Package: mlm4omics

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mlm4omics

StartedAt: 2019-10-15 23:37:07 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 23:37:48 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 41.8 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mlm4omics
###
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* checking for file ‘mlm4omics/DESCRIPTION’ ... OK
* preparing ‘mlm4omics’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘mlm4omics’ ...
** using staged installation
** libs
"/Library/Frameworks/R.framework/Resources/bin/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"
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c stan_files/mlmc_code.cc -o stan_files/mlmc_code.o
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use  instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
:93:2: note: expanded from here
 message("This header is deprecated. Use " "" " instead.")
 ^
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:41:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:27: error: no template named 'index_sequence' in namespace 'std'; did you mean 'boost::fusion::detail::index_sequence'?
                          std::index_sequence i) {
                          ^~~~~~~~~~~~~~~~~~~
                          boost::fusion::detail::index_sequence
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/fusion/support/detail/index_sequence.hpp:37:12: note: 'boost::fusion::detail::index_sequence' declared here
    struct index_sequence
           ^
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:41:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:30:11: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
constexpr auto apply_impl(const F& f, const Tuple& t,
          ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:48:11: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
constexpr auto apply(const F& f, const Tuple& t) {
          ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: no template named 'make_index_sequence' in namespace 'std'; did you mean 'boost::fusion::detail::make_index_sequence'?
  return apply_impl(f, t, std::make_index_sequence{}>{});
                          ^~~~~~~~~~~~~~~~~~~~~~~~
                          boost::fusion::detail::make_index_sequence
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/fusion/support/detail/index_sequence.hpp:59:12: note: 'boost::fusion::detail::make_index_sequence' declared here
    struct make_index_sequence
           ^
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:41:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:14: error: no template named 'result_of_t' in namespace 'std'; did you mean 'result_of'?
      = std::result_of_t;
        ~~~~~^~~~~~~~~~~
             result_of
/usr/local/clang4/bin/../include/c++/v1/type_traits:2763:34: note: 'result_of' declared here
template  class result_of;
                                 ^
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:41:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:6:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:408:3: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
  auto operator()(const Targs&... args) {
  ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:16: error: 'auto' not allowed in lambda parameter
        [this](auto&&... args) { this->accumulate_adjoints(args...); },
               ^~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:22: error: type 'int &&' of function parameter pack does not contain any unexpanded parameter packs
        [this](auto&&... args) { this->accumulate_adjoints(args...); },
               ~~~~~~^~~~~~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/adj_jac_apply.hpp:616:1: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
auto adj_jac_apply(const Targs&... args) {
^
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:41:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:60:3: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
  auto multiply_adjoint_jacobian(const std::array& needs_adj,
  ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:73:12: error: no viable conversion from returned value of type 'tuple &>::type>' (aka 'tuple >') to function return type 'int'
    return std::make_tuple(adj_times_jac);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_constrain.hpp:88:10: error: no matching function for call to 'adj_jac_apply'
  return adj_jac_apply(x);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:42:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:61:3: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
  auto multiply_adjoint_jacobian(const std::array& needs_adj,
  ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:71:12: error: no viable conversion from returned value of type 'tuple &>::type>' (aka 'tuple >') to function return type 'int'
    return std::make_tuple(adj_times_jac);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp:86:10: error: no matching function for call to 'adj_jac_apply'
  return adj_jac_apply(x);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:48:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:66:3: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
  auto multiply_adjoint_jacobian(const std::array& needs_adj,
  ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:79:12: error: no viable conversion from returned value of type 'tuple &>::type>' (aka 'tuple >') to function return type 'int'
    return std::make_tuple(adj_times_jac);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_constrain.hpp:97:10: error: no matching function for call to 'adj_jac_apply'
  return adj_jac_apply(y);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stan_files/mlmc_code.cc:3:
In file included from stan_files/mlmc_code.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:49:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hpp:78:10: error: no matching function for call to 'adj_jac_apply'
  return adj_jac_apply(alpha);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
18 warnings and 19 errors generated.
make: *** [stan_files/mlmc_code.o] Error 1
rm stan_files/mlmc_code.cc
ERROR: compilation failed for package ‘mlm4omics’
* removing ‘/private/tmp/RtmpOj9wv7/Rinst1546260e4e3fe/mlm4omics’
      -----------------------------------
ERROR: package installation failed