From cstrato at aon.at  Thu Aug 29 00:10:07 2013
From: cstrato at aon.at (cstrato)
Date: Thu, 29 Aug 2013 00:10:07 +0200
Subject: [Rd] Error when using buildVignettes()
In-Reply-To: <CAFDcVCSGCkxqYMC9MJAyLY6ybby6qX3mg+P97dX1yKA4ap7qFg@mail.gmail.com>
References: <521E5076.9020106@aon.at>
	<CAFDcVCSGCkxqYMC9MJAyLY6ybby6qX3mg+P97dX1yKA4ap7qFg@mail.gmail.com>
Message-ID: <521E753F.5030708@aon.at>

Dear Henrik,

Thank you for your suggestion, however the error was detected by a user 
who is already using R 3.0.1, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2013-August/054633.html

Best regards,
Christian


On 8/28/13 11:49 PM, Henrik Bengtsson wrote:
>>> sessionInfo()
>> R version 3.0.0 Patched (2013-04-11 r62551)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> I would check with R 3.0.1 patched and R devel before anything else,
> especially when troubleshooting vignette-related issues.
>
> /Henrik
>
>
> On Wed, Aug 28, 2013 at 12:33 PM, cstrato <cstrato at aon.at> wrote:
>> Dear all,
>>
>> When running function 'testQAReport()', which uses function
>> 'buildVignettes()' to create a pdf-file I get the following error:
>>
>>> source("testQAReport.R")
>>> testQAReport()
>> Error in .get_package_metadata(pkgdir) :
>>    Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
>>
>> Since I did not get this error in earlier versions of R, could you please
>> tell me what may be the reason for this error?
>>
>>
>> Here is the code for "testQAReport.R":
>>
>> #------------------------------------------------------------------------------#
>> # testQAReport.R: test quality control report
>> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> - -
>> testQAReport <-
>> function(dataset     = "My Dataset",
>>           title       = "Quality Report",
>>           date        = "October, 2011",
>>           author      = "Christian Stratowa",
>>           outdir      = file.path(getwd(), "TestQA"),
>>           ...)
>> {
>>     ## directory containing parts of QAReport.Rnw
>>     indir <- file.path(path.package("xps"), "QC");
>>
>>     ## create directory containing final QAReport.Rnw
>>     if (!dir.create(outdir))
>>        stop("could not create report directory");
>>     if (!dir.create(file.path(outdir, "inst")))
>>        stop("could not create report subdirectory 'inst'");
>>     if (!dir.create(file.path(outdir, "inst", "doc")))
>>        stop("could not create report subdirectory 'doc'");
>>     docdir <- file.path(outdir, "inst", "doc");
>>
>>     QCb <- readLines(file.path(indir, "QC.begin.Rnw"));
>>
>>     ## replace title, date, author
>>     QCb <- sub("@TITLE@",  title,  QCb);
>>     QCb <- sub("@DATE@",   date,   QCb);
>>     QCb <- sub("@AUTHOR@", author, QCb);
>>
>>     ## dataset info
>>     numtrees <- 6; chipname <- "Test3"; chiptype <- "GeneChip";
>>     QCb <- sub("@DATASET@",  dataset,  QCb);
>>     QCb <- sub("@NUMTREES@", numtrees, QCb);
>>     QCb <- sub("@CHIPNAME@", chipname, QCb);
>>     QCb <- sub("@CHIPTYPE@", chiptype, QCb);
>>
>>     write(QCb, file.path(docdir, "QAReport.Rnw"));
>>
>>     QCe <- readLines(file.path(indir, "QC.end.Rnw"));
>>     QCe <- sub("@DATASET@",  dataset,  QCe);
>>     QCe <- gsub("_","\\\\_", QCe);
>>
>>     write(QCe, file.path(docdir, "QAReport.Rnw"), append=TRUE);
>>
>>     ## build vignette QC.pdf
>>     if (require(tools)) {
>>        buildVignettes(dir=outdir, lib.loc=NULL, quiet=FALSE, clean=FALSE);
>>     }#if
>> }#xpsQAReport
>>
>> #------------------------------------------------------------------------------#
>>
>> The file "QC.begin.Rnw" is as follows:
>>
>> \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{@TITLE@}
>> \date{@DATE@}
>> \author{@AUTHOR@}
>> \maketitle
>>
>> \tableofcontents
>>
>>
>> \section{Introduction}
>>
>>   This is the quality assessment report for the dataset '@DATASET@'. The
>> dataset consists of
>>   @NUMTREES@ Affymetrix @CHIPTYPE@ arrays of type '@CHIPNAME@'. \\
>>
>>   This report was generated using function \Rfunction{xpsQAReport} of package
>> \xps. \\
>>
>>
>> The file "QC.end.Rnw" is as follows:
>>
>> \section{Summary}
>>
>>   The current quality report for dataset '@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}
>>
>>
>> Finally, the output which is located in TestQA/inst/doc/QAReport.Rnw is as
>> follows:
>>
>> \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}
>>
>>
>> Can you please tell me why function buildVignettes() of the tools package is
>> no longer able to convert this file into a pdf-file?
>> Thank you in advance.
>>
>>
>>> sessionInfo()
>> R version 3.0.0 Patched (2013-04-11 r62551)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] xps_1.21.4
>>
>> 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
>> _._._._._._._._._._._._._._._._._._
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Error when using buildVignettes()
cstrato