install.packages fails in knitr document: "trying to use CRAN without setting a mirror"

Question

Using the following code I got the data I wanted, but for some reason I can't figure out knitr doesn't let me compile a PDF document, as shown further below:

My code:

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

Works out with no problem but I get the following message trying 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

Propaedeutic

Answer 1

Knitr produces a R session, without a default cran mirror unless you specifically asked for one. We tend to forget we need to set up CRAN for every R session when we use Rstudio because it takes care of it, but only for interactive use, not for knitr.

You could try specifying a mirror as a install.packages argument:

install.packages("weatherData",repos = "http://cran.us.r-project.org")

Alternatively, you could set up your default CRAN mirror in your .Rprofile. See this answer.

That said, it is not a good idea to install packages through a knitr document that you will probably compile several times. You should assume people know how to install a missing package if needed, or at least test whether the package is installed before installing it again

if(!require(weatherData)) install.packages("weatherData",repos = "http://cran.us.r-project.org")

Fowkes

Interesting - can you explain why there is no default CRAN mirror in the new environment? – Chapell

I actually meant R session, not environment. Sorry for that. This is just a default R behavior we tend to forget when we use Rstudio, because it takes care of it. – Fowkes

No worrys, I was not confused about "environment" vs. "session" (this was clear from the context). However, I didn't know that RStudio is involved in setting such options. Thank you for the clarification. – Chapell

You can convert the package install code into a comment. This eliminates the error and also gives the user a hint about the package installation. #install.packages (" weatherData ", repos =" http://cran.us.r-project.org ") – Incandescence

I just started using R for the first time 5 minutes ago and the first thing I have to do is Google an obscure error message so I can configure the package download mirror?? Wtf are they smoking? – Hover

Answer 2

You must set the CRAN repository in your R. To do so, launch R or RStudio. in the R terminal run following codes.

r = getOption("repos")
r["CRAN"] = "http://cran.us.r-project.org"
options(repos = r)
install.packages("weatherData")

Above code defines CRAN repository in the R and in next package installation no need to define again.

Alternative way is to simply run install.packages("weatherData", repos="http://cran.us.r-project.org"). However, with the second solution the repository not set and you must pass it as a parameter in every package installation.

Edenedens

Answer 3

Honestly,

It would not work for me because I installed packages, and these lines of code were interrupting the knit function. When I removed all lines containing installing packages (and used the most updated R and R Markdown available) this error went away.

Fiddlededee