[Bioperl-l] BioPerl 1.6 RC1

Sendu Bala bix at sendu.me.uk
Fri Dec 26 17:07:46 EST 2008

Alex Lancaster wrote:
> Some other oddness: when the Build.PL script checks for the
> dependencies, it notes a few optional CPAN packages which aren't yet
> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random',
> are missing.  Since they are optional and missing dependencies, I
> would have expected that the relevant bioperl modules such
> Bio::PhyloNetwork should also not be installed, but it appears that
> the .pm files are installed, see lines like:
> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/Factory.pm
> from the full build.log:
> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log
> This causes problems because RPM then generates Requires such as:
> Requires: perl(Algorithm::Munkres)
> (see bottom of the build.log referred to above) which can't (yet) be
> fullfilled by any other package in the Fedora package set, leading to
> broken dependencies.
> Is this the expected behaviour upon missing optional dependencies?

Yes, though I can see how it's broken from your point of view. It is set 
up to install everything, but simply not everything will work without 
the optionals. I hadn't considered not installing the modules that won't 

Something to think about, but it's probably not going to happen for 1.6?

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