[Bioperl-l] BioPerl 1.6 RC1
cjfields at illinois.edu
Fri Jan 2 15:27:55 UTC 2009
On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote:
> 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/
>> from the full 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 work.
> Something to think about, but it's probably not going to happen for
Not for 1.6.0, maybe for 1.6.x. This would need to be worked out on
main trunk and merged over to the branch if it works.
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