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

    作者是因为安装中遇到了下面的问题：

    1. creating vignettes (8s)
    2.    --- re-building ‘FACETS.Rnw’ using Sweave
    3.    Loading required package: pctGCdata
    4.    Error: processing vignette 'FACETS.Rnw' failed with diagnostics:
    5.    Running 'texi2dvi' on 'FACETS.tex' failed.
    6.    --- failed re-building ‘FACETS.Rnw’
    8.    SUMMARY: processing the following file failed:
    9.      ‘FACETS.Rnw’
    11.    Error: Vignette re-building failed.
    12.    Execution halted
    13. Error: Failed to install 'facets' from GitHub:
    14.   System command error, exit status: 1, stdout + stderr (last 10 lines):
    15. E> Loading required package: pctGCdata
    16. E> Error: processing vignette 'FACETS.Rnw' failed with diagnostics:
    17. E> Running 'texi2dvi' on 'FACETS.tex' failed.
    18. E> --- failed re-building ‘FACETS.Rnw’
    19. E> 
    20. E> SUMMARY: processing the following file failed:
    21. E>   ‘FACETS.Rnw’
    22. E> 
    23. E> Error: Vignette re-building failed.
    24. E> Execution halted

    而我则是彻底的卡死在了等待下载的路上：

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

    这里git clone 下载一下：

    1. git clone https://github.com/mskcc/facets
    2. 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。

    1.  ./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：

    1. ~/archive
    3. R
    4. > getwd()
    5. [1] "/home/yzpen/archive"
    6. > list.files(recursive = TRUE)
    7. [1] "facets-master.zip"                    
    8. [2] "pctGCdata-master.zip"

    R中安装本地包：

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

    发生报错了：

    1. Error in rawToChar(block[seq_len(ns)]) : 
    2.   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'
    3. Warning message:
    4. In install.packages("facets-master.zip", repos = NULL, type = "source") :
    5.   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：

    1. > install.packages("facets-master", repos=NULL, type="source")
    2. * installing *source* package ‘facets’ ...
    3. ** using staged installation
    4. ** libs
    5. gfortran  -fPIC  -Wall -g -O2  -c cbs2rank.f -o cbs2rank.o
    6. make: gfortran: No such file or directory
    7. make: *** [cbs2rank.o] Error 1
    8. ERROR: compilation failed for package ‘facets’
    9. * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/facets’
    10. Warning message:
    11. In install.packages("facets-master", repos = NULL, type = "source") :
    12.   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：

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

    竟然就成功了。

    再来研究第一个安装失败的报错：

    1. make: gfortran: No such file or directory
    2. make: *** [cbs2rank.o] Error 1
    3. ERROR: compilation failed for package ‘facets’
    4. * 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：

    1. $ brew install gcc

    终于也成功安装了：

    1. ** R
    2. ** inst
    3. ** byte-compile and prepare package for lazy loading
    4. ** help
    5. *** installing help indices
    6. ** building package indices
    7. ** installing vignettes
    8. ** testing if installed package can be loaded from temporary location
    9. ** checking absolute paths in shared objects and dynamic libraries
    10. ** testing if installed package can be loaded from final location
    11. ** testing if installed package keeps a record of temporary installation path
    12. * DONE (facets)

    看来源码安装，还是麻烦啊！