I am getting an error installing Rcpp from source with R-2.15.3 and Rcpp 0.10.5:
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found
I am working in a non-standard environment; running R on a compute cluster,
similar to this thread:
https://github.com/molpopgen/devnotes/wiki/Rcpp-and-compiler-flags
Compute nodes on the cluster use 'environment modules' to load the environment
at runtime. E.g.
module load R-2.15
Rscript ...
In my particular case we are using 'dotkit' but the concept is the same. I don't
have permission to change the R installation; nor is it an option to update the
compute node VM or the version of R. I'd like to know what environment variables
to set to force g++ to use the correct flags.
# R installation dir
/pkgs/r_2.15.3
# custom package location
~/rhel6/Library/R/2.15
On my system, I have two different locations for the libstdc++.so.6 file.
/usr/lib64/libstdc++.so.6
/pkgs/gcc_4.9.0/lib64/libstdc++.so.6
The GLIBCXX in /pkgs is the correct version (GLIBCXX_3.4.20); the one in
'/usr/' is missing that version.
Here is a trace ...
---------------------
Installing from
http://cran.rstudio.com/src/contrib/Archive/Rcpp/Rcpp_0.10.5.tar.gz
---------------------
Installing package(s) into ~/rhel6/Library/R/2.15
* installing *source* package Rcpp ...
** package Rcpp successfully unpacked and MD5 sums checked
** libs
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c Date.cpp -o Date.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c Module.cpp -o Module.o
gcc -std=gnu99 -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/
-fpic -c Rcpp_init.c -o Rcpp_init.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c Timer.cpp -o Timer.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c api.cpp -o api.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c attributes.cpp -o attributes.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c barrier.cpp -o barrier.o
g++ -I/pkgs/r_2.15.3/lib64/R/include -DNDEBUG -I../inst/include/ -fpic -g
-O2 -c exceptions.cpp -o exceptions.o
g++ -shared -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o
barrier.o exceptions.o -L/pkgs/r_2.15.3/lib64/R/lib -lR
g++ -o libRcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o
barrier.o exceptions.o -shared -L/pkgs/r_2.15.3/lib64/R/lib -lR
ar qc libRcpp.a Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o
barrier.o exceptions.o
cp libRcpp.so ../inst/lib
cp libRcpp.a ../inst/lib
rm libRcpp.so libRcpp.a
installing to ~/rhel6/Library/R/2.15/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 '~/rhel6/Library/R/2.15/Rcpp/libs/Rcpp.so':
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by
~/rhel6/Library/R/2.15/Rcpp/libs/Rcpp.so)
Error: loading failed
Execution halted
ERROR: loading failed
Thanks for any pointers,
Peter
--
Peter Carr <pc...@broadinstitute.org>
Sr. Software Engineer
Broad Institute - GenePattern Team (http://genepattern.org/)
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