"install.packages 在 knitr 文档中失败：“尝试使用 CRAN 而不设置镜像”"

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

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")

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.

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.

Answer 4

Ramin Ar's solution worked for me.