11. R studio/R 工具指南（十：本地安装R 包）

北野茶缸子

发布于 2021-12-17 09:01:34

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发布于 2021-12-17 09:01:34

文章被收录于专栏：北野茶缸子的专栏

有的时候，包怎么都无法安装，可能是因为受制于网络，如github；也可能是某些玄学问题，只好将R 的源文件下载下来，自行本地安装。

参考：https://www.jianshu.com/p/6d5b5763c409

作者是因为安装中遇到了下面的问题：

creating vignettes (8s)
   --- re-building ‘FACETS.Rnw’ using Sweave
   Loading required package: pctGCdata
   Error: processing vignette 'FACETS.Rnw' failed with diagnostics:
   Running 'texi2dvi' on 'FACETS.tex' failed.
   --- failed re-building ‘FACETS.Rnw’
   
   SUMMARY: processing the following file failed:
     ‘FACETS.Rnw’
   
   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'facets' from GitHub:
  System command error, exit status: 1, stdout + stderr (last 10 lines):
E> Loading required package: pctGCdata
E> Error: processing vignette 'FACETS.Rnw' failed with diagnostics:
E> Running 'texi2dvi' on 'FACETS.tex' failed.
E> --- failed re-building ‘FACETS.Rnw’
E> 
E> SUMMARY: processing the following file failed:
E>   ‘FACETS.Rnw’
E> 
E> Error: Vignette re-building failed.
E> Execution halted

而我则是彻底的卡死在了等待下载的路上：

Downloading GitHub repo mskcc/facets@HEAD
Downloading GitHub repo veseshan/pctGCdata@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/veseshan/pctGCdata/tarball/HEAD' failed
Downloading GitHub repo veseshan/pctGCdata@HEAD

这里git clone 下载一下：

git clone https://github.com/mskcc/facets
git clone https://github.com/mskcc/pctGCdata

放在工作目录下，进行编译。

看到有两个版本的编译方法，第一个：https://blog.csdn.net/renyongzhe/article/details/101352683 采用了软件源码安装的configure-make-install 三部曲，比较麻烦：比如要配置下面这么多参数。

 ./configure  --prefix=/path/to/install/R_3.6.0  --enable-R-shlib  CPPFLAGS="-I/path_to/zlib_1.2.11/include -I/path_to/bzip2-1.0.6/include -I/path_to/xz-5.2.4/include -I/path_to/pcre-8.43/include -I/path_to/curl-7.65.3/include  -I/usr/include -fPIC" LDFLAGS="-L/path_to/zlib_1.2.11/lib -L/path_to/bzip2-1.0.6/lib -L/path_to/xz-5.2.4/lib  -L/path_to/pcre-8.43/lib -Wl,-rpath=/path_to/xz-5.2.4/lib -Wl,-rpath=/path_to/pcre-8.43/lib -L/path_to/curl-7.65.3/lib -L/path_to/icu/source/lib/ -L/usr/lib -L/usr/lib64 -fPIC"

还有一个就是：https://blog.csdn.net/huangfei711/article/details/51100155在R 中进行安装，使用本地的源码文件。

我们尝试在R 中操作一下。

进入R，并将工作目录设置为源码文件所在目录：

~/archive

R
> getwd()
[1] "/home/yzpen/archive"
> list.files(recursive = TRUE)
[1] "facets-master.zip"                    
[2] "pctGCdata-master.zip"

R中安装本地包：

install.packages("pctGCdata-master", repos=NULL, type="source")

发生报错了：

Error in rawToChar(block[seq_len(ns)]) : 
  字符串里嵌入了nul：'PK\003\004\n\0\0\0\0\0Ne^O\0\0\0\0\0\0\0\0\0\0\0\0\016\0\t\0facets-master/UT\005\0\001\xa5\xe7\xb9]PK\003\004\n\0\0\0\b\0Ne^O\xbc\024\x81\xabI\0\0\0W\0\0\0\033\0\t\0facets-master/.Rb'
Warning message:
In install.packages("facets-master.zip", repos = NULL, type = "source") :
  安装程序包‘facets-master.zip’时退出狀態的值不是0

接着尝试把文件解压缩，还是报错：

> install.packages("facets-master", repos=NULL, type="source")
* installing *source* package ‘facets’ ...
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c cbs2rank.f -o cbs2rank.o
make: gfortran: No such file or directory
make: *** [cbs2rank.o] Error 1
ERROR: compilation failed for package ‘facets’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/facets’
Warning message:
In install.packages("facets-master", repos = NULL, type = "source") :
  安装程序包‘facets-master’时退出狀態的值不是0

这也太可怕了吧！换一个安装：

> install.packages("pctGCdata-master", repos=NULL, type="source")
* installing *source* package ‘pctGCdata’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pctGCdata)

竟然就成功了。

再来研究第一个安装失败的报错：

make: gfortran: No such file or directory
make: *** [cbs2rank.o] Error 1
ERROR: compilation failed for package ‘facets’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/facets’

这里参考：https://www.jianshu.com/p/c63450e91a8c

发现是没有文件gfortran，简单查了一下这是一个非常古老的1956 年就开始使用的编程语言。那就下载一个，镜像：https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/tools/gfortran-6.1.pkg

我这里选择直接用brew 下载：

$ brew install gcc

终于也成功安装了：

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (facets)

看来源码安装，还是麻烦啊！

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原始发表：2021-09-04，如有侵权请联系 cloudcommunity@tencent.com 删除

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