[Rcpp-devel] Rcpp installation fails with undefined symbol: _ZTISo - what library am I missing?

Steven McKinney smckinney at bccrc.ca
Wed Dec 17 04:16:03 CET 2014


I installed R-3.1.2 today, and am having trouble installing Rcpp.

The error message is

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/share/data/apps/R/R-3.1.2/lib64/R/library/Rcpp/libs/Rcpp.so':
  /share/data/apps/R/R-3.1.2/lib64/R/library/Rcpp/libs/Rcpp.so: undefined symbol: _ZTISo

so there's some library I haven't linked against.  I've combed the vignettes and the web, but haven't found anything specific for this symbol, and haven't found a list of libraries that need to be specified when compiling Rcpp.  

Can anyone tell me what libraries I should be linking against?


Steven McKinney


This is a custom install for a cluster situation, so libraries are in non-standard locations so as to be accessible to all machines in the cluster and local network.

The error message in R is:

/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c Date.cpp -o Date.o
/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c Module.cpp -o Module.o
/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c Rcpp_init.cpp -o Rcpp_init.o
/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c api.cpp -o api.o
/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c attributes.cpp -o attributes.o
/share/data/usr/bin/gcc44 -I/share/data/apps/R/R-3.1.2/lib64/R/include -DNDEBUG -I../inst/include/ -I/share/data/usr/local/include -I/share/data/usr/include    -fpic  -g -O2  -c barrier.cpp -o barrier.o
/share/data/usr/bin/gcc44 -shared -L/share/data/usr/local/lib64 -L/share/data/usr/lib64 -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o
installing to /share/data/apps/R/R-3.1.2/lib64/R/library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/share/data/apps/R/R-3.1.2/lib64/R/library/Rcpp/libs/Rcpp.so':
  /share/data/apps/R/R-3.1.2/lib64/R/library/Rcpp/libs/Rcpp.so: undefined symbol: _ZTISo
Error: loading failed
Execution halted
ERROR: loading failed

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tcltk_3.1.2 tools_3.1.2

Steven McKinney, Ph.D.

Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3

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