Failing tests

[heikkil]

Do people run 'prove -w t/*' frequently or do you rely only on travis?

These tests fail before and after my commits today and yesterday.

This is perl 5, version 26, subversion 0 (v5.26.0) built for darwin-thread-multi-2level

Test Summary Report

t/LocalDB/Fasta.t (Wstat: 1024 Tests: 109 Failed: 4) Failed tests: 73, 91, 95, 101 Non-zero exit status: 4 t/LocalDB/Qual.t (Wstat: 1536 Tests: 56 Failed: 6) Failed tests: 7-9, 49-50, 52 Non-zero exit status: 6 t/Root/RootI.t (Wstat: 1024 Tests: 61 Failed: 4) Failed tests: 15-16, 22-23 Non-zero exit status: 4

[cjfields]

@heikkil we're currently relying on travis for checking, though if the tests are skipped there we'll miss changes that affect them.

These are passing for me, but it's using perl 5.24:

12:34 $ prove -lr t/LocalDB/
t/LocalDB/BioDBGFF.t ............. 1/275
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ............. ok
t/LocalDB/Fasta.t ................ ok
t/LocalDB/Flat.t ................. ok
t/LocalDB/Index/Blast.t .......... ok
t/LocalDB/Index/BlastTable.t ..... ok
t/LocalDB/Index/Index.t .......... ok
t/LocalDB/Qual.t ................. ok
t/LocalDB/Registry.t ............. ok
t/LocalDB/SeqFeature.t ........... ok
t/LocalDB/Taxonomy/greengenes.t .. ok
t/LocalDB/Taxonomy/silva.t ....... ok
t/LocalDB/Taxonomy/sqlite.t ...... ok
t/LocalDB/transfac_pro.t ......... ok
All tests successful.
Files=13, Tests=985,  5 wallclock secs ( 0.10 usr  0.03 sys +  2.77 cusr  1.29 csys =  4.19 CPU)
Result: PASS
✔ ~/bioperl/bioperl-live [master|…3⚑ 3]
12:35 $ perl -v

This is perl 5, version 24, subversion 1 (v5.24.1) built for darwin-2level
(with 1 registered patch, see perl -V for more detail)

Copyright 1987-2017, Larry Wall
...

[cjfields]

@heikkil to add to this, here is a run which shows a few warnings using prove -w:

12:37 $ prove -w t/LocalDB/
t/LocalDB/BioDBGFF.t ...... False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at Bio/DB/GFF/Typename.pm line 55.
t/LocalDB/BioDBGFF.t ...... 1/275
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ...... ok
t/LocalDB/Fasta.t ......... 1/109 Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1/darwin-2level/DynaLoader.pm line 214.
t/LocalDB/Fasta.t ......... ok
t/LocalDB/Flat.t .......... ok
t/LocalDB/Qual.t .......... 1/56 Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1/darwin-2level/DynaLoader.pm line 214.
t/LocalDB/Qual.t .......... ok
t/LocalDB/Registry.t ...... ok
t/LocalDB/SeqFeature.t .... 1/116 False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at Bio/DB/GFF/Typename.pm line 55.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1/darwin-2level/DynaLoader.pm line 214.
t/LocalDB/SeqFeature.t .... ok
t/LocalDB/transfac_pro.t .. ok
All tests successful.
Files=7, Tests=712,  2 wallclock secs ( 0.06 usr  0.02 sys +  1.57 cusr  1.05 csys =  2.70 CPU)
Result: PASS

[cjfields]

@heikkil I can confirm some of these using perl 5.26. It looks like they are due to a number of various issues that are worth breaking out into separate bugs, which I'll link back here.

[cjfields]

Interestingly enough, prove -w t/LocalDB/Fasta.t hangs completely for me. I'm not sure why, I can try running this on another system to see if the hang is just something local.

[cjfields]

@heikkil The hang was due to a bad BerkeleyDB install (I upgraded to High Sierra just recently which seemed to cause problems). It's now passing. This also seems to address the other issues, such as the Qual.t failures in #264.