we are trying to install lpsymphony in a local installation of R-3.3.2. A large part of the build process runs without problems, but at some point the build process ends with a linker error:
... g++ -I/home/kong/lib/R-3.3.2/include -DNDEBUG -ISYMPHONY/include -I/usr/local/include -fpic -g -O2 -c lp_symphony.cc -o lp_symphony.o g++ -shared -L/usr/local/lib64 -o lpsymphony.so lp_symphony.o -LSYMPHONY/lib -lSym -lCgl -lOsiClp -lClp -lOsi -lCoinUtils -L/home/kong/lib/R-3.3.2/lib -lRlapack -L/home/kong/lib/R-3.3.2/lib -lRblas -lgfortran -lm -lquadmath /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lSym /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lCgl /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lOsiClp /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lClp /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lOsi /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lCoinUtils collect2: error: ld returned 1 exit status make: * [lpsymphony.so] Error 1 ERROR: compilation failed for package ‘lpsymphony’ * removing ‘/tmp/RtmpPpE9zD/Rinst108f25132dc6/lpsymphony’
The LD_LIBRARY_PATH variable is set to the installation directory of SYMPHONY-5.6.16:
$ echo $LD_LIBRARY_PATH /home/kong/lib/SYMPHONY-5.6.16/lib64/
and that path contains all the shared libraries reported to be missing in the linker error.
Unfortunately, I have not yet been able to tell R to keep the build-directory or report the exact option to the configure script, which hampers the analysis of the issue.
Can anyone please help me?
Questions about bioconductor packages are better asked on the bioconductor site.
EDIT: I just saw you crossposted there.