Linux 下 R 源码安装指南

?? 本文章同步自作者的语雀知识库，请点击这里阅读原文。

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.。

?? 说明

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。

根据本教程，经过测试，以下版本均可以正常安装成功。

R-4.0.3

R-4.1.2

R-4.3.0

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。

# Rpy：--enable-R-shlib
# download list：https://mirrors.ustc.edu.cn/CRAN/src/base/
$ 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

关于 R 相关的动态库：

R 编译的过程中，如果想要在其他语言中集成 R 就必须选择--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——将 R 编译成动态库(libR.so)，然后 R 的执行程序与之链接；
- 例如，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。
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；

2. 基础环境

configure: error: No Fortran compiler found

# Ubuntu/Debian
apt install gfortran

# RHEL/openEluer
yum install gcc-gfortran

configure: error: C++ preprocessor "/lib/cpp" fails sanity check

# Ubuntu/Debian
apt install build-essential
apt install g++

# RHEL/openEluer
yum install glibc-headers
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

# Ubuntu/Debian
apt install install libreadline-dev

# RHEL/openEluer
yum install readline-devel

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

# Ubuntu/Debian
apt install libx11-dev xorg-dev libcurl4-openssl-dev

# RHEL/openEluer
yum install xorg-x11-server-devel libX11-devel libXt-devel

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

# Ubuntu/Debian
apt install liblzma-dev

# RHEL/openEluer
yum install lzma-devel xz xz-devel

configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support

# Ubuntu/Debian
apt install libpcre2-dev

# RHEL/openEluer 
yum install pcre pcre-devel			# 安装 PCRE1
yum install pcre2 pcre2-devel		# 安装 PCRE2

configure: error: libcurl >= 7.28.0 library and headers are required with support for https

# Ubuntu/Debian
apt install libcurl4-openssl-dev

# RHEL/openEluer 
yum install libcurl-devel

JPEG

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！

# Ubuntu/Debian
yum install libjpeg-dev

# RHEL/openEluer 
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！

# Ubuntu/Debian
yum install libtiff-dev

# RHEL/openEluer 
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！

# Ubuntu/Debian
apt install libcairo2-dev libxt-dev

# RHEL/openEluer 
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！

# Ubuntu/Debian
apt install libicu-dev

# RHEL/openEluer 
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。

Installations ofzlib(version 1.2.5 or later), libbz2(version 1.0.6 or later: called bzip2-libs/bzip2-devel or libbz2-1.0/libbz2-dev by some Linux distributions) andliblzmaversion 5.0.3 or later are required.

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

# 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.

Either PCRE1 (version 8.32 or later, formerly known as just PCRE) or PCRE2 is required: PCRE2 is preferred and using PCRE1 requires configure option --with-pcre1. Only the 8-bit library and headers are needed if these are packaged separately. JIT support (optional) is desirable for the best performance. For PCRE2 >= 10.30 (which is desirable as matching has been re-written not to use recursion and the Unicode tables were updated to version 10).

# 源码安装 PCRE1
$ 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

# root 安装 PCRE1
yum install pcre pcre-devel

# 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
# root 安装 PCRE2
yum install pcre2 pcre2-devel

注意:

R-3.4.2 要求 pcre 版本(>= 8.20, < 10.0)；
R-4.0.1 要求 PCRE >= 8.32 with UTF-8 support；
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:

$ 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

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：

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

注意:

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。
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:

$ ./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

如果你有管理员权限，你也可以直接使用 root 直接安装 libtiff：

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

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

http://libjpeg.sourceforge.net/

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

最后，CentOS 下 R 源码安装的完整 configure 命令如下（同样适用于 Ubuntu/Debian）：

# 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 \
  --with-x --with-cairo --with-pcre1\
  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
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
......
config.status: executing libtool commands
config.status: executing stamp-h commands

R is now configured for x86_64-pc-linux-gnu

  Source directory:            .
  Installation directory:      /Bioinfo/SoftWare/R-3.6.0

  C compiler:                  gcc -std=gnu99  -g -O2
  Fortran fixed-form compiler: gfortran  -g -O2

  Default C++ compiler:        g++ -std=gnu++11  -g -O2
  C++14 compiler:
  C++17 compiler:
  C++20 compiler:
  Fortran free-form compiler:  gfortran  -g -O2
  Obj-C compiler:

  Interfaces supported:        X11, tcltk
  External libraries:          pcre2, readline, curl
  Additional capabilities:     PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:             shared R library, shared BLAS, R profiling

  Capabilities skipped:
  Options not enabled:         memory profiling

  Recommended packages:        yes

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally

注意：

--with-x，--with-cairo 是开启 X11 图形化的参数，应该增加一下。
R-4.0 以上需要增加一个 --with-pcre1 参数，或者直接使用 PCRE2。
最后关于 HTML 的 WARNING 不会影响 R 的安装和使用，可以忽略。

最后，使用 make 和 make install 完成安装。

$ make 
$ make install

5. 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 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：

$ 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.。

6. 参考资料

R 官方文档，《R Installation and Administration》，CRAN
沈维燕，《非 root 用户手动编译安装 GCC》，语雀
沈维燕，《R 语言关于 SSL 证书异常处理笔记》，语雀

posted @ 2023-06-05 10:39 章鱼猫先生阅读(4) 评论(0) 编辑收藏举报

Linux下R源码安装指南

Linux 下 R 源码安装指南

1. 安装命令

2. 基础环境

3. 各种库和依赖解决

3.1 自动处理

JPEG

TIFF

cairo

ICU

3.2 手动处理

zlib

bzip2 or libbz2

PCRE

curl or libcurl

liblzma

libtiff

libjpeg and libpng16

4. 完整编译安装命令

5. 设置环境变量

6. 参考资料

张三（王者段位）

温馨提示

最新会员

Linux下R源码安装指南

Linux 下 R 源码安装指南

1. 安装命令

2. 基础环境

3. 各种库和依赖解决

3.1 自动处理

JPEG

TIFF

cairo

ICU

3.2 手动处理

zlib

bzip2 or libbz2

PCRE

curl or libcurl

liblzma

libtiff

libjpeg and libpng16

4. 完整编译安装命令

5. 设置环境变量

6. 参考资料

张三 （王者 段位）

温馨提示

最新会员

张三（王者段位）