Linking Rcpp to interp2d (GSL-type library)

Question

I need some help with a linker error I get during installation of an Rcpp package on a linux system where I don't have admin rights. In a nutshell, I get this error:

relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

I have a file solve.cpp that uses external library interp2d, which in turn has a GSL dependency. I specify my dependencies via [[Rcpp::depends(RcppArmadillo,RcppGSL)]] and in the DESCRIPTION. My Makevars is like the one from the RcppGSL package, with the addition of the linterp2d flag:

PKG_CPPFLAGS = -W $(GSL_CFLAGS) $(LOCAL_INCLUDE)
PKG_LIBS += $(GSL_LIBS) $(LOCAL_LIBS) -linterp2d $(RCPP_LDFLAGS) 

where I define the environement variables

export LOCAL_INCLUDE="-I/data/uctpfos/local/include/"
export LOCAL_LIBS="-L/data/uctpfos/local/lib/"

on the system.

I do R CMD INSTALL bkPackage and see:

g++ -I/cm/shared/apps/R/3.0.1/lib64/R/include -DNDEBUG -W -I/cm/shared/apps/gsl/1.15/include -I/data/uctpfos/local/include -fPIC -I/usr/local/include -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppArmadillo/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppGSL/include"   -fpic  -O3 -fPIC -c RcppExports.cpp -o RcppExports.o

g++ -I/cm/shared/apps/R/3.0.1/lib64/R/include -DNDEBUG -W -I/cm/shared/apps/gsl/1.15/include -I/data/uctpfos/local/include -fPIC -I/usr/local/include -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppArmadillo/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppGSL/include"   -fpic  -O3 -fPIC -c solve.cpp -o solve.o

The problems appears after that in the linking step:

g++ -shared -L/usr/local/lib64 -o bkPackage.so RcppExports.o solve.o -L/cm/shared/apps/gsl/1.15/lib -lgsl -lgslcblas -lm -L/data/uctpfos/local/lib -linterp2d -L/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/lib -lRcpp -Wl,-rpath,/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/lib

The error follows as:

/usr/bin/ld: /data/uctpfos/local/lib/libinterp2d.a(interp2d_spline.c.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC 
/data/uctpfos/local/lib/libinterp2d.a: could not read symbols: Bad value

As you can see I compiled this with -fPIC, so that can't be it.

Answer 1

It's complaining that libinterp2d.a was not compiled with -fPIC; are you sure that was also compiled with -fPIC on?

Also, it seems you both have -fpic and -fPIC in your flags; you probably just want -fPIC. I think R actually ensures that's on by default.