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) ; 同时你又不想入坑 conda, 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.


本文档以 R-3.6.0 为例, 但对于 R-3.6.x, R-4.0.x 的安装同样适用.


安装环境如下:

名称版本
系统Red Hat Enterprise Linux Server release 6.5 (Santiago), x86_64
gccgcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)



一、CentOS 安装 R


# 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:




二、各种库和依赖解决



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:

  1. R-3.4.2 要求 pcre 版本(>= 8.20, < 10.0);
  2. R-4.0.1 要求 PCRE >= 8.32 with UTF-8 support;
  3. configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support。R-4.0 以上在 configure 时,需要增加一个 --with-pcre1 参数。


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

## 不指定证书
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1

## 指定证书(推荐)
$ wget https://curl.haxx.se/ca/cacert.pem -O /Bioinfo/SoftWare/certs/ca-bundle.crt --no-check-certificate
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1 --with-ca-bundle=/Bioinfo/SoftWare/certs/ca-bundle.crt 

$ make
$ make install


注意:

  1. 有些情况下,R 在链接一些在线数据库,或者下载某些特殊包时,可能导致 SSL certificate problem: unable to get local issuer certificate 异常,这种情况可以通过 --with-ca-bundle 指定证书来解决。
  2. 参考下面的内容。
此处为语雀文档,点击链接查看:https://www.yuque.com/shenweiyan/cookbook/r-ssl-certificate



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, 如下所示, 首先修改 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-3.6.0:

$ ./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, 如果出现如下错误:

> 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




三、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:

此处为语雀文档,点击链接查看:https://www.yuque.com/shenweiyan/cookbook/linux-gcc-install