Compilation problem on Travis/linux (works fine on Travis/osx)

Developers
1

I see below errors when I test the CmdStan.jl examples. Could this, the bernoulli example, indicate a g++ version issue?

/tmp/jl_KYbVFF/bernoulli_make.log
--- Translating Stan model to C++ code ---
bin/stanc  --o=/tmp/jl_KYbVFF/bernoulli.hpp /tmp/jl_KYbVFF/bernoulli.stan
Model name=bernoulli_model
Input file=/tmp/jl_KYbVFF/bernoulli.stan
Output file=/tmp/jl_KYbVFF/bernoulli.hpp

g++ -std=c++1y -pthread -Wno-sign-compare     -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include    -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION     -c -MT /tmp/jl_KYbVFF/bernoulli.o -MT /tmp/jl_KYbVFF/bernoulli -include /tmp/jl_KYbVFF/bernoulli.hpp -include src/cmdstan/main.cpp -MM -E -MG -MP -MF /tmp/jl_KYbVFF/bernoulli.d /tmp/jl_KYbVFF/bernoulli.hpp
--- Linking C++ model ---
g++ -std=c++1y -pthread -Wno-sign-compare     -O3 -I src -I stan/src -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.3 -I stan/lib/stan_math/lib/boost_1.69.0 -I stan/lib/stan_math/lib/sundials_4.1.0/include    -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION             -include /tmp/jl_KYbVFF/bernoulli.hpp src/cmdstan/main.cpp        stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_4.1.0/lib/libsundials_idas.a  -o /tmp/jl_KYbVFF/bernoulli
/tmp/jl_KYbVFF/bernoulli_build.log
In file included from stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
                 from stan/lib/stan_math/stan/math/rev/mat.hpp:41,
                 from stan/lib/stan_math/stan/math.hpp:4,
                 from stan/src/stan/model/model_header.hpp:4,
                 from /tmp/jl_KYbVFF/bernoulli.hpp:3,
                 from <command-line>:0:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared
                           std::index_sequence<I...> i) {
                                ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token
                           std::index_sequence<I...> i) {
                                              ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’
   return apply_impl(f, t, std::make_index_sequence<std::tuple_size<Tuple>{}>{});
                           ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative:
In file included from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25,
                 from stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from stan/lib/stan_math/stan/math/prim/arr.hpp:46,
                 from stan/lib/stan_math/stan/math/prim/mat.hpp:344,
                 from stan/lib/stan_math/stan/math/rev/mat.hpp:12,
                 from stan/lib/stan_math/stan/math.hpp:4,
                 from stan/src/stan/model/model_header.hpp:4,
                 from /tmp/jl_KYbVFF/bernoulli.hpp:3,
                 from <command-line>:0:
stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note:   ‘boost::fusion::detail::make_index_sequence’
     struct make_index_sequence
            ^
In file included from stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
                 from stan/lib/stan_math/stan/math/rev/mat.hpp:41,
                 from stan/lib/stan_math/stan/math.hpp:4,
                 from stan/src/stan/model/model_header.hpp:4,
                 from /tmp/jl_KYbVFF/bernoulli.hpp:3,
                 from <command-line>:0:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token
   return apply_impl(f, t, std::make_index_sequence<std::tuple_size<Tuple>{}>{});
                                                                             ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier
       = std::result_of_t<F(decltype(is_var_), decltype(value_of(Targs()))...)>;
         ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope
   std::array<int, internal::compute_dims<FReturnType>::value> M_;
                                          ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid
   std::array<int, internal::compute_dims<FReturnType>::value> M_;
                                                     ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid
   std::array<int, internal::compute_dims<FReturnType>::value> M_;
                                                             ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector<stan::math::var> stan::math::adj_jac_vari<F, Targs>::build_return_varis_and_vars(const std::vector<double>&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript
     M_[0] = val_y.size();
         ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript
     std::vector<var> var_y(M_[0]);
                                ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix<stan::math::var, R, C> stan::math::adj_jac_vari<F, Targs>::build_return_varis_and_vars(const Eigen::Matrix<double, R, C>&)’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript
     M_[0] = val_y.rows();
         ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript
     M_[1] = val_y.cols();
         ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript
     Eigen::Matrix<var, R, C> var_y(M_[0], M_[1]);
                                        ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript
     Eigen::Matrix<var, R, C> var_y(M_[0], M_[1]);
                                               ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari<F, Targs>::chain()’:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope
     FReturnType y_adj;
     ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’
     FReturnType y_adj;
                 ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope
     internal::build_y_adj(y_vi_, M_, y_adj);
                                      ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs
         [this](auto&&... args) { this->accumulate_adjoints(args...); },
                          ^
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function:
stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope
         [this](auto&&... args) { this->accumulate_adjoints(args...); },
                                                            ^
make: *** [/tmp/jl_KYbVFF/bernoulli] Error 1
2

So -std=c++1y is a gcc/clang compiler flag for versions of the compiler for when they were still building out the C++14 features. Not having make_index_sequence probably means that your compiler version didn’t support that part of the 14 spec yet.

What version are you using?

Since we are using a good bit of C++14 features now I wonder whether it would be worth just bumping that flag up to -std=c++14

3

Thank you very much! I’ll go and figure out which version Julia’s CI is using.

4

Version info:

g++ (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Adding dist: xenial to .travis.yml provides a newer g++ which works fine! Thanks a lot!

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