如何在Ubuntu上设置R_LIBS_SITE，以便在启动时为所有用户正确设置.libPaths()? [英] How do I set R_LIBS_SITE on Ubuntu so that .libPaths() is set properly for all users at startup?

问题描述

我正在建立一个群集，其中所有节点都可以访问/nfs/software，因此install.packages()的好位置应该在/nfs/software/R下.如何设置R_LIBS_SITE，使其自动成为所有用户R环境的一部分?我尝试添加到/etc/R/Renviron中为R_LIBS_SITE给出的路径，但help(Startup)说请勿更改'R_HOME/etc/Renviron'本身"，由于R_HOME扩展为，但在任何情况下均无效.在各种Renviron.site和Rprofile.site文件中进行输入似乎没有达到预期的效果.我在这里想念什么?

I am setting up a cluster where all nodes have access to /nfs/software, so a good place to install.packages() would be under /nfs/software/R. How do I set R_LIBS_SITE so that this is automatically part of all users' R environment? I tried prepending to the path given for R_LIBS_SITE in /etc/R/Renviron but help(Startup) says "do not change ‘R_HOME/etc/Renviron’ itself", which I'm not sure is the same file since R_HOME expands to /usr/lib/R, but has no effect in any case. Making entries in the various Renviron.site and Rprofile.site files does not seem to have the desired effect. What am I missing here?

与此相关的还有其他一些问题(在此处和

Some other questions have danced around this (here and here, maybe others), but people seem to settle for having a user-specific library in their HOME.

推荐答案

确保对要写入的目录具有所有者和/或组写入权限.

Make sure you have owner and/or group write permissions for the directory you want to write into.

对于/etc/R/Renviron的本地替代，首选文件/etc/R/Renviron.site.

The file /etc/R/Renviron.site is the preferred choice for local overrides to /etc/R/Renviron.

另一种方法是在安装软件包时简单地添加目录.我倾向于通过以下脚本在(bash而非R)外壳上执行此操作，该脚本源自littler包中的示例:

Another way is to simply ... impose the directory when installing packages. I tend to do that on the (bash rather than R) shell via this script derived from an example in the littler package:

$ cat bin/install.r 
#!/usr/bin/env r
#
# a simple example to install one or more packages

if (is.null(argv) | length(argv)<1) {

  cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n")
  q()

}

## adjust as necessary, see help('download.packages')
repos <- "http://cran.us.r-project.org"
#repos <- "http://cran.r-project.org"

## this makes sense on Debian where no packages touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"

install.packages(argv, lib.loc, repos)

，您可以轻松地为您的首选位置自定义这样的帮助程序.在~/bin/中安装了脚本之后，我经常这样做

and you can easily customize a helper like this for your preferred location. With the script installed in ~/bin/, I often do

$ ~/bin/install.r xts plyr doRedis

，它将忠实地安装这些软件包及其依赖文件. littler程序包具有类似的脚本update.r.

and it will faithfully install these packages along with their depends. The littler package has a similar script update.r.

这篇关于如何在Ubuntu上设置R_LIBS_SITE，以便在启动时为所有用户正确设置.libPaths()?的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！