Question: Installation of Bioconductor package: lpsymphony
gravatar for haiying.kong
2.3 years ago by
haiying.kong270 wrote:

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 -o lp_symphony.o g++ -shared -L/usr/local/lib64 -o 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: * [] 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?

bioconductor • 947 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by haiying.kong270

Questions about bioconductor packages are better asked on the bioconductor site.

EDIT: I just saw you crossposted there.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Jean-Karim Heriche19k
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