Running ‘testthat.R’ [77s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Part of the rstanarm package for estimating model parameters
  > # Copyright (C) 2015 Trustees of Columbia University
  > # 
  > # This program is free software; you can redistribute it and/or
  > # modify it under the terms of the GNU General Public License
  > # as published by the Free Software Foundation; either version 3
  > # of the License, or (at your option) any later version.
  > # 
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > # 
  > # You should have received a copy of the GNU General Public License
  > # along with this program; if not, write to the Free Software
  > # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  > 
  > library(testthat)
  > library(rstanarm)
  Loading required package: Rcpp
  This is rstanarm version 2.21.1
  - See https://mc-stan.org/rstanarm/articles/priors for changes to default priors!
  - Default priors may change, so it's safest to specify priors, even if equivalent to the defaults.
  - For execution on a local, multicore CPU with excess RAM we recommend calling
    options(mc.cores = parallel::detectCores())
  > Sys.unsetenv("R_TESTS")
  > example(example_model)
  
  exmpl_> example_model <- 
  exmpl_+   stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
  exmpl_+              data = lme4::cbpp, family = binomial, QR = TRUE,
  exmpl_+              # this next line is only to keep the example small in size!
  exmpl_+              chains = 2, cores = 1, seed = 12345, iter = 1000, refresh = 0)
  
  exmpl_> example_model
  stan_glmer
   family:       binomial [logit]
   formula:      cbind(incidence, size - incidence) ~ size + period + (1 | herd)
   observations: 56
  ------
              Median MAD_SD
  (Intercept) -1.5    0.6  
  size         0.0    0.0  
  period2     -1.0    0.3  
  period3     -1.1    0.3  
  period4     -1.6    0.4  
  
  Error terms:
   Groups Name        Std.Dev.
   herd   (Intercept) 0.8     
  Num. levels: herd 15 
  
  ------
  * For help interpreting the printed output see ?print.stanreg
  * For info on the priors used see ?prior_summary.stanreg
  > test_check("rstanarm", invert = FALSE,
  +            filter = if (Sys.getenv("NOT_CRAN") != "true") "stan_functions")
  /home/ripley/developerstudio12.6/bin/CC -std=c++14 -I"/home/ripley/R/cc/include" -DNDEBUG   -I"/home/ripley/R/Lib32/Rcpp/include/"  -I"/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/"  -I"/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/unsupported"  -I"/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/BH/include" -I"/home/ripley/R/Lib32/StanHeaders/include/src/"  -I"/home/ripley/R/Lib32/StanHeaders/include/"  -I"/home/ripley/R/Lib32/RcppParallel/include/"  -I"/home/ripley/R/Lib32/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include '/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I"/home/ripley/R/Lib32/Rcpp/include" -I"/home/ripley/R/Lib32/StanHeaders/include" -I"/home/ripley/R/Lib32/rstan/include" -I"/home/ripley/R/Lib32/RcppEigen/include" -I"/home/ripley/R/Lib32/BH/include" -I"/tmp/RtmpI7aOjE/working_dir/RtmpSgaOWF/sourceCpp-i386-pc-solaris2.10-1.0.6" -I/usr/local/include -include '/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c file3f853225452.cpp -o file3f853225452.o
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 55: Warning: extra ";" ignored.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 64: Error: Multiple declaration for std::enable_if_t<!std::is_pointer<T>::value&&!is_fvar<T>::value&&!std::is_arithmetic<T>::value, reverse_return_t<T>> Eigen::MatrixBase<Derived>::val_Op::operator()<T>(T&) const.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 112: Warning: extra ";" ignored.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 143: Warning: extra ";" ignored.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 152: Error: Multiple declaration for std::enable_if_t<!std::is_pointer<T>::value, reverse_return_t<T>> Eigen::MatrixBase<Derived>::adj_Op::operator()<T>(T&) const.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 178: Warning: extra ";" ignored.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h", line 49: Error: Cannot define member of undefined specialization "unary_evaluator<CwiseUnaryOp<UnaryOp, ArgType>, Eigen::internal::IteratorBased>".
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h", line 100: Error: Cannot define member of undefined specialization "unary_evaluator<CwiseUnaryView<ViewOp, ArgType>, Eigen::internal::IteratorBased>".
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/SparseCore/SparseBlock.h", line 503: Error: Cannot define member of undefined specialization "unary_evaluator<Block<ArgType, BlockRows, BlockCols, InnerPanel>, Eigen::internal::IteratorBased>".
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/SparseCore/SparseBlock.h", line 529: Error: Cannot define member of undefined specialization "unary_evaluator<Block<ArgType, BlockRows, BlockCols, InnerPanel>, Eigen::internal::IteratorBased>".
  "/home/ripley/R/Lib32/rstan/include/exporter.h", line 72: Warning: "typename" must be used within a template.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/arr/meta/index_type.hpp", line 19: Error: Multiple definitions for stan::math::index_type<T, std::enable_if_t<std::is_pointer<T>::value, void>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/meta/index_type.hpp", line 19: Error: Multiple definitions for stan::math::index_type<T, std::enable_if_t<std::is_pointer<T>::value, void>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/meta/scalar_type.hpp", line 15: Error: Multiple definitions for stan::scalar_type<T, require_std_vector_t<T>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/arr/meta/value_type.hpp", line 17: Error: Multiple definitions for stan::value_type<T, std::enable_if_t<std::is_pointer<T>::value, void>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/meta/value_type.hpp", line 17: Error: Multiple definitions for stan::value_type<T, std::enable_if_t<std::is_pointer<T>::value, void>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/arr/meta/is_constant.hpp", line 19: Error: Multiple definitions for stan::is_constant<T, require_eigen_t<T>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/scal/meta/scalar_seq_view.hpp", line 44: Error: Multiple definitions for stan::scalar_seq_view<C, std::enable_if_t<is_vector_like<std::decay_t<C>>::value, void>>.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/gcc_itsx.h", line 39: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/gcc_itsx.h", line 52: Warning:  parameter in inline asm statement unused: %1.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 73: Warning:  parameter in inline asm statement unused: %4.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 73: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 73: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 74: Warning:  parameter in inline asm statement unused: %4.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 74: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 74: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 75: Warning:  parameter in inline asm statement unused: %4.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 75: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 75: Warning:  parameter in inline asm statement unused: %3.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 131: Warning:  parameter in inline asm statement unused: %2.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 150: Warning:  parameter in inline asm statement unused: %2.
  "/home/ripley/R/Lib32/RcppParallel/include/tbb/machine/linux_ia32.h", line 154: Warning:  parameter in inline asm statement unused: %2.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/scal/meta/index_type.hpp", line 33: Error: type is not a member of stan::math::index_type<Eigen::Matrix<double, -1, -1, 0, -1, -1>, void>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp", line 14: Error: Invalid type while substituting into index_type<T, void>::type.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp", line 67: Warning:  The template qualifier can only be used within a template.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp", line 71: Warning:  The template qualifier can only be used within a template.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp", line 73: Warning:  The template qualifier can only be used within a template.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/prob/categorical_log.hpp", line 27: Error: type is not a member of stan::math::index_type<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 55: Warning: extra ";" ignored.
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2346:     Where: While specializing "Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op".
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2346:     Where: Instantiated from static __success_type<decltype( std::declval<_Tp>()(std::declval<_Tp>()...) )> std::__result_of_other_impl::_S_test<_Fn, _Args...>(int).
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2357:     Where: Specialized in std::__result_of_impl<0, 0, Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, stan::math::vari*const&>.
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2362:     Where: Specialized in std::result_of<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op(stan::math::vari*const&)>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/util/Meta.h", line 320:     Where: Specialized in Eigen::internal::result_of<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op(stan::math::vari*const&)>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/CwiseUnaryView.h", line 20:     Where: Specialized in Eigen::internal::traits<Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/util/XprHelper.h", line 479:     Where: Specialized in Eigen::CwiseUnaryViewImpl<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>, Eigen::Dense>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/CwiseUnaryView.h", line 59:     Where: Specialized in Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp", line 40:     Where: Specialized in non-template code.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/eigen_plugins.h", line 64: Error: Multiple declaration for std::enable_if_t<!std::is_pointer<T>::value&&!is_fvar<T>::value&&!std::is_arithmetic<T>::value, reverse_return_t<T>> Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op::operator()<T>(T&) const.
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2346:     Where: While specializing "Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op".
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2346:     Where: Instantiated from static __success_type<decltype( std::declval<_Tp>()(std::declval<_Tp>()...) )> std::__result_of_other_impl::_S_test<_Fn, _Args...>(int).
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2357:     Where: Specialized in std::__result_of_impl<0, 0, Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, stan::math::vari*const&>.
  "/home/ripley/developerstudio12.6/lib/compilers/CC-gcc/include/c++/5.4.0/type_traits", line 2362:     Where: Specialized in std::result_of<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op(stan::math::vari*const&)>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/util/Meta.h", line 320:     Where: Specialized in Eigen::internal::result_of<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op(stan::math::vari*const&)>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/CwiseUnaryView.h", line 20:     Where: Specialized in Eigen::internal::traits<Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/util/XprHelper.h", line 479:     Where: Specialized in Eigen::CwiseUnaryViewImpl<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>, Eigen::Dense>.
  "/tmp/RtmpI7aOjE/RLIBS_3c4d4ad34d28/RcppEigen/include/Eigen/src/Core/CwiseUnaryView.h", line 59:     Where: Specialized in Eigen::CwiseUnaryView<Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>::val_Op, Eigen::Map<Eigen::Matrix<stan::math::vari*, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0>>>.
  "/home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp", line 40:     Where: Specialized in non-template code.
   >> Assertion:   (../lnk/tempparse.cc, line 2009)
      while processing /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp at line 54.
  *** Error code 2
  make: Fatal error: Command failed for target `file3f853225452.o'
  Current working directory /tmp/RtmpI7aOjE/working_dir/RtmpSgaOWF/sourceCpp-i386-pc-solaris2.10-1.0.6/sourcecpp_3f85acf761d
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_stan_functions.R:70:1): (code run outside of `test_that()`) ─────
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      █
   1. └─rstan::expose_stan_functions(stanc_ret, rebuild = TRUE, verbose = TRUE) test_stan_functions.R:70:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted