如果你使用的 Linux 系统 GCC 版本太低，又没有 root 权限（即使有 root 权限又担心升级 GCC 带来的风险）；同时你又不想额外多安装多一个 Anaconda 或者 Miniconda，但是你又希望安装一个最新版本的 R，那么恭喜你，这篇普通用户在 Linux（CentOS）下源码编译安装 R 的记录刚好满足了你想要的一切。
安装环境如下：
CentOS 安装 R-3.6.0
# Rpy：--enable-R-shlib
# download list：https://mirrors.ustc.edu.cn/CRAN/src/base/R-3/
$ wget https://mirrors.ustc.edu.cn/CRAN/src/base/R-3/R-3.6.0.tar.gz
$ tar zxvf R-3.6.0.tar.gz
$ cd R-3.6.0
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib --enable-BLAS-shlib --with-blas --with-lapack
报错：
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required
## 缺少zlib或者zlib版本过低, 要求 zlib 版本 >= 1.2.5 (Ribo log01 节点无法安装 zlib >= 1.2.8)关于 R 相关的动态库：
- R 编译的过程中，必须选择
--enable-R-shlib选项，将 R 编译成 lib 模式，在此模式下，会生成path-to-R/lib/libR.so - 同时，确保同目录下
libRblas.so、libRlapack.so两个链接库也被正确生成，这两个库默认会生成，如果没有，需要添加参数：--enable-BLAS-shlib--with-blas--with-lapack； - 如果不编译生成
libR.so，在安装 rpy2（python 中的 R 语言接口模块） 时就无法正确编译。
各种库和依赖
zlib
根据《R Installation and Administration: A.1 Essential programs and libraries》官方文档， zlib (version 1.2.5 or later)，至少需要 1.2.5 及以上版本。
# download list：http://www.zlib.net/fossils/
$ wget http://www.zlib.net/fossils/zlib-1.2.6.tar.gz
$ tar xvf zlib-1.2.6.tar.gz
$ cd zlib-1.2.6
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/zlib-1.2.6
$ make && make install接着安装 R-3.6.0：
$ cd ../R-3.6.0
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/lib" CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/include"
报错：
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking mmap support for zlib... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... no
checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required
## zlib 版本已经符合要求，bzip2 版本要求 >= 1.0.6
bzip2 or libbz2
根据《R Installation and Administration: A.1 Essential programs and libraries》官方文档，libbz2 (version 1.0.6 or later: called bzip2-libs/bzip2-devel or libbz2-1.0/libbz2-dev by some Linux distributions)，至少需要 1.0.6 及以上版本。
$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
$ tar zvxf bzip2-1.0.6.tar.gz
$ cd bzip2-1.0.6
$ make -f Makefile-libbz2_so
$ make clean
$ make
$ make install PREFIX=/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6重新安装 R-3.6.0：
$ cd ../R-3.6.0
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/lib -L/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib" CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/include -I/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/include"
报错：
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... yes
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... no
checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required
## 要求 pcre >= 8.10 (同时要求 pcre < 10.0, 否则再次安装 R-3.6.0 时报错)
# 安装 pcre-8.12，configure 编译 R-3.6.0 时报错:
checking for pcre/pcre.h... no
checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required
# PCRE 安装需要 --enable-utf8，同时版本 >= 8.10 且 < 10.0
pcre
在《R Installation and Administration: A.1 Essential programs and libraries》官方文档中要求，PCRE 版本最好在 8.32 及以上。
CRE (version 8.32 or later, although versions 8.20–8.31 will be accepted with a deprecation warning) is required (or just its library and headers if packaged separately). Only the '8-bit' interface is used (and only that is built by default when installing from sources). PCRE must be built with UTF-8 support (not the default, and checked by configure) and support for Unicode properties is assumed by some R packages. JIT support (optionally available) is desirable for the best performance: support for this and Unicode properties can be checked at run-time by calling pcre_config().
$ wget https://ftp.pcre.org/pub/pcre/pcre-8.40.tar.gz --no-check-certificate
$ tar zvxf pcre-8.40.tar.gz
$ cd pcre-8.40
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/pcre-8.40 --enable-utf8
$ make -j3 && make install注意：R-3.4.2 要求 pcre 版本(>= 8.20, < 10.0)
重新安装 R-3.6.0：
$ cd ../R-3.6.0
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/lib -L/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib -L/Bioinfo/SoftWare/NewLibs/pcre-8.40/lib" CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/include -I/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/include -I/Bioinfo/SoftWare/NewLibs/pcre-8.40/include"
报错：
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.28.0... no
configure: error: libcurl >= 7.28.0 library and headers are required with support for https
# 需要安装 curl >= 7.28.0
curl or libcurl
在《R Installation and Administration: A.1 Essential programs and libraries》要求，libcurl 大于或等于 7.22.0 版本。Library libcurl (version 7.22.0 or later) is required, with at least 7.28.0 being desirable.
$ wget https://curl.haxx.se/download/curl-7.64.1.tar.gz --no-check-certificate
$ tar zvxf curl-7.64.1.tar.gz
$ cd curl-7.64.1
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1
$ make
$ make install重新安装 R-3.6.0：
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/lib -L/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib -L/Bioinfo/SoftWare/NewLibs/pcre-8.40/lib -L/Bioinfo/SoftWare/NewLibs/curl-7.64.1/lib" CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/include -I/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/include -I/Bioinfo/SoftWare/NewLibs/pcre-8.40/include -I/Bioinfo/SoftWare/NewLibs/curl-7.64.1/include"
$ make
报错：
/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib/libbz2.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src'
make: *** [R] Error 1
# 需要使用64位元的方法重新编译 bzip2重装 bzip2-1.0.6：
首先，如下所示，修改 bzip2-1.0.6 的 Makefile 文件。
CC=gcc -fPIC
AR=ar
RANLIB=ranlib
LDFLAGS=
BIGFILES=-D_FILE_OFFSET_BITS=64然后，重新编译 bzip2-1.0.6：
$ make clean
$ make
$ make install PREFIX=/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6
liblzma
在编译过程中发现："configure: error: "liblzma library and headers are required""，需要安装 xz，对应主页：https://tukaani.org/xz/，安装如下：
$ wget https://nchc.dl.sourceforge.net/project/lzmautils/xz-5.2.3.tar.gz
$ tar zvxf xz-5.2.3.tar.gz
$ cd xz-5.2.3/
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/xz-5.2.3
$ make -j3
$ make install
libtiff
R shell 中使用 capabilities() 可以查看 R 已经编译支持的功能，对于画图可以增加下面几个参数，使 R 支持对应格式的图片保存，与此同时要确保对应库已经安装。
--with-cairo use cairo (and pango) if available [yes]
--with-libpng use libpng library (if available) [yes]
--with-jpeglib use jpeglib library (if available) [yes]
--with-libtiff use libtiff library (if available) [yes]
以 tiff 为例，需要安装 libtiff 库：
The bitmapped graphics devices jpeg(), png() and tiff() need the appropriate headers and libraries installed: jpeg (version 6b or later, or libjpeg-turbo) or libpng (version 1.2.7 or later) and zlib or libtiff(versions 4.0.[5-10] have been tested) respectively.
$ wget ftp://download.osgeo.org/libtiff/tiff-4.0.9.zip
$ unzip tiff-4.0.9.zip
$ cd tiff-4.0.9
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9
$ make
$ make install然后重新编译 R：
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 --enable-R-shlib --with-libtiff LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib" CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/include"如果 tiff 无法使用，可以考虑在 ~/.bashrc 中添加 libtiff 库路径，然后重新再编译 R 。
export LD_LIBRARY_PATH=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib/pkgconfig:$PKG_CONFIG_PATH
libjpeg and libpng16
R 安装完以后，使用 plot 进行画图，可能会导致错误：
> plot(1:0)
Error in (function (display = "", width, height, pointsize, gamma, bg, :
X11 module cannot be loaded
In addition: Warning message:
In (function (display = "", width, height, pointsize, gamma, bg, :
unable to load shared object '/Bioinfo/SoftWare/R-3.6.0/lib64/R/modules//R_X11.so':
libjpeg.so.9: cannot open shared object file: No such file or directory
> quit()
Save workspace image? [y/n/c]: n使用 ldd 命令如果看到 libjpeg.so.9、libpng16.so.16 not found，则可以考虑手动安装这两个包。
$ /Bioinfo/SoftWare/R-3.6.0/bin/R CMD ldd /Bioinfo/SoftWare/R-3.6.0/lib64/R/modules//R_X11.so
linux-vdso.so.1 => (0x00007fff3c79b000)
libtiff.so.5 => /Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib/libtiff.so.5 (0x00007f75369dc000)
libjpeg.so.9 => not found
libpng16.so.16 => not found
libpangocairo-1.0.so.0 => /usr/lib64/libpangocairo-1.0.so.0 (0x00007f75367ba000)
libpango-1.0.so.0 => /usr/lib64/libpango-1.0.so.0 (0x00007f753656e000)
libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00007f7536322000)
......libjpeg.so.9、libpng16.so.16 安装步骤如下：
$ wget http://www.ijg.org/files/jpegsrc.v9c.tar.gz
$ tar zvxf jpegsrc.v9c.tar.gz
$ cd jpeg-9c
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/jpeg-9c
$ make
$ make install
$ wget https://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz
$ tar zvxf libpng-1.6.37.tar.gz
$ cd libpng-1.6.37
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/libpng-1.6.37
$ make
$ make install- 参考：http://libjpeg.sourceforge.net/
完整编译安装命令
如果使用了自定义安装的 gcc/c++ 进行编译，需要在 configure 时候使用 CC/CXX 进行指定，否则使用系统默认的 gcc/c++。由于 CentOS-6.5 默认的 gcc==4.4.7，该版本的 gcc 会导致 R>=3.5.0 编译出现各种错误
# 粘贴到命令行时，请把 \ 去掉，连成一行命令再回车执行
$ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0 \
CC=/Bioinfo/SoftWare/gcc-4.8.5/bin/gcc \
CXX=/Bioinfo/SoftWare/gcc-4.8.5/bin/c++ \
--enable-R-shlib --with-libtiff --with-libpng --with-jpeglib \
LDFLAGS="-L/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/lib \
-L/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib \
-L/Bioinfo/SoftWare/NewLibs/pcre-8.40/lib \
-L/Bioinfo/SoftWare/NewLibs/curl-7.64.1/lib \
-L/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib \
-L/Bioinfo/SoftWare/NewLibs/jpeg-9c/lib \
-L/Bioinfo/SoftWare/NewLibs/libpng-1.6.37/lib" \
CPPFLAGS="-I/Bioinfo/SoftWare/NewLibs/zlib-1.2.6/include \
-I/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/include \
-I/Bioinfo/SoftWare/NewLibs/pcre-8.40/include \
-I/Bioinfo/SoftWare/NewLibs/curl-7.64.1/include \
-I/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/include \
-I/Bioinfo/SoftWare/NewLibs/jpeg-9c/include \
-I/Bioinfo/SoftWare/NewLibs/libpng-1.6.37/include"
# configure 的所有配置信息，都会保存在 ./Makeconf 文件中
$ make
$ make install
设置环境变量
最后，把安装完成的 R 添加至环境变量：
export R_HOME=path-to-R
export R_LIBS=$R_HOME/lib64/R/library
export LD_LIBRARY_PATH=$R_HOME/lib:$LD_LIBRARY_PATH
export PATH=$R_HOME/bin:$PATH- R_LIBS 的作用是 python 的 rpy2 调用安装的 R 包时，根据该变量寻找对应的包；
- LD_LIBRARY_PATH
- 环境变量设置中比较容易漏掉的是 PATH 和 LD_LIBRARY_PATH，如果是用 root 安装，可能会没有问题，如果安装到个人目录下，不添加这两个变量的话，就无法正确寻找需要的动态链接库，如下：
- LD_LIBRARY_PATH 则是相关动态依赖库需要查找的路径；
$ python
Python 2.7.14 (default, Mar 9 2018, 08:39:17)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy2
>>> import rpy2.robjects as robjects
Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Bioinfo/SoftWare/R-3.6.0/lib64/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
During startup - Warning message:
package ‘stats’ in options("defaultPackages") was not found
>>> robjects.r('library(splines)')
Error: package or namespace load failed for ‘splines’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Bioinfo/SoftWare/R-3.6.0/lib64/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Bioinfo/SoftWare/Python-2.7.14/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 269, in __call__
res = self.eval（p)
File "/Bioinfo/SoftWare/Python-2.7.14/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 170, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/Bioinfo/SoftWare/Python-2.7.14/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 100, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error: package or namespace load failed for ‘splines’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Bioinfo/SoftWare/R-3.6.0/lib64/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory$ ldd /Bioinfo/SoftWare/R-3.6.0/lib64/R/library/stats/libs/stats.so
linux-vdso.so.1 => (0x00007fffd65ba000)
libRlapack.so => not found
libRblas.so => not found
libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007fed38cbb000)
libm.so.6 => /lib64/libm.so.6 (0x00007fed389b9000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fed3877c000)
libR.so => not found
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007fed38556000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fed38339000)
libc.so.6 => /lib64/libc.so.6 (0x00007fed37f76000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fed37d60000)
/lib64/ld-linux-x86-64.so.2 (0x00005561aa2c3000)解决方法：
$ export LD_LIBRARY_PATH="/Bioinfo/SoftWare/R-3.6.0/lib64/R/lib:$LD_LIBRARY_PATH"
$ ldd /Bioinfo/SoftWare/R-3.5.0/lib64/R/library/stats/libs/stats.so
linux-vdso.so.1 => (0x00007ffd0f3af000)
libRlapack.so => /Bioinfo/SoftWare/R-3.6.0/lib64/R/lib/libRlapack.so (0x00007f6509c47000)
libRblas.so => /Bioinfo/SoftWare/R-3.6.0/lib64/R/lib/libRblas.so (0x00007f6509a19000)
libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f65096ee000)
libm.so.6 => /lib64/libm.so.6 (0x00007f65093ec000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f65091af000)
libR.so => /Bioinfo/SoftWare/R-3.6.0/lib64/R/lib/libR.so (0x00007f6508b81000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f650895b000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f650873e000)
libc.so.6 => /lib64/libc.so.6 (0x00007f650837b000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f6508165000)
/lib64/ld-linux-x86-64.so.2 (0x000055583c2da000)
libreadline.so.6 => /lib64/libreadline.so.6 (0x00007f6507f1e000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f6507cbc000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f6507a96000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f6507885000)
libz.so.1 => /lib64/libz.so.1 (0x00007f650766f000)
librt.so.1 => /lib64/librt.so.1 (0x00007f6507467000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f6507262000)
libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f6507038000)以上就是普通用户源码编译安装最新版本 R 的全部内容，总的一句话就是缺什么安装什么，从最基本的 gcc 编译器开始到 R 所需要的各种依赖库，直至最终安装完成。
—
本文章为转载内容，我们尊重原作者对文章享有的著作权。如有内容错误或侵权问题，欢迎原作者联系我们进行内容更正或删除文章。
