undefined symbol

[nfuhriman2]

I'm trying to install on a Centos6.2 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
CXXCPP = $(CXX) -E
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)
CXXPICFLAGS = -fpic
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
CXX98PICFLAGS = -fpic
CXX98STD =
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
CXX11PICFLAGS = -fpic
CXX11STD =
LD_LIBRARY_PATH=/share/apps/gcc/9.2.0/lib:/share/apps/gcc/9.2.0/lib64:/opt/openmpi/lib:/share/apps/update/lib:/opt/python/lib

[eddelbuettel]

That's at your end:

edd@rob:~$ c++filt _ZTVN10__cxxabiv120__si_class_type_infoE
vtable for __cxxabiv1::__si_class_type_info
edd@rob:~$ 

I suggest asking on r-sig-fedora, or maybe on rcpp-devel. There is nothing I can do for you; Rcpp appears to build fine on RH/FC systems that are properly setup. Snapshot right now:

(The windows error is a local file perm issue; the macos-oldrel seems like a toolchain issue, and as usual I have no idea what may be going on on Solaris and cannot reproduce. But note that the two Fedora systems are fine.)

So I am closing this. Please free to reopen if you have actual evidence that Rcpp is at fault. Otherwise, if you're stuck with CentOS 6.* maybe stick with a Rcpp release from a similar vintage. They are all still on CRAN.