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sestaton / HMMER2GO

Annotate DNA sequences for Gene Ontology terms
MIT License
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make test errors #6

Closed MDSharma closed 8 years ago

MDSharma commented 8 years ago

Hello,

I am trying to install hmmer2go as a module on a cluster. So far, I have installed all the dependencies:

perl Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for HMMER2GO
Writing MYMETA.yml and MYMETA.json

and also made sure that EMBOSS and HMMER 3 are in my path. I keep encountering the following problems during the make test step:

make test
PERL_DL_NONLAZY=1 "/data/cm/shared/apps/ActivePerl/5.22/bin/perl-static" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-load.t ........ 1/3 # Testing HMMER2GO 0.17, Perl 5.022001, /data/cm/shared/apps/ActivePerl/5.22/bin/perl-static
t/00-load.t ........ ok
t/01-fetchmap.t .... ok
t/02-getorf.t ...... ok
t/03-run.t ......... ok
t/04-mapterms.t .... 3/9
#   Failed test 'Correct number of GO terms mapped'
#   at t/04-mapterms.t line 63.
#          got: '3'
#     expected: '2'
t/04-mapterms.t .... 8/9 # Looks like you failed 1 test of 9.
t/04-mapterms.t .... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/9 subtests
t/05-map2gaf.t ..... ok
t/06-pfamsearch.t .. 2/10
#   Failed test 'Found the correct number of HMMs for the search term'
#   at t/06-pfamsearch.t line 39.
#          got: '7'
#     expected: '13'
t/06-pfamsearch.t .. 6/10 # Looks like you failed 1 test of 10.
t/06-pfamsearch.t .. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/10 subtests
t/07-customdb.t .... ok

Test Summary Report
-------------------
t/04-mapterms.t  (Wstat: 256 Tests: 9 Failed: 1)
  Failed test:  6
  Non-zero exit status: 1
t/06-pfamsearch.t (Wstat: 256 Tests: 10 Failed: 1)
  Failed test:  2
  Non-zero exit status: 1
Files=8, Tests=54, 36 wallclock secs ( 0.08 usr  0.01 sys + 12.09 cusr  2.55 csys = 14.73 CPU)
Result: FAIL
Failed 2/8 test programs. 2/54 subtests failed.
make: *** [test_dynamic] Error 255

Any thoughts on what could be the culprit here?

Best, MD

sestaton commented 8 years ago

Thanks for the report. If you try the latest release or the master branch it should work now. The issue was an unexpected result from Pfam based on new entries. So, not an issue with the methods, just the tests results.