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

[Qiang Kou]

Hi, Sariya,

I think you need to recompile the GSL library with "-fPIC".

Best,

KK

On 2/1/19, 9:54 AM, "Rcpp-devel on behalf of Sariya, Sanjeev" <rcpp-devel-bounces at lists.r-forge.r-project.org on behalf of ss5505 at cumc.columbia.edu> wrote:

    I'd requested IT/cluster person of my floor with this and see if could assist with error.
    
    It still fails after changing to "-fPIC" option. I changed the variable suggested by the developer, not sure what other variable to change.
    
    ##
    
    * installing *source* package ‘simplexreg’ ...
    ** package ‘simplexreg’ successfully unpacked and MD5 sums checked
    ** libs
    /usr/bin/g++-4.8 -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -I/gsl/win64/include  -I/usr/local/include   -fPIC  -g -O2  -c sim.gee.cpp -o sim.gee.o
    /usr/bin/g++-4.8 -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-3.4/share/make/shlib.mk:6: recipe for target 'simplexreg.so' failed
    make: *** [simplexreg.so] Error 1
    ERROR: compilation failed for package ‘simplexreg’
    * removing ‘/mnt/mfs/cluster/bin/R-3.4/library/simplexreg’
    
    The downloaded source packages are in
        ‘/tmp/RtmpAe9HMl/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    Warning message:
    In install.packages("simplexreg") :
      installation of package ‘simplexreg’ had non-zero exit status
    ##
    
    Thanks
    
    
    
    ---
    
    
    -----Original Message-----
    From: Rcpp-devel <rcpp-devel-bounces at lists.r-forge.r-project.org> On Behalf Of Serguei Sokol
    Sent: Friday, February 1, 2019 11:32 AM
    To: rcpp-devel at lists.r-forge.r-project.org
    Subject: Re: [Rcpp-devel] stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
    
    On 01/02/2019 17:22, Sariya, Sanjeev wrote:
    > 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 
    > g++ -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
    > 
    ...
    > 
    > May I know how to bypass this error?
    Try to do what error message says: "recompile with -fPIC" (you have -fpic instead). It is safer to get the exact syntax from $ R CMD config CXXPICFLAGS -fPIC
    
    Serguei.
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