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 <cstr...@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 <cstr...@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
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\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}
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