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 下源码编译安装 R 的记录刚好满足了你想要的一切.。

:::tips 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。例如 R-4.0.3、R-4.1.2 根据本教程，本人都测试过可以正常安装成功。 :::

本教程在以下的安装环境中，经过测试都可以正常操作：

系统（版本） GCC 版本
Red Hat Enterprise Linux Server release 6.5 (Santiago), x86_64 gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
CentOS Linux release 7.6.1810 (Core), x86_64 gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
openEuler 20.03 (LTS) gcc (GCC) 7.3.0

1. 安装命令

R 源码编译安装基本命令。

  1. # Rpy：--enable-R-shlib
  2. # download list：https://mirrors.ustc.edu.cn/CRAN/src/base/
  3. $ wget https://mirrors.ustc.edu.cn/CRAN/src/base/R-3/R-3.6.0.tar.gz 
  4. $ tar zxvf R-3.6.0.tar.gz
  5. $ cd R-3.6.0
  6. $ ./configure --prefix=/Bioinfo/SoftWare/R-3.6.0  --enable-R-shlib --enable-BLAS-shlib  --with-blas   --with-lapack

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。

2. 基础环境

  • configure: error: No Fortran compiler found ```bash

    Ubuntu/Debian

    apt install gfortran

RHEL/openEluer

yum install gcc-gfortran

  2. - **configure: error: C++ preprocessor "/lib/cpp" fails sanity check**
  3. ```bash
  4. # Ubuntu/Debian
  5. apt install build-essential
  6. apt install g++
  8. # RHEL/openEluer
  9. yum install glibc-headers
  10. yum install gcc-c++

3. 各种库和依赖解决

R 源码编译安装的时候需要的各种依赖库比较多，如果你有 root 的权限，建议使用 yum/apt 等系统命令解决；如果没有 root 权限，可以手动一个个去解决。

3.1 自动处理

针对 RHEL/Debian 一些常见的依赖，使用 yum/apt 自动解决的示例。

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

    Ubuntu/Debian

    apt install install libreadline-dev

RHEL/openEluer

yum install readline-devel 

  2. - **configure: error: --with-x=yes (default) and X11 headers/libs are not available**
  3. ```bash
  4. # Ubuntu/Debian
  5. apt install libx11-dev xorg-dev libcurl4-openssl-dev
  7. # RHEL/openEluer
  8. yum install xorg-x11-server-devel libX11-devel libXt-devel
  • configure: error: “liblzma library and headers are required” ```bash

    Ubuntu/Debian

    apt install liblzma-dev

RHEL/openEluer

yum install lzma-devel xz xz-devel

  2. - **configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support**
  3. ```bash
  4. # Ubuntu/Debian
  5. apt install libpcre2-dev
  7. # RHEL/openEluer 
  8. yum install pcre pcre-devel            # 安装 PCRE1
  9. yum install pcre2 pcre2-devel        # 安装 PCRE2
  • configure: error: libcurl >= 7.28.0 library and headers are required with support for https ```bash

    Ubuntu/Debian

    apt install libcurl4-openssl-dev

RHEL/openEluer

yum install libcurl-devel

  2. <a name="e5IX6"></a>
  3. ### JPEG
  4. R 安装过程中默认开启 --with-jpeglib（use jpeglib library (if available) [yes]），但是相关的依赖没有，依然可以正常安装（没有任何报错），但最后会提示：**Capabilities skipped: JPEG！**
  5. ```bash
  6. # Ubuntu/Debian
  7. yum install libjpeg-dev
  9. # RHEL/openEluer 
  10. yum install libjpeg-devel

TIFF

R 安装过程中默认开启 —with-tifflib（use libtiff library (if available) [yes]），但是相关的依赖没有，依然可以正常安装（没有任何报错），但最后会提示：Capabilities skipped: TIFF！

  1. # Ubuntu/Debian
  2. yum install libtiff-dev
  4. # RHEL/openEluer 
  5. yum install libtiff-devel

cairo

R 安装过程中默认开启 —with-cairo（use cairo (and pango) if available [yes]），但是相关的依赖没有，依然可以正常安装（没有任何报错），但最后会提示：Capabilities skipped: cairo！

  1. # Ubuntu/Debian
  2. apt install libcairo2-dev libxt-dev
  4. # RHEL/openEluer 
  5. yum install cairo-devel

ICU

R 安装过程中默认开启 —with-ICU（use ICU library (if available) [yes]），如果不可用，最后会提示：Capabilities skipped: ICU！

  1. # Ubuntu/Debian
  2. apt install libicu-dev
  4. # RHEL/openEluer 
  5. yum install libicu libicu-devel

3.2 手动处理

以下是一些常见的依赖手动解决的示例，可以参考。

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。

  1. 报错：
  2. checking for zlib.h... yes
  3. checking if zlib version >= 1.2.5... no
  4. checking whether zlib support suffices... configure: error: zlib library and headers are required  
  5. ## 缺少zlib或者zlib版本过低, 要求 zlib 版本 >= 1.2.5
  1. # download list：http://www.zlib.net/fossils/
  2. $ wget http://www.zlib.net/fossils/zlib-1.2.6.tar.gz
  3. $ tar xvf zlib-1.2.6.tar.gz
  4. $ cd zlib-1.2.6
  5. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/zlib-1.2.6
  6. $ make && make install

接着安装 R-3.6.0: 

  1. $ cd ../R-3.6.0
  2. $ ./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"
  4.     报错：
  5.     checking for zlib.h... yes
  6.     checking if zlib version >= 1.2.5... yes
  7.     checking whether zlib support suffices... yes
  8.     checking mmap support for zlib... yes
  9.     checking for BZ2_bzlibVersion in -lbz2... yes
  10.     checking bzlib.h usability... yes
  11.     checking bzlib.h presence... yes
  12.     checking for bzlib.h... yes
  13.     checking if bzip2 version >= 1.0.6... no
  14.     checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required
  15.     ## 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. 

  1. $ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
  2. $ tar zvxf bzip2-1.0.6.tar.gz
  3. $ cd bzip2-1.0.6
  4. $ make -f Makefile-libbz2_so
  5. $ make clean
  6. $ make
  7. $ make install PREFIX=/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6

重新安装 R-3.6.0: 

  1. $ cd ../R-3.6.0
  2. $ ./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"
  4.     报错：
  5.     checking if bzip2 version >= 1.0.6... yes
  6.     checking whether bzip2 support suffices... yes
  7.     checking for lzma_version_number in -llzma... yes
  8.     checking lzma.h usability... yes
  9.     checking lzma.h presence... yes
  10.     checking for lzma.h... yes
  11.     checking if lzma version >= 5.0.3... yes
  12.     checking for pcre_fullinfo in -lpcre... no
  13.     checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required
  14.     ## 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)
  16.     # 安装 pcre-8.12，configure 编译 R-3.6.0 时报错:
  17.     checking for pcre/pcre.h... no
  18.     checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... no
  19.     checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required
  20.     # 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().

  1. # 源码安装 PCRE1
  2. $ wget https://ftp.pcre.org/pub/pcre/pcre-8.40.tar.gz --no-check-certificate
  3. $ tar zvxf pcre-8.40.tar.gz
  4. $ cd pcre-8.40
  5. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/pcre-8.40 --enable-utf8
  6. $ make -j3 && make install
  8. # root 安装 PCRE1
  9. yum install pcre pcre-devel
  11. # 源码的方式安装 PCRE2，这里不介绍，跟源码安装 PCRE1 原理是一样的，自己去谷歌就好
  12. # root 安装 PCRE2
  13. yum install pcre2 pcre2-devel

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；或者安装 PCRE2！

重新安装 R-3.6.0: 

  1. $ cd ../R-3.6.0
  2. $ ./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"
  4.     报错：
  5.     checking curl/curl.h usability... yes
  6.     checking curl/curl.h presence... yes
  7.     checking for curl/curl.h... yes
  8.     checking if libcurl is version 7 and >= 7.28.0... no
  9.     configure: error: libcurl >= 7.28.0 library and headers are required with support for https
  10.     # 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.

  1. $ wget https://curl.haxx.se/download/curl-7.64.1.tar.gz --no-check-certificate
  2. $ tar zvxf curl-7.64.1.tar.gz
  3. $ cd curl-7.64.1
  5. ## 不指定证书
  6. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1
  8. ## 指定证书(推荐)
  9. $ wget https://curl.haxx.se/ca/cacert.pem -O /Bioinfo/SoftWare/certs/ca-bundle.crt --no-check-certificate
  10. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1 --with-ca-bundle=/Bioinfo/SoftWare/certs/ca-bundle.crt 
  12. $ make
  13. $ make install

如果你有管理员的权限，你也可以使用 root 的方法直接安装 libcurl：

  1. # CentOS 7.6 自带的 libcurl 最新版本应该是 7.29.0-59.el7_9.1
  2. yum install libcurl libcurl-devel

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。

R 语言关于 SSL 证书异常处理笔记

重新安装 R-3.6.0: 

  1. $ ./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"
  3. $ make 
  5.     报错：
  6.     /Bioinfo/SoftWare/NewLibs/bzip2-1.0.6/lib/libbz2.a: could not read symbols: Bad value
  7.     collect2: ld returned 1 exit status
  8.     make[3]: *** [libR.so] Error 1
  9.     make[3]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src/main'
  10.     make[2]: *** [R] Error 2
  11.     make[2]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src/main'
  12.     make[1]: *** [R] Error 1
  13.     make[1]: Leaving directory `/home/shenweiyan/inst/R-3.6.0/src'
  14.     make: *** [R] Error 1
  15.     # 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: 

  1. CC=gcc -fPIC
  2. AR=ar
  3. RANLIB=ranlib
  4. LDFLAGS=
  6. BIGFILES=-D_FILE_OFFSET_BITS=64

然后, 重新编译 bzip2-1.0.6: 

  1. $ make clean
  2. $ make
  3. $ 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: 

  1. $ wget https://nchc.dl.sourceforge.net/project/lzmautils/xz-5.2.3.tar.gz
  2. $ tar zvxf xz-5.2.3.tar.gz
  3. $ cd xz-5.2.3/
  4. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/xz-5.2.3
  5. $ make -j3
  6. $ 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. 

  1. --with-cairo            use cairo (and pango) if available [yes]
  2. --with-libpng           use libpng library (if available) [yes]
  3. --with-jpeglib          use jpeglib library (if available) [yes]
  4. --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.

  1. $ wget ftp://download.osgeo.org/libtiff/tiff-4.0.9.zip
  2. $ unzip tiff-4.0.9.zip
  3. $ cd tiff-4.0.9
  4. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9
  5. $ make
  6. $ make install

如果你有管理员权限，你也可以直接使用 root 直接安装 libtiff：

  1. # CentOS 7.6 自带的 libcurl 最新版本应该是 4.0.3-35.el7
  2. yum install libtiff libtiff-devel

然后重新编译 R-3.6.0: 

  1. $ ./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 . 

  1. export LD_LIBRARY_PATH=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib:$LD_LIBRARY_PATH
  2. export PKG_CONFIG_PATH=/Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib/pkgconfig:$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: 

  1. > plot(1:0)
  2. Error in (function (display = "", width, height, pointsize, gamma, bg,  :
  3.   X11 module cannot be loaded
  4. In addition: Warning message:
  5. In (function (display = "", width, height, pointsize, gamma, bg,  :
  6.   unable to load shared object '/Bioinfo/SoftWare/R-3.6.0/lib64/R/modules//R_X11.so':
  7.   libjpeg.so.9: cannot open shared object file: No such file or directory
  8. > quit()
  9. 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：

  1. $ /Bioinfo/SoftWare/R-3.6.0/bin/R CMD ldd /Bioinfo/SoftWare/R-3.6.0/lib64/R/modules//R_X11.so
  2.         linux-vdso.so.1 =>  (0x00007fff3c79b000)
  3.         libtiff.so.5 => /Bioinfo/SoftWare/NewLibs/tiff-4.0.9/lib/libtiff.so.5 (0x00007f75369dc000)
  4.         libjpeg.so.9 => not found
  5.         libpng16.so.16 => not found
  6.         libpangocairo-1.0.so.0 => /usr/lib64/libpangocairo-1.0.so.0 (0x00007f75367ba000)
  7.         libpango-1.0.so.0 => /usr/lib64/libpango-1.0.so.0 (0x00007f753656e000)
  8.         libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00007f7536322000)
  9.         ......

libjpeg.so.9, libpng16.so.16 安装步骤如下: 

  1. $ wget http://www.ijg.org/files/jpegsrc.v9c.tar.gz
  2. $ tar zvxf jpegsrc.v9c.tar.gz
  3. $ cd jpeg-9c
  4. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/jpeg-9c
  5. $ make
  6. $ make install
  8. $ wget https://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz
  9. $ tar zvxf libpng-1.6.37.tar.gz
  10. $ cd libpng-1.6.37
  11. $ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/libpng-1.6.37
  12. $ make
  13. $ make install

4. 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