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The other night I received the prompt suggesting for me to upgrade from 12.10 to 13.04. I figured why not, and accepted the upgrade. I had very little interaction, just clicked the accept button, and came back to an upgraded machine in an hour or so.

initramfs now fails on old linux headers which I do not believe exist on my system, and I am unable to update anything on my system which depends on it (which is, pretty much everything, including graphics drivers, system updates, etc). I have been trying to resolve this issue for nearly a month now, and have learned quite a lot about Ubuntu/Linux in the process, though I am still not sure what I have to do to get past the following error.

Whenever I run commands such as:

sudo apt-get install  (with -f or not)
sudo apt-get upgrade
sudo apt-get dist-upgrade
sudo apt-get remove
sudo apt-get autoremove
sudo update-initramfs -u

I will receive the following messages / errors and will not be able to continue the process:

Setting up initramfs-tools (0.103ubuntu0.7) ...
update-initramfs: deferring update (trigger activated)
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.8.0-31-generic
Fatal: open /boot/vmlinuz-3.5.0-21-generic: No such file or directory
run-parts: /etc/initramfs/post-update.d//runlilo exited with return code 1
dpkg: error processing initramfs-tools (--configure):
 subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
 initramfs-tools
E: Sub-process /usr/bin/dpkg returned an error code (1)

Both 'sudo apt-get clean' and 'sudo apt-get autoclean' seem to have no effect. Using 'sudo apt-get update' appears to run as expected, but no change as far as receiving the above error with subsequent commands.

Running 'sudo dpkg-reconfigure -a' did not make a difference.

Ive learned that there may be remnants of '3.5.0-21-generic' on my system. Ive done my best at locating them and moving them to a tmp dir in my home. Ive examined my /etc/apt/sources.list for any references to those headers, and there arent any.

Ive examined the contents of '/var/lib/dpkg/info/linux-image-generic.list' which is as follows:

/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/linux-image-generic
/usr/share/doc/linux-image-generic/copyright
/usr/share/doc/linux-image-generic/changelog.gz

Ive checked the contents of all of those locations, and found no references to anything with "3.5.0-21", and in fact searching my entire system, the only files with that string in the name now exist in my new tmp dir that I moved everything into. Ive also moved the references to linux-image-3.5.0-21-generic.* and linux-image-extra-3.5.0-22-generic.* that were in '/var/lib/dpkg/info' into my new tmp dir.

It seems to me that there isnt any place where vmlinuz-3.5.0-21-generic can be on my system. I cant find any when searching all files for anything containing '3.5.0-21'. I still cant use initramfs, which implies that I cant update/upgrade my system, install new packages, or fix a few other issues that sprung up when I upgraded to 13.04.

What follows is (some of) my output from: sudo update-initramfs -u -v

Available versions:  3.8.0-31-generic 3.5.0-41-generic
Keeping /boot/initrd.img-3.8.0-31-generic.dpkg-bak
update-initramfs: Generating /boot/initrd.img-3.8.0-31-generic
Adding module /lib/modules/3.8.0-31-generic/kernel/drivers/hid/hid.ko
... (mostly adding/calling happening here, hundreds of lines of output, seems successful)
Calling hook busybox
Adding binary /usr/lib/initramfs-tools/bin/busybox
Calling hook dmsetup
Adding binary /sbin/dmsetup
Adding library /lib/i386-linux-gnu/libdevmapper.so.1.02.1
rm -f ./etc/ld.so.conf.d/nvidia_settings.conf 
rm -f ./lib/firmware/cxgb4/t4fw.bin 
Building cpio /boot/initrd.img-3.8.0-31-generic.new initramfs
Fatal: open /boot/vmlinuz-3.5.0-21-generic: No such file or directory
run-parts: /etc/initramfs/post-update.d//runlilo exited with return code 1

Could anyone please help me understand this problem, and how I can alleviate it? What can I do to get past this? I really dont want to resort to completely reinstalling my system, is there any other way to fix this?

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What's the output of sudo dpkg --configure -a? –  Braiam Oct 15 '13 at 14:14
    
@Braiam - same issue as above - starting with the line "Setting up initramfs-tools (0.103ubuntu0.7) ..." and then the same exact output lines as pasted above. –  Todd Oct 16 '13 at 22:52
    
Use this instead apt-get download linux-image-3.5.0-21-generic then run sudo dpkg -i linux-image*.deb. –  Braiam Oct 16 '13 at 23:14
    
@Braiam thanks, but I get the following error when downloading that linux-image: E: Can't select candidate version from package linux-image-3.5.0-21-generic as it has no candidate –  Todd Oct 16 '13 at 23:35
    
Try sudo apt-get remove linux-image-3.5.0-21-generic, the sudo apt-get -f install –  minerz029 Oct 17 '13 at 0:14
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1 Answer

up vote 0 down vote accepted

I fixed the issue, and can now update my system as normal. However, I still dont understand how this issue began.

In any event, I went ahead and installed both the first listed missing kernel, 3.5.0-21. I have since edited this aspect of the question out, but after getting 3.5.0-21 installed, initramfs began whining about 3.5.0-17. So I decided I had delt with this issue and allowed it to consume way too much of my time, and backed up all my data, and prepared for the worst but hoped for the best.

I figured out how to download old/deprecated linux kernel/headers by searching for them on packages.ubuntu.com. I then edited my /etc/apt/sources.list file to allow the candidate versions associated with these two linux images to be downloaded. I then ran 'sudo apt-get update' to update the sources. Then I was able to run 'sudo apt-get download linux-image3.5.0-##-generic' and succesfully installed both packages.

After this, all my apt-get commands continued to function, I managed to get the latest updates to 13.04 installed and also all of my other user software updated.

Then, after restart, my mouse and keyboard were no longer responding! My grub menu disappeared! I couldnt get tty terminal up, or do anything really. From my windows computer, I downloaded a 13.10 image, created a usb flash ubuntu boot disk, and rescued grub after booting from this flash volume. After rescuing grub, I was able to boot into recovery mode, and fix any bad packages or whatever it was that happened. After rebooting into my machine, I could log in with full mouse and keyboard. Now my system seems stable and whoa am I amazed at what a learning experience this all is.

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