From cstrato at aon.at  Fri Aug 30 22:05:11 2013
From: cstrato at aon.at (cstrato)
Date: Fri, 30 Aug 2013 22:05:11 +0200
Subject: [Rd] Problem with texi2pdf(..,clean=TRUE)
In-Reply-To: <5220F780.8080507@aon.at>
References: <5220EBBE.8080504@aon.at>
	<D9E36BC9-3F08-4735-A61C-C183486D59C3@me.com>
	<5220EF23.5040400@gmail.com> <5220F0B7.2000107@aon.at>
	<CAFDcVCSRbFwDAee0sUtkQHwEK-488b=5uhq142n_eKgwCjV1RA@mail.gmail.com>
	<5220F780.8080507@aon.at>
Message-ID: <5220FAF7.5080603@aon.at>

Dear Henrik,

I am trying to attach the 'QAReport.Rnw' file which I am using on my Mac 
to reproduce your problem.

Best regards,
Christian


On 8/30/13 9:50 PM, cstrato wrote:
> Dear Henrik,
>
> Thank you for your explanation.
>
> Yes, this behavior is reproducible many times.
>
> When I copy both lines together into R, i.e.
>     Sweave("QAReport.Rnw")
>     tools::texi2pdf("QAReport.tex", clean = TRUE)
>
> then the auxiliary files are deleted. However, when I keep the *.tex
> file only and run:
>     tools::texi2pdf("QAReport.tex", clean = TRUE)
>
> then these files are not deleted. I can delete them manually many times
> and run texi2pdf() again, they will never be deleted.
>
> I really hope that your patch will be applied, so that it works as
> expected with the next Bioconductor release on October.
>
> Best regards,
> Christian
>
>
> On 8/30/13 9:36 PM, Henrik Bengtsson wrote:
>> On Fri, Aug 30, 2013 at 12:21 PM, cstrato <cstrato at aon.at> wrote:
>>> Dear Duncan, dear Marc,
>>>
>>> Thank you for your fast reply.
>>>
>>> Can you please tell me:
>>> If texi2pdf() won't delete files how are the files deleted when the
>>> directory structure is Test/inst/doc/?
>>
>> Check if what you're observing is reproducible when you run it *many*
>> times.  If not, see my previous reply.
>>
>> /Henrik
>>
>>> Is this done by Sweave()?
>>>
>>> Best regards,
>>> Christian
>>>
>>>
>>>
>>> On 8/30/13 9:14 PM, Duncan Murdoch wrote:
>>>>
>>>> On 30/08/2013 3:09 PM, Marc Schwartz wrote:
>>>>>
>>>>> On Aug 30, 2013, at 2:00 PM, cstrato <cstrato at aon.at> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> To create a *.pdf file from a *.Rnw file I do:
>>>>>>
>>>>>>       olddir <- getwd();
>>>>>>       setwd(outdir);
>>>>>>
>>>>>>       tryCatch({Sweave("QAReport.Rnw");
>>>>>>                 tools::texi2pdf("QAReport.tex", clean=TRUE)
>>>>>>                },
>>>>>>                finally = setwd(olddir)
>>>>>>               );
>>>>>>
>>>>>> This works fine, however 'clean=TRUE' does only work when:
>>>>>>      outdir <- "Test/inst/doc/"
>>>>>> but does not remove the files *.aux, *.log, *.toc when:
>>>>>>      outdir <- "Test/"
>>>>>>
>>>>>> Why does function texi2pdf() require the directory structure for
>>>>> vignettes for the deletion of interim files?
>>>>>>
>>>>>> (The help file?texi2pdf does not mention that this structure is
>>>>> necessary.)
>>>>>>
>>>>>> Best regards
>>>>>> Christian
>>>>>
>>>>>
>>>>> In the Details section of ?texi2pdf, there is:
>>>>>
>>>>> "Despite the name, this is used in R to compile LaTeX files,
>>>>> specifically those generated from vignettes."
>>>>>
>>>>>
>>>>> Since it is intended specifically for package vignettes, the path
>>>>> requirement should not be a surprise. :-)
>>>>>
>>>>
>>>> There is no path requirement.  Christian was incorrect in his
>>>> diagnosis.
>>>>
>>>> texi2pdf won't delete files that existed before it was run, whether or
>>>> not they were changed during the run.  That's likely what Christian was
>>>> seeing.
>>>>
>>>> Duncan Murdoch
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
-------------- next part --------------
\documentclass{article}


\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{\Cclass}[1]{{\textit{#1}}}
\newcommand{\Rexten}[1]{{\textit{#1}}}
\newcommand{\xps}{\Rpackage{xps}}
\newcommand{\ROOT}{\Robject{ROOT}}

\begin{document}

\title{Quality Report}
\date{October, 2011}
\author{Christian Stratowa}
\maketitle

\tableofcontents


\section{Introduction}

 This is the quality assessment report for the dataset 'My Dataset'. The dataset consists of
 6 Affymetrix GeneChip arrays of type 'Test3'. \\

 This report was generated using function \Rfunction{xpsQAReport} of package \xps. \\

\section{Summary}

 The current quality report for dataset 'My Dataset' displays the most important quality plots, using the
 default settings for most plots. Package \xps\ contains additional plots which can be used for further
 quality assessments. \\


\section*{Session Information:}

<<echo=FALSE>>=
sessionInfo()
@ 

\end{document}


[Rd] Problem with texi2pdf(..,clean=TRUE)
cstrato