Error(s) in re-building vignettes:
--- re-building ‘SBC.Rmd’ using rmarkdown
Creating a 'stanmodel' object beta_binomial
--- finished re-building ‘SBC.Rmd’

--- re-building ‘external.Rmd’ using rmarkdown
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
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Core:535:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/LU:47:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:12:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Jacobi:29:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:43:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/QR:17:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Householder:27:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SVD:48:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:6:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Geometry:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:66:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:71:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCholesky:43:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:32:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseQR:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from <built-in>:1:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:33:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from fileadf94129557b.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/CholmodSupport:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from fileadf94129557b.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:35:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from fileadf94129557b.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:39:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from fileadf94129557b.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:40:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:283:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:336:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:34:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:197:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
  inline static double square(double x) { return square(x); }
                                        ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
    const size_t coupled_size = cvodes_data.coupled_ode_.size();
                 ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/core.hpp:46:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
static void set_zero_all_adjoints() {
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/core.hpp:47:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints_nested() {
            ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from fileadf94129557b.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:51:
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_v>::type;
          ^
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_d>::type;
          ^
34 warnings generated.
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--- finished re-building ‘stanfit-objects.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted