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I have tried to install a few BioLinux packages -> several of the previous packages were 'broken'. After i ran :

apt-get -f install

apt-get upgrade 


apt-get upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages have been kept back:
r-cran-mass
The following packages will be upgraded:
desktop-file-utils

WARNING: The following packages cannot be authenticated!
desktop-file-utils
Install these packages without verification [y/N]? y
Reading changelogs... Done
(Reading database ... 
   dpkg: warning: files list file for package `desktop-file-utils' missing, assuming   package has no files currently installed.

Preparing to replace desktop-file-utils 0.15-2 (using .../desktop-file-utils_0.16- 0ubuntu2_amd64.deb) ...
Unpacking replacement desktop-file-utils ...
dpkg: error processing /var/cache/apt/archives/desktop-file-utils_0.16-0ubuntu2_amd64.deb (--unpack):
trying to overwrite '/etc/gnome/defaults.list', which is also in package gnome-session-common 2.30.2-3
 configured to not write apport reports
 Processing triggers for gnome-menus ...
 Processing triggers for man-db ...
 Errors were encountered while processing:
 /var/cache/apt/archives/desktop-file-utils_0.16-0ubuntu2_amd64.deb
 E: Sub-process /usr/bin/dpkg returned an error code (1)

I have also tried to reinstall it, updatem all,upgrade,reinstall agai, but i encounter the same issue.

Does anyone know the fix for this ? ( No OS reinstall though)

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up vote 0 down vote accepted

Don't really understand how you got yourself in this situation but apt is telling you it will overwrite /etc/gnome/defaults.list which is simply the list of default programs for gnome:

$ head /etc/gnome/defaults.list
[Default Applications]
application/rtf=abiword.desktop
application/x-abiword=abiword.desktop
text/abiword=abiword.desktop
text/richtext=abiword.desktop
text/rtf=abiword.desktop
text/x-abiword=abiword.desktop
text/x-xml-abiword=abiword.desktop
x-content/blank-bd=brasero-nautilus.desktop
x-content/blank-dvd=brasero-nautilus.desktop

You have a few options for "fixing" this problem:

  1. Do nothing. Unless there is a specific reason why you want to upgrade desktop-file-utils you can leave your system as is.

  2. Remove (rename) the offending file and try upgrading again. You can always move it back afterwards:

    mv /etc/gnome/defaults.list /etc/gnome/defaults.list.bak
    apt-get upgrade 
    

    Now you can compare the original file with the new one and decide which one to keep:

    diff /etc/gnome/defaults.list /etc/gnome/defaults.list.bak
    

    Or you can simply copy your old one back:

    mv /etc/gnome/defaults.list.bak /etc/gnome/defaults.list
    
  3. You can force the apt-get command to overwrite the file

    apt-get -o Dpkg::Options::="--force-overwrite" upgrade
    
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