I was trying to install the R gsl wrapper in our university's HPC cluster, with R version 3.1.1 and OS x86_64-redhat-linux-gnu (64-bit). But something weird happened:
R CMD INSTALL '/d1/pyangac/gsl_1.9-10.1.tar.gz'
* installing to library /d1/pyangac/R_libs/ installing *source* package gsl...
** package gsl successfully unpacked and MD5 sums checked
checking for gsl-config... /usr/local/gsl-1.16/bin/gsl-config
checking if GSL version >= 1.12... checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
ERROR: configuration failed for package gsl
* removing /d1/pyangac/R_libs/gsl
Here are some specifics I have made before I run the installation command. There are two gsl libraries already installed in the cluster, one is gsl, and the other is gsl-1.16 (version 1.16). As the R gsl wrapper requires external gsl library version >= 1.12, before installation, I have set the environments LDFLAGS="-L/usr/local/gsl-1.16/lib -lgsl -lgslcblas -lm"; export LDFLAGS and CPPFALGS="-I/usr/local/gsl-1.16/include"; export CPPFLAGS, so that R will install the wrapper based on version 1.16. I also added the following two paths to make sure R will find the gsl-config file export PATH=$PATH:/usr/local/gsl-1.16, and export PATH=$PATH:/usr/local/gsl-1.16/bin.
Then I run the previous installation command and the error suggests that the C compiler cannot work. After some searches I think it may be caused by the fact that the gsl library is not in the gcc include directory. After typing the following commands, I think the problem would be solved:
export CPATH=/usr/local/gsl-1.16/include
Unfortunately, when I reinstall the gsl wrapper, the same 'cannot run C compiled programs' error appears again. Sorry that I can't provide any further information, as I cannot find the config.log file.
Does anyone has any hint why this is happening, or how to find the config.log file?
Thanks.
