Issue with kernel upgrade

[daithi_dearg]

The system boots fine but I'm not able to run apt-get install commands.

It seems to me that the kernel has half installed. Through the update I was prompted to run following:

sudo apt --fix-broken install
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  linux-headers-5.4.0-45 linux-headers-5.4.0-45-generic linux-image-5.4.0-45-generic linux-modules-5.4.0-45-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  linux-modules-extra-5.4.0-51-generic
The following NEW packages will be installed:
  linux-modules-extra-5.4.0-51-generic
0 upgraded, 1 newly installed, 0 to remove and 195 not upgraded.
11 not fully installed or removed.
Need to get 0 B/38.6 MB of archives.
After this operation, 190 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 298176 files and directories currently installed.)
Preparing to unpack .../linux-modules-extra-5.4.0-51-generic_5.4.0-51.56_amd64.deb ...
Unpacking linux-modules-extra-5.4.0-51-generic (5.4.0-51.56) ...
dpkg: error processing archive /var/cache/apt/archives/linux-modules-extra-5.4.0-51-generic_5.4.0-51.56_amd64.deb (--unpack):
 unable to open '/lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new': Operation not permitted
Errors were encountered while processing:
 /var/cache/apt/archives/linux-modules-extra-5.4.0-51-generic_5.4.0-51.56_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

I thought I might be able to remove the offending kernel in /boot but I see no sign of this here.

Can provide more outputs as required.

[tea for one]

Can you successfully boot into a previous kernel via Grub > Advanced options?

[ActionParsnip]

What is the output of:

file /lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new

Thanks

[daithi_dearg]

Just to clarify I have no issue booting the machine. The issue is running apt-get to install updates.

Booted into previous kernel and while running the command does get me further still getting errors:

Unpacking linux-modules-extra-5.4.0-52-generic (5.4.0-52.57) ...
dpkg: error processing archive /tmp/apt-dpkg-install-ZFfVo9/2-linux-modules-extr
a-5.4.0-52-generic_5.4.0-52.57_amd64.deb (--unpack):
 unable to open '/lib/modules/5.4.0-52-generic/kernel/drivers/net/ethernet/qualc
omm/emac/qcom-emac.ko.dpkg-new': Operation not permitted
Preparing to unpack .../3-linux-generic_5.4.0.52.55_amd64.deb ...
Unpacking linux-generic (5.4.0.52.55) over (5.4.0.51.54) ...
Preparing to unpack .../4-linux-image-generic_5.4.0.52.55_amd64.deb ...
Unpacking linux-image-generic (5.4.0.52.55) over (5.4.0.51.54) ...
Selecting previously unselected package linux-headers-5.4.0-52.
Preparing to unpack .../5-linux-headers-5.4.0-52_5.4.0-52.57_all.deb ...
Unpacking linux-headers-5.4.0-52 (5.4.0-52.57) ...
Selecting previously unselected package linux-headers-5.4.0-52-generic.
Preparing to unpack .../6-linux-headers-5.4.0-52-generic_5.4.0-52.57_amd64.deb .
..
Unpacking linux-headers-5.4.0-52-generic (5.4.0-52.57) ...
Preparing to unpack .../7-linux-headers-generic_5.4.0.52.55_amd64.deb ...
Unpacking linux-headers-generic (5.4.0.52.55) over (5.4.0.51.54) ...
Errors were encountered while processing:
 /tmp/apt-dpkg-install-ZFfVo9/2-linux-modules-extra-5.4.0-52-generic_5.4.0-52.57
_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

Also that file command didn't find anything:

david@david-N7x0WU:~$ ls -l /boot/initrd.img*
lrwxrwxrwx 1 root root       27 Jul 23 06:42 /boot/initrd.img -> initrd.img-5.4.0-42-generic
-rw-r--r-- 1 root root 73149176 Aug 24 22:50 /boot/initrd.img-4.15.0-39-generic
-rw-r--r-- 1 root root 85569843 Aug 24 22:49 /boot/initrd.img-5.4.0-40-generic
-rw-r--r-- 1 root root 85569589 Aug 24 22:52 /boot/initrd.img-5.4.0-42-generic
lrwxrwxrwx 1 root root       27 Jul 23 06:42 /boot/initrd.img.old -> initrd.img-5.4.0-40-generic
david@david-N7x0WU:~$ file /lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new
/lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new: cannot open `/lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new' (No such file or directory)
david@david-N7x0WU:~$ ls /lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/
bnx2x  tg3.ko

[ActionParsnip]

If you run:

sudo touch /lib/modules/5.4.0-51-generic/kernel/drivers/net/ethernet/broadcom/cnic.ko.dpkg-new

Does it help?

[daithi_dearg]

Not really. Getting following below now:

sudo apt --fix-broken install
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  linux-headers-5.4.0-45 linux-headers-5.4.0-45-generic linux-headers-5.4.0-51 linux-headers-5.4.0-51-generic linux-image-5.4.0-45-generic linux-image-5.4.0-51-generic linux-modules-5.4.0-45-generic
  linux-modules-5.4.0-51-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  linux-modules-extra-5.4.0-52-generic
The following NEW packages will be installed:
  linux-modules-extra-5.4.0-52-generic
0 upgraded, 1 newly installed, 0 to remove and 196 not upgraded.
15 not fully installed or removed.
Need to get 0 B/38.6 MB of archives.
After this operation, 190 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 329190 files and directories currently installed.)
Preparing to unpack .../linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb ...
Unpacking linux-modules-extra-5.4.0-52-generic (5.4.0-52.57) ...
dpkg: error processing archive /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb (--unpack):
 unable to open '/lib/modules/5.4.0-52-generic/kernel/drivers/memstick/host/r592.ko.dpkg-new': Operation not permitted
Errors were encountered while processing:
 /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

[tea for one]

15 not fully installed or removed

As the kernel 5.4.0-52 (among other things) is causing a problem, possibly worth considering:-

Boot into previous working kernel.
Remove linux-modules-extra-5.4.0-52
Run updates and upgrades (without kernel components) so that other packages are up-to date
Also sudo update-grub

If successful, then try the the kernel again.
If unsuccessful, there may be other error messages.

[daithi_dearg]

Not using this kernel:

david@david-N7x0WU:~$ uname -r
5.4.0-42-generic

Continue to see same issues after removing that file:

david@david-N7x0WU:~$ sudo rm /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb 
david@david-N7x0WU:~$ sudo apt --fix-broken install
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  linux-headers-5.4.0-45 linux-headers-5.4.0-45-generic linux-headers-5.4.0-51 linux-headers-5.4.0-51-generic linux-image-5.4.0-45-generic linux-image-5.4.0-51-generic linux-modules-5.4.0-45-generic
  linux-modules-5.4.0-51-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  linux-modules-extra-5.4.0-52-generic
The following NEW packages will be installed:
  linux-modules-extra-5.4.0-52-generic
0 upgraded, 1 newly installed, 0 to remove and 196 not upgraded.
15 not fully installed or removed.
Need to get 38.6 MB of archives.
After this operation, 190 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://ie.archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-modules-extra-5.4.0-52-generic amd64 5.4.0-52.57 [38.6 MB]
Fetched 38.6 MB in 14s (2,720 kB/s)                                                                                                                                                                       
(Reading database ... 329190 files and directories currently installed.)
Preparing to unpack .../linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb ...
Unpacking linux-modules-extra-5.4.0-52-generic (5.4.0-52.57) ...
dpkg: error processing archive /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb (--unpack):
 unable to open '/lib/modules/5.4.0-52-generic/kernel/kernel/kheaders.ko.dpkg-new': Operation not permitted
Errors were encountered while processing:
 /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

Hope this is what you meant. Also tried apt-get remove but this didn't go anywhere.

[tea for one]

Not quite what I meant but let's persevere.

You still have 15 packages not fully installed or removed and I was hoping that you would be able to:-

Boot into a previous kernel
Remove all packages with 5.4.0-52 in the title.
Update and upgrade other packages but do not include anything with 5.4.0-52.

When you run sudo apt update, you can then run apt list --upgradable.

This will allow you to ignore the kernel upgrades pro tem.

If this is successful, we may have to double check that the following are still installed because it can cause kernel upgrade problems if they are missing.

linux-generic linux-headers-generic linux-image-generic

We are trying to reach the point where everything is up-to-date other than the kernel upgrade.

[tea for one]

[QUOTE=daithi_dearg;13994178]Not using this kernel:

david@david-N7x0WU:~$ uname -r
5.4.0-42-generic

Continue to see same issues after removing that file:

david@david-N7x0WU:~$ sudo rm /var/cache/apt/archives/linux-modules-extra-5.4.0-52-generic_5.4.0-52.57_amd64.deb

Is that the correct way to remove a package?

I would use synaptic and search for 5.4.0-52 and then sort by Installed Version