非root安装R以及依赖环境_非root 安装gfortran-优快云博客

转载：https://www.omicsclass.com/article/166

R当中有很多包，这些包之间有很多依赖关系，如果不是最新版本的R，在安装R各种包的时候，就会默认安装一些低版本的包。有些包更新频繁，例如：clusterprofile，如果你的R版本太低就只能安装低版本的，或者有些包根本安装不上去，所以必须更新一下自己linux 上的R版本了，这里我源码安装了一下R最新版本，分享一下。

一、安装依赖库：

可参照这个地方：http://pj.freefaculty.org/blog/?p=315

1.安装zlib1.2.5版本及以上

cd zlib-1.2.11 ./configure --prefix =/share/work/biosoft/zlib make make install

2.安装bzip

cd bzip2-1.0.6 make -f Makefile-libbz2_so 修改Makefile 中的PREFIX=/share/work/biosoft/bzip2 make && make install

3.安装liblzma5.0.3版本及以上

cd xz-5.2.3 ./configure -prefix=/share/work/biosoft/xz make make install

4.安装pcre

tar -zxvf pcre-8.41.tar.gz cd pcre-8.41 ./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp --prefix /share/work/biosoft/pcre##这个包的安装参数是有要求的，因此用的是官方文档的推荐命令
make make install
5.安装libcurl7.22.0及以上，但是不要超过版本8
tar -zxf curl-7.28.0.tar.gz cd curl-7.28.0 ./configure --prefix=/share/work/biosoft/curl make make install

二、安装R

提高GCC版本编译R，如果你的gcc版本太低有些包是安装不成功的，比如fgsea这个包，我这里用的是v6.4.0，我系统自带的4.4.7的编译安装的R在安装fgsea的时候就会报错；

1，设置环境变量：

export PATH=/share/work/biosoft/gcc/gcc-v6.4.0/bin/: $PATH export LD_LIBRARY_PATH=/share/work/biosoft/gcc/gcc-v6.4.0/lib64/:$ LD_LIBRARY_PATH
我这里的LD_LIBRARY_PATH：注意把/share/work/biosoft/gcc/gcc-v6.4.0/lib64/添加进去：
LD_LIBRARY_PATH=/share/work/biosoft/gcc/gcc-v6.4.0/lib64/:/share/work/biosoft/mpc/mpc-v1.0.2/lib/:/share/work/biosoft/cufflinks/samtools-0.1.18/htslib-1.3.2/htslib:/share/work/biosoft/samtools/htslib/:/share/work/biosoft/lib/atlas/:/share/work/biosoft/lib:/share/work/biosoft/Root/root/lib/:/share/work/biosoft/gsl/gsl-2.1/lib/:/share/work/biosoft/gcc/gcc-v4.7.3/lib64/:/share/work/biosoft/zlib/lib/:/share/work/biosoft/boost/boost.1.50/lib:/share/work/biosoft/xz/xz-v5.2.3/lib:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/opt/python/lib

2，设置R默认的GCC 最后两行：

编辑这个文件添加最后两行指定gcc：~/.R/Makevars
F77 = /usr/bin/gfortran
FC = $F77
FLIBS = -L/usr/bin/gfortran
CC=/share/work/biosoft/gcc/gcc-v6.4.0/bin/gcc
CXX=/share/work/biosoft/gcc/gcc-v6.4.0/bin/g++

3，配置R编译：

./configure --prefix=/share/work/biosoft/R/R-v3.5.0 --with-gnu-ld --with-cairo --with-x --enable-R-shlib --with-jpeglib --with-readline --with-tcltk --with-blas --with-lapack --enable-R-profiling --enable-memory-profiling CPPFLAGS="-I/share/work/biosoft/zlib/include -I/share/work/biosoft/bzip2/bzip2-v1.0.6/include/ -I/share/work/biosoft/xz/xz-v5.2.3/include -I/share/work/biosoft/pcre/pcre-v8.38/include -I/share/work/biosoft/curl/curl-v7.47.1/include" LDFLAGS="-L/share/work/biosoft/bzip2/bzip2-v1.0.6/lib/ -L/share/work/biosoft/zlib/lib/ -L/share/work/biosoft/xz/xz-v5.2.3/lib -L/share/work/biosoft/pcre/pcre-v8.38/lib -L/share/work/biosoft/curl/curl-v7.47.1/lib"