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I am dealing with a vanilla installation of Tex Live 2016 and with a Ubuntu 14.04 LTS. For the installation I lauched a sudo install-tl along the lines of the instructions on www.tug.org. On the whole this has been successful, since I can launch tex, xdvi, dvips and so forth on the example documents.

However, in my installation settings, I had chosen the following directories

TEXMFCONFIG: "~/.texlive2016/texmf-config"  
TEXMFHOME: "~/texmf"
TEXMFLOCAL: "/opt/texlive/texmf-local"
TEXMFSYSCONFIG: "/opt/texlive/2016/texmf-config"
TEXMFSYSVAR: "/opt/texlive/2016/texmf-var"
TEXMFVAR: "~/.texlive2016/texmf-var"

and yet I can't seem to find any of the directories that had to be placed under ~ (say, with cd && ls -a). These are TEXMFCONFIG, TEXMFHOME, and TEXMFVAR

Is this a flaw of the installation procedure or am I supposed to create those directories manually?

In case this is relevant, I also noted in the log file of install-tl (pasted here) that my chosen home directory had been reset in two cases

updmap [WARNING]: resetting $HOME value (was /home/user) to root's actual home (/root).  # line 1128
fmtutil [WARNING]: resetting $HOME value (was /home/user) to root's actual home (/root).   # line 1324
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    you do not need the directories at all: the paths are just set up to make it convenient if you need a local tex tree – David Carlisle Jan 3 '17 at 21:30

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