RInside segmentation fault and linking issue

Question

I'm trying to call R from c++ on linux via RInside, I compiled R-2.15.1 from source with gcc version 4.5.3 (Debian 4.5.3-1) , I don't have sudo rights to use apt-get install. I'm using OpenBlas and a system optimized lapack. The blas and lapack libraries work fine for many scalapack applications

I installed R with

./configure --with-blas="-I/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/include -L/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/lib -lopenblas -lgfortran" --with-lapack="/usr/lib/liblapack.so -lgfortran" --enable-BLAS-shlib=yes --enable-R-shlib --enable-R-static-lib --prefix= . 

which installed and runs fine,I ran make check with no errors, also all the packages (Rcpp and RInside) installed fine..

however when i use the given RInside makefile , the basic hello world example from /standard/rinside_sample0.cpp compiles! but it does not run and i get the following error

./rinside_sample0: error while loading shared libraries: libRblas.so: cannot open shared object file: No such file or directory

the file libRblas.so exists and is in the R/lib folder,

when i try to link it manually with the g++ command the make file creates or linking as follows i get a segmentation fault

/R/lib/libRblas.so ./hello_world
Segmentation fault

EDIT: heres how the example make file tries to compile an example, (which compiles fine) but won't run with the above missing libRblas.so error

g++ -I/nfs/user03/jimmie21/libs/lib64/R/include -I/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/include -I/nfs/user03/jimmie21/libs/lib64/R/library/RInside/include -g -O2 -Wall -I/usr/local/include   hello_world.cpp  -L/nfs/user03/jimmie21/libs/lib64/R/lib -lR  -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRlapack -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -L/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -lRInside -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -o hello_world

Answer 1

I fixed the problem by adding the R install path lib ../R/lib: to the beginning of LD_LIBRARY_PATH after that all the examples compiled and run fine

Answer 2

Couple of things:

1. Reproducible examples, please

2. You have a non-standard setup

3. With the script from 1), try it on a standard setting as that is how Rcpp / RInside get developed and tested (on Ubuntu / Debian)

4. The Rcpp test suite now contains almost 800 unit tests from around 350 unit test functions. These do not seg.fault, so the issue is at your end. Similarly, RInside has dozens of examples in the four examples/ subdirectories. This also works.

It may be as easy as tweaking the Makefile / Makevars files to make sure you get your libraries in all cases. But we can't tell as there is nothing reproducible here.

Edit If you want to link with libRblas.so then you have a completely non-standard setup as the R packages for Debian / Ubuntu as use the external BLAS. Again, not an RInside issue.