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
_._._._._._._._._._._._._._._._._._
C.h.r.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
e.m.a.i.l: cstrato at aon.at
_._._._._._._._._._._._._._._._._._
Problem with texi2pdf(..,clean=TRUE)
14 messages · cstrato, Marc Schwartz, Duncan Murdoch +1 more
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. :-) Regards, Marc Schwartz
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
On Fri, Aug 30, 2013 at 12:14 PM, Duncan Murdoch
<murdoch.duncan at gmail.com> 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.
Or, that the cleanup fails if the compilation is too quick, cf. PR#15394 'texi2dvi(..., clean=TRUE) sometimes too quick for "clean" (with PATCH)' submitted on July 17, 2013: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15394 /Henrik
Duncan Murdoch
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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/? 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
On 30/08/2013 3:21 PM, cstrato 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/? Is this done by Sweave()?
No. Duncan Murdoch
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
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
On Aug 30, 2013, at 2:20 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
On Fri, Aug 30, 2013 at 12:14 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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.
Or, that the cleanup fails if the compilation is too quick, cf. PR#15394 'texi2dvi(..., clean=TRUE) sometimes too quick for "clean" (with PATCH)' submitted on July 17, 2013: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15394 /Henrik
Interesting. It is late on a Friday, so perhaps I am short on functioning neurons. If the intent of 'clean = TRUE' is to remove the byproducts of compiling the .PDF file from the source .TEX file, why not just delete the resultant aux|log|tex|dvi files that match the basename of the source .TEX file rather than being dependent upon the time stamp? Is there a reason that I am failing to consider for a need to retain these files if older than the current time stamp? Perhaps if the compilation requires multiple cycles of latex processing (eg. the use of longtables, etc.), in which case, one could run texi2pdf(..., clean = FALSE) some number of times, then a final texi2pdf(..., clean = TRUE) when done. I actually have my own shell script that does this when creating Sweave files. Of course, the help file does have the following for the 'clean' argument: ...May not work on some platforms. Thanks, Marc
On Fri, Aug 30, 2013 at 12:40 PM, Marc Schwartz <marc_schwartz at me.com> wrote:
On Aug 30, 2013, at 2:20 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
On Fri, Aug 30, 2013 at 12:14 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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.
Or, that the cleanup fails if the compilation is too quick, cf. PR#15394 'texi2dvi(..., clean=TRUE) sometimes too quick for "clean" (with PATCH)' submitted on July 17, 2013: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15394 /Henrik
Interesting. It is late on a Friday, so perhaps I am short on functioning neurons. If the intent of 'clean = TRUE' is to remove the byproducts of compiling the .PDF file from the source .TEX file, why not just delete the resultant aux|log|tex|dvi files that match the basename of the source .TEX file rather than being dependent upon the time stamp?
I'm quite sure because it is not easy/impossible to predict which the byproducts are. To catch everything, you'd have to do something <basename>.* and that is certainly not safe. /Henrik
Is there a reason that I am failing to consider for a need to retain these files if older than the current time stamp? Perhaps if the compilation requires multiple cycles of latex processing (eg. the use of longtables, etc.), in which case, one could run texi2pdf(..., clean = FALSE) some number of times, then a final texi2pdf(..., clean = TRUE) when done. I actually have my own shell script that does this when creating Sweave files. Of course, the help file does have the following for the 'clean' argument: ...May not work on some platforms. Thanks, Marc
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
Dear Henrik,
Below is the 'QAReport.Rnw' file which I use on my Mac to reproduce your
problem. Maybe this will help others to reproduce this problem, too.
Best regards,
Christian
---- begin QAReport.Rnw ----
\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}
---- end QAReport.Rnw ----
On 8/30/13 9:46 PM, Henrik Bengtsson wrote:
On Fri, Aug 30, 2013 at 12:40 PM, Marc Schwartz <marc_schwartz at me.com> wrote:
On Aug 30, 2013, at 2:20 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
On Fri, Aug 30, 2013 at 12:14 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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.
Or, that the cleanup fails if the compilation is too quick, cf. PR#15394 'texi2dvi(..., clean=TRUE) sometimes too quick for "clean" (with PATCH)' submitted on July 17, 2013: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15394 /Henrik
Interesting. It is late on a Friday, so perhaps I am short on functioning neurons. If the intent of 'clean = TRUE' is to remove the byproducts of compiling the .PDF file from the source .TEX file, why not just delete the resultant aux|log|tex|dvi files that match the basename of the source .TEX file rather than being dependent upon the time stamp?
I'm quite sure because it is not easy/impossible to predict which the byproducts are. To catch everything, you'd have to do something <basename>.* and that is certainly not safe. /Henrik
Is there a reason that I am failing to consider for a need to retain these files if older than the current time stamp? Perhaps if the compilation requires multiple cycles of latex processing (eg. the use of longtables, etc.), in which case, one could run texi2pdf(..., clean = FALSE) some number of times, then a final texi2pdf(..., clean = TRUE) when done. I actually have my own shell script that does this when creating Sweave files. Of course, the help file does have the following for the 'clean' argument: ...May not work on some platforms. Thanks, Marc
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}
Just checked the SVN logs and the comparison towards file timestamps have been dropped in R devel and R 3.0.1 SVN r63690 (Aug 25, 2013) and newer. It is now simply comparing the set of files before and after. Try with one of those and I'll bet you that clean=TRUE does what it supposed to. /Henrik
On Fri, Aug 30, 2013 at 1:05 PM, cstrato <cstrato at aon.at> wrote:
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
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Dear Henrik, Thank you for this information, I will try to install the patched version. Best regards, Christian
On 8/30/13 10:23 PM, Henrik Bengtsson wrote:
Just checked the SVN logs and the comparison towards file timestamps have been dropped in R devel and R 3.0.1 SVN r63690 (Aug 25, 2013) and newer. It is now simply comparing the set of files before and after. Try with one of those and I'll bet you that clean=TRUE does what it supposed to. /Henrik On Fri, Aug 30, 2013 at 1:05 PM, cstrato <cstrato at aon.at> wrote:
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