[Bioperl-l] How to get rid of warnings

Hilmar Lapp hlapp at gmx.net
Sat Aug 19 08:47:30 EDT 2006


There is a variable Bio::Root::VERBOSITY which is returned by  
Bio::Root::Root::verbose() if called as a function (as opposed to a  
method).

The accompanying comment says that this would enable global verbosity  
setting, but I don't see the piece of code that would actually set  
the variable, let alone defaulting the per-instance value to it if a  
different one was never set.

I'm not sure whether I'm overlooking something (quite possible) but  
if I'm not this sounds like a bug. Also, I thought that the value of  
some environment variable would be taken into account but in the code  
I don't see any indication of that being true either.

If no-one sets me straight can you file this as a bug report?

	-hilmar

On Aug 18, 2006, at 11:28 AM, Niels Larsen wrote:

> I am a casual user of bioperl with my own error handling. Is there
> a way to switch off bioperls error handling? I switch off my own
> with
>
> $Common::Config::with_errors = 0;
> $Common::Config::with_warnings = 0;
>
> Sendu Bala wrote:
>> Jérémy JUST wrote:
>>>     Hello,
>>>
>>>   I can't manage to get rid of all warnings during a query from  
>>> GenBank
>>> with BioPerl 1.4. When the query doesn't give any result, I catch  
>>> the
>>> exception, but there is still a warning that is issued to STDERR.
>> [...]
>>> and the unwanted warning is:
>>> <<<<<
>>> Warning(s) from GenBank:
>>>                 <PhraseNotFound>FooBar</PhraseNotFound>
>>>
>>>   How could I set verbosity so that I don't get this warning?
>>
>> You can't easily or appropriately do it with bioperl 1.4, but I've  
>> just
>> fixed the problem in cvs. You might be able to just download revision
>> 1.18 of Bio/DB/Query/GenBank.pm from bioperl-live:
>>
>> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/Query/
>>
>> (The perl hack would be to redirect STDERR to /dev/null inside  
>> your eval.)
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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>>
>
> -- 
> ---------------------------------------------------------------------- 
> --
>
> Niels Larsen
> Danish Genome Institute
> Gustav Wieds vej 10 C
> DK-8000 Aarhus C
> Denmark
>
> Electronic mail: niels at genomics.dk
> Skype: niels_larsen_denmark
>
> Telephone: +45-8942-5268
> Telefax: +45-8620-1222
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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