Problems with installation R packages

This is something that pops up in R and RStudio only once in a while. RStudio changes quite a few settings, and the option "repos" is one of them. On Windows, the following is added

EDIT: It's not RStudio adding this extra repository. The repository is kindly provided by Dr. Brian Ripley for packages that for some reason can't be made available on CRAN (license, not building out of the box, requiring additional software, ...). This is called "CRANextra" in the settings:

> getOption("repos")
                                CRAN                            CRANextra 
         "https://cran.rstudio.com/" "http://www.stats.ox.ac.uk/pub/RWin" 
attr(,"RStudio")
[1] TRUE

So RStudio tries to access a specific repository when run on Windows, but that repository has had some connection issues in the past; it isn't always reachable, and when it's not, the warnings you report are issued.

You can get this warning to stop by resetting this option:

options(repos = "https://cran.rstudio.com") # or a repo of your choice.

Which allows you to install packages without the warning:

> install.packages("fortunes")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/fortunes_1.5-4.zip'
Content type 'application/zip' length 202721 bytes (197 KB)
downloaded 197 KB

package ‘fortunes’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Joris\AppData\Local\Temp\Rtmpu0febg\downloaded_packages

Even when this warning is displayed, packages still get installed from the rstudio CRAN mirror. The warning is reported as a bug, and RStudio has promised to tackle it soon.

EDIT: More information on the CRANextra repository in R FAQ (last paragraph):

Some CRAN packages that do not build out of the box on Windows, require additional software, or are shipping third party libraries for Windows cannot be made available on CRAN in form of a Windows binary packages. Nevertheless, some of these packages are available at the “CRAN extras” repository at https://www.stats.ox.ac.uk/pub/RWin/ kindly provided by Brian D. Ripley. Note that this repository is a default repository for recent versions of R for Windows.

In the mean while R Studio fixes the bug, a temporal solution for not having to especifie the CRAN repository every time we start an R session, is to edit your "Rprofile.site" file and add this line

options(repos = getOption("repos")["CRAN"])

That way every time an R session is started the CRANextra repository ("http://www.stats.ox.ac.uk/pub/RWin") is removed automatically. Just remember to delete or comment with # this line after the bug is solved.