ExtractProteomeFromGff.t failing tests 3.11.0

[tseemann]

Andrew,
Sarah here noticed that the gene_p_a.csv file was no longer putting anything in the gene and product columns.
I'm now noticing that roary is failing installation tests.

UPDATE: I think bedtools 2.27.0 is the culprit! Something is wrong with -s -name for bedtools getfasta ...
arq5x/bedtools2#609
Now need name+ ?

 * 64|>abc_00012(+)                                                 |>abc_00012                                                    *
# | 65|MRNQIQKLLDSDLSSLHISKQTGVPQSTIHRMRKKERSLDNMSLKNAELLYKFANSIFSN  |MRNQIQKLLDSDLSSLHISKQTGVPQSTIHRMRKKERSLDNMSLKNAELLYKFANSIFSN  |
# | 66|EN*                                                           |EN*                                                           |
# * 67|>abc_00014(+)                                                 |>abc_00014                                                    *
# | 68|MEGLFNAIKDTVTAAINNDGAKLGTSIVSIVENGVGLLGKLFGF*                 |MEGLFNAIKDTVTAAINNDGAKLGTSIVSIVENGVGLLGKLFGF*                 |
# * 69|>abc_00015(+)                                                 |>abc_00015                                                    *
# | 70|MTGLAEAIANTVQAAQQHDSVKLGTSIVDIVANGVGLLGKLFGF*                 |MTGLAEAIANTVQAAQQHDSVKLGTSIVDIVANGVGLLGKLFGF*                 |
# * 71|>abc_00016(+)                                                 |>abc_00016                                                    *
# | 72|LGYKNILIDFDDTIVDFYDAEEWAFHYMANVFNHKATKDDFLTFKKINHQHWEAFQQNKL  |LGYKNILIDFDDTIVDFYDAEEWAFHYMANVFNHKATKDDFLTFKKINHQHWEAFQQNKL  |
# | 73|TKSEVLSERFVNYFKHHQMEVDGHRADVLFRNGLAEAKVKYFDQTLETIVELSKRHDLYI  |TKSEVLSERFVNYFKHHQMEVDGHRADVLFRNGLAEAKVKYFDQTLETIVELSKRHDLYI  |
# | 74|VTNGVTETQKRRLNQTPLHKYIKKIFISEETGYQKPNPEFFNYVFNDIGEDERQHSIIVG  |VTNGVTETQKRRLNQTPLHKYIKKIFISEETGYQKPNPEFFNYVFNDIGEDERQHSIIVG  |
# +---+--------------------------------------------------------------+--------------------------------------------------------------+
# Looks like you failed 2 tests of 7.

Test Summary Report
-------------------
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t      (Wstat: 512 Tests: 7 Failed: 2)
  Failed tests:  5, 7
  Non-zero exit status: 2
t/Bio/Roary/CommandLine/QueryRoary.t                  (Wstat: 256 Tests: 37 Failed: 1)
  Failed test:  27
  Non-zero exit status: 1
t/Bio/Roary/CommandLine/Roary.t                       (Wstat: 1536 Tests: 67 Failed: 6)
  Failed tests:  4, 6, 13-14, 17, 27
  Non-zero exit status: 6
t/Bio/Roary/ExtractProteomeFromGFFs.t                 (Wstat: 2560 Tests: 20 Failed: 10)
  Failed tests:  4, 6, 9-11, 14-16, 19-20
  Non-zero exit status: 10
t/Bio/Roary/Output/GroupsMultifastasNucleotide.t      (Wstat: 1536 Tests: 16 Failed: 6)
  Failed tests:  5-9, 12
  Non-zero exit status: 6
Files=55, Tests=791, 109 wallclock secs ( 0.20 usr  0.07 sys + 87.05 cusr 22.00 csys = 109.32 CPU)
Result: FAIL
Failed 5/55 test programs. 25/791 subtests failed.
make: *** [test_dynamic] Error 255
FAIL

[andrewjpage]

Fixed in v3.11.1 PR #374
Thanks for the comprehensive bug report and for digging into the underlying issue.