mlm4omics 1.2.0
Irene SL Zeng
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/mlm4omics |
| Branch: RELEASE_3_9 |
| Last Commit: 8c2d5ac |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ ERROR ] | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | ERROR | ERROR | skipped | skipped | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/mlm4omics_1.2.0.tar.gz && rm -rf mlm4omics.buildbin-libdir && mkdir mlm4omics.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mlm4omics.buildbin-libdir mlm4omics_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL mlm4omics_1.2.0.zip && rm mlm4omics_1.2.0.tar.gz mlm4omics_1.2.0.zip
###
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install for i386
* installing *source* package 'mlm4omics' ...
** using staged installation
** libs
"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/mlmc_code.stan
Wrote C++ file "stan_files/mlmc_code.cc"
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c stan_files/mlmc_code.cc -o stan_files/mlmc_code.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("");
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function 'typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef 'T_alpha_val' locally defined but not used [-Wunused-local-typedefs]
typename partials_return_type::type>::type T_alpha_val;
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:41,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: 'std::index_sequence' has not been declared
std::index_sequence i) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ',' or '...' before '<' token
std::index_sequence i) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:54: error: 'apply_impl' function uses 'auto' type specifier without trailing return type
std::index_sequence i) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:54: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:48:48: error: 'apply' function uses 'auto' type specifier without trailing return type
constexpr auto apply(const F& f, const Tuple& t) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:48:48: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function 'constexpr auto stan::math::internal::apply(const F&, const Tuple&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/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{}>{});
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/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{}>{});
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ')' before '{' token
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:14: error: 'result_of_t' in namespace 'std' does not name a template type
= std::result_of_t;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: 'FReturnType' was not declared in this scope
std::array::value> M_;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid
std::array::value> M_;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid
std::array::value> M_;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:408:39: error: 'operator()' function uses 'auto' type specifier without trailing return type
auto operator()(const Targs&... args) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:408:39: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function 'std::vector stan::math::adj_jac_vari::build_return_varis_and_vars(const std::vector&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types 'int[int]' for array subscript
M_[0] = val_y.size();
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types 'int[int]' for array subscript
std::vector var_y(M_[0]);
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function 'Eigen::Matrix stan::math::adj_jac_vari::build_return_varis_and_vars(const Eigen::Matrix&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types 'int[int]' for array subscript
M_[0] = val_y.rows();
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types 'int[int]' for array subscript
M_[1] = val_y.cols();
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types 'int[int]' for array subscript
Eigen::Matrix var_y(M_[0], M_[1]);
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types 'int[int]' for array subscript
Eigen::Matrix var_y(M_[0], M_[1]);
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function 'void stan::math::adj_jac_vari::chain()':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: 'FReturnType' was not declared in this scope
FReturnType y_adj;
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/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);
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:15: warning: use of 'auto' in lambda parameter declaration only available with -std=c++1y or -std=gnu++1y
[this](auto&&... args) { this->accumulate_adjoints(args...); },
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:616:40: error: 'adj_jac_apply' function uses 'auto' type specifier without trailing return type
auto adj_jac_apply(const Targs&... args) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:616:40: note: deduced return type only available with -std=c++1y or -std=gnu++1y
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:41:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:61:62: error: 'multiply_adjoint_jacobian' function uses 'auto' type specifier without trailing return type
const Eigen::VectorXd& adj) const {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:61:62: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp: In function 'Eigen::Matrix stan::math::ordered_constrain(const Eigen::Matrix&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:88:57: error: invalid use of 'auto'
return adj_jac_apply(x);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:42:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:62:62: error: 'multiply_adjoint_jacobian' function uses 'auto' type specifier without trailing return type
const Eigen::VectorXd& adj) const {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:62:62: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp: In function 'Eigen::Matrix stan::math::positive_ordered_constrain(const Eigen::Matrix&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:86:66: error: invalid use of 'auto'
return adj_jac_apply(x);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:48:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:67:62: error: 'multiply_adjoint_jacobian' function uses 'auto' type specifier without trailing return type
const Eigen::VectorXd& adj) const {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:67:62: note: deduced return type only available with -std=c++1y or -std=gnu++1y
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp: In function 'Eigen::Matrix stan::math::simplex_constrain(const Eigen::Matrix&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:97:57: error: invalid use of 'auto'
return adj_jac_apply(y);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:49:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hpp: In function 'Eigen::Matrix stan::math::softmax(const Eigen::Matrix&)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hpp:78:51: error: invalid use of 'auto'
return adj_jac_apply(alpha);
^
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:41,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In instantiation of 'auto stan::math::adj_jac_apply(const Targs& ...) [with F = stan::math::internal::ordered_constrain_op; Targs = {Eigen::Matrix}]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:88:57: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:619:11: error: invalid use of 'auto'
return (*vi)(args...);
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In instantiation of 'auto stan::math::adj_jac_apply(const Targs& ...) [with F = stan::math::internal::positive_ordered_constrain_op; Targs = {Eigen::Matrix}]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:86:66: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:619:11: error: invalid use of 'auto'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In instantiation of 'auto stan::math::adj_jac_apply(const Targs& ...) [with F = stan::math::internal::simplex_constrain_op; Targs = {Eigen::Matrix}]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:97:57: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:619:11: error: invalid use of 'auto'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp: In instantiation of 'auto stan::math::adj_jac_apply(const Targs& ...) [with F = stan::math::internal::softmax_op; Targs = {Eigen::Matrix}]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hpp:78:51: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:619:11: error: invalid use of 'auto'
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:45:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/mlmc_code.hpp:18,
from stan_files/mlmc_code.cc:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^
make: *** [stan_files/mlmc_code.o] Error 1
rm stan_files/mlmc_code.cc
ERROR: compilation failed for package 'mlm4omics'
* removing 'C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.buildbin-libdir/mlm4omics'