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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Thu Sep 21 07:20:12 UTC 2006

Chris Fields wrote:
> My point was, is there any way we can have two sets of modules: one set that
> is 'required', and another that is 'optional' (for additional functionality,
> but not installed)?  And have Makefile.PL test for all of them?  
Something like this would definitely be my preference. It makes sense to 
document any/all dependencies in one place but to make a distinction 
between 2 or 3 "types" of dependencies. 1) core dependencies which are 
absolutely required for the functioning of the main modules in Bioperl; 
2) Optional dependencies which enhance the basic installation and 3) The 
dependencies which are only present in the odd module. It may be more 
straightforward to deal with 2 and 3 as one set of optional dependencies.

I know very little about Makefiles, but from my experience of 
installation of dependencies, it would be excellent if during the "perl 
Makefile.PL" that a summary table was produced at the end, either 
instead of, or in addition to the current verbose list of dependencies 
that are not met. This could make it much clearer as to which type of 
dependencies are missing and whether they need to be installed. A table 
such as this comes to mind:

Module			Dependency	Status

IO::String		Required	Installed
File::Temp		Required	
GD			Optional	
Convert::Binary::C	Optional	

If this information was coded into the Makefile.PL, much like the 
verbose description of the requirements currently is, you could just 
test that all "required" modules are installed before allowing the 
installation to proceed. All "optional" modules could also be added to 
Bundle::BioPerl for easy installation. This would also help with making 
a ppd by having all this info in one place.

Like I said, I don't know much about Makefiles, but that's my thoughts 

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