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

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Summary: Bioperl doesn't bootstrap on other platforms, circular dependencies

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

           Summary: Bioperl doesn't bootstrap on other platforms, circular
                    dependencies
           Product: Fedora
           Version: 11
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: low
         Component: perl-bioperl-run
        AssignedTo: alexl at users.sourceforge.net
        ReportedBy: loupgaroublond at gmail.com
         QAContact: extras-qa at fedoraproject.org
                CC: alexl at users.sourceforge.net,
                    fedora-perl-devel-list at redhat.com
    Classification: Fedora


Description of problem: perl-bioperl and perl-bioperl-run have circular build
dependencies effectively

While this situation is not explicit it's based on runtime only requirements
enforced by the packages. It makes it hard to bootstrap this on a system that
doesn't already have an earlier version of bioperl.

perl-bioperl has a runtime requirement on a dependency that is fulfilled by
perl-bioperl-run. perl-bioperl-run has a build time dependency on something
provided by perl-bioperl. Without a perl-bioperl-run package, it's impossible
to install bioperl to build a newer bioperl-run. This presents a problem when
trying to bootstrap this is centos.

Version-Release number of selected component (if applicable):
perl-bioperl 1.6.1 (based of the 1.6.0 spec file with only a version change)
perl-bioperl-run 1.6.1-1

How reproducible:
I'm guessing it is based on theory, i haven't tried to reproduce it on a second
machine.

Steps to Reproduce:
1. Build a perl-bioperl package on enterprise linux 5
2. Add it to a repo your system can access.
3. Try building a perl-bioperl-run package starting with rpmbuild -bs on the
.spec file.
4. Try installing perl-bioperl to fill the BR

Actual results:

[root at bofh016 SPECS]# rpmbuild -bs perl-bioperl-run.spec
error: Failed build dependencies:
        perl(Bio::Root::Version) >= 1.5.9 is needed by
perl-bioperl-run-1.6.1-1.noarch

[root at bofh016 SPECS]# yum install perl-bioperl-1.6.1-2.el5.noarch
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * addons: archive.cs.uu.nl
 * base: archive.cs.uu.nl
 * extras: archive.cs.uu.nl
 * updates: archive.cs.uu.nl
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(List::MoreUtils) for package: perl-bioperl
--> Processing Dependency: perl(Test::Warn) for package: perl-bioperl
--> Processing Dependency: perl(Test::Exception) for package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(XML::Simple) for package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Running transaction check
---> Package perl-List-MoreUtils.x86_64 0:0.22-2.el5 set to be updated
---> Package perl-Test-Exception.noarch 0:0.26-2.el5 set to be updated
--> Processing Dependency: perl(Sub::Uplevel) for package: perl-Test-Exception
---> Package perl-Test-Warn.noarch 0:0.11-2.el5 set to be updated
---> Package perl-XML-Simple.noarch 0:2.14-4.fc6 set to be updated
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Running transaction check
---> Package perl-Sub-Uplevel.noarch 0:0.18-2.el5 set to be updated
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Finished Dependency Resolution
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) is needed
by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::ASN1::EntrezGene) is needed by package
perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
  --> Missing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::ASN1::EntrezGene) is needed by package
perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) is needed
by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
 You could try using --skip-broken to work around the problem
 You could try running: package-cleanup --problems
                        package-cleanup --dupes
                        rpm -Va --nofiles --nodigest

Expected results:

A source package

Additional info:

I'm going to push a fedora package to our private repo to make this work, but
i'm wondering how this could be solved for EPEL in the future. Ideally we would
like to run bioperl out of EPEL directly rather than running our own private
builds.

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