R-devtools无法安装binmapr包

参考：
解决Package is not available (for R version XXX)？ - Bioinfarmer - 博客园 (cnblogs.com)
安装历史版本的R包 - 简书 (jianshu.com)

总结版：

1. 无ComplexHeatmap包
2. 又提示无GetoptLong包
3. 无rjson包(R版本过低<3.6>，最新rjson仅支持R≥4.0)

#①devtools指定版本安装
require(devtools)
install_version("rjson", version = "0.2.20", repos = "http://cran.us.r-project.org")
#②用源代码安装
packageurl <- "https://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

接着再转头安装GetoptLong

install.packages("GetoptLong")
#再安装ComplexHeatmap
install_github("jokergoo/ComplexHeatmap")

4. 无updog、viridis包

install.packages("updog")
install.packages("viridis")

再去安装binmapr

devtools::install_github("xuzhougeng/binmapr")

啰嗦版：

刚解决了devtools无法安装，又出现了通过它安装binmapr包的问题
首先来看看报错

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘ComplexHeatmap’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘binmapr’
* removing ‘/data/kesimin/R/x86_64-pc-linux-gnu-library/3.6/binmapr’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpxzWeiv/file7be4b54b4ca1c/binmapr_0.2.tar.gz’ had non-zero exit status

可以看到显示说没有ComplexHeatmap这个包，那就试试去安装ComplexHeatmap包

install.packages("ComplexHeatmap")
#又出现报错
Installing package into ‘/data/kesimin/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘ComplexHeatmap’ is not available (for R version 3.6.3)

这应该是说我的R版本太低了，不支持这个包555
于是我就去找了这个吧的官方文档
ComplexHeatmap Complete Reference (jokergoo.github.io)
上面推荐的安装方式是用devtools安装

library(devtools)
install_github("jokergoo/ComplexHeatmap")

安装过程中提示我需要update

Downloading GitHub repo jokergoo/ComplexHeatmap@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                             
2: CRAN packages only              
3: None                            
4: digest (0.6.27 -> 0.6.29) [CRAN]
#根据提示，输入1
Enter one or more numbers, or an empty line to skip updates: 1

updates

等啊等，发现继续报错

Installing package into ‘/data/xxx/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
ERROR: dependency ‘GetoptLong’ is not available for package ‘ComplexHeatmap’
* removing ‘/data/kesimin/R/x86_64-pc-linux-gnu-library/3.6/ComplexHeatmap’
Warning messages:
1: package ‘rjson’ is not available (for R version 3.6.3) 
2: In i.p(...) :
  installation of package ‘GetoptLong’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/tmp/RtmpxzWeiv/file7be4b4932f0d2/ComplexHeatmap_2.11.2.tar.gz’ had non-zero exit status

我们现在需要下载的是GetoptLong这个包

install.packages("GetoptLong")
#继续报错，需要rjson包
Installing package into ‘/data/kesimin/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependency ‘rjson’ is not available
trying URL 'https://cloud.r-project.org/src/contrib/GetoptLong_1.0.5.tar.gz'
Content type 'application/x-gzip' length 767681 bytes (749 KB)
==================================================
downloaded 749 KB

ERROR: dependency ‘rjson’ is not available for package ‘GetoptLong’
* removing ‘/data/kesimin/R/x86_64-pc-linux-gnu-library/3.6/GetoptLong’
Warning in install.packages :
  installation of package ‘GetoptLong’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpxzWeiv/downloaded_packages’

由于直接install.packages的话，会提示不支持R 3.6版本，最新的rjson仅支持R≥4.0

rjson
在R-CRAN上查看历史版本
Index of /src/contrib/Archive/rjson (r-project.org)
rjson-history

指定版本下载R包有两种方法
①用devtools

require(devtools)
install_version("rjson", version = "0.2.20", repos = "http://cran.us.r-project.org")

但是这个方法并不能保证所有情况适用
②源代码安装
a.Rstudio操作

#linux上下载相应版本的rjson包文件
wget https://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz

Rstudio-server上，tools→install packages→Browse，选择下载的文件→install

源代码安装

b.命令行操作

packageurl <- "https://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

rjson安装成功，现在是安装GetoptLong

install.packages("GetoptLong")

安装成功！
接着是ComplexHeatMap

install_github("jokergoo/ComplexHeatmap")

安装成功！

devtools::install_github("xuzhougeng/binmapr")
#又报错了
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘updog’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘binmapr’
* removing ‘/xxx/R/x86_64-pc-linux-gnu-library/3.6/binmapr’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpxzWeiv/file7be4b7ca07010/binmapr_0.2.tar.gz’ had non-zero exit status

那我们现在就去安装这个updog包,安装完后又是少了个viridis包

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘viridis’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

啥也别说了，继续install.packages("viridis")安装

最后！终于！把它装好了！

binmapr