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R在linux中的library path的问题:

R在linux中的library path的问题:

作者: 11的雾 | 来源:发表于2022-02-09 20:55 被阅读0次

问题:

非root权限下安装的R包都是默认安装在

/home/[yourname]/R/x86_64-pc-linux-gnu-library/[version]

这就导致一个问题,别的用户无法使用到你安装的包,需要自己再安装一遍,这样就很麻烦

解决办法:将别人的R library path 加载到自己的R环境变量中就可以了:

先查看一下包的安装路径:

.libPath()

[1] "/home/user2/R/x86_64-pc-linux-gnu-library/4.1"

[2] "/usr/local/lib/R/site-library"

[3] "/usr/lib/R/site-library"

[4] "/usr/lib/R/library"

安装时会按照顺序安装,

方法1:

.libPaths(new='/home/balter/conda/envs/dada2/lib/R/library')

.libPaths()

[1] "/home/balter/conda/envs/dada2/lib/R/library" "/usr/local/lib/R/site-library"

[3] "/usr/lib/R/site-library" "/usr/lib/R/library"

方法2:将别人的library 路径导入到自己的环境变量中,

export R_LIBS="/home/user2/R/x86_64-pc-linux-gnu-library/4.1"

即可凑合用。

更专业点就是修改R启动时候加载的Rprofile文件,参考:

https://www.cnblogs.com/jessepeng/p/10984983.html

将包安装到指定的path中:

args <- c("/xx/vdjtools/vdjtools-1.2.1/Rpackages/", "reshape2", "FField", "reshape", "gplots", "gridExtra", "circlize", "ggplot2", "grid", "VennDiagram", "RColorBrewer", "plotrix", "ape", "MASS", "scales")
libPath <- args[1]
# iterate over dependencies
for (i in 2:length(args)) {
   # install packages to local library, use 0-Cloud mirror
   # note that local library is set as default search path path by RUtil
   install.packages(args[i], lib=libPath, repos="http://cran.rstudio.com/")
}

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