General ⇒ TeXnicCenter and BibTeX — Citations appear as [??]

[kerenkapach]

Hello,

I am using TeXnicCenter and having troubles compiling tex file.
I am using bibtex, and the journal_names_long.bib and all.bib are in the same location as the tex file, and also the singlecol-new class.
I am building latex, bibtex and then latex twice. The PDF file is being updated with the changes I am doing although I am getting the error: "Couldn't find input index file". In addition, citation appears as [?] while the reference list is being built OK, and responds to different citation I use.

I read previous answers to the problem, and checked that the path in windows environmental variables and the path in Build->Defile output profiles both contain the 'makeindex.exe' correct location.
Can anyone tell me what I am doing wrong?

Code: Select all

%%%%%%%%%%%%%%%%%%%%%%
\documentclass{singlecol-new}
%%%%%%%%%%%%%%%%%%%%%%

\usepackage{cite}
\def\newblock{\hskip .11em plus .33em minus .07em}

\theoremstyle{TH}{
\newtheorem{theorem}{Theorem}[section]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{corollary}{Corollary}[section]
\newtheorem{conjecture}[theorem]{Conjecture}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{definition}[theorem]{Definition}
\newtheorem{claim}{Claim}
\newtheorem{stheorem}[theorem]{Wrong Theorem}
}

\theoremstyle{THhit}{
\newtheorem{aquestion}{Question}[section]
}

\theoremstyle{THrm}{
\newtheorem{remark}[theorem]{Remark}
\newtheorem{question}{Question}[section]
\newtheorem{example}[theorem]{Example}
\newtheorem{case}{Case}[section]
}

\makeatletter
\def\theequation{\arabic{equation}}
\makeatother

\def\bmD{\mbox{\boldmath $D$}}          %99.10.1
\def\bmE{\mbox{\boldmath $E$}}        %99.6.29
\def\bmg{\mbox{\boldmath $g$}}
\def\bmG{\mbox{\boldmath $G$}}
\def\bmM{\mbox{\boldmath $M$}}
\def\bmY{\mbox{\boldmath $Y$}}  %99.12.22
\def\bmW{\mbox{\boldmath $W$}}  %99.12.22
\def\bgamma{\mbox{\boldmath $\gamma$}}
\def\tc#1{\textcolor{red}{\bf #1}}

\spaceskip=3.5pt plus1.47pt minus0.77pt \makeatother
\newcommand{\CITE}[1]{\protect\cite{#1}}
%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
%%%%%%%%%%%%%%%%%%%%%%
\title{Some title}

\maketitle

\section{Introduction}
This is an attemp to cite an new article: \cite{Mokeichev}


\bibliographystyle{plain}
\bibliography{journal_names_long,all}
\end{document}

The citation in the bib file is:

Code: Select all

@ARTICLE(Mokeichev,
    AUTHOR      = "Mokeichev, A. and Okun, M. and Barak, O. and Katz, Y. and Ben-Shahar, O. and Lampl, I.",
    TITLE       = "Stochastic Emergence of Repeating Cortical Motifs in Spontaneous Membrane Potential Fluctuations  in vivo",
    JOURNAL     = "Neuron",
    YEAR        = "2007",
    VOLUME      = "53",
    PAGES       = "413-425",
    KEYWORDS    = "",
    KEYPOINTS   = "",
    ABSTRACT    = ""
)

Thanks a lot,
Keren

[localghost]

Which TeX distribution do you use (name, version)?


Best regards and welcome to the board
Thorsten

[kerenkapach]

MiKTex 2.9.

Thanks Thorsten.

[localghost]

In this version BibTeX as well as MakeIndex have got a security mechanism that doesn't allow absolute paths any more*. Therefore "%bm" has to be replaced by "%tm" in the corresponding settings of TeXnicCenter (TXC) as shown in the attachment. Start TXC and press Alt+F7 to get the »Profiles« dialog window.


* The same applies to TeX Live 2010.

[kerenkapach]

Thanks for the quick reply.
I changed the command line arguments for BiBTex and MakeIndex, and the error did disappear, but citations still appears as [?]. The references list is being built OK.
I noticed that our command line arguments to pass to the compiler are different:

profiles.jpg (94.92 KiB) Viewed 3828 times

Should I change that too? Can you please copy the full command line arguments?

Thanks again,
Keren

[localghost]

It will require at least two more compiler runs to get all things right. If the problem persists, attach a minimal example including the resulting log file to your next post by upload to the forum server.