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compilation of OpenMx fails in ubuntu 14.04

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Joined: 04/26/2018 - 12:53
compilation of OpenMx fails in ubuntu 14.04

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:
 
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> 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

jpritikin's picture
Offline
Joined: 05/24/2012 - 00:35
ubuntu 14.04 is really old

Which version of gcc are you using?

felix.fischer's picture
Offline
Joined: 04/26/2018 - 12:53
i upgraded to ubuntu 16.04.

i upgraded to ubuntu 16.04. gcc version is now 5.4.

gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.9' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.9) 

but compilation still fails, but throws another error

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-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 Compute.cpp -o Compute.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from Compute.cpp:25:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from Compute.cpp:19:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from Compute.cpp:25:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from Compute.cpp:19:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 ComputeGD.cpp -o ComputeGD.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from ComputeGD.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from ComputeGD.cpp:19:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from ComputeGD.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from ComputeGD.cpp:19:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 ComputeNM.cpp -o ComputeNM.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from ComputeNM.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from ComputeNM.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from ComputeNM.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from ComputeNM.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 ComputeNR.cpp -o ComputeNR.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from ComputeNR.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from /usr/include/c++/5/valarray:38,
                 from ComputeNR.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from ComputeNR.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from /usr/include/c++/5/valarray:38,
                 from ComputeNR.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 ComputeSD.cpp -o ComputeSD.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from Compute.h:22,
                 from ComputeGD.h:20,
                 from ComputeSD.cpp:3:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from Compute.h:22,
                 from ComputeGD.h:20,
                 from ComputeSD.cpp:3:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from Compute.h:22,
                 from ComputeGD.h:20,
                 from ComputeSD.cpp:3:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from Compute.h:22,
                 from ComputeGD.h:20,
                 from ComputeSD.cpp:3:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 FellnerFitFunction.cpp -o FellnerFitFunction.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from FellnerFitFunction.cpp:22:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from glue.h:21,
                 from FellnerFitFunction.cpp:22:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from FellnerFitFunction.cpp:22:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from glue.h:21,
                 from FellnerFitFunction.cpp:22:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 MarkovExpectation.cpp -o MarkovExpectation.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from MarkovExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from MarkovExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from MarkovExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from MarkovExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 MarkovFF.cpp -o MarkovFF.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from MarkovFF.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from MarkovFF.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from MarkovFF.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from MarkovFF.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 ba81quad.cpp -o ba81quad.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from ba81quad.h:21,
                 from ba81quad.cpp:18:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from glue.h:21,
                 from ba81quad.h:21,
                 from ba81quad.cpp:18:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxState.h:31,
                 from glue.h:23,
                 from ba81quad.h:21,
                 from ba81quad.cpp:18:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from glue.h:21,
                 from ba81quad.h:21,
                 from ba81quad.cpp:18:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 dmvnorm.cpp -o dmvnorm.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from dmvnorm.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from dmvnorm.cpp:1:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from dmvnorm.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from dmvnorm.cpp:1:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 fitMultigroup.cpp -o fitMultigroup.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from fitMultigroup.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from fitMultigroup.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from fitMultigroup.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from fitMultigroup.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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/include" -I"/usr/local/lib/R/site-library/rpf/include"    -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c general.c -o general.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 glue.cpp -o glue.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from glue.cpp:21:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from glue.cpp:21:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from glue.cpp:21:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from glue.cpp:21:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 matrix.cpp -o matrix.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from matrix.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from matrix.cpp:1:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from matrix.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from matrix.cpp:1:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 merge.cpp -o merge.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 nanotimer.cpp -o nanotimer.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 nloptcpp.cpp -o nloptcpp.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from nloptcpp.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from nloptcpp.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from nloptcpp.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from nloptcpp.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 omxAlgebra.cpp -o omxAlgebra.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxMatrix.h:37,
                 from omxAlgebra.cpp:30:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxMatrix.h:37,
                 from omxAlgebra.cpp:30:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxMatrix.h:37,
                 from omxAlgebra.cpp:30:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxMatrix.h:37,
                 from omxAlgebra.cpp:30:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxAlgebraFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxAlgebraFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxAlgebraFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxAlgebraFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 omxData.cpp -o omxData.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxData.h:33,
                 from omxData.cpp:27:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxData.h:33,
                 from omxData.cpp:27:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxData.h:33,
                 from omxData.cpp:27:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxData.h:33,
                 from omxData.cpp:27:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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 omxExpectation.cpp -o omxExpectation.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxExpectation.cpp:33:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxExpectation.cpp:33:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxExpectation.cpp:33:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxExpectation.cpp:33:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxExpectationBA81.h:20,
                 from omxExpectationBA81.cpp:20:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxExpectationBA81.h:20,
                 from omxExpectationBA81.cpp:20:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxExpectationBA81.h:20,
                 from omxExpectationBA81.cpp:20:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxExpectationBA81.h:20,
                 from omxExpectationBA81.cpp:20:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExportBackendState.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExportBackendState.cpp:19:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExportBackendState.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExportBackendState.cpp:19:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFIMLFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFIMLFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFIMLFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFIMLFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxFitFunction.cpp:31:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxFitFunction.cpp:31:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxFitFunction.cpp:31:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxFitFunction.cpp:31:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxFitFunctionBA81.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from omxFitFunctionBA81.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxFitFunctionBA81.cpp:19:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/random:40,
                 from /usr/include/c++/5/bits/stl_algo.h:66,
                 from /usr/include/c++/5/algorithm:62,
                 from omxFitFunctionBA81.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxGREMLExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxGREMLExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxGREMLExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxGREMLExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxGREMLfitfunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxGREMLfitfunction.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxFitFunction.h:32,
                 from omxGREMLfitfunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxFitFunction.h:32,
                 from omxGREMLfitfunction.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxHessianCalculation.cpp:29:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxHessianCalculation.cpp:29:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxHessianCalculation.cpp:29:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxHessianCalculation.cpp:29:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxImportFrontendState.cpp:20:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxImportFrontendState.cpp:20:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxImportFrontendState.cpp:20:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxImportFrontendState.cpp:20:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxLISRELExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxLISRELExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxExpectation.h:32,
                 from omxLISRELExpectation.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxExpectation.h:32,
                 from omxLISRELExpectation.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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/Core:276:0,
                 from omxDefines.h:247,
                 from omxMLFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2ndis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxMLFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:276:0,
                 from omxDefines.h:247,
                 from omxMLFitFunction.cpp:17:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1stis deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from omxDefines.h:31,
                 from omxMLFitFunction.cpp:17:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
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)
                              ^
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: candidate: 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: candidate: 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: candidate: 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: candidate: 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
/usr/lib/R/etc/Makeconf:168: recipe for target 'omxMLFitFunction.o' failed
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/RtmpGxd4Mb/downloaded_packages’
Warning message:
In install.packages("OpenMx", repos = "http://cran.rstudio.com") :
  installation of package ‘OpenMx’ had non-zero exit status
AdminRobK's picture
Offline
Joined: 01/24/2014 - 12:15
RcppEigen?

Here are the actual compiler errors, with immediate context:

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)
                              ^

How up-to-date is your installation of R package RcppEigen?

felix.fischer's picture
Offline
Joined: 04/26/2018 - 12:53
thanks!

thanks, after updating RcppEigen compilation worked!

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