[Rcpp-devel] stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC

[Sariya, Sanjeev]

Hi devs,



Platform - Unix

R version 3.4 and 3.5

Errors for -fPIC installation for two packages:



1)

I'm using r3.5 to install simplexreg on my local as:



/mnt/mfs/cluster/bin/R-3.5/bin/R  CMD INSTALL -l ./ simplexreg_1.3.tar.gz

When I do it, I get error as follows:



* installing *source* package 'simplexreg' ...

** package 'simplexreg' successfully unpacked and MD5 sums checked

** libs

g++  -I"/mnt/mfs/cluster/bin/R-3.5/include" -DNDEBUG -I/gsl/win64/include  -I/usr/local/include   -fpic  -g -O2  -c sim.gee.cpp -o sim.gee.o

g++ -shared -L/usr/local/lib -o simplexreg.so sim.gee.o -L/gsl/win64/lib -lgsl -lgslcblas -lm

/usr/bin/ld: /usr/local/lib/libgslcblas.a(xerbla.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC

/usr/bin/ld: final link failed: Bad value

collect2: error: ld returned 1 exit status

/mnt/mfs/cluster/bin/R-3.5/share/make/shlib.mk:6: recipe for target 'simplexreg.so' failed

make: *** [simplexreg.so] Error 1

ERROR: compilation failed for package 'simplexreg'


I get same error even when I try with R 3.4.

2)


I'm using r3.5 to install RcppGSL on my local as:

/mnt/mfs/cluster/bin/R-3.5/bin/R CMD INSTALL -l ./ RcppGSL_0.3.6.tar.gz

** libs
g++  -I"/mnt/mfs/cluster/bin/R-3.5/include" -DNDEBUG -I/usr/include -I../inst/include -I"/mnt/mfs/cluster/bin/R-3.5/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++  -I"/mnt/mfs/cluster/bin/R-3.5/include" -DNDEBUG -I/usr/include -I../inst/include -I"/mnt/mfs/cluster/bin/R-3.5/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c fastLm.cpp -o fastLm.o
gcc -I"/mnt/mfs/cluster/bin/R-3.5/include" -DNDEBUG -I/usr/include -I../inst/include -I"/mnt/mfs/cluster/bin/R-3.5/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
g++  -I"/mnt/mfs/cluster/bin/R-3.5/include" -DNDEBUG -I/usr/include -I../inst/include -I"/mnt/mfs/cluster/bin/R-3.5/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c setErrorHandler.cpp -o setErrorHandler.o
g++ -shared -L/usr/local/lib -o RcppGSL.so RcppExports.o fastLm.o init.o setErrorHandler.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm
/usr/bin/ld: /usr/local/lib/libgslcblas.a(xerbla.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
/mnt/mfs/cluster/bin/R-3.5/share/make/shlib.mk:6: recipe for target 'RcppGSL.so' failed
make: *** [RcppGSL.so] Error 1
ERROR: compilation failed for package 'RcppGSL'

I get the error with R 3.4 too.

May I know how to bypass this error?

Thanks,





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20190201/a21e4dc1/attachment.html>