[Rcpp-devel] Install failure undefined symbol

Fuhriman, Nathanael [US] (IS) (Contr) nate.fuhriman at ngc.com
Thu Jun 11 17:40:08 CEST 2020

I'm trying to install on a Centos6.10 system. I am using an updated gcc9.2 compiler that was installed on the system. I've searched the forum and the web and can't seem to find a solution to this. I did find one recommendation to use static compile but I don't know how to do that with R. Here is what I get when I try to install it:
R CMD INSTALL -d /share/apps/R/4.0.0/plugin/miniCRAN/src/contrib/Rcpp_1.0.4.6.tar.gz
processing '/share/apps/R/4.0.0/plugin/miniCRAN/src/contrib/Rcpp_1.0.4.6.tar.gz'
a file

  *   installing to library '/share/apps/R/4.0.0/plugin'
  *   build_help_types=
  *   DBG: 'R CMD INSTALL' now doing do_install()
  *   created lock directory '/share/apps/R/4.0.0/plugin/00LOCK-Rcpp'
  *   installing source package 'Rcpp' ...
** package 'Rcpp' successfully unpacked and MD5 sums checked
** using staged installation
** libs
about to run R CMD SHLIB -o Rcpp.so api.cpp attributes.cpp barrier.cpp date.cpp module.cpp rcpp_init.cpp
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c api.cpp -o api.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c attributes.cpp -o attributes.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c barrier.cpp -o barrier.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c date.cpp -o date.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c module.cpp -o module.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -I"/share/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_init.cpp -o rcpp_init.o
/share/apps/gcc/9.2.0/bin/gcc -m64 -shared -L/share/apps/update/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o
installing to /share/apps/R/4.0.0/plugin/00LOCK-Rcpp/00new/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'Rcpp' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/share/apps/R/4.0.0/plugin/00LOCK-Rcpp/00new/Rcpp/libs/Rcpp.so':
/share/apps/R/4.0.0/plugin/00LOCK-Rcpp/00new/Rcpp/libs/Rcpp.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
Error: loading failed
Execution halted
ERROR: loading failed
  *   removing '/share/apps/R/4.0.0/plugin/Rcpp'
Also here is my Makevars file
CXX = /share/apps/gcc/9.2.0/bin/gcc -m64
CXXFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic $(LTO)
CXX98 = /share/apps/gcc/9.2.0/bin/g++ -m64
CXX98FLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CXX11 = /share/apps/gcc/9.2.0/bin/g++ -m64
CXX11FLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -std=gnu++0x

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