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I have recently updated TexLive through tlmgr. After that I got several errors when running LaTeX saying that some .sty file was not found. Those files exist, and when I run texhash I recive:

texhash: Updating /home/markl/texlive/2013/texmf-config/ls-R... 
texhash: /home/markl/texlive/2013/texmf-dist/ls-R: no write permission, skipping...
texhash: Updating /home/markl/texlive/2013/../texmf-local/ls-R... 
texhash: Updating /home/markl/texlive/2013/texmf-var/ls-R... 
texhash: Done.

Any idea?

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    Try sudo texhash. – Sigur Dec 14 '13 at 18:34
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    Welcome to TeX.SX! It seems you have a TeX Live installed in your home. Check the owner of /home/markl/texlive and of directories below it. It should be you and not root or some other user. – egreg Dec 14 '13 at 19:11
  • Thanks @egreg. I've checked the file permission and found that /home/markl/texlive/2013/texmf-dist/ls-R was not owned by me (not sure the reason). After changing the owner now texhash can be run properly. Thank you very much! – markl Dec 14 '13 at 20:41
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The problem seems to be in wrong ownership of directories or files.

If TeX Live is installed in the home directory, it should be managed without ever using sudo and usually tlmgr does the right thing. But it can happen that ownerships or permissions get screwed. Check for them.

ls -dl /home/markl/texlive
ls -dl /home/markl/texlive/2013
ls -dl /home/markl/texlive/2013/texmf-dist
ls -l /home/markl/texlive/2013/texmf-dist/ls-R

might give the clue.

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