22.04 to 24.04 upgrade completed with errors. Unusable state warning.

**Phasmus** · September 19th, 2024

I kicked off my do-release-upgrade over ssh this morning and things are looking grim. It was working ok at first except during the upgrade it kept printing

Code:

 X11 connection rejected because of wrong authentication.

which sometimes forced useful information off the screen. Hopefully that's unrelated.

When the upgrade wrapped I saw this, before it got pushed off the screen by those X11 errors:

Code:

Upgrade complete 

The upgrade has completed but there were errors during the upgrade 
process.

I'm hoping there's a way to pull this out of the fire, ideally remotely, but I'm not sure where to start. I can still ssh to the system but I don't dare to reboot until I have a better idea what's going on. I'm happy to get rid of hdf5 and mpi but even if those are the cause of the issue, which isn't clear to me, I'm not sure how to restart the upgrade and turn this into a clean 24.04 install.

My /var/log/dist-upgrade/screenlog.0 is too big to upload, but here are the probably relevant excerpts, starting with the first obvious error.

Code:

Removing libhdf5-openmpi-dev (1.10.7+repack-4ubuntu2) ...
update-alternatives: warning: alternative /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc (part of link group hdf5.pc) doesn't exist; removing from list of alternatives
update-alternatives: warning: /etc/alternatives/hdf5.pc is dangling; it will be updated with best choice
update-alternatives: error: no alternatives for mpi
dpkg: error processing package libhdf5-openmpi-dev (--remove):
 installed libhdf5-openmpi-dev package pre-removal script subprocess returned error exit status 2
dpkg: too many errors, stopping
update-alternatives: using /usr/bin/h5pcc.openmpi to provide /usr/bin/h5pcc (h5pcc) in auto mode
update-alternatives: warning: /etc/alternatives/hdf5.pc is dangling; it will be updated with best choice
update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-openmpi.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
update-alternatives: error: no alternatives for mpi
dpkg: error while cleaning up:
 installed libhdf5-openmpi-dev package post-installation script subprocess returned error exit status 2
Errors were encountered while processing:
 libhdf5-openmpi-dev
Processing was halted because there were too many errors.
/usr/bin/gdbus: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory
ERROR: Cannot create report: [Errno 17] File exists: '/var/crash/libhdf5-openmpi-dev.0.crash'
/usr/bin/gdbus: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory
/usr/bin/gdbus: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory
Exception during pm.DoInstall():  E:Sub-process /usr/bin/dpkg returned an error code (1)

Could not install the upgrades 

The upgrade has aborted. Your system could be in an unusable state. A 
recovery will run now (dpkg --configure -a). 

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Errors were encountered while processing:
 libgs10:amd64
 libedataserverui4-1.0-0t64:amd64
 gnome-calculator
 libgweather-4-0t64:amd64
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 hplip
 gstreamer1.0-gl:amd64
 gir1.2-gtk-4.0:amd64
 libglib-object-introspection-perl
 libatk-bridge2.0-0t64:amd64
 graphviz
 libglib2.0-dev-bin
 unity-lens-video
 sssd-ad
 xdg-desktop-portal-gtk
 libreoffice-gtk3
 glib-networking-services
 unity-scope-home
 libchamplain-0.12-0:amd64
 indicator-appmenu
 gtk-update-icon-cache
 libxapp1:amd64
 libgts-bin
 tracker
 libdebuginfod1t64:amd64
 libqt6core6t64:amd64
 llvm-15
 unity-services
 bamfdaemon
 libwebkit2gtk-4.1-0:amd64
 python3-dbus
 libqt6widgets6t64:amd64
 unity
 libgck-2-2:amd64
 mailutils
 shotwell
 libnfsidmap1:amd64
 libproxy1v5:amd64
 timidity-interfaces-extra
 libglib-perl:amd64
 libgeoclue-2-0:amd64
 gstreamer1.0-x:amd64
 xdg-desktop-portal
 libgtksourceview-5-0:amd64
 gvfs:amd64
 libportal1:amd64
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 libgcr-4-4:amd64
Processing was halted because there were too many errors.
Starting upgrade of Ubuntu Pro service configuration
Finished upgrade of Ubuntu Pro service configuration

Upgrade complete 

The upgrade has completed but there were errors during the upgrade 
process.

**Phasmus** · September 19th, 2024

After trying a couple things some apt commands (apt --fix-broken install) are failing with errors like:

Code:

/usr/bin/gdbus: error while loading shared libraries: libgio-2.0.so.0: cannot open shared object file: No such file or directory

and

Code:

update-desktop-database: error while loading shared libraries: libglib-2.0.so.0: cannot open shared object file: No such file or directory

Trying to apt install individual packages fails with:

Code:

You might want to run 'apt --fix-broken install' to correct these.
The following packages have unmet dependencies:

...followed by a long list of packages with their missing dependencies, which seem to mostly come back to libglib2.0-0 and libgtk-3-0t64

**Phasmus** · September 19th, 2024

I think it's fixed. I grabbed the deb for the missing libglib2: wget http://archive.ubuntu.com/ubuntu/poo...u3.1_amd64.deb

And force installed it:

Code:

sudo dpkg -i  --force-overwrite  ./libglib2.0-0t64_2.80.0-6ubuntu3.1_amd64.deb

Before I did the force overwrite dpkg failed with:

Code:

dpkg: error processing archive ./libglib2.0-0t64_2.80.0-6ubuntu3.1_amd64.deb (--install):
 trying to overwrite shared '/usr/share/doc/libglib2.0-0t64/changelog.Debian.gz', which is different from other instances of package libglib2.0-0t64:amd64

I wonder if that is what caused the failure during the initial upgrade. I saw no sign of an error related to installing libglib2 in the log.

I got this warning during the forced dpkg which I hope I can ignore:

Code:

No such key “toggle-shaded” in schema “org.gnome.desktop.wm.keybindings:Unity” as specified in override file “/usr/share/glib-2.0/schemas/10_ubuntu-settings.gschema.override”; ignoring override for this key.

After an ldconfig, sudo apt --fix-broken install
worked.

Code:

sudo apt update

spits out a lot of messages like:

Code:

(appstreamcli:85449): GLib-GIO-CRITICAL **: 14:56:21.217: GFileInfo created without standard::is-hidden

(appstreamcli:85449): GLib-GIO-CRITICAL **: 14:56:21.217: file ../../../gio/gfileinfo.c: line 1632 (g_file_info_get_is_hidden): should not be reached

Code:

apt dist-upgrade

is cooking and I'll autoremove after that. Is there anything else I can do to finalize or clean up this upgrade since the initial do-release-upgrade didn't complete normally?

**unsound** · 2 Weeks Ago

Thanks for following up on this problem and taking the time to write down the solution. I had the same problem and managed to solve it in a similar way based on this thread, though the exact libglib2 download link is dead by now and I had to also install some dependencies manually since it wouldn't install otherwise. Also afterwards the dist-upgrade removed a lot of packages for me that shouldn't be removed (e.g. ubuntu-desktop + dependencies) so I'm going to have to reinstall some stuff manually.

I also had the "X11 connection rejected because of wrong authentication." messages due to connecting with ssh X forwarding enabled. This may have been the main problem as i believe that it triggered some code paths that would normally open up X11 window dialogs for user interaction but that wasn't possible and for some reason it got the upgrade into a place where it couldn't recover...

I guess this can be considered a bug in do-release-upgrade, but in the unlikely case that someone reads this before making the same mistake: Don't attempt a release upgrade over ssh with X forwarding enabled.

Thread: 22.04 to 24.04 upgrade completed with errors. Unusable state warning.

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