2

I want to disclaim that I am very inexperienced with latex. I am using Texmaker 4.3 with Miktex 2.9 on Windows 7.

I am writing an article (let's call it "test") which includes several packages to generate figures. One of them is pgfmolbio. When doing a Quickbuild , I am getting a Latex error that the environment pmbdomains is not defined. I understand from the documentation of this package that I have to run luatex on my file in order to get it to work. Now, when running luatex test it tells me that luatex.fmt was not found.

However, I find luatex on the dropdown list on top in texworks. Trying to use it there I get a similar error: I can't find the format file 'miktex-luatex.fmt'!.

From another answer with the same problem I learned that I should try to to run luatex -ini luatex.ini. When doing so, the Miktex package manager starts. The next error I get is I can't find etex.ini. I couldn't find any further solution and would be happy about help.

Edit: here is an example that produces the said error, taken from the pgfmolbio Package Manual:

\documentclass{article}
\usepackage[domains]{pgfmolbio}
\begin{document}
\begin{pmbdomains}[name=\TeX ase]{200}
\addfeature{disulfide}{40}{129}
\addfeature{disulfide}{53}{65}
\addfeature[description=Domain 1]{domain}{30}{80}
\addfeature[description=Domain 2]{domain}{93}{163}
\addfeature{domain}{168}{196}
\end{pmbdomains}
\end{document}

Edit 2: Log file of Lualatex (I redacted the path of the file):

This is LuaTeX, Version beta-0.70.2-2012060719 (MiKTeX 2.9 64-bit)  (format=lualatex 2014.9.10)  11 SEP 2014 14:37
**test2
("C:/.../test2.tex"
LaTeX2e <2011/06/27>
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Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
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\scratchdimen=\dimen152
\scratchbox=\box35
\nofMPsegments=\count110
\nofMParguments=\count111
\everyMPshowfont=\toks27
\MPscratchCnt=\count112
\MPscratchDim=\dimen153
\MPnumerator=\count113
\makeMPintoPDFobject=\count114
\everyMPtoPDFconversion=\toks28
) ABD: EveryShipout initializing macros
! LuaTeX error ...iles/MiKTeX 2.9/tex/lualatex/pgfmolbio/pgfmolbio.lua:54: atte
mpt to call field 'pack' (a nil value)
stack traceback:
    ...iles/MiKTeX 2.9/tex/lualatex/pgfmolbio/pgfmolbio.lua:54: in function 'getRa
nge'
    ...TeX 2.9/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua:407: in function '?'
    ...TeX 2.9/tex/lualatex/pgfmolbio/pgfmolbio.domains.lua:521: in function 'setP
arameters'
    <\directlua >:1: in main chunk.
\endpmbdomains ...Domains() \fi pmbProtein = nil }
                                                  \ifpmb@dom@tikzpicture \el...
l.11 \end{pmbdomains}

? x


Here is how much of LuaTeX's memory you used:
 10245 strings out of 495011
 100000,266212 words of node,token memory allocated 342 words of node memory still in use:
    nodes
   avail lists: 2:18,7:1,9:3
 13365 multiletter control sequences out of 65536+200000
 15 fonts using 602239 bytes
 63i,1n,57p,447b,239s stack positions out of 5000i,500n,10000p,200000b,50000s
No pages of output.

PDF statistics: 3 PDF objects out of 1000 (max. 8388607)
 0 named destinations out of 1000 (max. 131072)
 1 words of extra memory for PDF output out of 10000 (max. 10000000)
9
  • Welcome to TeX.SX! You should call lualatex instead of luatex. I don't know if that will solve your problem, but it's a step in the right direction.
    – mvkorpel
    Sep 10 '14 at 16:07
  • Thank you! This was one of the first things I tried but unfortunately I am getting the same error message that the environment pmbdomains specific to the package is not defined. Sep 11 '14 at 8:22
  • Could you post the contents of the .log file? This sounds like a path search problem. Sep 11 '14 at 9:26
  • I added the .log file for lualatex test2, no .log file is generated for luatex test2. Sep 11 '14 at 10:57
  • Another thing I forgot: you need to add the domains option to the pgfmolbio package: \usepackage[domains]{pgfmolbio}.
    – mvkorpel
    Sep 11 '14 at 11:14
5

With MiKTeX 2.9, your file compiles perfectly. But perhaps you should update your installation: your .log file mention LuaTeX, Version beta-0.70.2-2012060719 (MiKTeX 2.9 64-bit) and the beginning of my .log file is

This is LuaTeX, Version beta-0.76.0-2013062821 (rev 4627)  (format=lualatex 2013.6.28)  11 SEP 2014 13:54
\write18 enabled.

You also can try to redo the formats (although updating will certainly do it for you). To redo formats, launch MiKTeX Options (Settings) as administrator, select the Formats tab, select LuaLaTeX and click on build, as in this image:

enter image description here

2
  • Good answer. Looking at the error message in the log attached by the original poster, the reason why the older LuaTeX fails seems to be that table.pack() is not implemented. According to texdoc luatexref-t, "LuaTeX 0.74.0 is the first version with Lua 5.2". According to lua-users.org/wiki/LuaFiveTwo, Lua 5.2 adds the function table.pack().
    – mvkorpel
    Sep 11 '14 at 12:36
  • Oh my, that was it - I will update more frequently in the future. Thanks to all contributors, it works now. Sep 11 '14 at 16:37

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