集群上安装DESeq2遇到的困难及解决办法

Posted on | Edited on

  1. BiocManager::install(“DESeq2”, version = “3.8”)
    报错，错误内容：
    configure: WARNING: Only g++ version 4.7.2 or greater can be used with RcppArmadillo.
    configure: error: Please use a different compiler.
    ERROR: configuration failed for package ‘RcppArmadillo’

  2. 源码安装gcc
    参考
    ../configure –prefix=/home02/qizhengyang/packages -enable-checking=release -enable-languages=c,c++ -disable-multilib
    报错，错误内容：
    /usr/bin/ld: cannot find -lgfortran

  3. 重新安装gcc，增加fortran
    ../configure –prefix=/home02/qizhengyang/packages -enable-checking=release -enable-languages=c,c++,fortran -disable-multilib && make -j4 && make install

  4. 添加两个lib
    export LD_LIBRARY_PATH=$HOME/packages/lib64:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=$HOME/packages/lib:$LD_LIBRARY_PATH

  1. BiocManager::install(“DESeq2”, version = “3.8”)
    成功

备注：configure时间超级长。过程艰辛。还尝试过手动安装RcppArmadillo，失败。
.libPaths()
“/home02/qizhengyang/packages/R/lib64/R/library”
R CMD INSTALL -l /home02/qizhengyang/packages/R/lib64/R/library RcppArmadillo_0.3.6.3.tar.gz