Linux 下 R 源碼安裝指南

如果你使用的 Linux 系統 GCC 版本太低，又沒有 root 權限 (即使有 root 權限又擔心升級 GCC 帶來的風險) ；同時你又不想入坑 conda，但是你又希望安裝一個最新版本的 R，那么恭喜你，這篇普通用戶在 Linux 下源碼編譯安裝 R 的記錄剛好滿足了你想要的一切.。

?? 本文章同步自作者的語雀知識庫，請點擊這里閱讀原文。

如果你使用的 Linux 系統 GCC 版本太低, 又沒有 root 權限 (即使有 root 權限又擔心升級 GCC 帶來的風險) ; 同時你又不想入坑 conda, 但是你又希望安裝一個最新版本的 R, 那么恭喜你, 這篇普通用戶在 Linux 下源碼編譯安裝 R 的記錄剛好滿足了你想要的一切.。

?? 說明

本文檔以 R-3.6.0 為例, 但對于 R-3.6.x, R-4.0.x 的安裝同樣適用。

根據本教程，經過測試，以下版本均可以正常安裝成功。

R-4.0.3

R-4.1.2

R-4.3.0

本教程在以下的安裝環境中，經過測試都可以正常操作：

系統（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. 安裝命令

R 源碼編譯安裝基本命令。

# 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

關于 R 相關的動態庫：

R 編譯的過程中，如果想要在其他語言中集成 R 就必須選擇--enable-R-shlib選項，將 R 編譯成 lib 模式，在此模式下，會生成 path-to-R/lib/libR.so庫——將 R 編譯成動態庫(libR.so)，然后 R 的執行程序與之鏈接；
- 例如，如果不編譯生成 libR.so，在安裝 rpy2（Python 中的 R 語言接口模塊）時就無法正確編譯。
同時，確保同目錄下 libRblas.so,libRlapack.so 兩個鏈接庫也被正確生成，這兩個庫默認會生成，如果沒有，需要添加參數：--enable-BLAS-shlib,--with-blas,--with-lapack；

2. 基礎環境

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. 各種庫和依賴解決

R 源碼編譯安裝的時候需要的各種依賴庫比較多，如果你有 root 的權限，建議使用 yum/apt 等系統命令解決；如果沒有 root 權限，可以手動一個個去解決。

3.1 自動處理

針對 RHEL/Debian 一些常見的依賴，使用 yum/apt 自動解決的示例。

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			# 安裝 PCRE1
yum install pcre2 pcre2-devel		# 安裝 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 安裝過程中默認開啟 --with-jpeglib（use jpeglib library (if available) [yes]），但是相關的依賴沒有，依然可以正常安裝（沒有任何報錯），但最后會提示：Capabilities skipped: JPEG！

# Ubuntu/Debian
yum install libjpeg-dev

# RHEL/openEluer 
yum install libjpeg-devel

TIFF

R 安裝過程中默認開啟 --with-tifflib（use libtiff library (if available) [yes]），但是相關的依賴沒有，依然可以正常安裝（沒有任何報錯），但最后會提示：Capabilities skipped: TIFF！

# Ubuntu/Debian
yum install libtiff-dev

# RHEL/openEluer 
yum install libtiff-devel

cairo

R 安裝過程中默認開啟 --with-cairo（use cairo (and pango) if available [yes]），但是相關的依賴沒有，依然可以正常安裝（沒有任何報錯），但最后會提示：Capabilities skipped: cairo！

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

# RHEL/openEluer 
yum install cairo-devel

ICU

R 安裝過程中默認開啟 --with-ICU（use ICU library (if available) [yes]），如果不可用，最后會提示：Capabilities skipped: ICU！

# Ubuntu/Debian
apt install libicu-dev

# RHEL/openEluer 
yum install libicu libicu-devel

3.2 手動處理

以下是一些常見的依賴手動解決的示例，可以參考。

zlib

根據《R Installation and Administration: A.1 Essential programs and libraries》官方文檔，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.

報錯：
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版本過低, 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

接著安裝 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"

    報錯：
    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 版本已經符合要求，bzip2 版本要求 >= 1.0.6

bzip2 or libbz2

根據《R Installation and Administration: A.1 Essential programs and libraries》官方文檔, 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

重新安裝 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"

    報錯：
    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 (同時要求 pcre < 10.0, 否則再次安裝 R-3.6.0 時報錯)
    
    # 安裝 pcre-8.12，configure 編譯 R-3.6.0 時報錯:
    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 安裝需要 --enable-utf8，同時版本 >= 8.10 且 < 10.0

PCRE

在《R Installation and Administration: A.1 Essential programs and libraries》官方文檔中要求, 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).

# 源碼安裝 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 安裝 PCRE1
yum install pcre pcre-devel

# 源碼的方式安裝 PCRE2，這里不介紹，跟源碼安裝 PCRE1 原理是一樣的，自己去谷歌就好
# root 安裝 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 時，需要增加一個 --with-pcre1 參數；或者安裝 PCRE2！

重新安裝 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"

    報錯：
    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
    # 需要安裝 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

## 不指定證書
$ ./configure --prefix=/Bioinfo/SoftWare/NewLibs/curl-7.64.1

## 指定證書(推薦)
$ 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

如果你有管理員的權限，你也可以使用 root 的方法直接安裝 libcurl：

# CentOS 7.6 自帶的 libcurl 最新版本應該是 7.29.0-59.el7_9.1
yum install libcurl libcurl-devel

注意:

有些情況下，R 在鏈接一些在線數據庫，或者下載某些特殊包時，可能導致 SSL certificate problem: unable to get local issuer certificate 異常，這種情況可以通過 --with-ca-bundle 指定證書來解決。
參考下面的內容。

R 語言關于 SSL 證書異常處理筆記

重新安裝 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 

    報錯：
    /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位元的方法重新編譯 bzip2

重裝 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, 重新編譯 bzip2-1.0.6:

$ make clean
$ make
$ make install PREFIX=/Bioinfo/SoftWare/NewLibs/bzip2-1.0.6

liblzma

在編譯過程中發現: "configure: error: "liblzma library and headers are required", 需要安裝 xz, 對應主頁: https://tukaani.org/xz/, 安裝如下:

$ 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 已經編譯支持的功能, 對于畫圖可以增加下面幾個參數, 使 R 支持對應格式的圖片保存, 與此同時要確保對應庫已經安裝.

--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 為例, 需要安裝 libtiff 庫:

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

如果你有管理員權限，你也可以直接使用 root 直接安裝 libtiff：

# CentOS 7.6 自帶的 libcurl 最新版本應該是 4.0.3-35.el7
yum install libtiff libtiff-devel

然后重新編譯 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 無法使用, 可以考慮在 ~/.bashrc 中添加 libtiff 庫路徑, 然后重新再編譯 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 安裝完以后, 使用 plot 進行畫圖, 如果出現如下錯誤:

> 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，則可以考慮手動安裝這兩個包：

$ /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 安裝步驟如下:

$ 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. 完整編譯安裝命令

如果使用了自定義安裝的 gcc/c++ 進行編譯, 需要在 configure 時候使用 CC/CXX 進行指定, 否則使用系統默認的 gcc/c++，由于 CentOS-6.5 默認的 gcc==4.4.7, 該版本的 gcc 會導致 R>=3.5.0 編譯出現各種錯誤，非 root 用戶手動升級 gcc 可以參考：
非 root 用戶手動編譯安裝 GCC

最后，CentOS 下 R 源碼安裝的完整 configure 命令如下（同樣適用于 Ubuntu/Debian）：

# 粘貼到命令行時，請把 \ 去掉，連成一行命令再回車執行
$ ./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，都會保存在 ./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 是開啟 X11 圖形化的參數，應該增加一下。
R-4.0 以上需要增加一個 --with-pcre1 參數，或者直接使用 PCRE2。
最后關于 HTML 的 WARNING 不會影響 R 的安裝和使用，可以忽略。

最后，使用 make 和 make install 完成安裝。

$ make 
$ make install

5. 設置環境變量

最后, 把安裝完成的 R 添加至環境變量:

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 調用安裝的 R 包時，根據該變量尋找對應的包；
LD_LIBRARY_PATH 則是相關動態依賴庫需要查找的路徑；
環境變量設置中比較容易漏掉的是 PATH 和 LD_LIBRARY_PATH，如果是用 root 安裝，可能會沒有問題，如果安裝到個人目錄下，不添加這兩個變量的話，就無法正確尋找需要的動態鏈接庫，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)

解決方法:

$ 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)

以上就是普通用戶源碼編譯安裝最新版本 R 的全部內容, 總的一句話就是缺什么安裝什么, 從最基本的 gcc 編譯器開始到 R 所需要的各種依賴庫，直至最終安裝完成.。

6. 參考資料

R 官方文檔，《R Installation and Administration》，CRAN
沈維燕，《非 root 用戶手動編譯安裝 GCC》，語雀
沈維燕，《R 語言關于 SSL 證書異常處理筆記》，語雀

posted @ 2023-06-05 10:38 章魚貓先生閱讀(2431) 評論(2) 收藏舉報

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Linux 下 R 源碼安裝指南

1. 安裝命令

2. 基礎環境

3. 各種庫和依賴解決

3.1 自動處理

JPEG

TIFF

cairo

ICU

3.2 手動處理

zlib

bzip2 or libbz2

PCRE

curl or libcurl

liblzma

libtiff

libjpeg and libpng16

4. 完整編譯安裝命令

5. 設置環境變量

6. 參考資料

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