From cstrato at aon.at  Wed Aug 28 21:33:10 2013
From: cstrato at aon.at (cstrato)
Date: Wed, 28 Aug 2013 21:33:10 +0200
Subject: [Rd] Error when using buildVignettes()
Message-ID: <521E5076.9020106@aon.at>

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
_._._._._._._._._._._._._._._._._._



[Rd] Error when using buildVignettes()
cstrato