[Rcpp-devel] version GLIBCXX not found
Dirk Eddelbuettel
edd at debian.org
Tue Mar 15 12:27:02 CET 2016
On 15 March 2016 at 02:48, Peter Carr wrote:
| I did a little more investigating about the 'mixed g++' compilers. It appears
| as if R-2.15 was built with a different version of GCC than is available on my
| system.
|
| strings -a /pkgs/r_2.15.3/bin/Rscript | grep GCC
| GCC: (GNU) 4.4.6 20120305 (Red Hat 4.4.6-4)
| GCC: (GNU) 4.4.7 20120313 (Red Hat 4.4.7-3)
|
| $ gcc --version
| gcc (GCC) 4.9.0
It is relatively pretty easy to build R from source, maybe that would be
alternative. But you could simply jump three years forward: you have a
reasonably current compiler, so why stick with a seriously outdated R ? We
are R 3.2.4 now with R 3.3.0 scheduled to release next month.
|
| Furthermore, there was an additional set of paths added to the mix with the $
| {R_HOME}/etc/ldpaths file.
|
| : ${JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre}
| : ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server:${JAVA_HOME}/lib/
| amd64:${JAVA_HOME}/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/
| lib64:/lib:/usr/lib}
| if test -n ""; then
| : ${R_LD_LIBRARY_PATH=${R_HOME}/lib:}
| else
| : ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
| fi
| if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
| R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
| fi
| if test -z "${LD_LIBRARY_PATH}"; then
| LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
| else
| LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
| fi
| export LD_LIBRARY_PATH
|
| I got Rcpp to install with a simple workaround.
| module load R/2.15
| (This loads the GCC-4.9 dependency and sets up the path variables)
| I had to explicitly set R_JAVA_LD_LIBRARY_PATH to keep ldpaths from appending
| incorrect folders to my list:
| export R_JAVA_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
|
| It would be nice to know how this all works; but I am happy to have it working.
| As an occasional R user I was surprised to learn that my 'LD_LIBRARY_PATH' was
| automatically being changed.
Same motivation as your use of 'module load' on the cluster: to dynamically
load components.
Glad you have it working, but this is no longer an Rcpp discussion so might
be best to take this elsewhere...
Regards, Dirk
|
| Thanks,
| Peter
|
|
| On 3/14/16 8:38 PM, Dirk Eddelbuettel wrote:
|
| 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
| |
|
|
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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