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Upgrade to Fedora 27 problems with dnf and package removal

asked 2018-03-07 02:44:54 -0500

vancel35 gravatar image

updated 2018-03-07 10:18:37 -0500

I'm trying to upgrade my system from Fedora 25 to Fedora 27, and I've been removing packages that were causing problems. The last two packages don't seem to want to be removed, so I'm stuck. I've searched the Internet for various permutations of my problem, but nothing matches. The closest that I've found is that in Fedora 25, dnf seems to corrupt the rpm database regularly, but in those cases, they can't continue without rebuilding the rpm DB, and mine doesn't do that. Plus everything still functions other than removing these two packages.

Notes on the tests below:
- This happens both before and after doing a dnf clean all
- This happens both before and after doing an rpm --rebuilddb

Tried based on suggestions: (ran dnf clean all and rpm --rebuilddb after each repository was removed)
- Disabled fedora-steam repository -> error is the same
- Disabled google-chrome repository -> error is the same

Things I've tried since posting this question:
- dnf reinstall nss-softokn* -> all symptoms are the same.
-- Found this while trying to solve the rpmdbNextIterator error I've been getting.
-- It forced the re-download of all 3000+ upgrade packages
-- rpmdbNextIterator problem still exists.

dnf --best --allowerasing system-upgrade download --refresh --releasever=27
ends with the errors: (I'm not going to paste in the 3000+ packages that are going to be upgraded)
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction check error:
  file /usr/share/man/man3/Text::Diff.3pm.gz from install of perl-Text-Diff-1.44-5.fc27.noarch conflicts with file from package perl-Text-Diff-1.44-2.fc25.noarch
  file /usr/share/man/man3/Text::Diff::Config.3pm.gz from install of perl-Text-Diff-1.44-5.fc27.noarch conflicts with file from package perl-Text-Diff-1.44-2.fc25.noarch
  file /usr/share/man/man3/Text::Diff::Table.3pm.gz from install of perl-Text-Diff-1.44-5.fc27.noarch conflicts with file from package perl-Text-Diff-1.44-2.fc25.noarch
  file /usr/lib64/perl5/vendor_perl/auto/PadWalker/PadWalker.so from install of perl-PadWalker-2.2-7.fc27.x86_64 conflicts with file from package perl-PadWalker-2.2-3.fc25.x86_64
  file /usr/share/man/man3/PadWalker.3pm.gz from install of perl-PadWalker-2.2-7.fc27.x86_64 conflicts with file from package perl-PadWalker-2.2-3.fc25.x86_64

Error Summary
-------------

I then attempt to remove perl-Text-Diff and perl-PadWalker (focus on perl-Text-Diff in this post, but the same thing happens with perl-PadWalker)

dnf remove perl-Text-Diff

Which results in this:

Dependencies resolved.
=============================================================================================================================================================================================================================================
 Package                                                       Arch                                                  Version                                                    Repository                                              Size
=============================================================================================================================================================================================================================================
Removing:
 perl-Text-Diff                                                noarch                                                1.44-2.fc25                                                @fedora                                                 83 k

Transaction Summary
=============================================================================================================================================================================================================================================
Remove  1 Package

Installed size: 83 k
Is this ok [y/N]: y
Running transaction check
error: rpmdbNextIterator: skipping h#     880 Header V3 RSA/SHA256 Signature, key ID fdb19c98: BAD
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
perl-Text-Diff-1.44-2.fc25.noarch was supposed to be removed but is not!
  Verifying   : perl-Text-Diff-1.44-2.fc25.noarch                                                                                                                                                                                        1/1 

Removed:
  perl-Text-Diff.noarch 1.44-2.fc25                                                                                                                                                                                                          

Complete ...
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Comments

It looks like your rpm database might be corrupted. Did you try running rpm --rebuilddb?

ssieb gravatar imagessieb ( 2018-03-07 13:35:45 -0500 )edit

3 Answers

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answered 2018-03-08 08:25:10 -0500

villykruse gravatar image

updated 2018-03-08 08:25:44 -0500

dnf keeps track of packages in the directory /var/lib/dnf/yumdb. To find the specifics for the package perl-Text-Diff run

find /var/lib/dnf/yumdb -name '*perl-Text-Diff*'

That would give you the name of a directory, which you can remove using the rm -rf command.

If rpm -e is able to remove the package, then the package should be truly gone.

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answered 2018-11-30 11:46:40 -0500

Rebuild the RPM DB: 'sudo rpm --rebuilddb' and it will clear the error: "rpmdbNextIterator: skipping h#"

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answered 2018-03-07 03:44:34 -0500

Glenn gravatar image

updated 2018-03-07 03:45:14 -0500

Disable the steam repo and see if that helps to get the system updated. You can deal with the steam packages later.

dnf config-manager --set-disabled fedora-steam>
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Comments

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The errors are still the same (perl-Text-Diff-1.44-2.fc25.noarch was supposed to be removed but is not!). Even after dnf clean all and rpm --rebuilddb

I've also disabled the google-chrome repository and tried again, and the problem is exactly the same as above.

I'll add both of these to the top of my question so everyone knows both of these have been disabled.

vancel35 gravatar imagevancel35 ( 2018-03-07 09:39:32 -0500 )edit

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Asked: 2018-03-07 02:44:54 -0500

Seen: 717 times

Last updated: Mar 08 '18