[Bioperl-l] Optional 'circular dependency' ok?

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed Sep 20 04:32:17 UTC 2006

Chris Fields wrote:
> On Sep 19, 2006, at 5:25 PM, Sendu Bala wrote:
>> Aren't there already optional things in Bioperl that only begin to  
>> work
>> after you read the instructions and manually install something? Well,
>> there must be, since I've had to do exactly that to get all tests  
>> in the
>> suite to run (and not just skip).
> There shouldn't be!  All dependencies should be found in the  
> Makefile.PL and listed in the INSTALL file dependencies.  Using 'perl  
> Makefile.PL' doesn't force you to install them, but it does warn you  
> what Bioperl classes require them if they aren't present.

There shouldn't be, but they actually happen to exist. An example of 
this is the use of Regexp::Common in the 
bioperl-live/maintenance/check_URLs.pl script. Even though this script 
is supposed to be used only by developers, it introduces the condition 
that Sendu describes.

Other examples are version and Class::Inspector which are used by the 
Deobfuscator. These 3 dependencies haven't been added to the main 
Makefile.PL due to the intended use of the scripts that require them.

> I think the large dependency list is the reason there is a separate  
> Bundle::Bioperl installation.  And, even then, I don't get abi.t and  
> other similar tests to work b/c they require bioperl-ext (which I  
> find too much of a bother to install, really).
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
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arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM

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