mysql-server-5.6.postinst fails with: "cp: impossible d'écraser le répertoire «/var/lib/mysql-upgrade/DATADIR.link/mysql» par un non répertoire"

Thank you for taking the time to report this bug and helping to make Ubuntu better.

I believe this problem comes from the following code in mysql-server-5.6.preinst:

# if there's a symlink, let's store where it's pointing, because otherwise
# it's going to be lost in some situations
for dir in DATADIR LOGDIR; do
    checkdir=`eval echo "$"$dir`
    if [ -L "$checkdir" ]; then
        mkdir -p "$UPGRADEDIR"
        cp -d "$checkdir" "$UPGRADEDIR/$dir.link"
    fi
done

It isn't obvious to me why this would fail in this case, however. Please can you report the output of "stat /var/lib/mysql", "stat /var/lib/mysql-upgrade", "stat /var/lib/mysql-upgrade/DATADIR.link" and "stat /var/lib/mysql-upgrade/DATADIR.link/mysql" and then change the bug status back to New?

My MySQL 5.6's datadir is a symbolic link and I've the same issue.
To be honest this server uses using Debian v7.11:
Linux 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3~bpo70+1 (2016-07-07) x86_64 GNU/Linux

An `aptitude upgrade` fails:

----------8<----------
$ aptitude upgrade
The following packages will be upgraded:
  mysql-server-5.6
The following packages are RECOMMENDED but will NOT be installed:
  mysql-common-5.6
1 packages upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Need to get 0 B/14.7 MB of archives. After unpacking 8192 B will be used.
Do you want to continue? [Y/n/?] Y
Reading changelogs... Done
Preconfiguring packages ...
(Reading database ... 93574 files and directories currently installed.)
Preparing to replace mysql-server-5.6 5.6.32-1~dotdeb+7.1 (using .../mysql-server-5.6_5.6.34-1~dotdeb+7.2_amd64.deb) ...
Stopping MySQL database server: mysqld.
Stopping MySQL database server: mysqld.
cp: cannot overwrite directory `/var/lib/mysql-upgrade/DATADIR.link/mysql' with non-directory
dpkg: error processing /var/cache/apt/archives/mysql-server-5.6_5.6.34-1~dotdeb+7.2_amd64.deb (--unpack):
 subprocess new pre-installation script returned error exit status 1
Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld.
Checking for tables which need an upgrade, are corrupt or were
not closed cleanly..
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.6_5.6.34-1~dotdeb+7.2_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
A package failed to install. Trying to recover:
----------8<----------

Here are the asked `stat` outputs:
----------8<----------
$ stat /var/lib/mysql
  File: `/var/lib/mysql' -> `/home/.var/lib/mysql'
  Size: 20 Blocks: 0 IO Block: 4096 symbolic link
Device: 901h/2305d Inode: 394478 Links: 1
Access: (0777/lrwxrwxrwx) Uid: ( 105/ mysql) Gid: ( 0/ root)
Access: 2016-12-06 14:06:27.000000000 +0100
Modify: 2014-05-14 11:03:53.000000000 +0200
Change: 2014-10-01 17:09:49.000000000 +0200
 Birth: -

$ stat /var/lib/mysql-upgrade
  File: `/var/lib/mysql-upgrade'
  Size: 4096 Blocks: 8 IO Block: 4096 directory
Device: 901h/2305d Inode: 408247 Links: 2
Access: (0755/drwxr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2016-12-06 16:32:45.000000000 +0100
Modify: 2016-09-13 14:48:36.000000000 +0200
Change: 2016-09-13 14:48:36.000000000 +0200
 Birth: -

$ stat /var/lib/mysql-upgrade/DATADIR.link
  File: `/var/lib/mysql-upgrade/DATADIR.link' -> `/home/.var/lib/mysql'
  Size: 20 Blocks: 0 IO Block: 4096 symbolic link
Device: 901h/2305d Inode: 397993 Links: 1
Access: (0777/lrwxrwxrwx) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2016-12-06 16:31:58.000000000 +0100
Modify: 2016-09-13 14:48:36.000000000 +0200
Change: 2016-09-13 14:48:36.000000000 +0200
 Birth: -

$ stat /var/lib/mysql-upgrade/DATADIR.link/mysql
  File: `/var/lib/mysql-upgrade/DATADIR.link/mysql'
  Size: 4096 Blocks: 8 IO Block: 4096 directory
Device: 902h/2306d Inode: 56754435 Links: 2
Access: (0700/drwx---...

Workaround (found on "https://bugs.launchpad.net/ubuntu/+source/mariadb-10.0/+bug/1474212/comments/2"):

rm /var/lib/mysql-upgrade/DATADIR.link
apt-get -f install