Error(s) in re-building vignettes:
  ...
--- re-building ‘SBC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Creating a 'stanmodel' object beta_binomial
--- finished re-building ‘SBC.Rmd’

--- re-building ‘external.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 200-208 (external.Rmd) 
Quitting from lines 200-208 (external.Rmd) 
Error: processing vignette 'external.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘external.Rmd’

--- re-building ‘rstan.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5,
                 from file66136fff3810.cpp:5:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/get_pointer.hpp: At global scope:
/tmp/RtmpWCaaZT/RLIBS_5b9810891cc9/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /opt/csw/include/c++/5.2.0/bits/locale_conv.h:41:0,
                 from /opt/csw/include/c++/5.2.0/locale:43,
                 from /opt/csw/include/c++/5.2.0/iomanip:43,
                 from /home/ripley/R/Lib32/Rcpp/include/RcppCommon.h:52,
                 from /home/ripley/R/Lib32/rstan/include/exporter.h:1,
                 from file66136fff3810.cpp:1:
/opt/csw/include/c++/5.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
--- finished re-building ‘rstan.Rmd’

--- re-building ‘stanfit-objects.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘stanfit-objects.Rmd’

SUMMARY: processing the following file failed:
  ‘external.Rmd’

Error: Vignette re-building failed.
Execution halted