R – Trying to use CRAN without setting a mirror

I used the code below to obtain the desired data successfully, but I’m facing an issue when trying to compile a PDF document using knitr.

Here’s my code:

install.packages("weatherData")
library(weatherData)
istanbul <- getWeatherForDate("Istanbul",
                              start_date = Sys.Date() - 41, 
                              end_date = Sys.Date())

While the code works without any problem, I encounter the following error message when attempting to compile the PDF:

Quitting from lines 3-31 (ist_weather.spin.Rmd) 
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: <Anonymous> ... eval -> eval -> install.packages -> grep -> contrib.url
Execution halted

Can someone help me figure out what might be causing this error with knitr and how to resolve it?

Answer

Sure, I can provide a detailed explanation of the issue and how to resolve it.

Understanding the Issue

The error message you’re encountering when trying to compile your PDF document using knitr is related to the configuration of CRAN (Comprehensive R Archive Network), which is the repository for R packages.

The error message specifically states:

Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror

This error message is indicating that R is attempting to download packages from CRAN, but it doesn’t know which mirror (i.e., a server that hosts the CRAN repository) to use.

The Cause of the Error

The error occurs because when you run your R code within a knitr document (e.g., an R Markdown file), it operates within a different environment than your regular R console.

In this isolated environment, R doesn’t have access to your usual R settings and configurations, including the choice of CRAN mirror.

Solution: Set CRAN Mirror Explicitly

To resolve this issue and successfully compile your PDF document using knitr, you need to explicitly set a CRAN mirror within your R Markdown document.

You can do this by adding a code chunk at the beginning of your R Markdown file with the following code:

options(repos = CRANmirror)

Here, CRANmirror should be replaced with the URL of the CRAN mirror you want to use. You can choose a CRAN mirror that is geographically close to you to optimize package download speed.

Detailed Steps to Implement the Solution

  1. Identify a CRAN Mirror: Go to the CRAN mirror list (https://cran.r-project.org/mirrors.html) and choose a mirror that is geographically convenient for you. Copy the URL of the mirror.
  2. Edit Your R Markdown File: Open your R Markdown file (e.g., ist_weather.spin.Rmd) in a text editor or RStudio.
  3. Add the Code Chunk: At the beginning of your R Markdown document, add a code chunk to set the CRAN mirror using the URL you obtained in step 1:
{r setup, include=FALSE}
options(repos = "URL_of_your_chosen_CRAN_mirror")

Replace "URL_of_your_chosen_CRAN_mirror" with the actual URL of the CRAN mirror you selected.

  1. Save and Compile: Save your R Markdown file and then try to compile the PDF document again using knitr. This time, it should work without encountering the CRAN mirror error.

By explicitly setting the CRAN mirror within your R Markdown document, you ensure that knitr knows where to download packages from, even within its isolated environment.

This should resolve the issue and allow you to compile your PDF document successfully.

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