/5.14.2 .) at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  105. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
  106. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  107. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
  108. Compilation failed in require at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  109. BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.14.2/Bio/DB/SeqFeature/Store/memory.pm line 124.
  110. Compilation failed in require at (eval 55) line 2.
  111.  at bin/prepare-refseqs.pl line 130
  112.  
  113. #   Failed test 'yeast genbank formatting ran OK'
  114. #   at t/prepare-refseqs.pl.t line 55.
  115. # Looks like you failed 3 tests of 4.
  116. t/prepare-refseqs.pl.t ...... Dubious, test returned 3 (wstat 768, 0x300)
  117. Failed 3/4 subtests
  118. t/ucsc-to-json.pl.t ......... # writing output to /tmp/JrGAjUI4i_
  119. t/ucsc-to-json.pl.t ......... ok  
  120. t/wig-to-json.pl.t .......... # using temp dir /tmp/rRtZn6gS15
  121. t/wig-to-json.pl.t .......... ok  
  122.  
  123. Test Summary Report
  124. -------------------
  125. t/biodb-to-json.pl.t      (Wstat: 1024 Tests: 6 Failed: 4)
  126.   Failed tests:  1-4
  127.   Non-zero exit status: 4
  128. t/prepare-refseqs.pl.t    (Wstat: 768 Tests: 4 Failed: 3)
  129.   Failed tests:  1-2, 4
  130.   Non-zero exit status: 3
  131. Files=12, Tests=132, 17 wallclock secs ( 0.15 usr  0.01 sys + 15.71 cusr  0.68 csys = 16.55 CPU)
  132. Result: FAIL
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