[Bioperl-l] failures on the stable branch

[Dave Howorth]

Jason Stajich wrote:
> These are due to problems with Bio::DB::Query::GenBank
> 
> setting the env variable BIOPERLDEBUG=1 will give more information.
> 
> 
>>ok 62 # could not connect to Genbank
>>ok 63 # could not connect to Genbank
>>ok 64 # could not connect to Genbank
>>ok 65 # could not connect to Genbank
>>ok 66 # could not connect to Genbank
>>ok 67 # could not connect to Genbank
>>ok 68 # could not connect to Genbank
>>ok 69 # could not connect to Genbank
>>ok 70 # could not connect to Genbank
>>ok 71 # could not connect to Genbank
>>ok 72 # could not connect to Genbank
>>ok 73 # could not connect to Genbank
>>ok 74 # could not connect to Genbank
>>ok 75 # could not connect to Genbank
>>ok 76 # could not connect to Genbank
>>ok 77 # could not connect to Genbank
>>ok 78 # could not connect to Genbank

When I set BIOPERLDEBUG=1 I see:

t/DB.........................Warning: Couldn't connect to complete 
GenBank query tests!

------------- EXCEPTION  -------------
MSG: Error from Genbank: Range operation produced no results
STACK Bio::DB::Query::GenBank::_parse_response Bio/DB/Query/GenBank.pm:267
STACK Bio::DB::Query::WebQuery::_run_query Bio/DB/Query/WebQuery.pm:268
STACK Bio::DB::Query::GenBank::count Bio/DB/Query/GenBank.pm:225
STACK (eval) t/DB.t:251
STACK toplevel t/DB.t:245

--------------------------------------


FAILED tests 79-87
         Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay, 
87.18%)


I'm not sure why I see different results to you.

I think what you're telling me is that I don't need to worry about this 
failure of db.t as long as I don't want to access GenBank. Is that right?

Also, if I've understood you right, I'm not sure why the db.t test fails 
when BIOPERLDEBUG=0 when most (all?) other tests just skip the tests and 
output a warning like:

t/DBCUTG.....................ok
         20/22 skipped: tests which require remote servers - set env 
variable BIOPERLDEBUG to test

Cheers, Dave
-- 
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960