Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. 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@xxxxxxxxxxxxxxxxxxxxx ReportedBy: loupgaroublond@xxxxxxxxx QAContact: extras-qa@xxxxxxxxxxxxxxxxx CC: alexl@xxxxxxxxxxxxxxxxxxxxx, fedora-perl-devel-list@xxxxxxxxxx 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@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@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. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug. -- Fedora Extras Perl SIG http://www.fedoraproject.org/wiki/Extras/SIGs/Perl Fedora-perl-devel-list mailing list Fedora-perl-devel-list@xxxxxxxxxx https://www.redhat.com/mailman/listinfo/fedora-perl-devel-list
