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

Sariya, Sanjeev ss5505 at cumc.columbia.edu
Fri Feb 1 18:53:53 CET 2019


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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