Error when using buildVignettes()

Ok.  ...I've now read your original thread more carefully, and I'd say
that tools::buildVignettes() is intended for building vignettes within
packages, not for compiling vignette files in general.  This is most
likely why it complains - it simply looks for files that it expect to
see in a package source tree.  FYI, lots of changes were made to these
tools in R 3.0.0, which may explain why you didn't see them before
(not saying it was correct usage before either).

I'd say, use Sweave/Stangle "manually" and then pass it on to tools::texi2pdf().

<sales pitch>
1. For *.Rnw -> *.tex -> *.pdf, you can use R.rsp::compileRnw() that
does all this in one go with more sanity checks.

2. Instead of using all those sub("@TITLE@",  title, ...) coding to
generate the report Rnw from a main Rnw template, add a layer of RSP
markup and run it through the RSP compiler.  For instance, with a
template.Rnw.rsp containing:

  This is the quality assessment report for the dataset '<%=dataset%>'.
The dataset consists of
  <%=numtrees%> Affymetrix <%=chiptype%> arrays of type '<%=chipname%>'.

you can compile it all in one go into a final PDF by pdf <-
R.rsp::rfile("template.Rnw.rsp").  RSP supports <%@include
file="..."%> statements and more if you wish to bring multiple Rnw
templates into a final one.  See help("R.rsp") for vignettes etc.
</sales pitch>

On Wed, Aug 28, 2013 at 3:10 PM, cstrato <cstrato at aon.at> wrote:

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