FedUp 18 -> 19 Orphans

[Kevin H. Hobbs]

I just updated from Fedora 18 to 19 with fedup.

After the update I have many orphaned packages :

# package-cleanup --orphans | wc -l
635

When I examine them I see things like fedora-release, zlib, and such.

They mostly exist alongside their identical fedora 19 versions :

# package-cleanup --orphans | grep libogg
libogg-1.3.0-5.fc18.x86_64
# yum list libogg
Loaded plugins: auto-update-debuginfo, verify
Installed Packages
libogg.x86_64   2:1.3.0-5.fc18   installed
libogg.i686     2:1.3.0-5.fc19   installed
libogg.x86_64   2:1.3.0-5.fc19   installed

Any idea what's going on?

[Frank Murphy]

On Thu, 19 Dec 2013 12:16:16 -0500
"Kevin H. Hobbs"  wrote:
> I just updated from Fedora 18 to 19 with fedup.
> Any idea what's going on?

package-cleanup --dupes
packagecleanup --cleandupes

[Kevin H. Hobbs]

Frank wrote:
> package-cleanup --dupes
> packagecleanup --cleandupes

Somewhere in there some some dependency leaves fc18 and starts ripping
out large parts of fc19..

It looks to be perl

# yum remove `package-cleanup --dupes | grep perl | grep fc18`
...
Remove  67 Packages (+32 Dependent packages)...

It looks like I'm going to have to fix these in small batches...

[M A Young]

On Thu, 19 Dec 2013, Kevin H. Hobbs wrote:
> I just updated from Fedora 18 to 19 with fedup.
>
> After the update I have many orphaned packages :
>
> # package-cleanup --orphans | wc -l
> 635
>
> When I examine them I see things like fedora-release, zlib, and such.
>
> They mostly exist alongside their identical fedora 19 versions :
>
> # package-cleanup --orphans | grep libogg
> libogg-1.3.0-5.fc18.x86_64
> # yum list libogg
> Loaded plugins: auto-update-debuginfo, verify
> Installed Packages
> libogg.x86_64   2:1.3.0-5.fc18   installed
> libogg.i686     2:1.3.0-5.fc19   installed
> libogg.x86_64   2:1.3.0-5.fc19   installed
>
> Any idea what's going on?

You seem to have had an incomplete update. You will need to tidy up 
manually, eg. with package-cleanup --dupes and package-cleanup 
--cleandupes . You may also need to use yum or rpm to remove some of the 
duplicates by hand if package-cleanup can't work out how to solve all the 
dependencies.

Michael Young

[Kevin H. Hobbs]

Michael wrote:
> You may also need to use yum or rpm to remove some of the duplicates
> by hand if package-cleanup can't work out how to solve all the 
> dependencies.

The only bits of perl that I could not clean up seem to be perl and perl
libs.

I did :

# rpm -q --provides perl-5.16.3-266.fc19.x86_64 > /tmp/p19.txt
# rpm -q --provides perl-5.16.3-245.fc18.x86_64 > /tmp/p18.txt
# diff /tmp/p18.txt /tmp/p19.txt

and among the interesting bits of output was :

90d61
< perl(Fatal) = 2.10

so then I did :

# rpm -q --whatrequires "perl(Fatal)"
perl-5.16.3-245.fc18.x86_64
redhat-lsb-languages-4.1-14.fc19.x86_64
# rpm -q --whatprovides "perl(Fatal)"
perl-5.16.3-245.fc18.x86_64

so there is a F19 package that depends on a F18 package

Yum tells me that "perl(Fatal)" comes from :

# yum provides "perl(Fatal)"
Loaded plugins: auto-update-debuginfo, verify
perl-autodie-2.16-1.fc19.noarch : Replace functions with ones that
succeed or die
Repo        : fedora
Matched from:
Provides    : perl(Fatal) = 2.16

4:perl-5.16.3-245.fc18.x86_64 : Practical Extraction and Report Language
Repo        : @updates/18
Matched from:
Provides    : perl(Fatal) = 2.10
# yum list perl-autodie
Loaded plugins: auto-update-debuginfo, verify
Available Packages
perl-autodie.noarch                                          2.16-1.fc19
                                         fedora

which did not get installed...

# yum install perl-autodie
...
Transaction check error:
  file /usr/share/man/man3/Fatal.3pm.gz from install of
perl-autodie-2.16-1.fc19.noarch conflicts with file from package
perl-4:5.16.3-245.fc18.x86_64
  file /usr/share/man/man3/autodie.3pm.gz from install of
perl-autodie-2.16-1.fc19.noarch conflicts with file from package
perl-4:5.16.3-245.fc18.x86_64
  file /usr/share/man/man3/autodie::exception.3pm.gz from install of
perl-autodie-2.16-1.fc19.noarch conflicts with file from package
perl-4:5.16.3-245.fc18.x86_64
  file /usr/share/man/man3/autodie::exception::system.3pm.gz from
install of perl-autodie-2.16-1.fc19.noarch conflicts with file from
package perl-4:5.16.3-245.fc18.x86_64
  file /usr/share/man/man3/autodie::hints.3pm.gz from install of
perl-autodie-2.16-1.fc19.noarch conflicts with file from package
perl-4:5.16.3-245.fc18.x86_64

because it conflicts with perl from f18...

[M A Young]

On Thu, 19 Dec 2013, Kevin H. Hobbs wrote:
> # yum install perl-autodie
> ...
> Transaction check error:
>  file /usr/share/man/man3/Fatal.3pm.gz from install of
> perl-autodie-2.16-1.fc19.noarch conflicts with file from package
> perl-4:5.16.3-245.fc18.x86_64
>  file /usr/share/man/man3/autodie.3pm.gz from install of
> perl-autodie-2.16-1.fc19.noarch conflicts with file from package
> perl-4:5.16.3-245.fc18.x86_64
>  file /usr/share/man/man3/autodie::exception.3pm.gz from install of
> perl-autodie-2.16-1.fc19.noarch conflicts with file from package
> perl-4:5.16.3-245.fc18.x86_64
>  file /usr/share/man/man3/autodie::exception::system.3pm.gz from
> install of perl-autodie-2.16-1.fc19.noarch conflicts with file from
> package perl-4:5.16.3-245.fc18.x86_64
>  file /usr/share/man/man3/autodie::hints.3pm.gz from install of
> perl-autodie-2.16-1.fc19.noarch conflicts with file from package
> perl-4:5.16.3-245.fc18.x86_64
>
> because it conflicts with perl from f18...

You need to do both at the same time. Here yum shell is useful as it lets 
you gather a series of yum commands and run them in one batch. Try
something like

yum shell
> remove perl-5.16.3-245.fc18.x86_64
> install perl-autodie
> run

and if that works
> exit

you may need to add other commands as well to sort out the dependencies.

Michael Young

[Kevin H. Hobbs]

Michael Young said:
> You need to do both at the same time. Here yum shell is useful as it
> lets you gather a series of yum commands and run them in one batch.
> Try something like
>
> yum shell
> > remove perl-5.16.3-245.fc18.x86_64 install perl-autodie run
>
> and if that works
> > exit
>
> you may need to add other commands as well to sort out the
> dependencies.

Wow, Michael, thank you very much for that.

I don't know how I managed not to know about yum shell.