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If beaker-repo-update is run pointing at multiple different base URLs whose contents are not identical, it could use inconsistent cached repodata and become confused. One symptom is package checksum failures where there should be none: failure: ../../rpms/rhts-test-env-4.43-1.fc14.noarch.rpm from beaker-repo-update-harness-Fedora16: [Errno 256] No more mirrors to try. The cause is that the yum repodata caches are keyed on repo id (in this case, beaker-repo-update-harness-Fedora16) and this does not change even when a different base URL is used. Yum will therefore use the existing cache which might contain different repodata.
A workaround is to remove yum's cache in /var/tmp/yum-root-* before running beaker-repo-update.
Probably the easiest way to avoid the incorrect cache reuse is to base the repoids on the repo url.