R 重新编译包失败，因为失败

Question

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 在最新版本中删除了 libRcpp.so。最终目标是 让 R 包 DEseq2 运行。我们已经安装了新版本 /opt/bin 目录中的 g++ 在 /opt/lib64 中有新库。我有 还创建了具有以下指令的 .R/Makevars:

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

<小时/>

“各个版本的 Makevars 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 Armadillo 。如您所见，它正在查找 /usr/lib64 而不是 /opt/lib64。就好像我的 -Wl 指令被忽略了。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

<小时/>

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:

<小时/>

    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

警告消息:

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

Answer 1

两条简短的评论:

1. CXX=/opt/bin/g++ 中CXX的定义 -Wl,-rpath,/opt/lib64 -Wl,-L,/opt/lib64 有点不寻常，因为它混合了链接器指令(对于 ld 二进制文件)。如果没有，我会再试一次。

2. 编译 RcppArmadillo 时出现的错误没有什么意义，它应该尝试加载 libRcpp.so。 'GLIBCXX_3.4.9' not found 表明您可能设置了路径。

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。