Ubuntu 24.04 Upgrade Issue - Cannot upgrade system with unmerged /usr

[jcarson7]

I'm trying to upgrade to 24.04 from 22.04 but get the error of - Cannot upgrade system with unmerged /usr

I've installed usrmerge via the terminal

~$ sudo apt-get install usrmerge
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
usrmerge is already the newest version (25ubuntu2).
0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.

I am not prompted at any point to continue or anything. I've tried to re-run usrmerge via terminal

~$ sudo dpkg-reconfigure usrmerge

This produces no output at all.

I don't know that it matters but I have a duel boot system (Windows and Ubuntu) but that has never prevented an upgrade in the past.

I'm at a loss as to how to proceed. I've been on Linux for many years but I'm still somewhat of a noob so any assistance is greatly appreciated.

[Bashing-om]

Hello jcarson7 - Welcome to the Forums

As we have:

and 5 not upgraded.

what results:

sudo apt update
sudo apt full-upgrade
sudo do-release-upgrade

there is a path that seems right --- but ....

[jcarson7]

Thank you @Bashing-om for the quick reply. I have run those commands already and I end up with the same results. I'm assuming those 5 not upgrading are an issue but I'm at a loss on how to correct it.

[Bashing-om]

jcarson7; Well ---

Without information there is no way we can make a judgement for corrective action.

Please post back the outputs of those ups commands -

see then where we go from there

[jcarson7]

Below is the output from the commands.

~$ sudo apt update
[sudo] password for jscarson: 
Hit:1 http://archive.ubuntu.com/ubuntu jammy InRelease
Hit:2 http://archive.ubuntu.com/ubuntu jammy-updates InRelease                                    
Hit:3 http://archive.ubuntu.com/ubuntu jammy-security InRelease                                                   
Hit:4 https://dl.google.com/linux/chrome/deb stable InRelease                                                     
Hit:5 http://archive.ubuntu.com/ubuntu jammy-backports InRelease                            
Hit:6 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security InRelease                     
Hit:7 https://repo.nordvpn.com//deb/nordvpn/debian stable InRelease
Hit:8 https://esm.ubuntu.com/apps/ubuntu jammy-apps-updates InRelease
Hit:9 https://esm.ubuntu.com/infra/ubuntu jammy-infra-security InRelease
Hit:10 https://esm.ubuntu.com/infra/ubuntu jammy-infra-updates InRelease
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.

~$ sudo apt full-upgrade
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
  xdg-desktop-portal
1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/265 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] y
dpkg: warning: files list file for package 'usrmerge' missing; assuming package has no files currently installed
(Reading database ... 285979 files and directories currently installed.)
Preparing to unpack .../xdg-desktop-portal_1.14.4-1ubuntu2~22.04.2_amd64.deb ...
Unpacking xdg-desktop-portal (1.14.4-1ubuntu2~22.04.2) over (1.14.4-1ubuntu2~22.04.1) ...
Setting up xdg-desktop-portal (1.14.4-1ubuntu2~22.04.2) ...

~$ sudo do-release-upgrade
Checking for a new Ubuntu release

= Welcome to Ubuntu 24.04 LTS 'Noble Numbat' =

The Ubuntu team is proud to announce Ubuntu 24.04 LTS 'Noble Numbat'.

To see what's new in this release, visit:
  https://wiki.ubuntu.com/NobleNumbat/ReleaseNotes

Ubuntu is a Linux distribution for your desktop or server, with a fast
and easy install, regular releases, a tight selection of excellent
applications installed by default, and almost any other software you
can imagine available through the network.

We hope you enjoy Ubuntu.

== Feedback and Helping ==

If you would like to help shape Ubuntu, take a look at the list of
ways you can participate at

  http://www.ubuntu.com/community/participate/

Your comments, bug reports, patches and suggestions will help ensure
that our next release is the best release of Ubuntu ever.  If you feel
that you have found a bug please read:

  http://help.ubuntu.com/community/ReportingBugs

Then report bugs using apport in Ubuntu.  For example:

  ubuntu-bug linux

will open a bug report in Launchpad regarding the linux package.

If you have a question, or if you think you may have found a bug but
aren't sure, first try asking on the #ubuntu or #ubuntu-bugs IRC
channels on Libera.Chat, on the Ubuntu Users mailing list, or on the
Ubuntu forums:

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Continue [yN] y
Get:1 Upgrade tool signature [833 B]                                                                                                                                                                              
Get:2 Upgrade tool [1,277 kB]                                                                                                                                                                                     
Fetched 1,278 kB in 0s (0 B/s)                                                                                                                                                                                    
authenticate 'noble.tar.gz' against 'noble.tar.gz.gpg' 
extracting 'noble.tar.gz'

Reading cache

Checking package manager
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Hit http://archive.ubuntu.com/ubuntu jammy InRelease                                                                                                                                                              
Hit https://dl.google.com/linux/chrome/deb stable InRelease                                                                                                                                                       
Hit http://archive.ubuntu.com/ubuntu jammy-updates InRelease                                                                                                                                                      
Hit https://repo.nordvpn.com//deb/nordvpn/debian stable InRelease                                                                                                                                                 
Hit http://archive.ubuntu.com/ubuntu jammy-security InRelease                                                                                                                                                     
Hit http://archive.ubuntu.com/ubuntu jammy-backports InRelease                                                                                                                                                    
Hit https://esm.ubuntu.com/apps/ubuntu jammy-apps-security InRelease                                                                                                                                              
Hit https://esm.ubuntu.com/apps/ubuntu jammy-apps-updates InRelease                                                                                                                                               
Hit https://esm.ubuntu.com/infra/ubuntu jammy-infra-security InRelease                                                                                                                                            
Hit https://esm.ubuntu.com/infra/ubuntu jammy-infra-updates InRelease                                                                                                                                             
Fetched 0 B in 0s (0 B/s)                                                                                                                                                                                         
Reading package lists... Done    
Building dependency tree... Done 
Reading state information... Done

Cannot upgrade system with unmerged /usr 

Please install the usrmerge package to fix this, and then try the 
upgrade again. 


Restoring original system state

Aborting
Reading package lists... Done    
Building dependency tree... Done 
Reading state information... Done

[deadflowr]

dpkg: warning: files list file for package 'usrmerge' missing; assuming package has no files currently installed

Try reinstall

sudo apt install--reinstall usrmerge

File list should exist and look like this:

dpkg -L usrmerge
/.
/usr
/usr/lib
/usr/lib/usrmerge
/usr/lib/usrmerge/convert-etc-shells
/usr/lib/usrmerge/convert-usrmerge
/usr/lib/usrmerge/lib
/usr/lib/usrmerge/lib/Fatal.pm
/usr/lib/usrmerge/lib/File
/usr/lib/usrmerge/lib/File/Find
/usr/lib/usrmerge/lib/File/Find/Rule.pm
/usr/lib/usrmerge/lib/File/Find.pm
/usr/lib/usrmerge/lib/Number
/usr/lib/usrmerge/lib/Number/Compare.pm
/usr/lib/usrmerge/lib/Text
/usr/lib/usrmerge/lib/Text/Glob.pm
/usr/lib/usrmerge/lib/Tie
/usr/lib/usrmerge/lib/Tie/RefHash.pm
/usr/lib/usrmerge/lib/autodie
/usr/lib/usrmerge/lib/autodie/Scope
/usr/lib/usrmerge/lib/autodie/Scope/Guard.pm
/usr/lib/usrmerge/lib/autodie/Scope/GuardStack.pm
/usr/lib/usrmerge/lib/autodie/Util.pm
/usr/lib/usrmerge/lib/autodie.pm
/usr/lib/usrmerge/lib/if.pm
/usr/share
/usr/share/doc
/usr/share/doc/usrmerge
/usr/share/doc/usrmerge/README.Debian
/usr/share/doc/usrmerge/changelog.gz
/usr/share/doc/usrmerge/copyright

[1fallen]

Well yes and no to the above, ie:

 apt policy usrmerge
usrmerge:
  Installed: (none)
  Candidate: (none)
  Version table:

But may be related to:

dpkg -S {/usr,}/lib/a

Also Please have a look here: https://askubuntu.com/questions/1406...ge-fatal-error

dpkg -L usrmerge
dpkg-query: package 'usrmerge' is not installed
Use dpkg --contents (= dpkg-deb --contents) to list archive files contents.

apt show usrmerge
Package: usrmerge
State: not a real package (virtual)
Notice: Can't select candidate version from package usrmerge as it has no candidate
Notice: Can't select versions from package 'usrmerge' as it is purely virtual
Notice: No packages found

rmadison usrmerge
 usrmerge | 9         | xenial/universe | source, all
 usrmerge | 17        | bionic/universe | source, all
 usrmerge | 23        | focal/universe  | source, all
 usrmerge | 25ubuntu2 | jammy           | source, all

This on 24.10 upgrade from 20.04 thru 22.04, 24.04, 24.10

[leanderglanda]

Hi there,

I'm having the same issue described in the first post.

Output of `dpkg -L usermerge` looks different than the output from @1fallen2.
Also running `convert-usrmerge` works for me, but the `do-release-upgrade` still fails, because of an unmerged /usr.

Here my output:

leander@LeanderGlandaUbuntu:~$ dpkg -L usrmerge
/.
/usr
/usr/lib
/usr/lib/usrmerge
/usr/lib/usrmerge/convert-etc-shells
/usr/lib/usrmerge/convert-usrmerge
/usr/lib/usrmerge/lib
/usr/lib/usrmerge/lib/Fatal.pm
/usr/lib/usrmerge/lib/File
/usr/lib/usrmerge/lib/File/Find
/usr/lib/usrmerge/lib/File/Find/Rule.pm
/usr/lib/usrmerge/lib/File/Find.pm
/usr/lib/usrmerge/lib/Number
/usr/lib/usrmerge/lib/Number/Compare.pm
/usr/lib/usrmerge/lib/Text
/usr/lib/usrmerge/lib/Text/Glob.pm
/usr/lib/usrmerge/lib/Tie
/usr/lib/usrmerge/lib/Tie/RefHash.pm
/usr/lib/usrmerge/lib/autodie
/usr/lib/usrmerge/lib/autodie/Scope
/usr/lib/usrmerge/lib/autodie/Scope/Guard.pm
/usr/lib/usrmerge/lib/autodie/Scope/GuardStack.pm
/usr/lib/usrmerge/lib/autodie/Util.pm
/usr/lib/usrmerge/lib/autodie.pm
/usr/lib/usrmerge/lib/if.pm
/usr/share
/usr/share/doc
/usr/share/doc/usrmerge
/usr/share/doc/usrmerge/README.Debian
/usr/share/doc/usrmerge/changelog.gz
/usr/share/doc/usrmerge/copyright
leander@LeanderGlandaUbuntu:~$ sudo /usr/lib/usrmerge/convert-usrmerge
Smartmatch is experimental at /usr/lib/usrmerge/convert-usrmerge line 172.
The system has been successfully converted.
leander@LeanderGlandaUbuntu:~$

Any ideas on how to fix the upgrade?

[1fallen]

Any ideas on how to fix the upgrade?

Read through *all* on the link I provided.

[leanderglanda]

Okay I'm sorry. If I understood things correctly there isn't a fix right now and it seems that will take some time.
I thought things may be different for me as usrmerge says it has successfully merged /usr.