Description of problem: [root@bruno bruno]# yum install perl-bioperl perl-bioperl-run Loaded plugins: allowdowngrade, dellsysidplugin, dellsysidplugin2, keys, list- : data, priorities, protect-packages, protectbase, refresh- : packagekit, upgrade-helper, verify, versionlock 0 packages excluded due to repository protections Reading version lock configuration Setting up Install Process Resolving Dependencies --> Running transaction check ---> Package perl-bioperl.noarch 0:1.6.0-1.fc11 set to be updated --> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package: perl-bioperl ---> Package perl-bioperl-run.noarch 0:1.5.9-0.1.1.fc11 set to be updated --> Running transaction check ---> Package perl-Bio-ASN1-EntrezGene.noarch 0:1.091-6.fc9 set to be updated --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: perl-bioperl noarch 1.6.0-1.fc11 rawhide 6.0 M perl-bioperl-run noarch 1.5.9-0.1.1.fc11 rawhide 691 k Installing for dependencies: perl-Bio-ASN1-EntrezGene noarch 1.091-6.fc9 rawhide 41 k Transaction Summary ================================================================================ Install 3 Package(s) Update 0 Package(s) Remove 0 Package(s) Total download size: 6.7 M Is this ok [y/N]: y Downloading Packages: -------------------------------------------------------------------------------- Total 29 MB/s | 6.7 MB 00:00 Running rpm_check_debug Running Transaction Test Finished Transaction Test Transaction Check Error: file /usr/lib/perl5/vendor_perl/5.10.0/Bio/ConfigData.pm conflicts between attempted installs of perl-bioperl-1.6.0-1.fc11.noarch and perl-bioperl-run-1.5.9-0.1.1.fc11.noarch file /usr/share/man/man3/Bio::ConfigData.3pm.gz conflicts between attempted installs of perl-bioperl-1.6.0-1.fc11.noarch and perl-bioperl-run-1.5.9-0.1.1.fc11.noarch Error Summary ------------- [root@bruno bruno]# Version-Release number of selected component (if applicable): How reproducible: Steps to Reproduce: 1. 2. 3. Actual results: Expected results: Additional info:
This appears to be an inadvertant duplication of code in the two packages introduced upstream. I have reported the error here: http://lists.open-bio.org/pipermail/bioperl-l/2009-February/029213.html Once I know which package ConfigData should live in, I'll remove it from the other one.
*** Bug 484868 has been marked as a duplicate of this bug. ***
*** Bug 484867 has been marked as a duplicate of this bug. ***
Upstream is working on fixing this (which is related to an auto-generated ConfigData file in Perl): http://lists.open-bio.org/pipermail/bioperl-l/2009-February/029222.html and should have fixes out soon.
Should be fixed by 1.5.9 RC2: http://koji.fedoraproject.org/koji/buildinfo?buildID=82403 Leaving open until the file conflicts check is passed.
I assume that the file conflicts no longer exists in rawhide as there has been no additional report on this bug. Feel free to re-open if file conflicts re-occurs.