comment out some by not all highlight definitions which are now also pulled in via the highlight driver

Author: eddelbuettel

vignettes/Rcpp-attributes.Rnw

@@ -31,26 +31,26 @@ prettyDate <- format(Sys.Date(), "%B %e, %Y")
 \date{\pkg{Rcpp} version \Sexpr{prettyVersion} as of \Sexpr{prettyDate}}
 
 
-%% highlights macros
-%% Style definition file generated by highlight 2.7, http://www.andre-simon.de/
-% Highlighting theme definition:
-\newcommand{\hlstd}[1]{\textcolor[rgb]{0,0,0}{#1}}
-\newcommand{\hlnum}[1]{\textcolor[rgb]{0,0,0}{#1}}
+%% %% highlights macros
+%% %% Style definition file generated by highlight 2.7, http://www.andre-simon.de/
+%% % Highlighting theme definition:
+%% \newcommand{\hlstd}[1]{\textcolor[rgb]{0,0,0}{#1}}
+%% \newcommand{\hlnum}[1]{\textcolor[rgb]{0,0,0}{#1}}
 \newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}
-\newcommand{\hlesc}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
-%\newcommand{\hlstr}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
-\newcommand{\hlstr}[1]{\textcolor[rgb]{0.90,0.15,0.15}{#1}}
-%green: \newcommand{\hlstr}[1]{\textcolor[rgb]{0.13,0.67,0.13}{#1}} % 0.74 -> % 0.90; 0.55 -> 0.25
-\newcommand{\hldstr}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
-\newcommand{\hlslc}[1]{\textcolor[rgb]{0.67,0.13,0.13}{#1}}
-\newcommand{\hlcom}[1]{\textcolor[rgb]{0.67,0.13,0.13}{#1}}
-\newcommand{\hldir}[1]{\textcolor[rgb]{0,0,0}{#1}}
-\newcommand{\hlsym}[1]{\textcolor[rgb]{0,0,0}{#1}}
-\newcommand{\hlline}[1]{\textcolor[rgb]{0.33,0.33,0.33}{#1}}
-\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.61,0.13,0.93}{\bf{#1}}}
-\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.13,0.54,0.13}{#1}}
-\newcommand{\hlkwc}[1]{\textcolor[rgb]{0,0,1}{#1}}
-\newcommand{\hlkwd}[1]{\textcolor[rgb]{0,0,0}{#1}}
+%% \newcommand{\hlesc}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
+%% %\newcommand{\hlstr}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
+%% \newcommand{\hlstr}[1]{\textcolor[rgb]{0.90,0.15,0.15}{#1}}
+%% %green: \newcommand{\hlstr}[1]{\textcolor[rgb]{0.13,0.67,0.13}{#1}} % 0.74 -> % 0.90; 0.55 -> 0.25
+%% \newcommand{\hldstr}[1]{\textcolor[rgb]{0.74,0.55,0.55}{#1}}
+%% \newcommand{\hlslc}[1]{\textcolor[rgb]{0.67,0.13,0.13}{#1}}
+%% \newcommand{\hlcom}[1]{\textcolor[rgb]{0.67,0.13,0.13}{#1}}
+%% \newcommand{\hldir}[1]{\textcolor[rgb]{0,0,0}{#1}}
+%% \newcommand{\hlsym}[1]{\textcolor[rgb]{0,0,0}{#1}}
+%% \newcommand{\hlline}[1]{\textcolor[rgb]{0.33,0.33,0.33}{#1}}
+%% \newcommand{\hlkwa}[1]{\textcolor[rgb]{0.61,0.13,0.93}{\bf{#1}}}
+%% \newcommand{\hlkwb}[1]{\textcolor[rgb]{0.13,0.54,0.13}{#1}}
+%% \newcommand{\hlkwc}[1]{\textcolor[rgb]{0,0,1}{#1}}
+%% \newcommand{\hlkwd}[1]{\textcolor[rgb]{0,0,0}{#1}}
 \definecolor{bgcolor}{rgb}{1,1,1}
 \newcommand{\hlppc}[1]{\textcolor[rgb]{0,0.51,0}{#1}}
 
@@ -84,7 +84,7 @@ prettyDate <- format(Sys.Date(), "%B %e, %Y")
   functions as callable from \proglang{R} and automatically generating the code
   required to invoke them. Attributes are intended to facilitate both interactive use
   of \proglang{C++} within \proglang{R} sessions as well as to support \proglang{R}
-  package development. The implementation of attributes  is based on previous 
+  package development. The implementation of attributes  is based on previous
   work in the \pkg{inline} package \citep{CRAN:inline}.
 }
 
@@ -128,12 +128,12 @@ functions include:
 
 Attributes can also be used for package development via the
 \texttt{compileAttributes} function, which automatically generates
-\texttt{extern "C"} and \texttt{.Call} wrappers for \proglang{C++} 
+\texttt{extern "C"} and \texttt{.Call} wrappers for \proglang{C++}
 functions within pacakges.
 
 \section{Using Attributes}
 
-Attributes are annotations that are added to C++ source files to provide 
+Attributes are annotations that are added to C++ source files to provide
 additional information to the compiler. \pkg{Rcpp} supports attributes
 to indicate that C++ functions should be made available as R functions,
 as well as to optionally specify additional build dependencies for source files.
@@ -219,7 +219,7 @@ prompt:
 
 We can now write \proglang{C++} functions using built-in \proglang{C++} types
 and \pkg{Rcpp} wrapper types and then source them just as we would an
-\proglang{R} script. 
+\proglang{R} script.
 
 The \texttt{sourceCpp} function performs caching based on the last
 modified date of the source file so as long as the source file does not
@@ -233,7 +233,7 @@ the following C++ function:
 
 % \begin{verbatim}
 % DataFrame readData(
-%     CharacterVector file, 
+%     CharacterVector file,
 %     CharacterVector colNames = CharacterVector::create(),
 %     std::string commentChar = "#",
 %     bool header = true)
@@ -265,7 +265,7 @@ Will be exported to R as:
 \normalsize
 \end{kframe}
 
-Note that C++ rules for default arguments still apply: they must occur 
+Note that C++ rules for default arguments still apply: they must occur
 consecutively at the end of the function signature and (unlike R) can't rely
 on the values of other arguments.
 
@@ -275,18 +275,18 @@ Not all \proglang{C++} defualt argument values can be parsed into their
 \begin{itemize}
 \item
    String literals delimited by quotes (e.g. \texttt{"foo"})
-\item 
+\item
    Decimal numeric values (e.g. \texttt{10} or \texttt{4.5})
 \item
-   Pre-defined constants including \texttt{true}, \texttt{false}, 
+   Pre-defined constants including \texttt{true}, \texttt{false},
    \texttt{R\_NilValue}, \texttt{NA\_STRING}, \texttt{NA\_INTEGER},
    \texttt{NA\_REAL}, and \texttt{NA\_LOGICAL}.
 \item
-   Selected vector types (\texttt{CharacterVector}, \texttt{IntegerVector}, 
+   Selected vector types (\texttt{CharacterVector}, \texttt{IntegerVector},
    and \texttt{NumericVector}) instantiated using the \texttt{::create}
    static member function.
-\item 
-  \texttt{Matrix} types instantiated using the \texttt{rows}, 
+\item
+  \texttt{Matrix} types instantiated using the \texttt{rows},
   \texttt{cols} constructor.
 \end{itemize}
 
@@ -344,15 +344,15 @@ files. However, it's often convenient to bundle code from both languages into
 a common source file that can be executed using single call to \texttt{sourceCpp}.
 
 To embed chunks of \proglang{R} code within a \proglang{C++}
-source file you include the \proglang{R} code within a block comment that 
+source file you include the \proglang{R} code within a block comment that
 has the prefix of \texttt{/*** R}. For example:
 
 % \begin{verbatim}
 % /*** R
-% 
+%
 % # Call the fibonacci function defined in C++
 % fibonacci(10)
-% 
+%
 % */
 % \end{verbatim}
 \begin{kframe}
@@ -378,7 +378,7 @@ shared library and then source the embedded \proglang{R} code.
 \subsection{Modifying Function Names}
 
 You can change the name of an exported function as it appears to \proglang{R} by
-adding a name parameter to \texttt{Rcpp::export}. For example: 
+adding a name parameter to \texttt{Rcpp::export}. For example:
 
 % \begin{verbatim}
 % // [[Rcpp::export(".convolveCpp")]]
@@ -395,7 +395,7 @@ adding a name parameter to \texttt{Rcpp::export}. For example:
 \end{kframe}
 
 Note that in this case since the specified name is prefaced by a \code{.} the exported R
-function will be hidden. 
+function will be hidden.
 
 \subsection{Function Requirements}
 
@@ -407,24 +407,24 @@ requirements to be correctly handled:
    Be defined in the global namespace (i.e. not within a C++ namespace declaration)
 \item
    Have a return type that is either void or compatible with \texttt{Rcpp::wrap}
-   and parameter types that are compatible with \texttt{Rcpp::as} (see sections 
+   and parameter types that are compatible with \texttt{Rcpp::as} (see sections
    3.1 and 3.2 of the `\textsl{Rcpp-introduction}' vignette for more details).
  \item
    Use fully qualified type names for the return value and all parameters.
-   Rcpp types may however appear without a namespace qualifier (i.e. 
+   Rcpp types may however appear without a namespace qualifier (i.e.
    \texttt{DataFrame} is okay as a type name but \texttt{std::string} must be
-   specified fully).  
+   specified fully).
 \end{itemize}
 
 \subsection{Random Number Generation}
 
 \proglang{R} functions implemented in \proglang{C} or \proglang{C++} need
-to be careful to surround use of internal random number geneneration routines 
-(e.g. \texttt{unif\_rand}) with calls to \texttt{GetRNGstate} and 
-\texttt{PutRNGstate}. 
+to be careful to surround use of internal random number geneneration routines
+(e.g. \texttt{unif\_rand}) with calls to \texttt{GetRNGstate} and
+\texttt{PutRNGstate}.
 
-Within \pkg{Rcpp}, this is typically done using the \texttt{RNGScope} class. 
-However, this is not necessary for \proglang{C++} functions exported using 
+Within \pkg{Rcpp}, this is typically done using the \texttt{RNGScope} class.
+However, this is not necessary for \proglang{C++} functions exported using
 attributes because an \texttt{RNGScope} is established for them automatically.
 Note that \pkg{Rcpp} implements \texttt{RNGScope} using a counter, so it's
 still safe to execute code that may establish it's own \texttt{RNGScope} (such
@@ -517,7 +517,7 @@ and by invoking \pkg{inline} plugins if they are available for a package.
 
 Note that while the \texttt{Rcpp::depends} attribute establishes dependencies
 for \texttt{sourceCpp}, it's important to note that if you include the same
-source file in an \proglang{R} package these dependencies must still be 
+source file in an \proglang{R} package these dependencies must still be
 listed in the \texttt{Depends} and \texttt{LinkingTo} fields of the package
 \texttt{DESCRIPTION} file.
 
@@ -527,10 +527,10 @@ listed in the \texttt{Depends} and \texttt{LinkingTo} fields of the package
 Maintaining C++ code in it's own source file provides several benefits including
 the ability to use \proglang{C++} aware text-editing tools and straightforward
 mapping of compilation errors to lines in the source file. However, it's also
-possible to do inline declaration and execution of C++ code. 
+possible to do inline declaration and execution of C++ code.
 
 There are several ways to accomplish this, including passing a code
-string to \texttt{sourceCpp} or using the shorter-form \texttt{cppFunction} 
+string to \texttt{sourceCpp} or using the shorter-form \texttt{cppFunction}
 or \texttt{evalCpp} functions. For example:
 
 % \begin{verbatim}
@@ -600,11 +600,11 @@ moving code from a standalone \proglang{C++} source file to a package:
 
 \subsection{Package Creation}
 
-To create a package that is based on \pkg{Rcpp} you should follow the 
+To create a package that is based on \pkg{Rcpp} you should follow the
 guidelines in the `\textsl{Rcpp-package}' vignette. For a new package this
 is most conveniently done using  the \texttt{Rcpp.package.skeleton} function.
 
-To generate a new package with a simple hello, world function that uses 
+To generate a new package with a simple hello, world function that uses
 attributes you can do the following:
 
 % \begin{verbatim}
@@ -641,7 +641,7 @@ with \texttt{sourceCpp} you can use the \texttt{cpp\_files} parameter:
 Once you've migrated \proglang{C++} code into a package, the dependencies for
 source files are derived from the \texttt{Depends} and \texttt{LinkingTo} fields
 in the package \texttt{DESCRIPTION} file rather than the \texttt{Rcpp::depends}
-attribute. For every package you import C++ code from (including \pkg{Rcpp}) 
+attribute. For every package you import C++ code from (including \pkg{Rcpp})
 you need to add these entries.
 
 For example, if your package depends on \pkg{Rcpp} and \pkg{RcppArmadillo}
@@ -664,7 +664,7 @@ LinkingTo:\ Rcpp,\ RcppArmadillo}\hspace*{\fill}
 \subsection{Exporting R Functions}
 
 Within interactive sessions you call the \texttt{sourceCpp} function
-on individual files to export \proglang{C++} functions into the global 
+on individual files to export \proglang{C++} functions into the global
 environment. However, for packages you call a single utility function to
 export all \proglang{C++} functions within the package.
 
@@ -696,13 +696,13 @@ Results in the generation of the following two source files:
   the \texttt{extern "C"} functions defined in \texttt{RcppExports.cpp}.
 \end{itemize}
 
-You should re-run \texttt{compileAttributes} whenever functions are added, 
+You should re-run \texttt{compileAttributes} whenever functions are added,
 removed, or have their signatures changed.
 
 The \texttt{compileAttributes} function deals only with exporting
-\proglang{C++} functions to \proglang{R}. If you want the functions to 
-additionally be publicly available from your package's namespace another 
-step may be required. Specifically, if your package \texttt{NAMESPACE} file 
+\proglang{C++} functions to \proglang{R}. If you want the functions to
+additionally be publicly available from your package's namespace another
+step may be required. Specifically, if your package \texttt{NAMESPACE} file
 does not use a pattern to export functions then you should add an explicit
 entry to \texttt{NAMESPACE} for each R function you want publicly available.
 
@@ -767,10 +767,10 @@ The interface exposed from \proglang{R} packages is most typically a set of
 \proglang{R} functions. However, the \proglang{R} package system also provides
 a mechanism to allow the exporting of \proglang{C} and \proglang{C++}
 interfaces using package header files.  This is based on the
-\texttt{R\_RegisterCCallable} and \texttt{R\_GetCCallable} functions described in 
+\texttt{R\_RegisterCCallable} and \texttt{R\_GetCCallable} functions described in
 `\textsl{Writing R Extensions}' \citep{R:Extensions}.
 
-\proglang{C++} interfaces to a package are published within the 
+\proglang{C++} interfaces to a package are published within the
 top level \texttt{include} directory of the package (which within the package
 source directory is located at \texttt{inst/include}). The \proglang{R} build
 system automatically adds the required \texttt{include} directories for all
@@ -779,12 +779,12 @@ packages specified in the \texttt{LinkingTo} field of the package
 
 \subsubsection{Interfaces Attribute}
 
-The \texttt{Rcpp::interfaces} attribute can be used to automatically 
+The \texttt{Rcpp::interfaces} attribute can be used to automatically
 generate a header-only interface to your \proglang{C++} functions
 within the \texttt{include} directory of your package.
 
 The \texttt{Rcpp::interfaces} attribute is specified on a per-source
-file basis, and indicates which interfaces (\proglang{R}, \proglang{C++}, 
+file basis, and indicates which interfaces (\proglang{R}, \proglang{C++},
 or both) should be provided for exported functions within the file.
 
 For example, the following specifies that both R and \proglang{C++} interfaces
@@ -809,7 +809,7 @@ is not included in a source file is to generate an R interface only.
 \subsubsection{Generated Code}
 
 If you request a \texttt{cpp} interface for a source file then
-\texttt{compileAttributes} generates the following header files 
+\texttt{compileAttributes} generates the following header files
 (substituting \emph{Package} with the name of the package code is being
 generated for):
 
@@ -827,14 +827,14 @@ inst/include/Package\textunderscore RcppExports.h}\hspace*{\fill}
 \normalsize
 \end{kframe}
 
-The \texttt{Package\_RcppExports.h} file has inline definitions for all 
+The \texttt{Package\_RcppExports.h} file has inline definitions for all
 exported \proglang{C++} functions that enable calling them using the
-\texttt{R\_GetCCallable} mechanism. 
+\texttt{R\_GetCCallable} mechanism.
 
 The \texttt{Package.h} file does nothing other than include the
-\texttt{Package\_RcppExports.h} header. This is done so 
+\texttt{Package\_RcppExports.h} header. This is done so
 that package authors can replace the \texttt{Package.h} header with
-a custom one and still be able to include the automatically generated exports 
+a custom one and still be able to include the automatically generated exports
 (details on doing this are provided in the next section).
 
 The exported functions are defined within a \proglang{C++} namespace that matches
@@ -869,23 +869,23 @@ the name of the package. For example, an exported \proglang{C++} function
 \subsubsection{Including Additional Code}
 
 You might wish to use the \texttt{Rcpp::interfaces} attribute to generate
-a part of your package's \proglang{C++} interface but also provide 
-additional custom \proglang{C++} code. In this case you 
-should replace the generated \texttt{Package.h} file with one of your own. 
+a part of your package's \proglang{C++} interface but also provide
+additional custom \proglang{C++} code. In this case you
+should replace the generated \texttt{Package.h} file with one of your own.
 
 Note that the way \pkg{Rcpp} distinguishes user verses generated files is by checking
 for the presence a special token in the file (if it's present then it's known
 to be generated and thus safe to overwrite). You'll see this token at the top
-of the generated \texttt{Package.h} file, be sure to remove it if you want 
+of the generated \texttt{Package.h} file, be sure to remove it if you want
 to provide a custom header.
 
-Once you've established a custom package header file, you need only include the 
-\texttt{Package\_RcppExports.h} file within your header to make available 
+Once you've established a custom package header file, you need only include the
+\texttt{Package\_RcppExports.h} file within your header to make available
 the automatically generated code alongside your own.
 
-If you need to include code from your custom header files within the 
+If you need to include code from your custom header files within the
 compilation of your package source files, you will also need to add the
-following entry to \texttt{Makevars} and \texttt{Makevars.win} (both are 
+following entry to \texttt{Makevars} and \texttt{Makevars.win} (both are
 in the \texttt{src} directory of your package):
 
 % \begin{verbatim}