R error in contrib.url(repos source )

3.2K Asked by JanFerguson in Data Science , Asked on Jul 12, 2021

 I am using shell commands to install some packages in R.  I have an R file "installDependencies.R" for installing packages, this is the content of the file:

packages <- c("xts","stringr","log4r")
# Function to check whether package is installed
is.installed <- function(mypkg){
  is.element(mypkg, installed.packages()[,1])
}
for(package in packages){
  # check if package is installed
  if (!is.installed(package)){
    install.packages(package)
  }
}

Next, I'm running this on the terminal. This is the shell script I created:

#!/bin/bash
Rscript installDependencies.R
I get the following error while running the file:
algotree@algotree-900X3C-900X4C-900X4D:~$ ./inst.sh
Installing package into ‘/usr/local/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

Execution halted

algotree@algotree-900X3C-900X4C-900X4D:~$

Answered by Yajaira Satchell

To resolve this error, set a CRAN mirror like so:

for(x in pkgs){

  if(!is.element(x, installed.packages()[,1]))

    {install.packages(x, repos="http://cran.fhcrc.org")

  } else {print(paste(x, " library already installed"))}

}

The cause of the “error in contrib. url repos source r markdown” message is more than a simple matter of the R app software not being able to find the installed package. This code attempts the installation of a non-existing package.

R error in contrib.url(repos source )

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