[Bioc-devel] executable vignette?

[cstrato]

Dear James

Thank you for your comments.
I made a simple mistake:
It turns out that the vignette file itself is an executable on Linux 
because my Mac
makes it an executable. (Robert Gentleman was so kind to clarify this 
issue.)
Sorry for this confusion, my mistake.

Best regards
Christian

James W. MacDonald wrote:
> Hi Christian,
>
> cstrato wrote:
>> Dear all
>>
>> Can you tell me when is a vignette for a package, e.g. "mypkg", an 
>> executable file?
>> How can I avoid that my vignette is an executable file?
>> Is there something special that I have to add to my vignette?
>
> Not sure what you are getting at here. Why would you have a vignette 
> that isn't executable? That is the main rationale for having one in 
> the first place.
>
> If you want to make certain code chunks not evaluated, you can put 
> <<eval=false>>=
> in the chunk header. This will also cause that chunk to be commented 
> out if someone were to Stangle() your .Rnw file. Of course that won't 
> keep a determined person from executing your code, but it will keep it 
> from executing unintentionally.
>
> Best,
>
> Jim
>
>
>>
>> In "mypkg" the vignette  with example name "mypkg.Snw" is located in 
>> subdirectory
>> "inst/doc" as suspected, and it looks as follows:
>>
>> %\VignetteIndexEntry{MyPkg Vignette: Overview}
>> %\VignetteDepends{mypkg}
>> %\VignetteKeywords{Expression}
>> %\VignettePackage{mypkg}
>> \documentclass{article}
>>
>> \usepackage{hyperref}
>>
>> \textwidth=6.2in
>> \textheight=8.5in
>> %\parskip=.3cm
>> \oddsidemargin=.1in
>> \evensidemargin=.1in
>> \headheight=-.3in
>>
>> \newcommand{\Rfunction}[1]{{\texttt{#1}}}
>> \newcommand{\Rmethod}[1]{{\texttt{#1}}}
>> \newcommand{\Rcode}[1]{{\texttt{#1}}}
>> \newcommand{\Robject}[1]{{\texttt{#1}}}
>> \newcommand{\Rpackage}[1]{{\textsf{#1}}}
>> \newcommand{\Rclass}[1]{{\textit{#1}}}
>> \newcommand{\mypkg}{\Rpackage{mypkg}}
>>
>> \begin{document}
>>
>> \title{Introduction}
>> \date{July, 2007}
>> \author{Christian Stratowa}
>> \maketitle
>>
>> \tableofcontents
>>
>> \section{Introduction}
>>
>> some text
>>
>> <<>>=
>> library(mypkg)
>> @
>>  
>> some text
>>
>> \end{document}
>>
>>
>> Thank you in advance
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._
>> C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
>> V.i.e.n.n.a       A.u.s.t.r.i.a
>> _._._._._._._._._._._._._._._._
>>
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>