Failed during make test
0
0
Entering edit mode
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
ADD COMMENT •
0
Entering edit mode

Did you follow the installation instructions, in particular with regards to installing dependencies and setting the CGL_[SG]O_SOURCE environment variables?

ADD REPLY •
0
Entering edit mode

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

ADD REPLY •
0
Entering edit mode

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.

ADD REPLY •
0
Entering edit mode

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.
ADD REPLY •
0
Entering edit mode

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

ADD REPLY •
0
Entering edit mode

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
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 2500 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6