Sorry to reactivate this old post but there was no correct answer.
The message :
(running on Debian, switching to user mode!) cannot setup TLPDB in /home/USER/texmf at /usr/bin/tlmgr line 5308.
is generated when tlmgr was not initialized. In most cases, launching the following command (as a normal user) solves the problem :
$ tlmgr init-usertree
This command will create few folders inside your home directory. See the man page for explanation :
Before using tlmgr in user mode, you have to set up the user tree with the init-usertree action. This creates usertree/web2c and usertree/tlpkg/tlpobj, and a minimal usertree/tlpkg/texlive.tlpdb. At that point, you can tell tlmgr to do the (supported) actions by adding the --usermode command line option.
If you have both a GNU/Linux distribution provided TeX Live and a manually installed one, you'll have two different tlmgr.
The one in /usr/bin will not update packages, but just change configuration parameters.
The one in /usr/local/texlive/<YEAR>/bin/<ARCH>, instead, will do updates to the manually installed TeX Live. Here <YEAR> stands for the version you have, probably 2014, while <ARCH> is the standard symbolic name for the processor, say x86_64-linux or i386-linux.
The correct call, if your data is as above, is
sudo /usr/local/texlive/2014/bin/x86_64-linux/tlmgr --gui
When doing a manual installation of TeX Live, I recommend doing
sudo ln -s /usr/local/texlive/2014/bin/x86_64-linux /opt/texbin
so you just need to add to your PATH the simpler /opt/texbin and have another benefit: when TeX Live 2015 is released and you install it, you just have to do
sudo rm /opt/texbin
sudo ln -s /usr/local/texlive/2015/bin/x86_64-linux /opt/texbin
and do no other change to your setup, because your PATH variable will already point to the correct location. If you create this symbolic link, then
sudo /opt/texbin/tlmgr --gui
will become the correct call.
See this article on TUGboat which explains the installation procedure I recommend and that's still valid provided you just change the year from 2010 to the current release year.
Best Answer
Short answer
The Ubuntu package seems to be fairly broken, so remove it and install via https://tug.org/texlive/acquire.html.
Long answer
Find out which package you have installed:
Kill it with prejudice:
sudo apt purge texlive-baseFollow instructions in link (above) to install working TexLive.