kng kng - 2 months ago 17
R Question

Package error when running r code on command line

I have some code that I run that includes this part:

if (!require("yaml")) {
install.packages("yaml")
library("yaml")
}


When I run in it rstudio, everything runs seamlessly and there are no bugs. However, when I try running my code on the command line, I get this error:

$ Rscript.exe file.R
Loading required package: yaml
Installing package(s) into ‘/usr/lib/R/site-library’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
Calls: install.packages -> grep -> contrib.url
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘yaml’
Execution halted

Answer

RStudio sets a default repository when you call install.packages from within RStudio. When you run the script via the command line, you have to tell R which repository to use (or set a global default repository).

You can easily fix this problem by telling R to use your favorite repository.

For example, if you want to use RStudio's package repository, set repos="http://cran.rstudio.com/" inside the install.packages call.

if (!require("yaml")) {
  install.packages("yaml", repos="http://cran.rstudio.com/") 
  library("yaml")
}

This should work!