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I've just did an update.

$ sudo tlmgr update --self
tlmgr: package repository http://sunsite.informatik.rwth-aachen.de/ftp/pub/mirror/ctan/systems/texlive/tlnet
tlmgr: saving backups to /usr/local/texlive/2013/tlpkg/backups
tlmgr: no updates for tlmgr present.
tlmgr: no updates available
$ sudo tlmgr update --all
[...]
[108/109, 06:49/06:49] update: collection-pictures [1k] (32769 -> 33307) ... done
[109/109, 06:51/06:51] update: collection-publishers [1k] (32864 -> 33330) ... done
tlmgr: package log updated: /usr/local/texlive/2013/texmf-var/web2c/tlmgr.log
running mktexlsr ...

mktexlsr failed (status -1), output:

running mtxrun --generate ...

mtxrun --generate failed (status -1), output:

Can't exec "kpsewhich": No such file or directory at ./tlmgr line 679.
Use of uninitialized value $TEXMFSYSVAR in scalar chomp at ./tlmgr line 679.
Can't exec "kpsewhich": No such file or directory at ./tlmgr line 680.
Use of uninitialized value $TEXMFSYSCONFIG in scalar chomp at ./tlmgr line 680.
Can't exec "kpsewhich": No such file or directory at ./tlmgr line 681.
Use of uninitialized value $TEXMFLOCAL in scalar chomp at ./tlmgr line 681.
Can't exec "kpsewhich": No such file or directory at ./tlmgr line 682.
Use of uninitialized value $TEXMFDIST in scalar chomp at ./tlmgr line 682.
Use of uninitialized value $TEXMFDIST in concatenation (.) or string at ./tlmgr line 693.
Can't exec "kpsewhich": No such file or directory at /usr/local/texlive/2013/tlpkg/TeXLive/TLUtils.pm line 2785.
Use of uninitialized value $tmfsysconf in scalar chomp at /usr/local/texlive/2013/tlpkg/TeXLive/TLUtils.pm line 2785.
Use of uninitialized value $tmfsysconf in concatenation (.) or string at /usr/local/texlive/2013/tlpkg/TeXLive/TLUtils.pm line 2786.
Cannot open /web2c/updmap.cfg for writing: No such file or directory at /usr/local/texlive/2013/tlpkg/TeXLive/TLUtils.pm line 2928.

Then I run mtxrun --generate which seemed to work.

Then I've tried to compile this file and got:

(/usr/local/texlive/2013/texmf-dist/tex/generic/pgfplots/pgfplots.revision.tex)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/frontendlayer/tikz.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/basiclayer/pgf.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/pgf/utilities/pgfrcs.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfutil-common.te
x
! I can't find file `pgfutil-common-lists.tex'.
l.556 \input pgfutil-common-lists.tex

(Press Enter to retry, or Control-D to exit)
Please type another input file name:

When I enter /usr/local/texlive/2013/texmf-dist/tex/generic/pgf/utilities/pgfutil-common-lists.tex it seems to work until it gets to pgfmathfunctions.integerarithmetics.code.tex which it also doesn't find.

As one other question with the same problem had problems with the path, I checked it (added breaks to make it easier to read):

$ echo $PATH
/usr/local/texlive/2013/bin/x86_64-linux:
/usr/local/texlive/2013/bin/x86_64-linux:
/usr/local/texlive/2013/bin/x86_64-linux:
/usr/local/texlive/2013/bin/x86_64-linux:
/usr/local/texlive/2013/bin/x86_64-linux:
/usr/local/sbin:/usr/local/bin:
/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:
/usr/local/games

I don't know why TexLive is there 5 times, but that should not be a problem (?)

Before the update, I had pgfplot 1.09.

Can anybody please tell me how to fix this problem?

share|improve this question
1  
    
@ClaudioFiandrino I saw this question. Wehn You look at my path, this should not be the same problem. –  moose Apr 2 at 9:55
1  
@ClaudioFiandrino: I've just did run sudo mktexlsr and then kpsewhich pgfutil-common-lists.tex again and it worked ... very strange. And somehow my sudo PATH seems not to be the same as my usual PATH. –  moose Apr 2 at 9:57
    
I guess this can be closed. Perhaps I should ask a question on unix.stackexchange.com why my sudo path is different from my usual path and how I can display the sudo path. –  moose Apr 2 at 9:58

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