diff --git a/src/docs/stan-reference/appendices.tex b/src/docs/stan-reference/appendices.tex
index ef219d467ce..a33aa7a5fbb 100644
--- a/src/docs/stan-reference/appendices.tex
+++ b/src/docs/stan-reference/appendices.tex
@@ -430,7 +430,7 @@ \subsubsection{Boost C++ Library Source}
 \begin{itemize}
 \item Home: http://www.boost.org/users/license.html
 \item License: Boost Software License
-\item Tested Version: 1.51.0
+\item Tested Version: 1.52.0
 \end{itemize}
 %
 The Boost source code is distributed with \Stan.
@@ -444,7 +444,7 @@ \subsubsection{Eigen Matrix and Linear Algebra Library Source}
 \begin{itemize}
 \item Home: \url{http://eigen.tuxfamily.org}
 \item License: Mozilla Public License, version 2.0
-\item Tested Version: 3.1.1
+\item Tested Version: 3.1.2
 \end{itemize}
 %
 The Eigen source code is distributed with \Stan.
diff --git a/src/docs/stan-reference/commands.tex b/src/docs/stan-reference/commands.tex
index b6a01293c2b..4f466802013 100644
--- a/src/docs/stan-reference/commands.tex
+++ b/src/docs/stan-reference/commands.tex
@@ -442,8 +442,8 @@ \subsection{Compiling a \Stan Model}
 \begin{quote}
 \begin{Verbatim}[fontshape=sl]
 > cd <stan-home>
-> g++ -O3 -Lbin -Isrc -Ilib/boost_1.51.0 \
-  -Ilib/eigen_3.1.0 my_model.cpp -o my_model -lstan
+> g++ -O3 -Lbin -Isrc -Ilib/boost_1.52.0 \
+  -Ilib/eigen_3.1.2 my_model.cpp -o my_model -lstan
 \end{Verbatim}
 \end{quote} %
 The backslash (\Verb|\|) is used to indicate that the command is
@@ -457,9 +457,9 @@ \subsection{Compiling a \Stan Model}
   directory,
 \item[\code{-Isrc}] specifies that the directory \code{src} should be
   searched for code (it contains the top-level \Stan headers),
-\item[\code{-Ilib/eigen\_3.1.0}] specifies the directory for
+\item[\code{-Ilib/eigen\_3.1.2}] specifies the directory for
   the Eigen library,
-\item[\code{-Ilib/boost\_1.51.0}] specifies the directory for the 
+\item[\code{-Ilib/boost\_1.52.0}] specifies the directory for the 
   Boost library,
 \item[\code{my\_model.cpp}] specifies the name of the source file to
   compile, and 
diff --git a/src/stan/gm/generator.hpp b/src/stan/gm/generator.hpp
index 7f25b345adb..7a17258435b 100644
--- a/src/stan/gm/generator.hpp
+++ b/src/stan/gm/generator.hpp
@@ -1383,6 +1383,7 @@ namespace stan {
       o << INDENT << "             std::ostream* pstream__ = 0) {" << EOL2;
 
       // use this dummy for inits
+      o << INDENT2 << "// Note: this is not a memory leak. Memory will be cleaned up with the arena allocator" << EOL;
       o << INDENT2 << "stan::agrad::vari* DUMMY_VARI_PTR__ = new vari(std::numeric_limits<double>::quiet_NaN(),false);" << EOL;
       o << INDENT2 << "stan::agrad::var DUMMY_VAR__ = var(DUMMY_VARI_PTR__);" << EOL2;