Many files in /var/lib/dpkg/info/ corrupted; how to recover

Question

When I run sudo apt-get (anything), I invariably get this error:

dpkg: unrecoverable fatal error, aborting:
 files list file for package 'thunderbird-gnome-support' is missing final newline
E: Sub-process /usr/bin/dpkg returned an error code (2)

After some Googling, I learn that this is because /var/lib/dpkg/info/thunderbird-gnome-support.list is corrupt. I cat that file, and it most certainly is corrupt - it should be a plain text file containing a list of absolute file paths, but instead is a binary file.

Now I inspect the other files in the same directory, and it appears that many of them are corrupt in the same way. This indicates that something went severely wrong in my file system, that caused many files to get corrupted. Unfortunately, it happened to affect system files.

How do I recover from this?

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More details:

Just prior to this, I installed a routine update when Ubuntu prompted me. It was a new Linux kernel, and some system file headers.

After restarting, these were my specs:

OS specs:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 13.10
Release:    13.10
Codename:   saucy
$ uname -a
Linux brendang-linux 3.11.0-24-generic #41-Ubuntu SMP Mon Jun 9 20:36:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Immediately after restarting for the first time, the entire file system appeared to be mounted as read only (which has not been the case previously). Subsequently I have had to reboot several times before the system worked. I have done touch /forcefsck in between them to ensure that fsck runs, and am not sure what else needs to be done.

Answer 1

In my case i got a lot of *.list files corrupted. If you do

file /var/lib/dpkg/info/<package_name>.list

you should usually get:

/var/lib/dpkg/info/<package_name>.list: ASCII text

but if your list files are corrupted you will get:

/var/lib/dpkg/info/<package_name>.list: data

I made two scripts to fix this problem.

The first script check for this and rename each corrupted .list file into *.list.broken

move_broken_list_files.sh

The second script cycle for each *.list.broken file and force reinstallation of the package.

install_missing_list.sh

sometimes the install fails because of problems with triggers:

fgets gave an empty string from '/var/lib/dpkg/info/libnih1:amd64.triggers'

in that case you have to move/rename that file like:

mv /var/lib/dpkg/info/libnih1:amd64.triggers /var/lib/dpkg/info/libnih1:amd64.triggers.broken

Hope this helps someone facing the same mess.

Answer 2

I solved this as follows:

• delete the offending file (in the OP case /var/lib/dpkg/info/thunderbird-gnome-support.list
• reinstall the offending package using apt-get install --reinstall thunderbird-gnome-support

This recreated the deleted file list for me as well.

Of course, this can be cumbersome if a lot of files are corrupt, but in my case it was only a single file and the solution was quite easy in this case.

Answer 3

Backup your damaged list (you can move all .list files)

mkdir /tmp/damaged && mv /var/lib/dpkg/info/*.list /tmp/damaged

Then, you can install your new package

apt install thunderbird-gnome-support