Edgy update problem(s)

[marc]

Hi,

I attempted an update to edgy (from dapper) via

  kdesu "update-manager -c"

After a few hours of downloads it spewed out the following message:

  This upgrade requires that the /usr/X11R6/bin directory be removed and
  replaced with a symlink. An attempt was made to do so, but it failed,
  most likely because the directory is not yet empty. You must move the
  files that are currently in the directory out of the way so that the
  installation can complete. If you like, you may move them back after 
  the symlink is in place.

  This package installation will now fail and exit so that you can do
  this. Please re-run your upgrade procedure after you have cleaned out
  the directory.

After making this change, rerunning update-manager halts with:

  Software index is broken

  it is impossible to install or remove any software. Please use
  the package manager "Synaptic" or run "sudo apt-get install -f"
  in a terminal to fix this issue first.

Running

  sudo apt-get install -f

produces the following:

  Reading package lists... Done
  Building dependency tree... Done
  Correcting dependencies...Done
  The following extra packages will be installed:
    x11-common
  The following packages will be upgraded:
    x11-common
  1 upgraded, 0 newly installed, 0 to remove and 1200 not upgraded.
  40 not fully installed or removed.
  Need to get 0B/291kB of archives.
  After unpacking 418kB of additional disk space will be used.
  Do you want to continue [Y/n]? y
  DESTROY created new reference to dead object ' Qt::VBoxLayout', <> 
line 1 during global destruction.
  Preconfiguring packages ...
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 4.
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 9.
        
and a dialogue opens that says:

  Debconf on <machine name>
  Incorrect nice value
  Please enter an integer between -20 and 19

There is no field in which to enter a value and the only options are 
provided by three buttons:

  1. Help: which does nothing when clicked
  2. Next >: which redisplays the same dialogue while adding another 
     error message in the terminal

    Use of uninitialized value in join or string at 
    /usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 17.

    Repeatedly pressing Next > does the same as above, seemingly 
    endlessly, but adding 8 to the line number each time.

  3. Cancel: produces the following

  DESTROY created new reference to dead object ' Qt::VBoxLayout' during 
global destruction.
  (Reading database ... 169571 files and directories currently 
installed.)
  Preparing to replace x11-common 7.0.0-0ubuntu45 (using .../x11-common_
1%3a7.1.1ubuntu6.2_i386.deb) ...
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 4.
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 9.

  and the same dialogue as above opens once more.

  Cancelling this dialgue produces

  DESTROY created new reference to dead object ' Qt::VBoxLayout' during 
global destruction.
  dpkg: error processing /var/cache/apt/archives/x11-common_1%
3a7.1.1ubuntu6.2_i386.deb (--unpack):
  subprocess pre-installation script returned error exit status 255
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 4.
  Use of uninitialized value in join or string at 
/usr/share/perl5/Debconf/DbDriver/Stack.pm line 104, <GEN1> line 9.
  
  and, once again, open the debconf dialogue. Cancelling this dialogue 
ends the command with:

  DESTROY created new reference to dead object ' Qt::VBoxLayout' during 
global destruction.
  dpkg: error while cleaning up:
   subprocess post-installation script returned error exit status 255
  Errors were encountered while processing:
 /var/cache/apt/archives/x11-common_1%3a7.1.1ubuntu6.2_i386.deb
  E: Sub-process /usr/bin/dpkg returned an error code (1)

So, that doesn't work - confirmed by rerunning kdesu "update-manager -c"

Time to try Synaptic, as suggested.

On loading, Synaptic reports a broken package; this package is "xserver-
xorg-core". Removing this isn't an option, so I tried a reinstall. This 
marks x11-common for upgrade.

Using Synaptic's "Apply", the result is:

  E: /var/cache/apt/archives/x11-common_1%3a7.1.1ubuntu6.2_i386.deb: 
trying to overwrite `/usr/X11R6/bin', which is also in package xli


So, the problem is with /usr/X11R6/bin, but how to fix it?

(Since there seems to be a conflict with the xli package, I looked at
removing it, but it would remove ubuntu-desktop, all xserver packages
and a more, so that's not an option.)

-- 
Cheers,
Marc