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R-IQ-OQ.Rnw
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright 2013, Marc Schwartz <[email protected]>
%
% This software is distributed under the terms of the GNU General
% Public License Version 2, June 1991.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% IMPORTANT NOTES FOLLOW. REVIEW ALL OF THEM.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% RUN THIS BEFORE INSTALLING CRAN PACKAGES!!!!!!!!!!!!!!!!!!
% DO NOT RUN THIS FROM ANY R GUI'S, AS THEY MAY AFFECT THE ENVIRONMENT
% IN WHICH R IS RUNNING, COMPROMISING THE INTEGRITY OF THE CHECKS. THE
% DEFAULT USER .Rprofile MAY ALSO AFFECT THE ENVIRONMENT AS CAN THE PRESENCE
% OF ANY CRAN PACKAGES THAT ARE NOT PART OF THE OFFICIAL R DISTRIBUTION.
% NOTE THAT YOU MAY NEED TO RUN THE FOLLOWING:
%
% export LC_COLLATE=C LANG=en LC_TIME=C
%
% IN YOUR TERMINAL SHELL BEFORE RUNNING R BELOW IN ORDER TO MATCH REFERENCE TEST RESULTS DUE
% TO LOCALE ISSUES. IF YOU GET ANY TEXT COMPARISON (DIFF) ERRORS, TRY THIS TO
% RESOLVE THOSE ISSUES. ON OSX MOUNTAIN LION I USE THIS INCANTATION AS PER THE
% R INSTALLATION AND ADMINISTRATION MANUAL
% http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Testing-a-Unix_002dalike-Installation
% RUN R FROM THE TERMINAL/CONSOLE COMMAND LINE USING:
% R --vanilla (For Windows: Rterm.exe --vanilla)
% Then run:
% Sweave("R-IQ-OQ.Rnw")
% OR YOU CAN RUN R IN BATCH MODE:
% R --vanilla CMD Sweave R-IQ-OQ.Rnw (For Windows: Rterm.exe --vanilla CMD Sweave R-IQ-OQ.Rnw )
% Note that while this program is running, test result files will be created in a sub-directory
% called 'IQ-OQ-TestOutput'. You may wish to inspect these files as part of
% your review and, if part of your operating procedures, tar/zip the folder tree and
% archive it as part of your testing documentation.
% The above steps will take approximately 20 minutes to run on current hardware and create a LaTeX source document called R-IQ-OQ.tex
% Then run:
% pdflatex R-IQ-OQ.tex (Likely more than once. Look for messages output regarding running it again)
% The final result will be R-IQ-OQ.pdf, which will be the final report file.
% CODING NOTES:
% SWEAVE CANNOT CAPTURE OUTPUT TO STDERR, THOUGH SOME WORKAROUNDS HAVE BEEN POSTED.
% SO CANNOT JUST CALL THE TEST FUNCTIONS DIRECTLY HERE.
% ATTEMPTS TO USE EITHER capture.output() or sink() PLUS sink(type = "messages")
% DO NOT IN FACT CAPTURE ALL OF THE OUTPUT GENERATED BY THE PACKAGE TESTS. MOST
% OF THE OUTPUT GOES TO STDERR AND IS CAUGHT BY THE DOUBLE sink() APPROACH, HOWEVER
% SOME OUTPUT FROM THE PACKAGE TESTS, SUCH AS DIFF ERRORS IN THE SHELL ARE NOT CAPTURED AND END
% UP IN THE DOCUMENT BODY, SEPARATE FROM THE LISTINGS OUTPUT WHICH ARE OUT OF
% SEQUENCE AND NOT HELPFUL IN BEING ASSOCIATED WITH A SPECIFIC TEST.
% THE USE OF system(CMD) IN THE VARIOUS PACKAGE TESTS NEEDS TO BE VERIFIED ON
% WINDOWS BASED SYSTEMS FOR CORRECT FUNCTIONING AND PORTABILITY.
% IQ refers to Installation Qualification: has the software been installed correctly?
% OQ refers to Operational Qualification: is the software operating correctly?
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[10pt]{article}
\usepackage[paperwidth=8.5in,paperheight=11in,includefoot=false,lmargin=0.5in,rmargin=0.5in,tmargin=1.0in,bmargin=1.0in]{geometry}
\usepackage{colortbl}
\usepackage{color}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage{array}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{textcomp}
\usepackage{stmaryrd}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{fancyhdr}
\usepackage[linktocpage=true,colorlinks=true,urlcolor=blue,linkcolor=black]{hyperref}
\usepackage[format=hang,font=bf,belowskip=1ex,singlelinecheck=off]{caption}
\usepackage[hang,norule,stable,multiple]{footmisc}
\usepackage{listings}
\lstloadlanguages{R}
\begin{document}\pagestyle{fancy}
\fancyhf{}
\fancyfoot[L]{R Software IQ OQ}
\fancyfoot[C]{\thepage}
\fancyfoot[R]{\today}
\renewcommand\footnotemargin{1em}
\renewcommand\headrulewidth{0pt}
\renewcommand\footrulewidth{0.4pt}
\addtocontents{toc}{\protect\thispagestyle{fancy}}
\addtocontents{lof}{\protect\thispagestyle{fancy}}
\addtocontents{lot}{\protect\thispagestyle{fancy}}
%% Reset table/figure counters with each new section
\makeatletter\@addtoreset{table}{section}\makeatother
\makeatletter\@addtoreset{figure}{section}\makeatother
%% Table/Figure counter format to Section.Table
\renewcommand{\thetable}{\arabic{section}.\arabic{table}}
\renewcommand{\thefigure}{\arabic{section}.\arabic{figure}}
%% Adjust numwidth wider so that table/figure number in the LOT/LOF do
%% not collide with the text descriptions
\makeatletter
\renewcommand\l@figure{\@dottedtocline{1}{1.5em}{3em}}
\makeatother
\makeatletter
\renewcommand\l@table{\@dottedtocline{1}{1.5em}{3em}}
\makeatother
%% Set for no paragraph indentation and skip a line between paragraphs
\setlength\parindent{0in}
\addtolength{\parskip}{\baselineskip}
%% Set R for listings package
%% http://en.wikibooks.org/wiki/LaTeX/Colors
%% separate additional keywords with commas
\lstset{
language=R,
caption=,
basicstyle=\scriptsize\ttfamily,
commentstyle=\ttfamily\color{Gray},
numbers=left,
numberstyle=\ttfamily\color{Gray}\footnotesize,
stepnumber=1,
numbersep=5pt,
backgroundcolor=\color{White},
showspaces=false,
showstringspaces=false,
showtabs=false,
xleftmargin=0.25in,
xrightmargin=0.25in,
frame=single,
tabsize=2,
captionpos=b,
breaklines=true,
breakatwhitespace=false,
title=\lstname,
escapeinside={},
keywordstyle=\ttfamily\color{Red},
stringstyle=\ttfamily\color{ForestGreen},
morekeywords={OK,NA,PASS,FAIL,FAILED,failed,Execution,halted},
deletekeywords={R,C,for,terms,is,if,file,path,For,Platform,machine,system,status,rev,packages,factor,
package,graphics,methods,class,grid,Version,or,as,double,min,exp,integer,max,var,
q,inherits,report,ifelse,on,help,browser,quit,try,options,plot,ps,save,lines,list,
character,attr,se,~,_,/}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
<<results=hide,echo=false>>=
RVersionInfo <- R.Version()
Version <- RVersionInfo$version.string
Arch <- gsub("_", "\\\\\\\\_", RVersionInfo$arch)
Platform <- gsub("_", "\\\\\\\\_", RVersionInfo$platform)
require("tools")
options(width = 120)
# Disable fancy "curly" quotes for LaTeX
options(useFancyQuotes = FALSE)
# Check to be sure that the external code files are present.
CMDFileNames <- paste("CMDFile", 1:7, ".r", sep = "")
CMDFileResults <- sapply(CMDFileNames,
function(x) if (file_test("-f", x)) TRUE else FALSE)
if (any(!CMDFileResults))
stop("One or more of the CMDFile*.r files is missing. Cannot continue.")
# Clean up test output folder, create it
if(file.exists("IQ-OQ-TestOutput")) {
unlink("IQ-OQ-TestOutput", recursive = TRUE)
}
stopifnot(dir.create("IQ-OQ-TestOutput"))
@
%% START OF TITLE PAGE
\begin{titlepage}
\begin{center}
\textbf{\Large{
Installation and Operational Qualification Testing For R Statistical Software\\
\Sexpr{Version}\\
Architecture: \Sexpr{Arch}\\
Platform: \Sexpr{Platform}\\
}}
\vspace{1.5in}
\textbf{\Large{\emph{
\today\\
}}}
\end{center}
\end{titlepage}
\tableofcontents
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Introduction}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% THE LANGUAGE BELOW WOULD NEED TO BE MODIFIED IF A BINARY INSTALLATION OF R
%% IS FROM A THIRD PARTY REPOSITORY, SUCH AS FROM DEBIAN OR FEDORA LINUX
%% REPOSITORIES.
The R software being tested in this report was downloaded from The Comprehensive R Archive Network (CRAN):
\hspace{20pt}\url{http://cran.r-project.org/}
or a CRAN mirror:
\hspace{20pt}\url{http://cran.us.r-project.org/mirrors.html}
if this is a stable release or from:
\hspace{20pt}\url{http://R.research.att.com/}
if a patched release for Apple's OSX operating system.
The R software was installed on this computer in a manner consistent with
``The R Installation and Administration Manual'' (the Manual) which is available from:
\hspace{20pt}\url{http://cran.r-project.org/doc/manuals/R-admin.html}
The Manual provides recommendations for the post-installation testing of R. The procedures for this
testing are described in:
\hspace{20pt}\url{http://cran.r-project.org/doc/manuals/R-admin.html#Testing-a-Unix_002dalike-Installation}
for Unix, Linux and OSX installations and:
\hspace{20pt}\url{http://cran.r-project.org/doc/manuals/R-admin.html#Testing-a-Windows-Installation}
for Windows installations. The results contained within this report are based upon an automated implementation of the
procedures described in the Manual.
General guidance for the use of R in regulated clinical trials has been provided by the R Foundation
in a document entitled:
\begin{center}
R: Regulatory Compliance and Validation Issues\\
A Guidance Document for the Use of R in Regulated Clinical Trial Environments
\end{center}
which is available from:
\hspace{20pt}\url{http://www.r-project.org/doc/R-FDA.pdf}
The above document describes various characteristics of R, including the Software Development Life Cycle (SDLC)
and relevant aspects of 21 CFR Part 11 compliance issues as they may pertain to the use of R for statistical analysis
applications for clinical trials.
The output on the following pages of this report describe various technical characteristics of the computer upon which R
is running, the R installation, current R session information and is followed by a series of tests for the so-called ``Base''
and ``Recommended'' packages which are a part of the official R distribution, as released by the R Foundation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Installation Qualification (IQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{R.home()}, showing where R was installed on this computer:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output the R startup banner
cat(R.home(), sep = "\n")
@
\end{lstlisting}
The following is the output of \texttt{system("R -e 'q()'")}, presenting the R welcome banner
as displayed from a default R console (terminal) to show the R console correctly running and then exiting:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output the R startup banner
Result0 <- try(system(paste(shQuote(file.path(R.home("bin"), "R")), "-e", shQuote("q()")), intern = TRUE))
if (class(Result0) != "try-error")
cat(Result0, sep = "\n")
@
\end{lstlisting}
\clearpage
<<results=hide,echo=false>>=
# Check to see if only Base and Recommended packages are installed
BaseRecommendedOnly <- all(installed.packages()[, "Priority"] %in% c("base", "recommended"))
MSG <- ifelse(BaseRecommendedOnly,
"\\\\textcolor{ForestGreen}{\\\\textbf{Only Base and Recommended packages are currently installed.}}",
"\\\\textcolor{Red}{\\\\textbf{WARNING: There are packages currently installed that are NOT part of the official R Foundation distribution of R.}}")
@
Only ``Base'' and ``Recommended'' packages, which are a part of the official R Foundation distribution of R,
should be installed while running these tests. A scan of the currently installed packages indicates:
\begin{center}
\Sexpr{MSG}
\end{center}
The following is the output of \texttt{installed.packages()}.
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output currently installed packages
installed.packages()
@
\end{lstlisting}
\clearpage
The following is the output of \texttt{Sys.info()}, defining some details about the current system upon which R is running
and user information:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output current system information
Sys.info()
@
\end{lstlisting}
\clearpage
The following is the output of \texttt{.Platform}, defining some details of the platform upon which R was built (compiled):
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output .Platform details for current installation
.Platform
@
\end{lstlisting}
\clearpage
The following is the output of \texttt{R.version}, defining detailed information on the currently running version of R:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output R.version information for current installation
R.version
@
\end{lstlisting}
\clearpage
The following is the output of \texttt{.Machine}, defining the numerical characteristics of the computer upon which R
is running:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output current Machine specific information
.Machine
@
\end{lstlisting}
\clearpage
The following is the output of \texttt{sessionInfo()}, defining current R version, locale information and attached packages:
\begin{lstlisting}
<<results=tex,echo=false>>=
# Output current session information
sessionInfo()
@
\end{lstlisting}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Core Operational Qualification - System Tests (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledBasic("both")}, which runs a series of core system-wide operational
tests of the R installation, including various regression tests:
<<results=tex,echo=false>>=
InFile <- "CMDFile1.r"
OutFile <- "CMDFile1Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result1 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile1Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Base Package Operational Qualification - Package Examples (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledPackages(outDir = "IQ-OQ-TestOutput", scope = "base", types = "examples")},
which runs a series of operational tests of the R Base package code examples:
<<results=tex,echo=false>>=
InFile <- "CMDFile2.r"
OutFile <- "CMDFile2Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result2 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile2Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
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\section{R Base Package Operational Qualification - Package Vignettes (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledPackages(outDir = "IQ-OQ-TestOutput", scope = "base", types = "vignettes")},
which runs a series of operational tests of the R Base package vignette code examples:
<<results=tex,echo=false>>=
InFile <- "CMDFile3.r"
OutFile <- "CMDFile3Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result3 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile3Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Recommended Package Operational Qualification - Package Examples (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledPackages(outDir = "IQ-OQ-TestOutput", scope = "recommended", types = "examples")},
which runs a series of operational tests of the R Recommended package code examples:
<<results=tex,echo=false>>=
InFile <- "CMDFile4.r"
OutFile <- "CMDFile4Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result4 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile4Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Recommended Package Operational Qualification - Package Vignettes (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledPackages(outDir = "IQ-OQ-TestOutput", scope = "recommended", types = "vignettes")},
which runs a series of operational tests of the R Recommended package vignette code examples:
<<results=tex,echo=false>>=
InFile <- "CMDFile5.r"
OutFile <- "CMDFile5Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result5 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile5Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Base Package Operational Qualification - Package Tests (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The following is the output of \texttt{testInstalledPackages(outDir = "IQ-OQ-TestOutput", scope = "base", types = "tests")},
which runs a series of operational tests of the R Base package code tests:
<<results=tex,echo=false>>=
InFile <- "CMDFile6.r"
OutFile <- "CMDFile6Out.txt"
CMD <- paste(shQuote(file.path(R.home("bin"), "R")),
"CMD BATCH --vanilla --no-timing", shQuote(InFile), shQuote(OutFile))
Result6 <- try(system(CMD))
@
\lstinputlisting[caption={}]{CMDFile6Out.txt}
The final line of the above output displays the status of running the above tests. ``PASS'' indicates a successful
running of the tests, a ``FAIL'' would indicate that an error was detected during the running of the tests.
There may be some tests where the result of performing a ``diff'' on two files that were being compared demonstrate a content
difference that may or may not be relevant and may be dependent upon locale settings. Any such differences displayed in the
above output should be reviewed in detail to determine their relevance to the Operational Qualification of this R installation.
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{R Recommended Package Operational Qualification - Package Tests (OQ)}
\addtocontents{lot}{\hfil}
\addtocontents{lof}{\hfil}
\clearpage