史上最棘手的Linux下R源代码安装指南：区分root权限与无root权限情况

本文记录的是linux下R安装的心得，windows下的安装方法请自行google：
先说有root权限的时候：
官网上下载R源码：找到latest release 版本：R-3.5.1.tar.gz

https://mirrors.tuna.tsinghua.edu.cn/CRAN/

解压，进入路径

tar -zxvf R-3.5.1.tar.gz 
cd R-3.5.1
./configure

有报错：

configure: error: --with-readline=yes (default) and headers/libs are not available

设置如下参数： ./configure --with-readline=no
或者centos系统:安装readline：yum install readline-devel
或者ubuntu系统：安装readline：

安装成功后继续./configure 又出现报错：

configure: error: --with-x=yes (default) and X11 headers/libs are not available

设置参数 --with-x=no
或者安装x：

yum install libX11-devel 
yum install libXt-devel  

继续
./configure --with-readline=no --with-x=no
还报错：没有装libzma

configure: error: "liblzma library and headers are required"

解决方法：

wget https://tukaani.org/xz/xz-5.2.4.tar.gz
tar -zxvf xz-5.2.4.tar.gz
cd xz-5.2.4/
./configure
make
make install

安装完成xz，无报错，再来继续编译R
./configure --with-readline=no --with-x=no
又报错：没有pcre

checking whether PCRE support suffices... configure: error: pcre >= 8.20 library and headers are required

解决方法：

wget https://nchc.dl.sourceforge.net/project/pcre/pcre/8.42/pcre-8.42.tar.gz
tar -zxvf pcre-8.42.tar.gz
cd pcre-8.42.tar.gz
./configure
make
make install

安装完成pcre，无报错，再来继续编译R
./configure --with-readline=no --with-x=no
又报错：没有libcurl

configure: error: libcurl >= 7.22.0 library and headers are required with support for https

解决方法：

wget https://curl.haxx.se/download/curl-7.61.0.tar.gz
tar -zxvf curl-7.61.0.tar.gz
cd curl-7.61.0/
./configure
make
make install

安装完成curl，无报错,再来继续编译R
./configure --with-readline=no --with-x=no
又报错：

configure: error: libcurl >= 7.22.0 library and headers are required with support for https

好像上一步的libcurl没有安装成功呐？奇怪，
仔细观察了一下，发现虽然是以root下载的，但是解压后的目录是以用户拥有的方式，于是
用sudo的方式试一次：

sudo ./configure
make
make install
安装完成，无报错

再来安装R
./configure --with-readline=no --with-x=no
报错：

configure: error: libcurl >= 7.22.0 library and headers are required with support for https

还是这个错。。。。。
已奔溃。。。

$ curl -V
curl 7.60.0 (x86_64-conda_cos6-linux-gnu) libcurl/7.60.0 OpenSSL/1.0.2o zlib/1.2.11
Release-Date: 2018-05-16
Protocols: dict file ftp ftps gopher http https imap imaps pop3 pop3s rtsp smb smbs smtp smtps telnet tftp
Features: AsynchDNS IPv6 Largefile NTLM NTLM_WB SSL libz TLS-SRP UnixSockets HTTPS-proxy

看版本，已经是7.60了呀。
有人说要下载libcurl-devel，

wget http://mirrors.163.com/centos/7/os/x86_64/Packages/libcurl-devel-7.29.0-46.el7.x86_64.rpm
wget http://mirrors.163.com/centos/7/os/x86_64/Packages/libcurl-7.29.0-46.el7.x86_64.rpm

rpm -ivh libcurl-devel-7.29.0-46.el7.x86_64.rpm libcurl-7.29.0-46.el7.x86_64.rpm

试了还是不行，最后。。。
用别的用户名登录，不用root登录

./configure --with-readline=no --with-x=no
···
R is now configured for x86_64-pc-linux-gnu
  Source directory:          .
  Installation directory:    /usr/local
  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2
  Default C++ compiler:      g++   -g -O2
  C++98 compiler:            g++ -std=gnu++98 -g -O2
  C++11 compiler:            g++ -std=gnu++11 -g -O2
  C++14 compiler:
  C++17 compiler:
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:
  Interfaces supported:
  External libraries:        readline, curl
  Additional capabilities:   NLS
  Options enabled:           shared BLAS, R profiling
  Capabilities skipped:      PNG, JPEG, TIFF, cairo, ICU
  Options not enabled:       memory profiling
  Recommended packages:      yes
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages

最后只有三个无关紧要的提醒。
赶紧
sudo make
输入了密码
sudo make install
成功了 但是使用时还是没有有问题，没有libR.so？？

当没有安装bzip2时会报错如下：

checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required

最后。。。
一怒之下删掉了安装了所有版本R，

rm -rf /usr/bin/R*
rm -rf /usr/local/bin/R*
删掉了安装的所有bzip2,
rm -rf /usr/local/bin/bz*
rm -rf /usr/local/include/bz*
yum remove bzip2
重新解压 bzip2
tar -zxvf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6
make -f Makefile-libbz2_so
修改Makefile其中两行。
vi Makefile
CC=gcc -fPIC
CFLAGS=-Wall -fPIC -Winline -O2 -g $(BIGFILES)

然后
make
make install
然后安装R
将原来R解压的路径也删掉了
重新解压R包

tar -zxvf R-3.5.1.tar.gz
cd R-3.5.1
./configure --enable-R-shlib
居然没有报错
make
make install

都没有报错。。。。。。

---

重点来了

将R安装到指定路径下：在没有root权限时，我们只能安装在指定目录下。

要想安装到指定目录中则需要指定： --prefix=/path/to/install/
./configure --enable-R-shlib,先根据报错将依赖的各种库都装上。安装时也要指定路径，一般情况下我会将其安装在解压后的该目录。
先后安装了zlib，bzip2,xz,curl.
然后编译的时候要加上LDFLAGS和CPPFLAGS相关的路径：

./configure --prefix=$HOME/Programme/R-3.3.1 --enable-R-shlib LDFLAGS="-L/$HOME/Programme/zlib-1.2.11/lib -L/$HOME/Programme/bzip2-1.0.6/lib -L/$HOME/Programme/xz-5.2.3/lib -L/$HOME/Programme/pcre-8.40/lib -L/$HOME/Programme/curl-7.52.1/lib" CPPFLAGS="-I/$HOME/Programme/zlib-1.2.11/include -I/$HOME/Programme/bzip2-1.0.6/include -I/$HOME/Programme/xz-5.2.3/include -I/$HOME/Programme/pcre-8.40/include -I/$HOME/Programme/curl-7.52.1/include"

然而还是会报错：

报错：

/usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link) 
/usr/bin/ld: warning: liblzma.so.5, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link) 
../../lib/libR.so: undefined reference to `pcre_fullinfo' 
../../lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0' 
../../lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0' 
../../lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0' 
../../lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_config' 
../../lib/libR.so: undefined reference to `lzma_code@XZ_5.0' 
../../lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_free' 
../../lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_free_study' 
../../lib/libR.so: undefined reference to `pcre_assign_jit_stack' 
../../lib/libR.so: undefined reference to `pcre_exec' 
../../lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_maketables' 
../../lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_compile' 
../../lib/libR.so: undefined reference to `pcre_study' 
../../lib/libR.so: undefined reference to `pcre_version' 
../../lib/libR.so: undefined reference to `lzma_end@XZ_5.0' 
../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc' 
collect2: error: ld returned 1 exit status 
make[3]: *** [R.bin] Error 1 
make[3]: Leaving directory `/builder/software/R/src/main' 
make[2]: *** [R] Error 2 
make[2]: Leaving directory `/builder/software/R/src/main' 
make[1]: *** [R] Error 1 
make[1]: Leaving directory `/builder/software/R/src' 
make: *** [R] Error 1

重点来了：

/usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
怎么会有这样的报错？编译的时候不是已经将这两个库的路径传入了呀？
一番搜索后，
有人提出

要添加动态库
#cat /etc/ld.so.conf
include ld.so.conf.d/*.conf
/opt/pcre-8.39/lib
/opt/xz-5.2.2/lib
然后执行
#ldconfig

但是我没有root权限啊，于是再一帆研究，根据报错提示，设置一下-rpath看行不行。
修改Makeconf文件，再LDFLAGS这里加上了-Wl,-rpath后面跟这两个库的路径，

LDFLAGS = -L/BIGDATA1/cygene_sydu_1/02.dropEst/zlib-1.2.11/lib -L/BIGDATA1/cygene_sydu_1/02.dropEst/bzip2-1.0.6/lib -L/BIGDATA1/cygene_sydu_1/02.dropEst/xz-5.2.4/lib -L/BIGDATA1/cygene_sydu_1/02.dropEst/pcre-8.42/lib -L/BIGDATA1/cygene_sydu_1/02.dropEst/curl-7.61.0/lib -Wl,-rpath=/BIGDATA1/cygene_sydu_1/02.dropEst/pcre-8.42/lib -Wl,-rpath=/BIGDATA1/cygene_sydu_1/02.dropEst/xz-5.2.4/lib

再进行make,make install就不会报错，完成安装。
或者在编译的时候直接将-Wl,-rpath=/的路径跟在LDFLAGS里面，要写两次哦。

补充：
如果遇到如下报错

begin installing recommended package Matrix
ERROR: failed to lock directory ‘/BIGDATA1/cygene_sydu_1/software/R-3.5.1/library’ for modifying
Try removing ‘/BIGDATA1/cygene_sydu_1/software/R-3.5.1/library/00LOCK-Matrix’
make[2]: *** [Matrix.ts] Error 1
make[2]: Leaving directory `/BIGDATA1/cygene_sydu_1/software/R-3.5.1/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/BIGDATA1/cygene_sydu_1/software/R-3.5.1/src/library/Recommended'
make: *** [stamp-recommended] Error 2

这里是开始安装某个package时失败了，那么想让它跳过，不安装就好了，在提示的报错信息中找到安装该package的路径，把里面的相应的package删掉即可，我这里删掉了Martrix包；
rm /BIGDATA1/cygene_sydu_1/software/R-3.5.1/src/library/Recommended/Matrix*

等R安装成功后再手动将这些包装上。

R 包的安装

R的package安装时遇到错误可以换镜像路径，举例如下：
install.packages("Rcpp",dependencies=TRUE, repos='http://cran.rstudio.com/')
install.packages("ggplot2",dependencies=TRUE, repos='http://cran.rstudio.com/')

R ggforce 包安装

install.packages("ggforce")
library(ggforce)

# geom_circle() 是来自ggforce这个包。用法跟ggplot一样：

ggplot(df.venn, aes(x0=x, y0=y, r= 1.5, fill = labels)) +
  geom_circle(alpha=.3, size=1, colour='grey') +
  coord_fixed() + theme_void()

关于bioconductor

R limma 包安装

source("http://www.bioconductor.org/biocLite.R")
biocLite("limma")
library(limma)

R tidyverse包安装

source("http://www.bioconductor.org/biocLite.R")
biocLite("tidyverse")
library(tidyverse)

其他包安装

source("[http://bioconductor.org/biocLite.R](http://bioconductor.org/biocLite.R)")
biocLite("ALL") 安装 ALL
biocLite("hgu95av2.db")

library(ALL)
library(hgu95av2.db)

总结：

Ubuntu下基本上可以通过安装这些库解决：

sudo apt-get install build-essential
sudo apt-get install fort77 （error）
sudo apt-get install xorg-dev
sudo apt-get install liblzma-dev libblas-dev gfortran
sudo apt-get install gcc-multilib
sudo apt-get install gobjc++ （error）
sudo apt-get install aptitude
sudo apt-get install libreadline-dev

最简单的安装R的方法是：通过conda安装，先安装annaconda2或3，再通过conda install R，就可以一键安装R，非常方便，绕过手动源码安装。省好多事