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在我的Linux集群上，我遇到了重编译R包需要重新编译 并删除了libRcpp.so的最新版本。最终目标是 以运行R包DEseq2。我们在/opt/bin目录中安装了g ++的新版本 ，在/opt/lib64中有新库。我已经 也创造.R/Makevars具有这些指令：R重编译包失败，因为失败
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
“的Makevars失败的各种版本，这只是我的最新尝试 克服它没有找到的libstdC++，当它连接 犰狳装载机问题正如你所看到的，它是在寻找/usr/lib64代替 /opt/lib64。这是因为如果我的-Wl指令被忽略。我 运行R作为sudo的。
也是我的.bashrc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
这里是我所得到的，当我尝试R中编译新的软件包需要重新编译 ：
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
警告消息：
In install.packages(onCRAN, lib = lib, repos = rep) :
installation of package RcppArmadillo had non-zero exit code