[Bioperl-l] Failed tests for FeatureIO

Chris Fields cjfields at uiuc.edu
Mon Sep 25 11:34:45 EDT 2006


Sendu,

After updating from CVS, now passes on this end using Mac OS X and  
WinXP.  Nice catch!

Chris

PS: is there any point to using mode() here?  As Sendu points out, no  
other Bioperl modules use it.  Just curious...

On Sep 25, 2006, at 10:02 AM, Sendu Bala wrote:

> Torsten Seemann wrote:
>> Chris,
>>
>>> I am getting failed tests for FeatureIO.t on make test using  
>>> bioperl-
>>> live on Mac OS X (10.4.7, perl 5.8.6):
>>> pyr:~/src/bioperl-live cjfields$ perl -I. -w t/FeatureIO.t
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: Invalid protein count
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:331
>>> STACK: Bio::FeatureIO::ptt::_initialize Bio/FeatureIO/ptt.pm:147
>>> STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:266
>>> STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:286
>>> STACK: t/FeatureIO.t:189
>>> -----------------------------------------------------------
>>
>> Hmmm, I committed that module last week. I just did a fresh  
>> complete checkout
>> of current CVS, and all the tests pass fine for me on Linux 2.6 +  
>> Perl 5.8.5 ?
>
> The problem is your use of Bio::Root::IO::mode. Your's is the only
> module in bioperl that seems to use it, and for good reason: it was
> broken. I've fixed it and tested under Linux and Mac OS X, not tried
> Windows but hopefully that's ok too.
>
> (Briefly, mode() would call IO::Handle::getline which would return a
> seemingly random (but consistent per platform) line from the file, and
> then mode() would happily push that random line into the buffer.  
> Worse,
> under Mac OS X, getlines() would leave Root::IO's filehandle at the
> point after that random line, so all subsequent _readline's would be
> from the wrong point in the file)
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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