R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) > TARGETLIB <- "/crmda/tools/lib64/R/3.3/site-library" > .libPaths(c(.libPaths(), TARGETLIB)) > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base > failsfrominstall <- c("OpenMx") > install.packages(failsfrominstall, lib=TARGETLIB) trying URL 'http://rweb.crmda.ku.edu/cran/src/contrib/OpenMx_2.6.9.tar.gz' Content type 'application/x-gzip' length 2998542 bytes (2.9 MB) ================================================== downloaded 2.9 MB * installing *source* package 'OpenMx' ... ** package 'OpenMx' successfully unpacked and MD5 sums checked Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars ** libs g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c Compute.cpp -o Compute.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c ComputeGD.cpp -o ComputeGD.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c ComputeNR.cpp -o ComputeNR.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c ComputeSD.cpp -o ComputeSD.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c FellnerFitFunction.cpp -o FellnerFitFunction.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c ba81quad.cpp -o ba81quad.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c dmvnorm.cpp -o dmvnorm.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c fitMultigroup.cpp -o fitMultigroup.o gcc -std=gnu99 -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fpic -I/tools/cluster/6.2/R/3.3.1/include -c general.c -o general.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c glue.cpp -o glue.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c matrix.cpp -o matrix.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c merge.cpp -o merge.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c nloptcpp.cpp -o nloptcpp.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxAlgebra.cpp -o omxAlgebra.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxCsolnp.cpp -o omxCsolnp.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxData.cpp -o omxData.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxExpectation.cpp -o omxExpectation.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxExpectationBA81.cpp -o omxExpectationBA81.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxExportBackendState.cpp -o omxExportBackendState.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxFIMLSingleIteration.cpp -o omxFIMLSingleIteration.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxFitFunction.cpp -o omxFitFunction.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxHessianCalculation.cpp -o omxHessianCalculation.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxImportFrontendState.cpp -o omxImportFrontendState.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o g++ -std=c++0x -I/tools/cluster/6.2/R/3.3.1/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/Rcpp/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/RcppEigen/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/BH/include" -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/rpf/include" -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto -fpic -g -O2 -c omxMLFitFunction.cpp -o omxMLFitFunction.o In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/fwd/core/fvar.hpp:5:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/fwd/core.hpp:4, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:4, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/is_nan.hpp: In function 'bool stan::math::is_nan(double)': /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/is_nan.hpp:18:14: error: 'boost' has not been declared return boost::math::isnan(x); ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core.hpp:34, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:8, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp: At global scope: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:14:22: error: 'boost' has not been declared const double E = boost::math::constants::e(); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:14:48: error: expected primary-expression before 'double' const double E = boost::math::constants::e(); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:78:16: error: 'boost' has not been declared = std::log(boost::math::constants::pi()) / 4.0; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:78:43: error: expected primary-expression before 'double' = std::log(boost::math::constants::pi()) / 4.0; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp: In function 'double stan::math::pi()': /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:86:14: error: 'boost' has not been declared return boost::math::constants::pi(); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:86:41: error: expected primary-expression before 'double' return boost::math::constants::pi(); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:86:41: error: expected ';' before 'double' /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:86:47: error: expected unqualified-id before '>' token return boost::math::constants::pi(); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp: At global scope: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:154:17: error: 'boost' has not been declared = std::sqrt(boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:154:44: error: expected primary-expression before 'double' = std::sqrt(boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:164:29: error: 'boost' has not been declared = 1.0 / std::sqrt(2.0 * boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:164:56: error: expected primary-expression before 'double' = 1.0 / std::sqrt(2.0 * boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:167:16: error: 'boost' has not been declared = std::log(boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:167:43: error: expected primary-expression before 'double' = std::log(boost::math::constants::pi()); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:181:34: error: 'boost' has not been declared = - std::log(std::sqrt(2.0 * boost::math::constants::pi())); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:181:61: error: expected primary-expression before 'double' = - std::log(std::sqrt(2.0 * boost::math::constants::pi())); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:186:27: error: 'boost' has not been declared = -std::log(std::sqrt(boost::math::constants::pi())); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:186:54: error: expected primary-expression before 'double' = -std::log(std::sqrt(boost::math::constants::pi())); ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core/std_isinf.hpp:4:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core.hpp:45, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:8, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/is_inf.hpp: In function 'int stan::math::is_inf(double)': /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/is_inf.hpp:19:14: error: 'boost' has not been declared return boost::math::isinf(x); ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/arr/meta/is_constant_struct.hpp:4:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/mat/meta/is_constant_struct.hpp:4, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/mat.hpp:12, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:12, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp: At global scope: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:20: error: 'boost' has not been declared enum { value = boost::is_convertible::value }; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:43: error: expected primary-expression before ',' token enum { value = boost::is_convertible::value }; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:45: error: expected identifier before 'double' enum { value = boost::is_convertible::value }; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:45: error: expected '}' before 'double' /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:27:51: error: expected unqualified-id before '>' token enum { value = boost::is_convertible::value }; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:30:1: error: expected declaration before '}' token } ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core.hpp:34, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:8, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:161:18: warning: 'stan::math::NEG_TWO_OVER_SQRT_PI' defined but not used [-Wunused-variable] const double NEG_TWO_OVER_SQRT_PI = -TWO_OVER_SQRT_PI; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:172:18: warning: 'stan::math::LOG_ZERO' defined but not used [-Wunused-variable] const double LOG_ZERO = std::log(0.0); ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:178:18: warning: 'stan::math::NEG_LOG_TWO' defined but not used [-Wunused-variable] const double NEG_LOG_TWO = - LOG_TWO; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:183:18: warning: 'stan::math::NEG_LOG_PI' defined but not used [-Wunused-variable] const double NEG_LOG_PI = - LOG_PI; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:188:18: warning: 'stan::math::NEG_LOG_TWO_OVER_TWO' defined but not used [-Wunused-variable] const double NEG_LOG_TWO_OVER_TWO = - LOG_TWO / 2.0; ^ /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:192:18: warning: 'stan::math::NEG_LOG_TWO_PI' defined but not used [-Wunused-variable] const double NEG_LOG_TWO_PI = - LOG_TWO_PI; ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core.hpp:42:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:8, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core.hpp:43:0, from /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/mix/mat.hpp:8, from omxMLFitFunction.cpp:19: /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:17: warning: 'void stan::math::set_zero_all_adjoints_nested()' defined but not used [-Wunused-function] static void set_zero_all_adjoints_nested() { ^ make: *** [omxMLFitFunction.o] Error 1 ERROR: compilation failed for package 'OpenMx' * removing '/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.3/site-library/OpenMx' The downloaded source packages are in '/library/tmp/RtmpWNzqyx/downloaded_packages' Warning message: In install.packages(failsfrominstall, lib = TARGETLIB) : installation of package 'OpenMx' had non-zero exit status >