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<<echo=FALSE,print=FALSE>>=
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prettyDate <- format(Sys.Date(), "%B %e, %Y")
require(Rcpp)
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@

\author{Dirk Eddelbuettel \and Romain Fran\c{c}ois}
\title{Frequently Asked Questions about \pkg{Rcpp}}
\date{\pkg{Rcpp} version \Sexpr{prettyVersion} as of \Sexpr{prettyDate}}


\begin{document}
\maketitle

\abstract{
  \noindent This document attempts to answer the most Frequently Asked
  Questions (FAQ) regarding the \pkg{Rcpp}
  \citep{CRAN:Rcpp,JSS:Rcpp,Eddelbuettel:2013:Rcpp} package. 
}

\tableofcontents

\section{Getting started}

\subsection{How do I get started ?}

If you have \pkg{Rcpp} installed, please execute the following command in \proglang{R}
to access the introductory vignette (which is a variant of the \citet{JSS:Rcpp}
paper) for a detailed introduction:

<<eval=FALSE>>=
vignette("Rcpp-introduction")
@

If you do not have \pkg{Rcpp} installed, the document should also be available
whereever you found this document, \textsl{i.e.,} on every mirror of CRAN site.

\subsection{What do I need ?}

Obviously, \proglang{R} must be installed. \pkg{Rcpp} provides a
\proglang{C++} API as an extension to the \proglang{R} system.  As such, it
is bound by the choices made by \proglang{R} and is also influenced by how
\proglang{R} is configured.

In general, the standard environment for building a CRAN package from source
(particularly when it contains \proglang{C} or \proglang{C++} code) is required. This
means one needs:
\begin{itemize}
\item a development environment with a suitable compiler (see
  below), header files and required libraries;
\item \proglang{R} should be built in a way that permits linking and possibly
  embedding of \proglang{R}; this is typically ensured by the
  \texttt{--enable-shared-lib} option;
\item standard development tools such as \texttt{make} etc.
\end{itemize}

Also see the \href{http://www.rstudio.com/ide/docs/packages/prerequisites}{RStudio
  documentation} on pre-requisites for R package development.

\subsection{What compiler can I use ?}

On almost all platforms, the GNU Compiler Collection (or \texttt{gcc}, which
is also the name of its \proglang{C} language compiler) has to be used along
with the corresponding \texttt{g++} compiler for the \proglang{C++} language.
A minimal suitable version is a final 4.2.* release; earlier 4.2.* were
lacking some \proglang{C++} features (and even 4.2.1, still used on OS X as the
last gcc release), has issues).  

Generally speaking, the default compilers on all the common platforms are suitable.

Specific per-platform notes:
\begin{description}
  \item[Windows] users need the \texttt{Rtools} package from the site maintained by
    Duncan Murdoch which contains all the required tools in a single package;
    complete instructions specific to Windows are in the `R Administration'
    manual \citep[Appendix D]{R:Administration}. As of August 2014, it still
    installs the \texttt{gcc/g++} 4.6.* compiler which limits the ability to use
    modern C++ standards so only \code{s-std=c++0x} is supported. R 3.1.0 and
    above detect this and set appropriate flags.
  \item[OS X] users, as noted in the `R Administration' manual \citep[Appendix
    C.4]{R:Administration}, need to install the Apple Developer Tools
    (\textsl{e.g.}, \href{https://itunes.apple.com/us/app/xcode/id497799835?mt=12}{Xcode} (OS X $\le 10.8$) or \href{https://developer.apple.com/library/ios/technotes/tn2339/_index.html}{Xcode Command Line Tools} (OS X $\ge 10.9$) (as well as \texttt{gfortran} if \proglang{R} or
    Fortran-using packages are to be built); also see \faq{q:OSX} and
    \faq{q:OSXArma} below. Depending on whether on OS X release before or after
    Mavericks is used, different additional installation may be needed. Consult
    the \code{r-sig-mac} list (and its archives) for (current) details.
  \item[Linux] user need to install the standard developement packages. Some
    distributions provide helper packages which pull in all the required
    packages; the \texttt{r-base-dev} package on Debian and Ubuntu is an example.
\end{description}

The \texttt{clang} and \texttt{clang++} compilers from the LLVM project can
also be used. On Linux, they are inter-operable with \texttt{gcc} et al. On
OS X, they are unfortunately not ABI compatible.  The \texttt{clang++}
compiler is interesting as it emits much more comprehensible error messages
than \texttt{g++} (though \texttt{g++} 4.8 and 4.9 have caught up).

The Intel \texttt{icc} family has also been used successfully  as its output
files can also be combined with those from \texttt{gcc}.

\subsection{What other packages are useful ?}

Additional packages that we have found useful are

\begin{description}
\item[\pkg{inline}] which is invaluable for direct compilation, linking and loading
  of short code snippets---but now effectively superseded by the Rcpp
  Attributes (see \faq{using-attributes} and
  \faq{prototype-using-attributes}) feature provided by \pkg{Rcpp};
\item[\pkg{RUnit}] is used for unit testing; the package is recommended and
  will be needed to re-run some of our tests but it is not strictly required
  during use of \pkg{Rcpp};
\item[\pkg{rbenchmark}] to run simple timing comparisons and benchmarks; it is also
  recommended but not required.
\item[\pkg{microbenchmark}] is an alternative for benchmarking.
\item[\pkg{devtools}] can help the process of building, compiling and testing
  a package but it too is entirely optional.
\end{description}

\subsection{What licenses can I choose for my code?}

The \pkg{Rcpp} package is licensed under the terms of the
\href{http://www.gnu.org/licenses/gpl-2.0.html}{GNU GPL 2 or later}, just like
\proglang{R} itself. A key goal of the \pkg{Rcpp} package is to make
extending \proglang{R} more seamless.  But by \textsl{linking} your code against
\proglang{R} (as well as \pkg{Rcpp}), the combination is bound by the GPL as
well.  This is very clearly 
stated at the 
\href{https://www.gnu.org/licenses/gpl-faq.html#GPLStaticVsDynamic}{FSF website}:

\begin{quote}
  Linking a GPL covered work statically or dynamically with other modules is
  making a combined work based on the GPL covered work. Thus, the terms and
  conditions of the GNU General Public License cover the whole combination. 
\end{quote}

So you are free to license your work under whichever terms you find suitable
(provided they are GPL-compatible, see the 
\href{http://www.gnu.org/licenses/licenses.html}{FSF site for details}). However,
the combined work will remain under the terms and conditions of the GNU General
Public License.  This restriction comes from both \proglang{R} which is GPL-licensed
as well as from \pkg{Rcpp} and whichever other GPL-licensed components you may
be linking against.  


\section{Compiling and Linking}

\subsection{How do I use \pkg{Rcpp} in my package ?}
\label{make-package}

\pkg{Rcpp} has been specifically designed to be used by other packages.
Making a package that uses \pkg{Rcpp} depends on the same mechanics that are
involved in making any \proglang{R} package that use compiled code --- so
reading the \textsl{Writing R Extensions} manual \citep{R:Extensions} is a required
first step.

Further steps, specific to \pkg{Rcpp}, are described in a separate vignette.

<<eval=FALSE>>=
vignette("Rcpp-package")
@

\subsection{How do I quickly prototype my code?}

There are two toolchains which can help with this:
\begin{itemize}
\item The older one is provided by the \pkg{inline} package and described in
  Section~\ref{using-inline}. 
\item Starting with \pkg{Rcpp} 0.10.0, the Rcpp Attributes feature (described
  in Section~\ref{using-attributes}) offered an even easier alternative via
  the function \rdoc{Rcpp}{evalCpp}, \rdoc{Rcpp}{cppFunction} and
  \rdoc{Rcpp}{sourceCpp}.
\end{itemize}
The next two subsections show an example each.

\subsubsection{Using inline}
\label{using-inline}

The \pkg{inline} package \citep{CRAN:inline} provides the functions
\rdoc{inline}{cfunction} and \rdoc{inline}{cxxfunction}. Below is a simple
function that uses \texttt{accumulate} from the (\proglang{C++}) Standard
Template Library to sum the elements of a numeric vector.

<<>>=
fx <- cxxfunction(signature(x = "numeric"),
    'NumericVector xx(x);
     return wrap(std::accumulate(xx.begin(), xx.end(), 0.0));',
    plugin = "Rcpp")
res <- fx(seq(1, 10, by=0.5))
res
<<echo=FALSE>>=
stopifnot(identical(res, sum(seq(1, 10, by=0.5))))
@

%\pkg{Rcpp} uses \pkg{inline} to power its entire unit test suite. Consult the
%\texttt{unitTests} directory of \pkg{Rcpp} for several hundred further examples.
%
%< < eval=FALSE>>=
% \list.files( system.file( "unitTests", package = "Rcpp" ), pattern = "^runit[.]" )
% @

One might want to use code that lives in a \proglang{C++} file instead of writing
the code in a character string in R. This is easily achieved by using
\rdoc{base}{readLines}:

<<eval=FALSE>>=
fx <- cxxfunction(signature(), paste(readLines("myfile.cpp"), collapse="\n"),
                  plugin = "Rcpp")
@

The \texttt{verbose} argument of \rdoc{inline}{cxxfunction} is very
useful as it shows how \pkg{inline} runs the show.

\subsubsection{Using Rcpp Attributes}
\label{using-attributes}

Rcpp Attributes \citep{CRAN:Rcpp:Attributes}, and also discussed in
\faq{prototype-using-attributes} below, permits an even easier 
route to integrating R and C++.  It provides three key functions. First, \rdoc{Rcpp}{evalCpp}
provide a means to evaluate simple C++ expression which is often useful for
small tests, or to simply check if the toolchain is set up
correctly. Second, \rdoc{Rcpp}{cppFunction} can be used to create C++ functions
for R use on the fly.  Third, \code{Rcpp}{sourceCpp} can integrate entire files in
order to define multiple functions.

The example above can now be rewritten as:

<<>>=
cppFunction('double accu(NumericVector x) {
   return(std::accumulate(x.begin(), x.end(), 0.0));
}')
res <- accu(seq(1, 10, by=0.5))
res
@

The \rdoc{Rcpp}{cppFunction} parses the supplied text, extracts the desired
function names, creates the required scaffolding, compiles, links and loads
the supplied code and makes it available under the selected identifier.

Similarly, \rdoc{Rcpp}{sourceCpp} can read in a file and compile, link and load
the code therein.

\subsection{How do I convert my prototyped code to a package ?}
\label{from-inline-to-package}

Since release 0.3.5 of \pkg{inline}, one can combine \faq{using-inline} and
\faq{make-package}. See \verb|help("package.skeleton-methods")| once
\pkg{inline} is loaded and use the skeleton-generating functionality to
transform a prototyped function into the minimal structure of a package.
After that you can proceed with working on the package in the spirit of
\faq{make-package}.

Rcpp Attributes \citep{CRAN:Rcpp:Attributes} also offers a means to convert
functions written using Rcpp Attributes into a function via the
\rdoc{Rdoc}{compileAttributes} function; see the vignette for details.

\subsection{How do I quickly prototype my code in a package?}
\label{using-a-package}

The simplest way may be to work directly with a package.  Changes to both the
\proglang{R} and \proglang{C++} code can be compiled and tested from the
command line via:

<<lang=bash>>=
$ R CMD INSTALL mypkg && Rscript --default-packages=mypkg -e 'someFunctionToTickle(3.14)'
@

This first installs the packages, and then uses the command-line tool
\rdoc{utils}{Rscript} (which ships with \code{R}) to load the package, and execute
the \proglang{R} expression following the \code{-e} switch. Such an
expression can contain multiple statements separated by semicolons.
\rdoc{utils}{Rscript} is available on all three core operating systems.

On Linux, one can also use \code{r} from the \code{littler} package by Horner
and Eddelbuettel which is an alternative front end to \proglang{R} designed
for both \verb|#!| (hashbang) scripting and command-line use. It has slightly
faster start-up times than \rdoc{utils}{Rscript}; and both give a guaranteed clean
slate as a new session is created.

The example then becomes

<<lang=bash>>=
$ R CMD INSTALL mypkg && r -l mypkg -e 'someFunctionToTickle(3.14)'
@

The \code{-l} option calls 'suppressMessages(library(mypkg))' before executing the
\proglang{R} expression. Several packages can be listed, separated by a comma.

More choice are provide by the \pkg{devtools} package, and by using
RStudio. See the respective documentation for details.

\subsection{But I want to compile my code with R CMD SHLIB !}
\label{using-r-cmd-shlib}

The recommended way is to create a package and follow \faq{make-package}. The
alternate recommendation is to use \pkg{inline} and follow \faq{using-inline}
because it takes care of all the details.

However, some people have shown that they prefer not to follow recommended
guidelines and compile their code using the traditional \texttt{R CMD SHLIB}. To
do so, we need to help \texttt{SHLIB} and let it know about the header files
that \pkg{Rcpp} provides and the \proglang{C++} library the code must link
against.

On the Linux command-line, you can do the following:\newline
<<lang=bash>>=
$ export PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"`  # if Rcpp older than 0.11.0
$ export PKG_CXXFLAGS=`Rscript -e "Rcpp:::CxxFlags()"`
$ R CMD SHLIB myfile.cpp
@
which first defines and exports two relevant environment variables which
\texttt{R CMD SHLIB} then relies on.  On other operating systems, appropriate
settings may have to be used to define the environment variables.

This approach corresponds to the very earliest ways of building programs and
can still be found in some deprecated documents (as \textit{e.g.} some of
Dirk's older 'Intro to HPC with R' tutorial slides).  It is still not
recommended as there are tools and automation mechanisms that can do the work
for you.

\pkg{Rcpp} versions 0.11.0 or later can do with the definition of
\code{PKG\_LIBS} as a user-facing library is no longer needed (and hence no
longer shipped with the package).  One still needs to set \code{PKG\_CXXFLAGS}
to tell R where the \pkg{Rcpp} headers files are located.  

Once \code{R CMD SHLIB} has created the dyanmically-loadable file (with
extension \code{.so} on Linux, \code{.dylib} on OS X or \code{.dll} on
Windows), it can be loaded in an R session via \rdoc{base}{dyn.load}, and the
function can be executed via \rdoc{base}{.Call}.  Needless to say, we
\emph{strongly} recommend using a package, or at least Rcpp Attributes as
either approach takes care of a lot of these tedious and error-prone manual
steps.


\subsection{But R CMD SHLIB still does not work !}

We have had reports in the past where build failures occurred when users had
non-standard code in their \verb|~/.Rprofile| or \texttt{Rprofile.site} (or
equivalent) files.

If such code emits text on \texttt{stdout}, the frequent and implicit
invocation of \texttt{Rscript -e "..."} (as in \faq{using-r-cmd-shlib}
above) to retrieve settings directly from \pkg{Rcpp} will fail.

You may need to uncomment such non-standard code, or protect it by wrapping
it inside \texttt{if (interactive())}, or possibly try to use \texttt{Rscript
  --vanilla} instead of plain \texttt{Rscript}.


\subsection{What about \texttt{LinkingTo} ?}

\proglang{R} has only limited support for cross-package linkage.

We now employ the \texttt{LinkingTo} field of the \texttt{DESCRIPTION} file
of packages using \pkg{Rcpp}. But this only helps in having \proglang{R}
compute the location of the header files for us.

The actual library location and argument still needs to be provided by the
user. How to do so has been shown above, and we recommned you use either
\faq{make-package} or \faq{using-inline} both which use the \pkg{Rcpp}
function \texttt{Rcpp:::LdFlags()}.

If and when \texttt{LinkingTo} changes and lives up to its name, we will be
sure to adapt \pkg{Rcpp} as well. 

An important change arrive with \pkg{Rcpp} release 0.11.0 and concern the
automatic registration of functions; see Section~\ref{function-registration} below.


\subsection{Does \pkg{Rcpp} work on windows ?}

Yes of course. See the Windows binaries provided by CRAN.

\subsection{Can I use \pkg{Rcpp} with Visual Studio ?}

Not a chance.

And that is not because we are meanies but because \proglang{R} and Visual
Studio simply do not get along. As \pkg{Rcpp} is all about extending
\proglang{R} with \proglang{C++} interfaces, we are bound by the available
toolchain.  And \proglang{R} simply does not compile with Visual Studio. Go
complain to its vendor if you are still upset.

\subsection{I am having problems building Rcpp on OS X, any help ?}
\label{q:OSX}

There are three known issues regarding Rcpp build problems on OS X.  If you are
building packages with RcppArmadillo, there is yet another issue that is
addressed separately in \faq{q:OSXArma} below.

\subsubsection{Lack of a Compiler}
By default, OS X does not ship with an active compiler. To enable a compiler one
must either install
\href{https://itunes.apple.com/us/app/xcode/id497799835?mt=12}{Xcode} (OS X
$\le 10.8$) or
\href{https://developer.apple.com/library/ios/technotes/tn2339/_index.html}{Xcode
  Command Line Tools} (OS X $\ge 10.9$). We will focus on the later as the
installation requires the use of \texttt{Terminal} and the install size is
significantly less than the prior, which is setup using an installer.

To install XCode Command Line Tools, one must do the following:

\begin{enumerate}
    \item Open \texttt{Terminal} found in \texttt{/Applications/Utilities/}
    \item Type the following: 

<<lang=bash>>=
$ xcode-select --install
@
    \item Press "Install" on the window that pops up.
    \item After the installation is complete, type the following in \texttt{Terminal} to ensure the installation was successful:
 
<<lang=bash>>=
$ gcc --version
@
\end{enumerate}

After major system updates, e.g. going from version 10.11 to 10.12, you may need
to accept the terms and licenses associated the the Xcode command line tools
prior to being allowed to compile again.

To do so, open the \texttt{Terminal} found in \texttt{/Applications/Utilities/} and type:

<<lang=bash>>=
$ git
@

Press spacebar to move down to the end of the file. There, you should see a
prompt asking whether or not you accept the terms via either "Yes" or
"No". Enter "Yes" if you agree to the terms to have the command line tools
reactivated.

\subsubsection{Differing Mac OS X R Versions Leading to Binary Failures}

There are currently two distinct versions of R for OS X. The first version is a
legacy version meant for Mac OS X 10.6 (Snow Leopard) - 10.8 (Mountain
Lion). The second version is for more recent system Mac OS X 10.9 (Mavericks),
10.10 (Yosemite), 10.11 (El Capitan). The distinction comes as a result of a
change in the compilers shipped with the operating system. As a result, avoid
sending package binaries if it is known that your collaborators are working on
older systems as the R binaries for these two versions will not be able to mix.

\subsubsection{No OpenMP Support}
The OS X operating environment lacks the ability to parallelize sections of code
using the \href{http://openmp.org/wp/}{OpenMP} standard. As a result, make sure
to protect any reference to OpenMP. In this case, protect the inclusion of
headers with:

<<lang=cpp>>=
#ifdef _OPENMP
  #include <omp.h>
#endif
@

And when one goes to parallelize portions of code use:

<<lang=cpp>>=
#ifdef _OPENMP
    // multithreaded OpenMP version of code
#else
    // single-threaded version of code
#endif
@

Doing so will enable the parallelization of the process on Linux and Windows. In
the event that Apple enables OpenMP later on, this code will also allow for
parallelization to occur.

The reason for the lack of OpenMP support is because under OS X, you are not
using the \texttt{gcc} compiler. Instead, all the requests are being redirected
to \texttt{llvm}. As of LLVM 3.7, the
\href{https://clang-omp.github.io/}{community initiative} to enable OpenMP has
been merged into the \href{http://openmp.llvm.org/}{official branch}. Thus,
there is hope in the next release of Xcode (around WWDC in June 2016) that
OpenMP will work on OS X.


\subsubsection{Additional Information / Help}

Below are additional resources that provide information regarding compiling Rcpp code on OS X.

\begin{enumerate}
    \item A helpful post was provided by Brian Ripley regarding the use of
      compiling R code with OS X in April 2014
      \href{https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/010835.html}{on
        the \code{r-sig-mac} list}, which is generally recommended for OS
      X-specific questions and further consultation. 
    \item Another helpful write-up for installation / compilation on OS X Mavericks is provided
      \href{http://www.bioconductor.org/developers/how-to/mavericks-howto/}{by the BioConductor project}. 
    \item Lastly, another resource that exists for installation / compilation
      help is provided at
      \url{http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/}. 
\end{enumerate}

\textbf{Note:} If you are running into trouble compiling code with RcppArmadillo, please also see \faq{q:OSXArma} listed below. 

%At the time of writing this paragraph (in the spring of 2011), \pkg{Rcpp}
%(just like CRAN) supports all OS X releases greater or equal to 10.5.
%However, building \pkg{Rcpp} from source (or building packages using
%\pkg{Rcpp}) also requires a recent-enough version of Xcode. For the
%\textsl{Leopard} release of OS X, the current version is 3.1.4 which can be
%downloaded free of charge from the Apple Developer site. Users may have to
%manually select \code{g++-4.2} via the symbolic link \code{/usr/bin/g++}.
%The \textsl{Snow Leopard} release already comes with Xcode 3.2.x and work as
%is.

\subsection{Does \pkg{Rcpp} work on solaris/suncc ?}

Yes, it generally does.  But as we do not have access to such systems, some
issues persist on the CRAN test systems.

\subsection{Does \pkg{Rcpp} work with Revolution R ?}

We have not tested it yet. \pkg{Rcpp} might need a few tweaks to work
with the compilers used by Revolution R (if those differ from the defaults).

\subsection{Is it related to CXXR ?}

CXXR is an ambitious project that aims to totally refactor the \proglang{R}
interpreter in \proglang{C++}. There are a few similaritites with \pkg{Rcpp}
but the projects are unrelated.

CXXR and \pkg{Rcpp} both want \proglang{R} to make more use of \proglang{C++}
but they do it in very different ways.

\subsection{How do I quickly prototype my code using Attributes?}
\label{prototype-using-attributes}

\pkg{Rcpp} version 0.10.0 and later offer a new feature 'Rcpp Attributes'
which is described in detail in its own vignette
\citep{CRAN:Rcpp:Attributes}.  In short, it offers functions \rdoc{Rcpp}{evalCpp},
\rdoc{Rcpp}{cppFunction} and \rdoc{Rcpp}{sourceCpp} which extend the functionality of the
\rdoc{Rcpp}{cxxfunction} function.


\subsection{What about the new 'no-linking' feature??}
\label{function-registration}

Starting with \pkg{Rcpp} 0.11.0, functionality provided by \pkg{Rcpp} and
used by packages built with \pkg{Rcpp} accessed via the registration facility
offered by R (and which is used by \pkg{lme4} and \pkg{Matrix}, as well as by
\pkg{xts} and \pkg{zoo}).  This requires no effort from the user /
programmer, and even frees us from explicit linking instruction. In most
cases, the files \code{src/Makevars} and \code{src/Makevars.win} can now be
removed. Exceptions are the use of \pkg{RcppArmadillo} (which needs an entry
\verb|PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)|) and packages linking 
to external libraries they use.

But for most packages using \pkg{Rcpp}, only two things are required:
\begin{itemize}
\item an entry in \code{DESCRIPTION} such as \code{Imports: Rcpp} (which may
  be versioned as in \code{Imports: Rcpp (>= 0.11.0)}), and
\item an entry in \code{NAMESPACE} to ensure \pkg{Rcpp} is correctly
  instantiated, for example \code{importFrom(Rcpp, evalCpp)}.
\end{itemize}

The name of the symbol does really matter; once one symbol is important all
should be available.

\subsection{I am having problems building RcppArmadillo on OS X, any help ?}
\label{q:OSXArma}

Odds are your build failures are due to the absence of \texttt{gfortran}
and its associated libraries. The errors that you may receive are related to either: 
\begin{center}
\textbf{``-lgfortran''} or \textbf{``-lquadmath''}
\end{center}

To rectify the root of these errors, there are two options available. The first option is to download and use a fixed set of \texttt{gfortran} binaries that are used to compile R for OS X (e.g. given by the maintainers of the OS X build). The second option is to either use pre-existing \texttt{gfortran} binaries on your machine or download the latest.

\subsubsection{Fixed set of \texttt{gfortran} binaries}

Within this option, you will install a pre-compiled \code{gfortran} binary from
\href{http://r.research.att.com/libs/}{\texttt{r.research.att.com/libs/}}. The binary listed here was compiled by Simon Urbanek the maintainer of the OS X R versions.

To install the pre-compiled \code{gfortran} binary, do the following:
\begin{enumerate}
    \item Open \texttt{Terminal} found in \texttt{/Applications/Utilities/}
    \item Type the following: 

<<lang=bash>>=
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
@

\end{enumerate}

For more information on this error, please see TheCoatlessProfessor's  \href{http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/}{Rcpp, RcppArmadillo and OS X Mavericks "-lgfortran" and "-lquadmath" error}.

\subsubsection{Pre-existing or latest \texttt{gfortran} binaries}

Most OS X users that have a pre-existing \texttt{gfortran} binaries or want the latest version, typically use a custom packaging solution to install \texttt{gfortran}; 
\href{https://www.macports.org/}{\texttt{macports}},
\href{http://brew.sh/}{\texttt{homebrew}}, and
\href{http://www.finkproject.org/}{\texttt{fink}} are the usual suspects
here. In general, we recommend using homebrew, and we provide a short
set of instructions for installing \texttt{gfortran} below.

After installing \texttt{homebrew} by
\href{http://brew.sh/}{following the instructions here},
you can install the latest version of \texttt{gfortran} with:

    \code{brew install gcc}

Note that \texttt{gfortran} is available as part of the \texttt{gcc}
'formula' by default and cannot be downloaded separately, but one can
freely use \texttt{gfortran} with Apple (or LLVM) \texttt{clang}
compilers (as used by default on OS X since Mavericks).

You may need to set the \code{FLIBS} variable in your
\texttt{~/.R/Makevars} to point to the location of the \texttt{gfortran}
library paths. A solution is outlined
\href{http://stackoverflow.com/questions/29992066/rccp-warning-directory-not-found-for-option-l-usr-local-cellar-gfortran-4-8/29993906#29993906}{on
  StackOverflow}, but the relevant details are copied in brief here.

In short, you want to add this entry to your \texttt{~/.R/Makevars}:

\begin{verbatim}
FLIBS=`gfortran -print-search-dirs | grep ^libraries: | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`
\end{verbatim}

This invocation explicitly asks and constructs the library link paths
from the \texttt{gfortran}'s reported search paths, and produces a set
of paths suitable to be passed to \code{FLIBS}. \R will then search
these paths when attempting to locate e.g \code{libgfortran} when
compiling \pkg{RcppArmadillo} or other FORTRAN-dependent code.

Also see \faq{q:OSX} above, and the links provided in that answer. In the event
the above solution does not satisfy all the OS X build problems.  

\section{Examples}

The following questions were asked on the
\href{https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel}{Rcpp-devel}
mailing list, which is our preferred place to ask questions as it guarantees
exposure to a number of advanced Rcpp users.  The
\href{http://stackoverflow.com/questions/tagged/rcpp}{StackOverflow tag for
  rcpp} is an alternative; that site is also easily searchable.

Several dozen fully documented examples are provided at the
\href{http://gallery.rcpp.org}{Rcpp Gallery} -- which is also open for new contributions.

\subsection{Can I use templates with \pkg{Rcpp} ? }

\begin{quote}
  \emph{I'm curious whether one can provide a class definition inline in an R
    script and then initialize an instance of the class and call a method on
    the class, all inline in R.}
\end{quote}

This question was initially about using templates with \pkg{inline}, and we
show that (older) answer first. It is also easy with Rcpp Attributes which is
what we show below.

\subsubsection{Using inline}

\noindent Most certainly, consider this simple example of a templated class
which squares its argument:

<<lang=r>>=
inc <- 'template <typename T>
        class square : public std::unary_function<T,T> {
        public:
            T operator()( T t) const { return t*t ;}
        };
       '

src <- '
       double x = Rcpp::as<double>(xs);
       int i = Rcpp::as<int>(is);
       square<double> sqdbl;
       square<int> sqint;
       return Rcpp::DataFrame::create(Rcpp::Named("x", sqdbl(x)),
                                      Rcpp::Named("i", sqint(i)));
       '
fun <- cxxfunction(signature(xs="numeric", is="integer"),
                   body=src, include=inc, plugin="Rcpp")

fun(2.2, 3L)
@

\subsubsection{Using Rcpp Attributes}

We can also use 'Rcpp Attributes' \citep{CRAN:Rcpp:Attributes}---as described
in \faq{using-attributes} and \faq{prototype-using-attributes} above. Simply
place the following code into a file and use \rdoc{Rcpp}{sourceCpp} on it. It
will even run the R part at the end.

<<lang=cpp>>=
#include <Rcpp.h>

template <typename T> class square : public std::unary_function<T,T> {
public:
    T operator()( T t) const { return t*t ;}
};

// [[Rcpp::export]]
Rcpp::DataFrame fun(double x, int i) {
       square<double> sqdbl;
       square<int> sqint;
       return Rcpp::DataFrame::create(Rcpp::Named("x", sqdbl(x)),
                                      Rcpp::Named("i", sqint(i)));
}

/*** R
fun(2.2, 3L)
*/
@ 

\subsection{Can I do matrix algebra with \pkg{Rcpp} ?}
\label{matrix-algebra}

\begin{quote}
  \emph{\pkg{Rcpp} allows element-wise operations on vector and matrices through
    operator overloading and STL interface, but what if I want to multiply a
    matrix by a vector, etc ...}
\end{quote}

\noindent Currently, \pkg{Rcpp} does not provide binary operators to allow operations
involving entire objects. Adding operators to \pkg{Rcpp} would be a major
project (if done right) involving advanced techniques such as expression
templates. We currently do not plan to go in this direction, but we would
welcome external help. Please send us a design document.

However, we have developed the \pkg{RcppArmadillo} package
\citep{CRAN:RcppArmadillo,Eddelbuettel+Sanderson:2014:RcppArmadillo} that
provides a bridge between \pkg{Rcpp} and \pkg{Armadillo}
\citep{Sanderson:2010:Armadillo}. \pkg{Armadillo}
supports binary operators on its types in a way that takes full advantage of
expression templates to remove temporaries and allow chaining of
operations. That is a mouthful of words meaning that it makes the code go
faster by using fiendishly clever ways available via the so-called template
meta programming, an advanced \proglang{C++} technique.
Also, the \pkg{RcppEigen} package \citep{JSS:RcppEigen} provides an alternative using the
\href{http://eigen.tuxfamily.org}{Eigen} template library.

\subsubsection{Using inline}

The following example is adapted from the examples available at the project
page of Armadillo. It calculates $ x' \times Y^{-1} \times z$

<<lang=cpp>>=
    // copy the data to armadillo structures
    arma::colvec x = Rcpp::as<arma::colvec> (x_);
    arma::mat Y = Rcpp::as<arma::mat>(Y_) ;
    arma::colvec z = Rcpp::as<arma::colvec>(z_) ;

    // calculate the result
    double result = arma::as_scalar(arma::trans(x) * arma::inv(Y) * z);

    // return it to R
    return Rcpp::wrap( result );
@

%% Running this now makes the package depend on RcppArmadillo being installed
%% and would require at least a Suggests

If stored in a file \code{myfile.cpp}, we can use it via \pkg{inline}:

<<eval=FALSE>>=
fx <- cxxfunction(signature(x_="numeric", Y_="matrix", z_="numeric" ),
                  paste(readLines("myfile.cpp"), collapse="\n"),
                  plugin="RcppArmadillo" )
fx(1:4, diag(4), 1:4)
@
<<echo=FALSE>>=
unlink("myfile.cpp")
@

The focus is on the code \verb|arma::trans(x) * arma::inv(Y) * z|, which
performs the same operation as the R code \verb|t(x) %*% solve(Y) %*% z|,
although Armadillo turns it into only one operation, which makes it quite fast.
Armadillo benchmarks against other \proglang{C++} matrix algebra libraries
are provided on \href{http://arma.sourceforge.net/speed.html}{the Armadillo website}.

It should be noted that code below depends on the version \texttt{0.3.5} of
\pkg{inline} and the version \texttt{0.2.2} of \pkg{RcppArmadillo}

\subsubsection{Using Rcpp Attributes}

We can also write the same example for use with Rcpp Attributes:

<<lang=cpp>>=
#include <RcppArmadillo.h>

// [[Rcpp::depends(RcppArmadillo)]]

// [[Rcpp::export]]
double fx(arma::colvec x, arma::mat Y, arma::colvec z) {
    // calculate the result
    double result = arma::as_scalar(arma::trans(x) * arma::inv(Y) * z);
    return result;
}

/*** R
fx(1:4, diag(4), 1:4)
*/
@ 

Here, the additional \code{Rcpp::depends(RcppArmadillo)} ensures that code
can be compiled against the \pkg{RcppArmadillo} header, and that the correct
libraries are linked to the function built from the supplied code example.

Note how we do not have to concern ourselves with conversion; R object
automatically become (Rcpp)Armadillo objects and we can focus on the single
computing a (scalar) result.



\subsection{Can I use code from the Rmath header and library with \pkg{Rcpp} ?}

\begin{quote}
  \emph{Can I call functions defined in the Rmath header file and the
    standalone math library for R--as for example the random number generators?}
\end{quote}

\noindent Yes, of course. This math library exports a subset of R, but \pkg{Rcpp} has
access to much more.  Here is another simple example. Note how we have to use
and instance of the \texttt{RNGScope} class to set and re-set the
random-number generator. This also illustrates Rcpp sugar as we are using a
vectorised call to \texttt{rnorm}. Moreover, because the RNG is reset, the
two calls result in the same random draws. If we wanted to control the draws,
we could explicitly set the seed after the \texttt{RNGScope} object has been
instantiated.

<<>>=
fx <- cxxfunction(signature(), 
                  'RNGScope();
                   return rnorm(5, 0, 100);',
                  plugin="Rcpp")
set.seed(42)
fx()
fx()
@

Newer versions of Rcpp also provide the actual Rmath function in the \code{R}
namespace, \textsl{i.e.} as \code{R::rnorm(m,s)} to obtain a scalar
random variable distributed as $N(m,s)$.

Using Rcpp Attributes, this can be as simple as 

<<>>=
cppFunction('Rcpp::NumericVector ff(int n) { return rnorm(n, 0, 100); }')
set.seed(42)
ff(5)
ff(5)
set.seed(42)
rnorm(5, 0, 100)
rnorm(5, 0, 100)
@ 

This illustrates the Rcpp Attributes adds the required \code{RNGScope} object
for us. It also shows how setting the seed from R affects draws done via C++
as well as R, and that identical random number draws are obtained.

\subsection{Can I use NA and Inf with \pkg{Rcpp} ?}

\begin{quote}
  \emph{R knows about NA and Inf. How do I use them from C++?}
\end{quote}

\noindent Yes, see the following example:

<<>>=
src <- 'Rcpp::NumericVector v(4);
        v[0] = R_NegInf;  // -Inf
        v[1] = NA_REAL;   // NA
        v[2] = R_PosInf;  // Inf
        v[3] = 42;        // see the Hitchhiker Guide
        return Rcpp::wrap(v);'
fun <- cxxfunction(signature(), src, plugin="Rcpp")
fun()
@

Similarly, for Rcpp Attributes:

<<lang=cpp>>=
#include <Rcpp.h>

// [[Rcpp::export]]
Rcpp::NumericVector fun(void) {
    Rcpp::NumericVector v(4);
    v[0] = R_NegInf;  // -Inf
    v[1] = NA_REAL;   // NA
    v[2] = R_PosInf;  // Inf
    v[3] = 42;        // see the Hitchhiker Guide
    return v;
}
@ 

\subsection{Can I easily multiply matrices ?}

\begin{quote}
  \emph{Can I multiply matrices easily?}
\end{quote}

\noindent Yes, via the \pkg{RcppArmadillo} package which builds upon \pkg{Rcpp} and the
wonderful Armadillo library described above in \faq{matrix-algebra}:

<<eval=FALSE>>=
txt <- 'arma::mat Am = Rcpp::as< arma::mat >(A);
        arma::mat Bm = Rcpp::as< arma::mat >(B);
        return Rcpp::wrap( Am * Bm );'
mmult <- cxxfunction(signature(A="numeric", B="numeric"),
                     body=txt, plugin="RcppArmadillo")
A <- matrix(1:9, 3, 3)
B <- matrix(9:1, 3, 3)
C <- mmult(A, B)
@
% < < echo=FALSE,print=FALSE > > =
% A <- matrix(1:9, 3, 3)
% B <- matrix(9:1, 3, 3)
% A %*% B
% @

Armadillo supports a full range of common linear algebra operations.

The \pkg{RcppEigen} package provides an alternative using the
\href{http://eigen.tuxfamily.org}{Eigen} template library.

Rcpp Attributes, once again, makes this even easier:

<<lang=cpp>>=

#include <RcppArmadillo.h>

// [[Rcpp::depends(RcppArmadillo)]] 

// [[Rcpp::export]]
arma::mat mult(arma::mat A, arma::mat B) { 
    return A*B; 
}

/*** R
A <- matrix(1:9, 3, 3)
B <- matrix(9:1, 3, 3)
mult(A,B)
*/
@ 

which can be built, and run, from R via a simple \rdoc{Rcpp}{sourceCpp}
call---and will also run the small R example at the end.


\subsection{How do I write a plugin for \pkg{inline} and/or Rcpp Attributes?}

\begin{quote}
  \emph{How can I create my own plugin for use by the \pkg{inline} package?}
\end{quote}

\noindent Here is an example which shows how to it using GSL libraries as an
example.  This is merely for demonstration, it is also not perfectly general
as we do not detect locations first---but it serves as an example:

<<eval=FALSE>>=
## simple example of seeding RNG and drawing one random number
gslrng <- '
int seed = Rcpp::as<int>(par) ;
gsl_rng_env_setup();
gsl_rng *r = gsl_rng_alloc (gsl_rng_default);
gsl_rng_set (r, (unsigned long) seed);
double v = gsl_rng_get (r);
gsl_rng_free(r);
return Rcpp::wrap(v);'

plug <- Rcpp:::Rcpp.plugin.maker(
    include.before = "#include <gsl/gsl_rng.h>",
    libs = paste("-L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp",
                 "-Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib",
                 "-L/usr/lib -lgsl -lgslcblas -lm"))
registerPlugin("gslDemo", plug )
fun <- cxxfunction(signature(par="numeric"), gslrng, plugin="gslDemo")
fun(0)
@
%

Here the \pkg{Rcpp} function \code{Rcpp.plugin.maker} is used to create a
plugin 'plug' which is then registered, and subsequently used by \pkg{inline}.

The same plugins can be used by Rcpp Attributes as well.

\subsection{How can I pass one additional flag to the compiler?}

\begin{quote}
  \emph{How can I pass another flag to the \code{g++} compiler without writing a new plugin?}
\end{quote}

The quickest way is to modify the return value from an existing plugin. Here
we use the default one from \pkg{Rcpp} itself in order to pass the new flag
\verb|-std=c++0x|. As it does not set the \verb|PKG_CXXFLAGS| variable, we
simply assign this. For other plugins, one may need to append to the existing
values instead.

<<eval=FALSE>>=
myplugin <- getPlugin("Rcpp")
myplugin$env$PKG_CXXFLAGS <- "-std=c++11"
f <- cxxfunction(signature(), settings=myplugin, body='
+    std::vector<double> x = { 1.0, 2.0, 3.0 };  // fails without -std=c++0x
+    return Rcpp::wrap(x);
+ ')
f()
@

For Rcpp Attributes, the attributes \code{Rcpp::plugin()} can be
used. Currently supported plugins are for C++11 as well as for OpenMP.

\subsection{How can I set matrix row and column names ?}

\begin{quote}
  \emph{Ok, I can create a matrix, but how do I set its row and columns names?}
\end{quote}

Pretty much the same way as in \proglang{R} itself: We define a list with two
character vectors, one each for row and column names, and assign this to the
\code{dimnames} attribute:

<<eval=FALSE>>=
src <- '
  Rcpp::NumericMatrix x(2,2);
  x.fill(42);                           // or more interesting values
  Rcpp::List dimnms =                   // two vec. with static names
      Rcpp::List::create(Rcpp::CharacterVector::create("cc", "dd"),
                         Rcpp::CharacterVector::create("ee", "ff"));
  // and assign it
  x.attr("dimnames") = dimnms;
  return(x);
'
fun <- cxxfunction(signature(), body=src, plugin="Rcpp")
fun()
@
%

The same logic, but used with Rcpp Attributes:

<<lang=cpp>>=
#include <Rcpp.h>

// [[Rcpp::export]]
Rcpp::List fun(void) {
    Rcpp::NumericMatrix x(2,2);
    x.fill(42);                           // or more interesting values
    Rcpp::List dimnms =                   // two vec. with static names
        Rcpp::List::create(Rcpp::CharacterVector::create("cc", "dd"),
                           Rcpp::CharacterVector::create("ee", "ff"));
    // and assign it
    x.attr("dimnames") = dimnms;
    return(x);
}
@ 

\subsection{Why can long long types not be cast correctly?}

That is a good and open question. We rely on the basic \proglang{R} types,
notably \code{integer} and \code{numeric}.  These can be cast to and from
\proglang{C++} types without problems.  But there are corner cases.  The
following example, contributed by a user, shows that we cannot reliably cast
\code{long} types (on a 64-bit machines).

<<eval=FALSE>>=
BigInts <- cxxfunction(signature(),
  'std::vector<long> bigints;
   bigints.push_back(12345678901234567LL);
   bigints.push_back(12345678901234568LL);
   Rprintf("Difference of %ld\\n", 12345678901234568LL - 12345678901234567LL);
   return wrap(bigints);', plugin="Rcpp", includes="#include <vector>")

retval<-BigInts()

# Unique 64-bit integers were cast to identical lower precision numerics
# behind my back with no warnings or errors whatsoever.  Error.


stopifnot(length(unique(retval)) == 2)
@
%

While the difference of one is evident at the \proglang{C++} level, it is no
longer present once cast to \proglang{R}. The 64-bit integer values get cast
to a floating point types with a 53-bit mantissa. We do not have a good
suggestion or fix for casting 64-bit integer values: 32-bit integer values
fit into \code{integer} types, up to 53 bit precision fits into
\code{numeric} and beyond that truly large integers may have to converted
(rather crudely) to text and re-parsed. Using a different representation as
for example from the \href{http://gmplib.org/}{GNU Multiple Precision Arithmetic
  Library} may be an alternative.

\subsection{What LaTeX packages do I need to typeset the vignettes ?}

\begin{quote}
  \emph{I would like to typeset the vignettes. What do I need?}
\end{quote}

The \href{https://www.tug.org/texlive/}{TeXLive} distribution seems to get
bigger and bigger.  What you need to install may depend on your operating
system.

Specific per-platform notes:
\begin{description}
  \item[Windows] users probably want the \href{http://miktex.org/}{MiKTeX}.
    Suggestions for a more detailed walk through would be appreciated.
  \item[OS X] users seem to fall into camps which like or do not like brew /
    homebrew. One suggestion was to install
    \href{https://tug.org/mactex/mactex-download.html}{MacTeX} but at
    approximately 2.5gb (as of January 2016) this is not lightweight.
  \item[Linux] users probably want the full
    \href{https://www.tug.org/texlive/}{TeXLive} set from their distribution. On
    \href{http://www.debian.org}{Debian} these packages are installed to build
    the R package itself: \texttt{texlive-base, texlive-latex-base,
      texlive-generic-recommended, texlive-fonts-recommended,
      texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended,
      texlive-latex-extra}.  Using \texttt{texlive-full} may be a shortcut.
    Fedora and other distributions should have similar packages.
\end{description}

\subsection{Why is there a limit of 20 on some constructors?}

\begin{quote}
  \emph{Ok, I would like to pass $N$ object but you only allow 20. How come?}
\end{quote}

In essence, and in order to be able to compile it with the largest number of
compilers, \pkg{Rcpp} is constrained by the older C++ standards which do not
support variadic function arguments.  So we actually use macros and code
generator scripts to explicitly enumerate arguments, and that number has to stop
at some limit. We chose 20.

A good discussion is available at
\href{http://stackoverflow.com/questions/27371543}{this StackOverflow question}
concering data.frame creation with \pkg{Rcpp}. One solution offers a custom
\code{ListBuilder} class to circumvent the limit; another suggests to simply
nest lists.


\section{Support}

\subsection{Is the API documented ?}

You bet. We use \proglang{doxygen} to generate html, latex and man page
documentation from the source. The html documentation is available for
\href{http://dirk.eddelbuettel.com/code/rcpp/html/index.html}{browsing}, as a
\href{http://dirk.eddelbuettel.com/code/rcpp/Rcpp_refman.pdf}{very large pdf file},
and all three formats are also available a zip-archives:
\href{http://dirk.eddelbuettel.com/code/rcpp/rcpp-doc-html.zip}{html},
\href{http://dirk.eddelbuettel.com/code/rcpp/rcpp-doc-latex.zip}{latex}, and
\href{http://dirk.eddelbuettel.com/code/rcpp/rcpp-doc-man.zip}{man}.

\subsection{Does it really work ?}

We take quality seriously and have developped an extensive unit test suite to
cover many possible uses of the \pkg{Rcpp} API.

We are always on the look for more coverage in our testing. Please let us know
if something has not been tested enough.


\subsection{Where can I ask further questions ?}

The
\href{https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel}{Rcpp-devel}
mailing list hosted at R-forge is by far the best place.  You may also want
to look at the list archives to see if your question has been asked before.

You can also use \href{http://stackoverflow.com/questions/tagged/rcpp}{Stack
  Overflow via its 'rcpp' tag}.

\subsection{Where can I read old questions and answers ?}

The normal \href{https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel}{Rcpp-devel}
mailing list hosting at R-forge contains an archive, which can be
\href{http://lists.r-forge.r-project.org/mailman/swish.cgi?query=listname=rcpp-devel}{searched via swish}.

Alternatively, one can also use
\href{http://thread.gmane.org/gmane.comp.lang.r.rcpp/}{Gmane on Rcpp-devel} as well as
\href{http://www.mail-archive.com/rcpp-devel@lists.r-forge.r-project.org/info.html}{Mail-Archive
  on Rcpp-devel} both of which offer web-based interfaces, including
searching.

\subsection{I like it. How can I help ?}
\label{helping}

We maintain a list of
\href{https://github.com/RcppCore/Rcpp/issues?state=open}{open issues in the
  Github repository}. We welcome pull requests and suggest that code submissions
come corresponding unit tests and, if applicable, documentation.

If you are willing to donate time and have skills in C++, let us know. If you are
willing to donate money to sponsor improvements, let us know too.

You can also spread the word about \pkg{Rcpp}. There are many packages on CRAN
that use \proglang{C++}, yet are not using \pkg{Rcpp}. You could blog about
it, or get the word out otherwise.

Last but not least the \href{http://gallery.rcpp.org}{Rcpp Gallery} is open
for user contributions.


\subsection{I don't like it. How can I help ?}

It is very generous of you to still want to help. Perhaps you can tell us
what it is that you dislike. We are very open to \emph{constructive} criticism.

\subsection{Can I have commercial support for \pkg{Rcpp} ?}

Sure you can. Just send us an email, and we will be happy to discuss the
request.

\subsection{I want to learn quickly. Do you provide training courses ?}

Yes. Just send us an email.

\subsection{Where is the code repository ?}

From late 2008 to late 2013, we used the
\href{https://r-forge.r-project.org/scm/?group_id=155}{Subversion repository at R-Forge}
which contained \pkg{Rcpp} and a number of related packages. It still has the full
history as well as number of support files.

We have since switched to a \href{http://github.com/RcppCore/Rcpp}{Git
  repository at Github} for \pkg{Rcpp} (as well as for \pkg{RcppArmadillo} and
\pkg{RcppEigen}).

\bibliographystyle{plainnat}
\bibliography{Rcpp}

\end{document}

