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