[Bug 537138] Bioperl doesn't bootstrap on other platforms, circular dependencies

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https://bugzilla.redhat.com/show_bug.cgi?id=537138


Alex Lancaster <alexl at users.sourceforge.net> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|skasal at redhat.com           |alexl at users.sourceforge.net




--- Comment #2 from Alex Lancaster <alexl at users.sourceforge.net>  2009-11-12 15:42:36 EDT ---
If you look at the .spec file:

http://cvs.fedoraproject.org/viewvc/rpms/perl-bioperl/devel/perl-
bioperl.spec?revision=1.23&view=markup

you'll notice that we have:

#cat << \EOF > %{_builddir}/BioPerl-%{version}/%{name}-req
##!/bin/sh
#%{__perl_requires} $* |\
#   sed -e '/perl(Bio::Tools::Run::Alignment::Clustalw)/d;
/perl(Bio::Tools::Run::GenericParameters)/d;
/perl(Bio::Tools::Run::Phylo::Molphy::ProtML)/d;
/perl(Bio::Tools::Run::Phylo::Phylip::Neighbor)/d;
/perl(Bio::Tools::Run::Phylo::Phylip::ProtDist)/d;
/perl(Bio::Tools::Run::Phylo::Phylip::ProtPars)/d;
/perl(Bio::Tools::Run::RemoteBlast)/d'
#EOF

#%%define __perl_requires %{_builddir}/BioPerl-%{version}/%{name}-req
#chmod +x %{__perl_requires}

to handle the bootstrapping problem.  So simply enable those sections of the
spec on first build, then build perl-bioperl-run against them, then comment
them out again.  Not pretty but it works (more requires may need to be filtered
since new requires may have been added since the first bootstrap).  

(In reply to comment #1)
> Thanks for the report.
> 
> I think that it makes sense to filter the perl-bioperl requires so that
> perl-bioperl-run is not required by them. 

Right and that's what the above does, although I'm not sure if that's a good
idea to permanently filter them.

> (Otherwise the two packages could  probably be merged.)

No that should not be done, because they are two tarballs maintained separately
with different release schedules upstream.  I have already discussed this
problem with upstream and if anything they are moving in the direction of more
modularisation of bioperl into separate packages than less.

> I'm going to fix this in devel; I doubt it is worth to issue a F11 update for
> this bug.

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