R recompile packages failing because failing

问题

On my linux cluster, I am having trouble recompiling R packages that need to be recompiled with the removal of libRcpp.so in the latest release. The end goal is to get the R package DEseq2 running. We have installed a new version of g++ in /opt/bin directory have new libraries in /opt/lib64. I have also created .R/Makevars that has these directives:

CXX=/opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64

 -Wl,-llibstdc++ CC=/opt/bin/c++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 -Wl,-llibstdc++ 
SHLIB_OPENMP_CXXFLAGS= -fopenmp

"Various versions of Makevars fail, this is just my latest attempt to overcome a loader problem of it not finding libstdc++ when it links armadillo. As you can see, it is looking in /usr/lib64 instead of /opt/lib64. It is as if my -Wl directives are ignored. I am running R as sudo.

Also my .bashrc has:

LD_LIBRARY_PATH=/opt/lib64:/opt/lib64/R/library/Rcpp/libs:$LD_LIBRARY_PATH:~/lib:~/perl/lib:~/lib/bamtools

LD_RUN_PATH=/opt/lib64:$LD_RUN_PATH:~/lib

export LD_LIBRARY_PATH 
export LD_RUN_PATH

Here is what I get when I try to compile in R the new packages needing recompilation:

    install.packages(onCRAN, lib=lib, repos=rep)
     trying URL 'http://cran.rstudio.com/src/contrib/RcppArmadillo_0.4.000.2.tar.gz'
    Content type 'application/x-gzip' length 892941 bytes (872 Kb)
     opened URL
     ==================================================
     downloaded 872 Kb

     * installing *source* package âRcppArmadilloâ ...
     ** package âRcppArmadilloâ successfully unpacked and MD5 sums checked
     * checking LAPACK_LIBS divide-and-conquer complex SVD unavailable via R-supplied LAPACK
     * divide-and-conquer algorithm for complex SVD will be redirected to default
     ** libs
     /opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 -Wl,-llibstdc++ -I/opt/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/opt/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
     /opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 -Wl,-llibstdc++ -I/opt/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/opt/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
     /opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 -Wl,-llibstdc++ -I/opt/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/opt/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c fastLm.cpp -o fastLm.o
     Error in dyn.load(file, DLLpath = DLLpath, ...) : 
       unable to load shared object '/opt/lib64/R/library/Rcpp/libs/Rcpp.so':
       /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/lib64/R/library/Rcpp/libs/Rcpp.so)
     Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
     Execution halted
     /opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 -Wl,-llibstdc++ -shared -L/usr/local/lib64 -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/opt/lib64/R/lib -lRlapack
 -L/opt/lib64/R/lib -lRblas -lgfortran -lm
     Error in dyn.load(file, DLLpath = DLLpath, ...) : 
       unable to load shared object '/opt/lib64/R/library/Rcpp/libs/Rcpp.so':
       /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by        /opt/lib64/R/library/Rcpp/libs/Rcpp.so)`
     Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
     Execution halted
     /usr/bin/ld: cannot find -llibstdc++
     collect2: error: ld returned 1 exit status
     make: *** [RcppArmadillo.so] Error 1
     ERROR: compilation failed for package âRcppArmadilloâ
     * removing â/opt/lib64/RcppArmadilloâ

The downloaded source packages are in

 /tmp/RtmpZty35f/downloaded_packages

Warning message:

In install.packages(onCRAN, lib = lib, repos = rep) :
   installation of package RcppArmadillo had non-zero exit code

回答1:

Two quick comments:

The definition of CXX in CXX=/opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 is a little, ahem, unusual as it mixes linker instructions (for the ld binary). I would try again without.
The errors in compiling RcppArmadillo make little sense, it should try to load libRcpp.so. And 'GLIBCXX_3.4.9' not found suggests that you may have a path setup.

I would try a simpler setup, fewer bells and whistles, and then work from the inside out: Rebuild / reinstall Rcpp, then RcppArmadillo and so on. It works for a lot of people using more standard setups.

来源：https://stackoverflow.com/questions/21597018/r-recompile-packages-failing-because-failing

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rcpp