R 重新编译包失败，因为失败 [英] R recompile packages failing because failing

问题描述

在我的 linux 集群上，我无法重新编译需要重新编译的 R 包在最新版本中删除了 libRcpp.so.最终目标是让 R 包 DEseq2 运行.我们安装了新版本/opt/bin 目录下的 g++ 在 /opt/lib64 中有新的库.我有还创建了具有以下指令的 .R/Makevars:

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

<小时>

各种版本的 Makevars 都失败了，这只是我最近的一次尝试克服了链接时找不到 libstdc++ 的加载程序问题犰狳如您所见，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.

---

"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.

我的 .bashrc 也有:

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

<小时>

这是我尝试在 R 中编译需要的新包时得到的结果重新编译:

---

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

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

推荐答案

两个快速评论:

1. CXX中CXX的定义=/opt/bin/g++ -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).我会再试一次.

1. 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.

编译 RcppArmadillo 的错误意义不大，它应该尝试加载 libRcpp.so.并且 'GLIBCXX_3.4.9' not found 表明您可能设置了路径.

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.

我会尝试更简单的设置，更少的花里胡哨，然后从内到外工作:重建/重新安装 Rcpp，然后是 RcppArmadillo，依此类推.它适用于使用更标准设置的很多人.

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.

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