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OpenMx

Package: OpenMx
Date: 2016-06-22
Title: Extended Structural Equation Modelling
Authors@R: c(person(c("Steven", "M."), "Boker", role="aut"),
person(c("Michael", "C."), "Neale", role="aut"), person(c("Hermine", "H."),
"Maes", role="aut"), person(c("Michael", "J."), "Wilde", role="ctb"), person("Michael",
"Spiegel", role="aut"), person(c("Timothy", "R."), "Brick", role="aut"),
person("Ryne", "Estabrook", role="aut"), person(c("Timothy", "C."),
"Bates", role="aut"), person("Paras", "Mehta", role="ctb"), person("Timo", c("von",
"Oertzen"), role="ctb"), person(c("Ross", "J."), "Gore", role="aut"),
person(c("Michael", "D."), "Hunter", role="aut"), person(c("Daniel", "C."), "Hackett", role="ctb"),
person("Julian", "Karch", role="ctb"), person(c("Andreas", "M."), "Brandmaier", role="ctb"),
person(c("Joshua", "N."), "Pritikin", email="jpritikin@pobox.com",
role=c("aut", 'cre')), person("Mahsa", "Zahery", role="aut"),
person(c("Robert", "M."), "Kirkpatrick", role="aut"),
person(c("Yang"), "Wang", role="ctb"),
person(c("Charles"), "Driver", email="driver@mpib-berlin.mpg.de", role="ctb"),
person("Massachusetts Institute of Technology", role="cph"),
person("S. G.", "Johnson", role="cph"),
person("Association for Computing Machinery", role="cph"),
person("Dieter", "Kraft", role="cph"))
URL: http://openmx.psyc.virginia.edu
BugReports: http://openmx.psyc.virginia.edu/forums
Description: Facilitates treatment of statistical model specifications as things
that can be generated and manipulated programmatically. Structural equation
models may be specified with reticular action model matrices or paths, linear
structural relations matrices or paths, or directly in matrix algebra. Fit
functions include full information maximum likelihood, maximum likelihood, and
weighted least squares. Example models include confirmatory factor, multiple
group, mixture distribution, categorical threshold, modern test theory,
differential equations, state space, and many others.
SystemRequirements: GNU make
License: Apache License (== 2.0)
LinkingTo: Rcpp, RcppEigen, StanHeaders (>= 2.7), BH, rpf (>= 0.45)
Depends: R (>= 3.0.2), digest, MASS, methods, Matrix, Rcpp, parallel
Suggests: mvtnorm, numDeriv, roxygen2 (>= 3.1), Rmpi, rpf (>= 0.45),
snowfall, lme4
LazyLoad: yes
LazyData: yes
Collate: '0ClassUnion.R' 'cache.R' 'MxBaseNamed.R' 'MxData.R'
'MxDataWLS.R' 'DefinitionVars.R' 'MxReservedNames.R'
'MxNamespace.R' 'MxSearchReplace.R' 'MxFlatSearchReplace.R'
'MxUntitled.R' 'MxAlgebraFunctions.R' 'MxExponential.R'
'MxMatrix.R' 'DiagMatrix.R' 'FullMatrix.R' 'IdenMatrix.R'
'LowerMatrix.R' 'SdiagMatrix.R' 'StandMatrix.R' 'SymmMatrix.R'
'UnitMatrix.R' 'ZeroMatrix.R' 'MxMatrixFunctions.R'
'MxAlgebra.R' 'MxCycleDetection.R' 'MxDependencies.R'
'MxAlgebraConvert.R' 'MxAlgebraTransform.R' 'MxSquareBracket.R'
'MxEval.R' 'MxRename.R' 'MxPath.R' 'MxObjectiveMetaData.R'
'MxRAMMetaData.R' 'MxExpectation.R' 'MxExpectationNormal.R'
'MxExpectationRAM.R' 'MxExpectationLISREL.R' 'MxFitFunction.R'
'MxFitFunctionAlgebra.R' 'MxFitFunctionML.R'
'MxFitFunctionMultigroup.R' 'MxFitFunctionRow.R'
'MxFitFunctionWLS.R' 'MxRAMObjective.R' 'MxLISRELObjective.R'
'MxFIMLObjective.R' 'MxMLObjective.R' 'MxRowObjective.R'
'MxAlgebraObjective.R' 'MxBounds.R' 'MxConstraint.R'
'MxInterval.R' 'MxTypes.R' 'MxCompute.R' 'MxModel.R'
'MxRAMModel.R' 'MxLISRELModel.R' 'MxModelDisplay.R'
'MxFlatModel.R' 'MxMultiModel.R' 'MxModelFunctions.R'
'MxModelParameters.R' 'MxUnitTesting.R' 'MxApply.R' 'MxRun.R'
'MxRunHelperFunctions.R' 'MxSummary.R' 'MxCompare.R'
'MxSwift.R' 'MxOptions.R' 'MxThreshold.R' 'OriginalMx.R'
'MxGraph.R' 'MxGraphviz.R' 'MxDeparse.R' 'MxCommunication.R'
'MxRestore.R' 'MxVersion.R' 'MxPPML.R' 'MxRAMtoML.R' 'MxDiff.R'
'MxErrorHandling.R' 'MxDetectCores.R' 'MxSaturatedModel.R'
'omxBrownie.R' 'omxConstrainThresholds.R' 'omxGetNPSOL.R'
'MxFitFunctionR.R' 'MxRObjective.R' 'MxExpectationStateSpace.R'
'MxExpectationBA81.R' 'MxFitFunctionGREML.R'
'MxExpectationGREML.R' 'MxMI.R' 'MxFactorScores.R'
'MxRobustSE.R' 'MxAvailableOptimizers.R' 'MxTryHard.R' 'zzz.R'
Version: 2.6.7
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-22 10:22:28 UTC; joshua
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Repository: CRAN
Date/Publication: 2016-06-23 00:35:57

● 19 images, 228 functions, 40 datasets
● Reverse Depends: 4

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* 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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"   -fpic  -g -O2  -c general.c -o general.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/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 /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0,
                 from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:34,
                 from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math.hpp:4,
                 from omxMLFitFunction.cpp:19:
/home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:66:18: warning: 'stan::math::NEGATIVE_EPSILON' defined but not used [-Wunused-variable]
     const double NEGATIVE_EPSILON
                  ^
In file included from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:42:0,
                 from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/ddbj/local/lib64/R/library/StanHeaders/include/stan/math.hpp:4,
                 from omxMLFitFunction.cpp:19:
/home/ddbj/local/lib64/R/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() {
                 ^
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxMatrix.cpp -o omxMatrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxNPSOLSpecific.cpp -o omxNPSOLSpecific.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxNormalExpectation.cpp -o omxNormalExpectation.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxRAMExpectation.cpp -o omxRAMExpectation.o
In file included from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:56:0,
                 from RAMInternal.h:10,
                 from omxRAMExpectation.cpp:20:
/home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/DataFrame.h: In instantiation of 'Rcpp::DataFrame_Impl<StoragePolicy>::DataFrame_Impl(const Rcpp::DataFrame_Impl<StoragePolicy>&) [with StoragePolicy = Rcpp::PreserveStorage]':
/home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/generated/DataFrame_generated.h:41:68:   required from 'static Rcpp::DataFrame_Impl<StoragePolicy> Rcpp::DataFrame_Impl<StoragePolicy>::create(const T1&, const T2&, const T3&) [with T1 = Rcpp::traits::named_object<SEXPREC*>; T2 = Rcpp::traits::named_object<SEXPREC*>; T3 = Rcpp::traits::named_object<SEXPREC*>; StoragePolicy = Rcpp::PreserveStorage]'
omxRAMExpectation.cpp:1729:42:   required from here
/home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/DataFrame.h:46:9: warning: base class 'class Rcpp::Vector<19>' should be explicitly initialized in the copy constructor [-Wextra]
         DataFrame_Impl( const DataFrame_Impl& other){
         ^
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxRFitFunction.cpp -o omxRFitFunction.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxRowFitFunction.cpp -o omxRowFitFunction.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxSadmvnWrapper.cpp -o omxSadmvnWrapper.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxState.cpp -o omxState.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxStateSpaceExpectation.cpp -o omxStateSpaceExpectation.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxSymbolTable.cpp -o omxSymbolTable.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c omxWLSFitFunction.cpp -o omxWLSFitFunction.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"   -fpic  -g -O2  -c optimize.c -o optimize.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"   -fpic  -g -O2  -c options.c -o options.o
f95   -fpic  -g -O2  -c sadmvn.f -o sadmvn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"   -fpic  -g -O2  -c slsqp.c -o slsqp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"   -fpic  -g -O2  -c stop.c -o stop.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include" -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/rpf/include"  -fopenmp -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -fdiagnostics-color=auto    -fpic  -g -O2  -c subnp.cpp -o subnp.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o OpenMx.so Compute.o ComputeGD.o ComputeNR.o ComputeSD.o FellnerFitFunction.o ba81quad.o dmvnorm.o fitMultigroup.o general.o glue.o matrix.o merge.o nloptcpp.o omxAlgebra.o omxAlgebraFitFunction.o omxCsolnp.o omxData.o omxExpectation.o omxExpectationBA81.o omxExportBackendState.o omxFIMLFitFunction.o omxFIMLSingleIteration.o omxFitFunction.o omxFitFunctionBA81.o omxGREMLExpectation.o omxGREMLfitfunction.o omxHessianCalculation.o omxImportFrontendState.o omxLISRELExpectation.o omxMLFitFunction.o omxMatrix.o omxNPSOLSpecific.o omxNormalExpectation.o omxRAMExpectation.o omxRFitFunction.o omxRowFitFunction.o omxSadmvnWrapper.o omxState.o omxStateSpaceExpectation.o omxSymbolTable.o omxWLSFitFunction.o optimize.o options.o sadmvn.o slsqp.o stop.o subnp.o -fopenmp -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lRblas -L/home/ddbj/local/lib64/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
mkdir -p ../inst/debug
cp *.gcno ../inst/debug/
cp: cannot stat '*.gcno': No such file or directory
Makevars:43: recipe for target 'save-gcno' failed
make: [save-gcno] Error 1 (ignored)
installing to /home/ddbj/local/lib64/R/library/OpenMx/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'OpenMx'
Creating a generic function for 'ncol' from package 'base' in package 'OpenMx'
** help
*** installing help indices
  converting help for package 'OpenMx'
    finding HTML links ... done
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    mxRename                                html  
    mxRestore                               html  
    mxRowObjective                          html  
    mxRun                                   html  
    mxSave                                  html  
    mxSetDefaultOptions                     html  
    mxSimplify2Array                        html  
    mxStandardizeRAMpaths                   html  
    mxThreshold                             html  
    mxTryHard                               html  
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/mxTryHard.Rd:54: missing file link 'runif'
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/mxTryHard.Rd:54: missing file link 'rnorm'
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/mxTryHard.Rd:54: missing file link 'rcauchy'
    mxTypes                                 html  
    mxVersion                               html  
    myAutoregressiveData_data               html  
    myFADataRaw                             html  
    myGrowthKnownClassData_data             html  
    myGrowthMixtureData_data                html  
    myLongitudinalData_data                 html  
    myRegDataRaw_data                       html  
    myRegData_data                          html  
    myTwinData_data                         html  
    mzfData                                 html  
    mzmData                                 html  
    nuclear_twin_design_data                html  
    numHess1                                html  
    numHess2                                html  
    omxAllInt                               html  
    omxApply                                html  
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/omxApply.Rd:22: missing file link 'sfApply'
    omxAssignFirstParameters                html  
    omxBrownie                              html  
    omxCheckCloseEnough                     html  
    omxCheckEquals                          html  
    omxCheckError                           html  
    omxCheckIdentical                       html  
    omxCheckNamespace                       html  
    omxCheckSetEquals                       html  
    omxCheckTrue                            html  
    omxCheckWarning                         html  
    omxCheckWithinPercentError              html  
    omxConstrainMLThresholds                html  
    omxDetectCores                          html  
    omxGetNPSOL                             html  
    omxGetParameters                        html  
    omxGetRAMDepth                          html  
    omxGraphviz                             html  
    omxLapply                               html  
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/omxLapply.Rd:22: missing file link 'sfLapply'
    omxLocateParameters                     html  
    omxLogical                              html  
    omxManifestModelByParameterJacobian     html  
    omxMatrixOperations                     html  
    omxMnor                                 html  
    omxNameAnonymousParameters              html  
    omxNormalQuantiles                      html  
    omxParallelCI                           html  
    omxQuotes                               html  
    omxRAMtoML                              html  
    omxRMSEA                                html  
    omxSapply                               html  
Rd warning: /tmp/RtmpfzsrX1/R.INSTALL5492176dfa62/OpenMx/man/omxSapply.Rd:22: missing file link 'sfSapply'
    omxSaturatedModel                       html  
    omxSelectRowsAndCols                    html  
    omxSetParameters                        html  
    omxSymbolTable                          html  
    ordinalTwinData                         html  
    rvectorize                              html  
    summary.MxModel                         html  
    tr                                      html  
    twinData                                html  
    twin_NA_dot_data                        html  
    vec2diag                                html  
    vech                                    html  
    vech2full                               html  
    vechs                                   html  
    vechs2full                              html  
** building package indices
** testing if installed package can be loaded
* DONE (OpenMx)
Making 'packages.html' ... done