Hi,
i am trying to install OpenMx on a ubuntu server, R version 3.4.4, 64 bit, but compilation fails and i cannot really make sense of the error message. I ran sudo apt-get upgrade and dist-upgrade, but it did not help.
ffischer@common-metrics:~$ sudo su -c "R -e \"install.packages('OpenMx', repos = 'http://cran.rstudio.com' )\"" [sudo] password for ffischer: R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > install.packages('OpenMx', repos = 'http://cran.rstudio.com' ) Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/OpenMx_2.9.6.tar.gz' Content type 'application/x-gzip' length 3197289 bytes (3.0 MB) ================================================== downloaded 3.0 MB * installing *source* package ‘OpenMx’ ... ** package ‘OpenMx’ successfully unpacked and MD5 sums checked NOTE: ./configure is not an autoconf generated script. Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars ** libs g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Compute.cpp -o Compute.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ComputeGD.cpp -o ComputeGD.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ComputeNM.cpp -o ComputeNM.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ComputeNR.cpp -o ComputeNR.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ComputeSD.cpp -o ComputeSD.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c FellnerFitFunction.cpp -o FellnerFitFunction.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c MarkovExpectation.cpp -o MarkovExpectation.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c MarkovFF.cpp -o MarkovFF.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ba81quad.cpp -o ba81quad.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dmvnorm.cpp -o dmvnorm.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitMultigroup.cpp -o fitMultigroup.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library /Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local /lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/inc lude" -I"/usr/local/lib/R/site-library/rpf/include" -fpic -g -O2 -fstack-pro tector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOU RCE=2 -g -c general.c -o general.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c glue.cpp -o glue.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matrix.cpp -o matrix.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c merge.cpp -o merge.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nanotimer.cpp -o nanotimer.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nloptcpp.cpp -o nloptcpp.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxAlgebra.cpp -o omxAlgebra.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxData.cpp -o omxData.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-libra ry/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/loc al/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/i nclude" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g - O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxExpectation.cpp -o omxExpectation.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxExpectationBA81.cpp -o omxExpectationBA81.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxExportBackendState.cpp -o omxExportBackendState.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxFitFunction.cpp -o omxFitFunction.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxHessianCalculation.cpp -o omxHessianCalculation.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxImportFrontendState.cpp -o omxImportFrontendState.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/StanHeaders/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/rpf/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c omxMLFitFunction.cpp -o omxMLFitFunction.o In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Cholesky:23:0, from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:3, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat/fun/typedefs.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat.hpp:4, from omxMLFitFunction.cpp:19: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h: In instantiation of ‘class Eigen::LLT<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 1>’: /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/cholesky_decompose.hpp:247:73: required from here /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:54:10: error: ‘Options’ is not a member of ‘Eigen::LLT<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 1>::MatrixType {aka Eigen::Ref<Eigen::Matrix<double, -1, -1> >}’ enum { ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h: In instantiation of ‘Eigen::LLT<MatrixType, UpLo>::LLT(const MatrixType&) [with _MatrixType = Eigen::Ref<Eigen::Matrix<double, -1, -1> >; int _UpLo = 1; Eigen::LLT<MatrixType, UpLo>::MatrixType = Eigen::Ref<Eigen::Matrix<double, -1, -1> >]’: /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/cholesky_decompose.hpp:247:73: required from here /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:91:30: error: no matching function for call to ‘Eigen::Ref<Eigen::Matrix<double, -1, -1> >::Ref(Eigen::MapBase<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 0>::Index, Eigen::MapBase<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 0>::Index)’ m_isInitialized(false) ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:91:30: note: candidates are: In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:308:0, from omxDefines.h:247, from omxMLFitFunction.cpp:17: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:211:12: note: template<class Derived> Eigen::Ref<PlainObjectType, Options, StrideType>::Ref(const Eigen::DenseBase<OtherDerived>&, typename Eigen::internal::enable_if<(bool)(typename Eigen::internal::traits<Eigen::Ref<_PlainObjectType, _Options, _StrideType> >::match<Derived>::MatchAtCompileTime), Derived>::type*) inline Ref(const DenseBase<Derived>& expr, ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:211:12: note: template argument deduction/substitution failed: In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Cholesky:23:0, from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:3, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat/fun/typedefs.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat.hpp:4, from omxMLFitFunction.cpp:19: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:91:30: note: mismatched types ‘const Eigen::DenseBase<Derived>’ and ‘Eigen::MapBase<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 0>::Index {aka int}’ m_isInitialized(false) ^ In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:308:0, from omxDefines.h:247, from omxMLFitFunction.cpp:17: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:204:12: note: template<class Derived> Eigen::Ref<PlainObjectType, Options, StrideType>::Ref(Eigen::PlainObjectBase<OtherDerived>&, typename Eigen::internal::enable_if<(bool)(typename Eigen::internal::traits<Eigen::Ref<_PlainObjectType, _Options, _StrideType> >::match<Derived>::MatchAtCompileTime), Derived>::type*) inline Ref(PlainObjectBase<Derived>& expr, ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:204:12: note: template argument deduction/substitution failed: In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Cholesky:23:0, from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:3, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat/fun/typedefs.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat.hpp:4, from omxMLFitFunction.cpp:19: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:91:30: note: mismatched types ‘Eigen::PlainObjectBase<OtherDerived>’ and ‘Eigen::MapBase<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 0>::Index {aka int}’ m_isInitialized(false) ^ In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:308:0, from omxDefines.h:247, from omxMLFitFunction.cpp:17: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:194:12: note: template<class Derived> Eigen::Ref<PlainObjectType, Options, StrideType>::Ref(const Eigen::PlainObjectBase<OtherDerived>&, typename Eigen::internal::enable_if<(bool)(typename Eigen::internal::traits<Eigen::Ref<_PlainObjectType, _Options, _StrideType> >::match<Derived>::MatchAtCompileTime), Derived>::type*) inline Ref(const PlainObjectBase<Derived>& expr, ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:194:12: note: template argument deduction/substitution failed: In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Cholesky:23:0, from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:3, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat/fun/typedefs.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/mix/mat.hpp:4, from omxMLFitFunction.cpp:19: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Cholesky/LLT.h:91:30: note: mismatched types ‘const Eigen::PlainObjectBase<OtherDerived>’ and ‘Eigen::MapBase<Eigen::Ref<Eigen::Matrix<double, -1, -1> >, 0>::Index {aka int}’ m_isInitialized(false) ^ In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:308:0, from omxDefines.h:247, from omxMLFitFunction.cpp:17: /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:188:76: note: Eigen::Ref<Eigen::Matrix<double, -1, -1> >::Ref(const Eigen::Ref<Eigen::Matrix<double, -1, -1> >&) template<typename PlainObjectType, int Options, typename StrideType> class Ref ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Ref.h:188:76: note: candidate expects 1 argument, 2 provided make: *** [omxMLFitFunction.o] Error 1 ERROR: compilation failed for package ‘OpenMx’ * removing ‘/usr/local/lib/R/site-library/OpenMx’ The downloaded source packages are in ‘/tmp/RtmpF6fbPp/downloaded_packages’ Warning message: In install.packages("OpenMx", repos = "http://cran.rstudio.com") : installation of package ‘OpenMx’ had non-zero exit status
would be great if someone could help me sort this out!
Best, Felix
Which version of gcc are you using?
i upgraded to ubuntu 16.04. gcc version is now 5.4.
but compilation still fails, but throws another error
Here are the actual compiler errors, with immediate context:
How up-to-date is your installation of R package RcppEigen?
thanks, after updating RcppEigen compilation worked!
Thank you we were confronted with the same problem on our site, thank you for helping us, cordially.