How to install OpenMx on 64-bit Ubuntu 9.10 with R 2.10.0?

4 replies [Last post]
sgsong's picture
Offline
Joined: 11/15/2009

I am new to this community and am very excited to find out more about OpenMx. Now I can get it installed on my Windows box using the binary package, but cannot seem to get it installed on my 64-bit Linux box. Has anybody succeed on 64-bit Linux with R 2.10.0? Many thanks.

Best,
Shige

mspiegel's picture
Offline
Joined: 07/31/2009
What error message do you get

What error message do you get when you try to install OpenMx on R 2.10.0 on 64-bit linux?

sgsong's picture
Offline
Joined: 11/15/2009
Here is what I

Here is what I got:

--------------------------
shige@MEMORY:~/Downloads$ sudo R CMD INSTALL OpenMx_0.2.2-951.tar.gz
* installing to library ‘/usr/local/lib64/R/library’
* 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... 4.4.1
checking for gawk... mawk
checking for inst/npsol/linux/x86_64/gcc4.4/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/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c npsolWrap.c -o npsolWrap.o
npsolWrap.c: In function ‘callNPSOL’:
npsolWrap.c:494: warning: ‘ans’ may be used uninitialized in this function
npsolWrap.c:494: warning: ‘names’ may be used uninitialized in this function
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebra.c -o omxAlgebra.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebraFunctions.c -o omxAlgebraFunctions.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxAlgebraObjective.c -o omxAlgebraObjective.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxData.c -o omxData.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxFIMLObjective.c -o omxFIMLObjective.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxMLObjective.c -o omxMLObjective.o
omxMLObjective.c: In function ‘omxCallMLObjective’:
omxMLObjective.c:125: warning: unused variable ‘n’
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxMatrix.c -o omxMatrix.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxObjective.c -o omxObjective.o
omxObjective.c: In function ‘omxFillMatrixFromMxObjective’:
omxObjective.c:98: warning: array subscript is above array bounds
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxObjectiveTable.c -o omxObjectiveTable.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxRAMObjective.c -o omxRAMObjective.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxRObjective.c -o omxRObjective.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxState.c -o omxState.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -Wall -fpic -g -O2 -c omxSymbolTable.c -o omxSymbolTable.o
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 omxState.o omxSymbolTable.o sadmvn.o -lgfortran -lm -L/usr/local/lib64/R/lib -lRblas -L/usr/local/lib64/R/lib -lRlapack -lnpsol -L../inst/npsol/linux/x86_64/gcc4.4 -lgfortran -lm -L/usr/local/lib64/R/lib -lR
/usr/bin/ld: ../inst/npsol/linux/x86_64/gcc4.4/libnpsol.a(npsolsubs.o): relocation R_X86_64_32 against `.data' can not be used when making a shared object; recompile with -fPIC
../inst/npsol/linux/x86_64/gcc4.4/libnpsol.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [OpenMx.so] Error 1
ERROR: compilation failed for package ‘OpenMx’
* removing ‘/usr/local/lib64/R/library/OpenMx’
---------------------------

mspiegel's picture
Offline
Joined: 07/31/2009
Thanks. Looks like we need

Thanks. Looks like we need to recompile 64-bit npsol with -fPIC. I'll post to the forum when it's finished.

sgsong's picture
Offline
Joined: 11/15/2009
Many thanks. I look forward

Many thanks. I look forward to it.