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

Chris Fields cjfields at uiuc.edu
Wed Sep 20 00:48:36 EDT 2006


On Sep 19, 2006, at 11:32 PM, Mauricio Herrera Cuadra wrote:
..

>> 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.
> ...

...which makes sense.  For those scripts we could add README files  
stating their use and requirements, or run eval(require) blocks to  
catch and throw if a required module isn't present.  We should  
probably be stricter with regards to the core modules ('core' being  
anything that resides in the Bio namespace in the distribution).

>
> -- 
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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