Unable to fix broken package system

Question

After I (painfully) managed to install Skype on my Ubuntu 12.04 LTS, I'm experiencing since months ago a packages issue I cannot fix.

Have a look to my last post in order to know what caused this issue: Install Skype on Ubuntu 12.04 LTS 64-bit

If I try to install system Updates the Update Manager closes unexpectedly stating that the package system is broken and throws the following error:

The following packages have unmet dependencies:

grub-efi-amd64: Depends: grub2-common (= 1.99-21ubuntu3.9) but 1.99-21ubuntu3.10 is installed
                Depends: grub-efi-amd64-bin (= 1.99-21ubuntu3.9) but 1.99-21ubuntu3.10 is installed

If I run sudo apt-get -f install in order to fix potential packages issues I get the following:

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-image-3.5.0-26-generic linux-headers-3.5.0-26
  linux-headers-3.5.0-26-generic
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  grub-efi-amd64
The following packages will be upgraded:
  grub-efi-amd64
1 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
2 not fully installed or removed.
Need to get 39.5 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue [Y/n]? y
Get:1 http://archive.ubuntu.com/ubuntu/ precise-updates/main grub-efi-amd64 amd64 1.99-21ubuntu3.10 [39.5 kB]
Fetched 39.5 kB in 0s (154 kB/s)        
dpkg: dependency problems prevent configuration of grub-efi-amd64:
 grub-efi-amd64 depends on grub2-common (= 1.99-21ubuntu3.9); however:
  Version of grub2-common on system is 1.99-21ubuntu3.10.
 grub-efi-amd64 depends on grub-efi-amd64-bin (= 1.99-21ubuntu3.9); however:
  Version of grub-efi-amd64-bin on system is 1.99-21ubuntu3.10.
dpkg: error processing grub-efi-amd64 (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of grub-efi-amd64-signed:
 grub-efi-amd64-signed depends on grub-efi-amd64 (>= 1.99-21ubuntu3.5); however:
  Package grub-efi-amd64 is not configured yet.
dpkg: error processing grub-efi-amd64-signed (--configure):
 dependency problems - leaving unconfiguredNo apport report written because the error message indicates its a followup error from a previous failure.
                                                                     No apport report written because the error message indicates its a followup error from a previous failure.

Errors were encountered while processing:
 grub-efi-amd64
 grub-efi-amd64-signed
E: Sub-process /usr/bin/dpkg returned an error code (1)

If I run sudo dpkg --configure -a I get:

dpkg: dependency problems prevent configuration of grub-efi-amd64:
 grub-efi-amd64 depends on grub2-common (= 1.99-21ubuntu3.9); however:
  Version of grub2-common on system is 1.99-21ubuntu3.10.
 grub-efi-amd64 depends on grub-efi-amd64-bin (= 1.99-21ubuntu3.9); however:
  Version of grub-efi-amd64-bin on system is 1.99-21ubuntu3.10.
dpkg: error processing grub-efi-amd64 (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of grub-efi-amd64-signed:
 grub-efi-amd64-signed depends on grub-efi-amd64 (>= 1.99-21ubuntu3.5); however:
  Package grub-efi-amd64 is not configured yet.
dpkg: error processing grub-efi-amd64-signed (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 grub-efi-amd64
 grub-efi-amd64-signed

My understanding is that the root cause is unmet dependecies of packages grub-efi-amd64 and grub-efi-amd64-signed, so I have tried what is described here How do I resolve unmet dependencies after adding a PPA? but the problem still persist.

I'm not sure if the removal of the conflicting packages would fix the issue, but I haven't done it yet as I'm afraid I could ruin my system as it has EFI boot and I'm booting it with GRUB. For the same reason I haven't tried to run sudo apt-get -u dist-upgrade, as perhaps the conflicting packages could be automatically removed.

I'd like to know if others have had a similar experience as well as possible solutions to this.

Just as additional info this is the output of gedit /etc/apt/sources.list:

# deb cdrom:[Ubuntu 12.04.2 LTS _Precise Pangolin_ - Release amd64 (20130213)]/ dists/precise/main/binary-i386/

# deb cdrom:[Ubuntu 12.04.2 LTS _Precise Pangolin_ - Release amd64 (20130213)]/ dists/precise/restricted/binary-i386/
# deb cdrom:[Ubuntu 12.04.2 LTS _Precise Pangolin_ - Release amd64 (20130213)]/ precise main restricted

# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://archive.ubuntu.com/ubuntu precise main restricted

## Major bug fix updates produced after the final release of the
## distribution.
deb http://archive.ubuntu.com/ubuntu precise-updates main restricted

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://archive.ubuntu.com/ubuntu precise universe
deb http://archive.ubuntu.com/ubuntu precise-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu 
## team, and may not be under a free licence. Please satisfy yourself as to 
## your rights to use the software. Also, please note that software in 
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://archive.ubuntu.com/ubuntu precise multiverse
deb http://archive.ubuntu.com/ubuntu precise-updates multiverse

## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.

deb http://archive.ubuntu.com/ubuntu precise-security main restricted
deb http://archive.ubuntu.com/ubuntu precise-security universe
deb http://archive.ubuntu.com/ubuntu precise-security multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
deb http://archive.canonical.com/ubuntu precise partner
deb-src http://archive.canonical.com/ubuntu precise partner

## This software is not part of Ubuntu, but is offered by third-party
## developers who want to ship their latest software.
# deb http://extras.ubuntu.com/ubuntu precise main
# deb-src http://extras.ubuntu.com/ubuntu precise main
deb http://archive.canonical.com/ precise partner
deb-src http://archive.canonical.com/ precise partner

And gedit /etc/apt/sources.list.d/* (different files):

deb-src http://ppa.launchpad.net/cassou/emacs/ubuntu precise main

### THIS FILE IS AUTOMATICALLY CONFIGURED ###
# You may comment out this entry, but any other modifications may be lost.
deb http://dl.google.com/linux/chrome/deb/ stable main

### THIS FILE IS AUTOMATICALLY CONFIGURED ###
# You may comment out this entry, but any other modifications may be lost.
deb http://dl.google.com/linux/chrome/deb/ stable main

deb http://ppa.launchpad.net/guilhem-fr/swftools/ubuntu precise main
deb-src http://ppa.launchpad.net/guilhem-fr/swftools/ubuntu precise main

deb-src http://ppa.launchpad.net/rabbitvcs/ppa/ubuntu precise main

deb http://ppa.launchpad.net/yannubuntu/boot-repair/ubuntu precise main
deb-src http://ppa.launchpad.net/yannubuntu/boot-repair/ubuntu precise main

deb http://ppa.launchpad.net/yannubuntu/boot-repair/ubuntu precise main
deb-src http://ppa.launchpad.net/yannubuntu/boot-repair/ubuntu precise main

Solution

I finally solved my issue by removing with Synaptic the problematic packages grub-efi-amd64 and grub-efi-amd64-signed.

After that, I installed and applied all the pending system updates which seem to have installed again the mentioned packages.

Once all the update process finished I rebooted the system and everything is fine now.

Comments

[Alejandro García Seco]

Won't work, I get this either way: E: grub-efi-amd64: dependency problems - leaving unconfigured E: grub-efi-amd64-signed: dependency problems - leaving unconfigured

[Kanthala Raghu]

You seem to have added other repositories to your update manager. try not to add any third party (if your not sure) also untick unsupported updates/ pre-release updates from update manager. check this out for more information google.co.in/…

[Alejandro García Seco]

I have always had disabled "updates/ pre-release updates" in the update manager. Disabling third party repositories the outcome is the same.

[thewebjackal]

so you are suggesting sudo apt-get remove grub-efi-amd64 grub-efi-amd64-signed ??? Is it safe?