[Bioperl-l] Optional 'circular dependency' ok?
cjfields at uiuc.edu
Wed Sep 20 04:48:36 UTC 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
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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