It may be that I'm receiving a corrupted tarball.
I'm running Linux version 2.6.18-164.11.1.el5 (mockbuild@builder10.centos.org) (gcc version
4.1.2 20080704 (Red Hat 4.1.2-46)) #1 SMP Wed Jan 20 07:32:21 EST 2010
On a Quad-Core AMD Opteron(tm) Processor 2378
I get the following long list of warnings. OpenMx appears to install and load without errors, but then I get segmentation faults when calling the optimizer. The model to optimize is the first optimization example in the user guide.
-Scott
$ R
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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> source('https://openmx.ssri.psu.edu/getOpenMx.R')
Warning in install.packages(pkgs = c("OpenMx"), repos = repos) :
argument 'lib' is missing: using '/home/vrie0006/R/x86_64-unknown-linux-gnu-library/2.10'
trying URL 'https://openmx.ssri.psu.edu/packages/src/contrib/OpenMx_0.4.1-1320.tar.gz'
Content type 'application/x-gzip' length 4445964 bytes (4.2 Mb)
opened URL
downloaded 4.2 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... 4.1.2
checking for gawk... gawk
checking for inst/npsol/linux/x86_64/gcc4.1/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/share/apps/R-2.10.1/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c merge.c -o merge.o
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxState.h:64,
from npsolWrap.c:28:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxState.h:64,
from npsolWrap.c:28:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxState.h:64,
from npsolWrap.c:28:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebra.c:30:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebra.c:30:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebra.c:30:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:27,
from omxAlgebraFunctions.c:30:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxAlgebraFunctions.c:30:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxAlgebraFunctions.c:30:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxAlgebraFunctions.c:30:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:27,
from omxAlgebraObjective.c:17:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxAlgebraObjective.c:17:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxAlgebraObjective.c:17:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxAlgebraObjective.c:17:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxObjective.h:43,
from omxMatrix.h:44,
from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxData.h:43,
from omxData.c:27:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxData.h:43,
from omxData.c:27:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxData.h:43,
from omxData.c:27:
omxSymbolTable.h:65:7: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxFIMLObjective.c:24:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxFIMLObjective.c:24:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxFIMLObjective.c:24:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:27,
from omxMLObjective.c:23:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxMLObjective.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxMLObjective.c:23:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxMLObjective.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxMatrix.c:28:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxMatrix.c:28:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxMatrix.c:28:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxObjective.h:43,
from omxObjective.c:31:
omxMatrix.h:155:27: 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:65:7: warning: no newline at end of file
In file included from omxObjective.h:43,
from omxObjective.c:31:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:65:7: warning: no newline at end of file
In file included from omxState.h:64,
from omxAlgebra.h:43,
from omxMatrix.h:43,
from omxSymbolTable.h:10,
from omxObjectiveTable.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxObjectiveTable.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxObjectiveTable.c:23:
omxSymbolTable.h:65:7: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxRAMObjective.c:17:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxObjective.h:43,
from omxRAMObjective.c:17:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxObjective.h:43,
from omxRAMObjective.c:17:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxObjective.h:43,
from omxRAMObjective.c:17:
omxMatrix.h:155:27: warning: no newline at end of file
omxRAMObjective.c: In function 'omxCallRAMObjective':
omxRAMObjective.c:78: warning: unused variable 'Ax'
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:27,
from omxRObjective.c:23:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxRObjective.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxRObjective.c:23:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxRObjective.c:23:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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 omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxRowObjective.c:24:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxAlgebraFunctions.h:27,
from omxRowObjective.c:24:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxAlgebraFunctions.h:27,
from omxRowObjective.c:24:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxState.c -o omxState.o
In file included from omxState.h:53,
from omxState.c:27:
omxDefines.h:73:28: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxState.h:64,
from omxState.c:27:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxAlgebra.h:42,
from omxMatrix.h:43,
from omxState.h:64,
from omxState.c:27:
omxSymbolTable.h:65:7: warning: no newline at end of file
In file included from omxState.h:64,
from omxState.c:27:
omxMatrix.h:155:27: warning: no newline at end of file
gcc -std=gnu99 -I/share/apps/R-2.10.1/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:65:7: warning: no newline at end of file
In file included from omxState.h:64,
from omxAlgebra.h:43,
from omxMatrix.h:43,
from omxSymbolTable.h:10,
from omxSymbolTable.c:7:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxSymbolTable.h:10,
from omxSymbolTable.c:7:
omxMatrix.h:155:27: warning: no newline at end of file
In file included from omxSymbolTable.c:7:
omxSymbolTable.h:65:7: warning: no newline at end of file
omxSymbolTable.c:54:3: 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 merge.o 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/share/apps/R-2.10.1/lib64/R/lib -lRblas -L/share/apps/R-2.10.1/lib64/R/lib -lRlapack -lnpsol -L../inst/npsol/linux/x86_64/gcc4.1 -lgfortran -lm
** 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/RtmpWaPihM/downloaded_packages'
> q()
Save workspace image? [y/n/c]: n
$ R --vanilla < test.r > test.r.out
Loading required package: OpenMx
Loading required package: MASS
*** caught segfault ***
address 0x81fe262f8, cause 'memory not mapped'
Traceback:
1: .Call("callNPSOL", objective, startVals, constraints, matrices, parameters, algebras, data, intervalList, communication, options, state, PACKAGE = "OpenMx")
2: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket)
3: mxRun(bivCorModel)
aborting ...
Segmentation fault
$