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I was trying to make a chromatogram today using pgfmolbio using pdfTeX from TeX Live 2013.

The code I was using is:

\documentclass{article} 
\usepackage[chromatogram]{pgfmolbio}
\pagestyle{empty}
\begin{document}
\pmbchromatogram{seq.scf}
\end{document} 

The code gives me following error:

./figures-1.tex:5: Undefined control sequence.
l.5 \pmbchromatogram
                {seq.scf}

I tried my best to follow the manual page. However, even if I load the convert module, the same error message still occurs. I saw Package ifluatex Info: LuaTeX not detected. in the log. Could this be the source of the problem?

edit:

I also tried run the file with luatex after read Paul's comment. It gives me the following result:

This is LuaTeX, Version beta-0.76.0-2013061817 (rev 4627) 
 restricted \write18 enabled.
(./figures-1.tex
! Undefined control sequence.
l.1 \documentclass
                {article}
? 

edit:

Here is the result from lualatex.

This is LuaTeX, Version beta-0.76.0-2013061817 (rev 4627) 
 restricted \write18 enabled.
(./figures-1.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/size10.clo))
(/usr/local/texlive/2013/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ifluatex.sty)
(/usr/local/texlive/2013/texmf-dist/tex/luatex/luatexbase/luatexbase-modutils.s
ty
(/usr/local/texlive/2013/texmf-dist/tex/luatex/luatexbase/luatexbase-loader.sty

(/usr/local/texlive/2013/texmf-dist/tex/luatex/luatexbase/luatexbase-compat.sty
)
(/usr/local/texlive/2013/texmf-dist/tex/luatex/luatexbase/luatexbase.loader.lua)
)
(/usr/local/texlive/2013/texmf-dist/tex/luatex/luatexbase/modutils.lua))
(/usr/local/texlive/2013/texmf-dist/tex/luatex/lualibs/lualibs.lua)
! LuaTeX error ...xlive/2013/texmf-dist/tex/luatex/luatexbase/modutils.lua:57: m
odule 'pgfmolbio' not found:
    no field package.preload['pgfmolbio']
    [luatexbase.loader] Search failed
    [kpse lua searcher] file not found: 'pgfmolbio'
    [kpse C searcher] file not found: 'pgfmolbio'
stack traceback:
    [C]: in function 'require'
    ...xlive/2013/texmf-dist/tex/luatex/luatexbase/modutils.lua:57: in function 're
quire_module'
    [string "\directlua "]:1: in main chunk.
\lltxb@requirelua ...xluaescapestring {#2}" \fi )}

l.44 \fi

The log file is attached:

This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) (format=pdflatex 2013.7.20)  29 JUL 2013 23:36
entering extended mode
 \write18 enabled.
 %&-line parsing enabled.
**figures-1.tex
(./figures-1.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
)
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\c@table=\count86
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(/usr/local/texlive/2013/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.sty
Package: pgfmolbio 2012/10/01 v0.2 Molecular biology graphs with TikZ

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Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
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The pgfmolbio package needs the luatex engine! –  Paul Gaborit Jul 30 '13 at 6:50
    
Is it means I need to compile the figures-1.tex with luatex? –  Mys_721tx Jul 30 '13 at 6:52
    
Yes (look at p.44 of the pgfmolbio manual). –  Paul Gaborit Jul 30 '13 at 6:54
    
Welcome to TeX-SX! Have a look at our starter page for a quick intro if you wish to familiarize yourself with our format. –  Claudio Fiandrino Jul 30 '13 at 7:04
    
@Mys_721tx As others comment, the key features of mgfmolbio require LuaTeX, but the package does not really issue suitable warning/error messages about this. However, LuaTeX was updated for TeX Live 2013 in a way that requires changes to module loading, and pgfmolbio hasn't been modified to reflect that. So with your installation I suspect this isn't going to work. I suggest a bug report to the package author. –  Joseph Wright Jul 30 '13 at 7:20
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1 Answer

up vote 1 down vote accepted

Apparently the missing pgfmolbio.lua is a part of the problem. However, this can be solved by putting all the files from pgfmolbio package to the . directory of the tex file I was trying to compile. However, a bug report should be made to Tex Live.

The compatibility problem has been solved by Wolfgang himself. The update has been reflected on CRAN.

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