_gfortran_copy_string

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pdeboeck's picture
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Joined: 08/04/2009

Hi Everyone,

I ran into this problem today while doing a new installation of OpenMx, and I was just curious if this looked familiar to anyone: "/nfs/home/pascal/R/x86_64-redhat-linux-gnu-library/2.15/OpenMx/libs/OpenMx.so: undefined symbol: _gfortran_copy_string"

Thanks!

> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
1. single-threaded
2. multi-threaded [default]
Which version of OpenMx should I install? 1
Installing package(s) into '/nfs/home/pascal/R/x86_64-redhat-linux-gnu-library/2.15'
(as 'lib' is unspecified)
trying URL 'http://openmx.psyc.virginia.edu/sequential/src/contrib/OpenMx_1.3.2-2301.tar.gz'
Content type 'application/x-gzip' length 7964596 bytes (7.6 Mb)
opened URL
==================================================
downloaded 7.6 Mb

* installing *source* package 'OpenMx' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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

[...]

** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/nfs/home/pascal/R/x86_64-redhat-linux-gnu-library/2.15/OpenMx/libs/OpenMx.so':
/nfs/home/pascal/R/x86_64-redhat-linux-gnu-library/2.15/OpenMx/libs/OpenMx.so: undefined symbol: _gfortran_copy_string
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/nfs/home/pascal/R/x86_64-redhat-linux-gnu-library/2.15/OpenMx'

The downloaded source packages are in
'/library/tmp/Rtmp48ZKUq/downloaded_packages'
Warning message:
In install.packages(pkgs = c("OpenMx"), repos = repos, configure.args = c("--disable-openmp")) :
installation of package 'OpenMx' had non-zero exit status

pdeboeck's picture
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Joined: 08/04/2009
Env Variables

Got some help with the environmental variables so that I'm now using gcc4.4. I think that did the trick.