wilde@login3:~/R$ ./ubuntu8/bin/R R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. > source('http://openmx.psyc.virginia.edu/getOpenMx.R') trying URL 'http://openmx.psyc.virginia.edu/packages/src/contrib/OpenMx_0.2.5-1050.tar.gz' Content type 'application/x-gzip' length 4555680 bytes (4.3 Mb) opened URL ================================================== downloaded 4.3 Mb * installing *source* package 'OpenMx' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc is installed... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking if gcc accepts -dumpversion option... yes checking gcc version... 4.2.4 checking for gawk... gawk checking for inst/npsol/linux/x86_64/gcc4.2/libnpsol.a... yes configure: creating ./config.status config.status: creating src/Makevars config.status: executing src/omxSymbolTable.h commands config.status: executing src/omxSymbolTable.c commands ** libs gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c npsolWrap.c -o npsolWrap.o In file included from npsolWrap.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxState.h:44, from npsolWrap.c:26: omxSymbolTable.h:57:7: warning: no newline at end of file npsolWrap.c: In function 'callNPSOL': npsolWrap.c:579: warning: 'names' may be used uninitialized in this function npsolWrap.c:579: warning: 'ans' may be used uninitialized in this function gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebra.c -o omxAlgebra.o In file included from omxMatrix.h:39, from omxAlgebra.c:30: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebra.c:30: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebraFunctions.c -o omxAlgebraFunctions.o In file included from omxMatrix.h:39, from omxAlgebraFunctions.h:26, from omxAlgebraFunctions.c:30: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxAlgebraFunctions.c:30: omxSymbolTable.h:57:7: warning: no newline at end of file omxAlgebraFunctions.c: In function 'omxMatrixDeterminant': omxAlgebraFunctions.c:539: warning: too few arguments for format omxAlgebraFunctions.c: In function 'omxMatrixFromDiagonal': omxAlgebraFunctions.c:723: warning: unused variable 'value' omxAlgebraFunctions.c: In function 'omxMultivariateNormalIntegration': omxAlgebraFunctions.c:985: warning: passing argument 2 of 'omxStandardizeCovMatrix' from incompatible pointer type omxAlgebraFunctions.c:985: warning: passing argument 3 of 'omxStandardizeCovMatrix' from incompatible pointer type omxAlgebraFunctions.c:1051:2: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebraObjective.c -o omxAlgebraObjective.o In file included from omxMatrix.h:39, from omxAlgebraFunctions.h:26, from omxAlgebraObjective.c:17: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxAlgebraObjective.c:17: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxData.c -o omxData.o In file included from omxData.h:39, from omxData.c:27: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxData.h:43, from omxData.c:27: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxFIMLObjective.c -o omxFIMLObjective.o In file included from omxFIMLObjective.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxFIMLObjective.c:24: omxSymbolTable.h:57:7: warning: no newline at end of file omxFIMLObjective.c: In function 'omxInitFIMLObjective': omxFIMLObjective.c:618: warning: assignment from incompatible pointer type gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxMLObjective.c -o omxMLObjective.o In file included from omxMatrix.h:39, from omxAlgebraFunctions.h:26, from omxMLObjective.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxMLObjective.c:23: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxMatrix.c -o omxMatrix.o In file included from omxMatrix.h:39, from omxMatrix.c:28: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxMatrix.c:28: omxSymbolTable.h:57:7: warning: no newline at end of file omxMatrix.c:528: warning: C99 inline functions are not supported; using GNU89 omxMatrix.c:528: warning: to disable this warning use -fgnu89-inline or the gnu_inline function attribute omxMatrix.h:123: warning: 'omxRecompute' declared inline after being called omxMatrix.h:123: warning: previous declaration of 'omxRecompute' was here omxMatrix.c:535: warning: C99 inline functions are not supported; using GNU89 gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxObjective.c -o omxObjective.o In file included from omxObjective.h:38, from omxObjective.c:31: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxObjective.h:43, from omxObjective.c:31: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxObjectiveTable.c -o omxObjectiveTable.o In file included from omxMatrix.h:39, from omxSymbolTable.h:10, from omxObjectiveTable.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxSymbolTable.h:10, from omxObjectiveTable.c:23: omxSymbolTable.h:57:7: warning: no newline at end of file In file included from omxObjectiveTable.c:23: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxRAMObjective.c -o omxRAMObjective.o In file included from omxObjective.h:38, from omxObjectiveTable.h:29, from omxRAMObjective.c:17: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxObjective.h:43, from omxObjectiveTable.h:29, from omxRAMObjective.c:17: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxRObjective.c -o omxRObjective.o In file included from omxMatrix.h:39, from omxAlgebraFunctions.h:26, from omxRObjective.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxRObjective.c:23: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxRowObjective.c -o omxRowObjective.o In file included from omxRowObjective.c:23: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxAlgebraFunctions.h:26, from omxRowObjective.c:24: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxState.c -o omxState.o In file included from omxState.h:37, from omxState.c:27: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxState.h:44, from omxState.c:27: omxSymbolTable.h:57:7: warning: no newline at end of file gcc -std=gnu99 -I/home/wilde/R/ubuntu8/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxSymbolTable.c -o omxSymbolTable.o In file included from omxMatrix.h:39, from omxSymbolTable.h:10, from omxSymbolTable.c:7: omxDefines.h:73:28: warning: no newline at end of file In file included from omxAlgebra.h:42, from omxMatrix.h:43, from omxSymbolTable.h:10, from omxSymbolTable.c:7: omxSymbolTable.h:57:7: warning: no newline at end of file In file included from omxSymbolTable.c:7: omxSymbolTable.h:57:7: warning: no newline at end of file omxSymbolTable.c:46:3: warning: no newline at end of file gfortran -fpic -g -O -c sadmvn.f -o sadmvn.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o OpenMx.so npsolWrap.o omxAlgebra.o omxAlgebraFunctions.o omxAlgebraObjective.o omxData.o omxFIMLObjective.o omxMLObjective.o omxMatrix.o omxObjective.o omxObjectiveTable.o omxRAMObjective.o omxRObjective.o omxRowObjective.o omxState.o omxSymbolTable.o sadmvn.o -lgfortran -lm -L/home/wilde/R/ubuntu8/lib64/R/lib -lRblas -L/home/wilde/R/ubuntu8/lib64/R/lib -lRlapack -lnpsol -L../inst/npsol/linux/x86_64/gcc4.2 -lgfortran -lm -L/home/wilde/R/ubuntu8/lib64/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading Creating a new generic function for "print" in "OpenMx" Creating a new generic function for "nrow" in "OpenMx" Creating a new generic function for "ncol" in "OpenMx" Creating a new generic function for "summary" in "OpenMx" ** help *** installing help indices ** building package indices ... * DONE (OpenMx) The downloaded packages are in '/tmp/RtmpO1V6Ia/downloaded_packages' Updating HTML index of packages in '.Library' > require(OpenMx) Loading required package: OpenMx > > data(demoOneFactor) > manifests <- names(demoOneFactor) > latents <- c("G") > > factorModel <- mxModel("One Factor", + type="RAM", + manifestVars = manifests, + latentVars = latents, + mxPath(from=latents, to=manifests), + mxPath(from=manifests, arrows=2), + mxPath(from=latents, arrows=2, free=F, values=1.0), + mxData(observed=cov(demoOneFactor), type="cov", numObs=500)) > > summary(mxRun(factorModel)) Running One Factor Error in mxVersion() : subscript out of bounds Error in summary(mxRun(factorModel)) : error in evaluating the argument 'object' in selecting a method for function 'summary' > traceback() 1: summary(mxRun(factorModel)) > mxVersion() Error in mxVersion() : subscript out of bounds > require(OpenMx) > mxVersion() Error in mxVersion() : subscript out of bounds > mxVersion function () { libMatrix <- installed.packages() return(libMatrix["OpenMx", "Version"]) } > installed.packages() Package LibPath Version KernSmooth "KernSmooth" "/home/wilde/R/ubuntu8/lib64/R/library" "2.23-3" MASS "MASS" "/home/wilde/R/ubuntu8/lib64/R/library" "7.3-4" Matrix "Matrix" "/home/wilde/R/ubuntu8/lib64/R/library" "0.999375-33" base "base" "/home/wilde/R/ubuntu8/lib64/R/library" "2.10.1" boot "boot" "/home/wilde/R/ubuntu8/lib64/R/library" "1.2-41" class "class" "/home/wilde/R/ubuntu8/lib64/R/library" "7.3-1" cluster "cluster" "/home/wilde/R/ubuntu8/lib64/R/library" "1.12.1" codetools "codetools" "/home/wilde/R/ubuntu8/lib64/R/library" "0.2-2" datasets "datasets" 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