[Bioperl-l] BioPerl 1.6 RC1

[Alex Lancaster]

>>>>> "AL" == Alex Lancaster  writes:

[...]

AL> Also is the version number 1.5.9 or 1.5.9.1 and will the next RC
AL> candidate be 1.5.9.2?  Can you tell me the exact sequence of
AL> version numbers you expect before going to 1.6.0?  From a Linux
AL> distribution POV the exact version numbers are very important
AL> because they are used to determine whether one release is more
AL> recent than another and therefore whether to update a package or
AL> not.  Having release candidate tarball with the version 1.5.9._1
AL> (i.e. with the underscore) is very non-standard and can confuse
AL> package managers.

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?

Alex