Failed during make test
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5.1 years ago
ashaneev07 ▴ 40

Hiii...i'm getting the following error message during the installation of CGL, its essential for repeatrunner. Could u please have look into this problem and help me out of this..Thank you.

Test Summary Report
-------------------
t/embedded-Bio-Search-Hit-PhatHit-Base.t       (Wstat: 65280 Tests: 9 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit-blastn.t     (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit-blastp.t     (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit-blastx.t     (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit-tblastn.t    (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit-tblastx.t    (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-Hit-PhatHit.t            (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-Bio-Search-HSP-PhatHSP-blastx.t     (Wstat: 1536 Tests: 26 Failed: 6)
  Failed tests:  13-14, 16, 22, 25-26
  Non-zero exit status: 6
t/embedded-Bio-Search-HSP-PhatHSP.t            (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Annotation-Feature-Contig.t     (Wstat: 512 Tests: 4 Failed: 1)
  Failed test:  1
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Feature-Exon.t       (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Annotation-Feature-Gene.t       (Wstat: 512 Tests: 4 Failed: 1)
  Failed test:  1
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Feature-Intron.t     (Wstat: 512 Tests: 4 Failed: 1)
  Failed test:  1
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Feature-Protein.t    (Wstat: 512 Tests: 4 Failed: 1)
  Failed test:  1
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Feature-Transcript.t (Wstat: 512 Tests: 4 Failed: 1)
  Failed test:  1
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Feature.t            (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Annotation-Iterator.t           (Wstat: 512 Tests: 1 Failed: 0)
  Non-zero exit status: 2
t/embedded-CGL-Annotation-Trace.t              (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Annotation.t                    (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Ontology-GO.t                   (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Ontology-Node.t                 (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Ontology-NodeRelationship.t     (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Ontology-SO.t                   (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-Ontology-Trace.t                (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL-TranslationMachine.t            (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-CGL.t                               (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/embedded-PROTO.t                             (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
t/PhatHSP-isContained.t                        (Wstat: 768 Tests: 45 Failed: 3)
  Failed tests:  24-25, 31
  Non-zero exit status: 3
Files=41, Tests=464,  7 wallclock secs ( 0.14 usr  0.02 sys +  5.77 cusr  0.50 csys =  6.43 CPU)
Result: FAIL
Failed 28/41 test programs. 14/464 subtests failed.
Makefile:1186: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
Reapeatmasking repeatrunner CGL • 1.3k views
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Did you follow the installation instructions, in particular with regards to installing dependencies and setting the CGL_[SG]O_SOURCE environment variables?

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i didn't install Chaos-xml and data store. But, they are optional.Otherwise I've complete prerequisites installation.

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Do you see any error message before the failed tests? Without more indications, it's going to be hard to figure out what's going on.

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Please have a look into this...

t/embedded-Bio-Search-HSP-PhatHSP-blastx.t ....... 2/? 
#   Failed test 'check base at postition 9118 in query.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 223.
#          got: 'H'
#     expected: 'M'

#   Failed test 'check base at postition 1328 in hit.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 224.
#          got: 'H'
#     expected: 'M'

#   Failed test 'check base at postition 1394 in hit.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 226.
#          got: 'E'
#     expected: 'N'

#   Failed test 'Check the query's natural begin.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 379.
#          got: '9119'
#     expected: '9118'

#   Failed test 'Check the query's natural end.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 435.
#          got: '8286'
#     expected: '8354'

#   Failed test 'Check the hit's natural end.'
#   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 436.
#          got: '1606'
#     expected: '1583'
# Looks like you failed 6 tests of 26.
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Where is your code coming from? A quick look at the code for CGL-0.08 here shows there is no t/embedded-Bio-Search-HSP-PhatHSP-blastx.t

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I've downloaded from https://github.com/Yandell-Lab/CGL and this gave me the above error.When i was downloaded it from https://www.yandell-lab.org/software/cgl.html shows the following error message. 

    #   Failed test 'check base at postition 9118 in query.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 218.
    #          got: 'H'
    #     expected: 'M'

    #   Failed test 'check base at postition 1328 in hit.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 219.
    #          got: 'H'
    #     expected: 'M'

    #   Failed test 'check base at postition 1394 in hit.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 221.
    #          got: 'E'
    #     expected: 'N'

    #   Failed test 'Check the query's natural begin.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 374.
    #          got: '9119'
    #     expected: '9118'

    #   Failed test 'Check the query's natural end.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 430.
    #          got: '8286'
    #     expected: '8354'

    #   Failed test 'Check the hit's natural end.'
    #   at lib/Bio/Search/HSP/PhatHSP/blastx.pm line 431.
    #          got: '1606'
    #     expected: '1583'
    # Looks like you failed 6 tests of 26.
#   Failed test 'Checking for correct version number.'
#   at lib/CGL/Version.pm line 79.
#          got: 'CGL Version 0.08CGL Version 0.08'
#     expected: 'CGL Version 0.08'

#   Failed test 'Checking exported call.'
#   at lib/CGL/Version.pm line 90.
#          got: 'CGL Version 0.08CGL Version 0.08CGL Version 0.08'
#     expected: 'CGL Version 0.08'
# Looks like you failed 2 tests of 6.
t/embedded-CGL-Version.t ......................... Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/6 subtests 
t/embedded-CGL.t ................................. UNIVERSAL does not export anything at lib/CGL.pod line 10.
BEGIN failed--compilation aborted at lib/CGL.pod line 10.
t/embedded-CGL.t ................................. skipped: (no reason given)
t/embedded-PROTO.t ............................... UNIVERSAL does not export anything at PROTO.pm line 10.
BEGIN failed--compilation aborted at PROTO.pm line 10.
t/embedded-PROTO.t ............................... skipped: (no reason given)
t/PhatHSP-isContained.t .......................... 1/? 
#   Failed test 'Is this the right hsp?'
#   at t/PhatHSP-isContained.t line 78.
#          got: '280'
#     expected: '256'

#   Failed test 'blastx: Check for position before the query sequence.'
#   at t/PhatHSP-isContained.t line 81.
#          got: '1'
#     expected: '0'

#   Failed test 'blastx: Check for position after the hit sequence.'
#   at t/PhatHSP-isContained.t line 94.
#          got: '1'
#     expected: '0'
# Looks like you failed 3 tests of 45.
t/PhatHSP-isContained.t .......................... Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/45 subtests 
t/PhatHSP-whatIsThere.t .......................... ok
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