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

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

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.
_______________________________________________
Rcpp-devel mailing list
Rcpp-devel at lists.r-forge.r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_rcpp-2Ddevel&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=rDmT5PX8EcARMO0vn_gzxM5_ETquAxRXGQ9goqf94_I&m=WPEqcxOt_kOucDCNIFifRu618CnhlQMjEyoyIiJRi-w&s=Ja3gdUYYGsZjiJyNsKirbSvCwqLG9vidkeIpeixLV84&e=