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 库；

• 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 -fPICAR=arRANLIB=ranlibLDFLAGS=

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:$LD_LIBRARY_PATHexport PKG_CONFIG_PATH=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib/pkgconfig:$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 loadedIn 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，非 root 用户手动升级 gcc 可以参考：《非 root 用户手动编译安装 GCC》。

# 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-Rexport R_LIBS=$R_HOME/lib64/R/libraryexport LD_LIBRARY_PATH=$R_HOME/lib:$LD_LIBRARY_PATHexport PATH=$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 则是相关动态依赖库需要查找的路径；

• 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；

$ pythonPython 2.7.14 (default, Mar  9 2018, 08:39:17)[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2Type "help", "copyright", "credits" or "license" for more information.>>> import rpy2>>> import rpy2.robjects as robjectsError: 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 directoryDuring 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 directoryTraceback (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。

——The  End——