R 重新编译包失败，因为失败

在我的 Linux 集群上，我在重新编译需要重新编译的 R 包时遇到问题 随着去除libRcpp.so在最新版本中。最终目标是 让 R 包 DEseq2 运行。我们已经安装了新版本 g++ 中的/opt/bin目录中有新库/opt/lib64。我有 还创建了.R/Makevars有这些指令：

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

“Makevars 的各种版本都失败了，这只是我的最新尝试 克服链接时找不到 libstdc++ 的加载程序问题 犰狳。正如你所看到的，它正在寻找/usr/lib64代替/opt/lib64。就好像我的-Wl指令被忽略。我是 以 sudo 身份运行 R。

我的 .bashrc 也有：

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

这是当我尝试在 R 中编译需要的新包时得到的结果 重新编译：

    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

下载的源码包在

 /tmp/RtmpZty35f/downloaded_packages

警告信息：

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

两个快速评论：

1. 的定义CXX in CXX=/opt/bin/g++ -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64有点，咳咳，不寻常，因为它混合了链接器指令（对于ld二进制）。没有的话我会再试一次。

2. 编译 RcppArmadillo 时出现的错误没有什么意义，应该尝试加载libRcpp.so. And 'GLIBCXX_3.4.9' not found表明您可能有一个路径设置。

我会尝试更简单的设置，更少的花哨的东西，然后从内到外工作：重建/重新安装 Rcpp，然后是 RcppArmadillo 等等。它适用于很多使用更标准设置的人。