On 14 March 2016 at 20:07, Peter Carr wrote: | 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
That almost always means that you have mixed g++ compilers. C++ can be picky. In short, you need to _consistently_ use the same compiler. We just ran into this on machines from this decade as g++-5 came out and is NOT compatible to g++-4 and earlier. So at work I wrote some ltitle helper scripts looking at DESCRIPTION (or rather, installed.packages()) and everything involving C++ (Rcpp dependence is a good proxy) got reinstalled. Painful once, but then things work. | 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 See above. I fear that two get mixed that should not get mixed. You will undoubtedly managed to make it work, but it may involve quite some housekeeping. C'est la vie with C++. Dirk | 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/) | | _______________________________________________ | Rcpp-devel mailing list | Rcpp-devel@lists.r-forge.r-project.org | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
