How to select a CRAN mirror in R

Question

I'm trying to install a package through the R prompt by doing the following:

install.packages('RMySQL')

But the output is as follows:

--- Please select a CRAN mirror for use in this session ---

And nothing else! I can't find a solution to this very basic problem. What am I supposed to type in order to select a CRAN mirror?

EDIT:

OS: Mac-OS X 10.6.8 R Version: 2.15.0

Jacket

it should come up with a list of numbers from 1 - 100 coresponding to the mirror , try typing 84 and hit enter – Rancho

also add what OS you are using , and which version of R – Rancho

Either a window should pop up with selections or a list of selections should appear in the console. Did you check for a separate window with choices? How are you running R? – Equilateral

@Rancho I typed 84, but nothing is returned. – Jacket

@Equilateral I'm simply running R by calling the prompt from my terminal. I just type in r, and the interpreter comes up. I've never had any separate windows popping up asking for choices. – Jacket

in that case the list of mirrors should appear in the console. fwiw 70 is the mirror at Berkeley that I use. What OS do you use? If you are using linux try sudo apt-get update. – Equilateral

it's because you need X windows to allow Rconsole can throw a graphical dialog... R should detect you don't have windowing, and fall back to printing a list and asking for input, but doesn't... – Pernas

Answer 1

You should either get a window with a list of repositories or a text menu with some options. But if that is not appearing, you can always specify the mirror from where to download the packages yourself by using repos parameter. By doing that, R will not ask you anymore about the repository. Example:

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

Here you have a list of mirrors for R.

Desert

For me, the repos pop-up came, I clicked a mirror, and then nothing happened; meanwhile, this worked fine. Programmatic solution > interactive solution, as usual! Thanks! – Antipole

And here are some mirrors to chose from, to be kind to cran: cran.r-project.org/mirrors.html – Keon

I found this a useful workaround to install a recent package into MRO. I spent a day trying to get a recent build of a package installed but the checkpoint function did not work as described using Anaconda's distribution of R, v3.4.3, with the snapshot set to 2017-09-01. – Damien

Answer 2

Here is what I do, which is basically straight from the example(Startup) page:

## Default repo
local({r <- getOption("repos")
       r["CRAN"] <- "https://cran.r-project.org" 
       options(repos=r)
})

which is in ~/.Rprofile.

Edit: As it is now 2018, we can add that for the last few years the URL "https://cloud.r-project.org" has been preferable as it reflects a) https access and b) an "always-near-you" CDN.

Edit 2: And these days we want https:// so updated accordingly.

Hamulus

I think this should be the accepted answer. It Just Works(tm), in all cases, including on headless systems (servers, IoT, etc.). Thanks, Dirk. – Incorporate

And with the hindsight of several years later we now a proper CDN that is guaranteed to be network-close to everybody, and we use https now so make this https://cloud.r-project.org as the URL. – Hamulus

I hope you don't mind, Dirk, but I just edited your post to reflect your suggestion. – Incorporate

If I had wanted that I could have done it four hours ago myself. I prefer to let the historical record speak. But because vandals will come, I put a postscriptum in. – Hamulus

Edit queue now full. I think the ideal answer here would 1) have the new URL in the main code block to enable easy copy-paste and 2) include this useful note as well: https://mcmap.net/q/117030/-how-to-select-a-cran-mirror-in-r – Misjudge

Answer 3

I'm a fan of:

chooseCRANmirror()

Which will print the list of mirrors in the output (no worrying a popup window since you are running it from the terminal) and then you enter the number you want.

Serviceman

Oops, do chooseCRANmirror(81) and it brings up a prompt for you to enter a number. All in the console. – Serviceman

Note: this doesn't appear to update either /etc/R/Rprofile.site or ~/.Rprofile. (So, it is not good for choosing an alternative old mirror that has disappeared. Better to edit the above files directly.) – Mooch

@DarrenCook You might be right but I find a lot of people can be intimidated by those files. I know I was. – Serviceman

chooseCRANmirror(ind=81) is what Jared probably meant. It will bypass the prompt. – Katelyn

Can set options(menu.graphics = FALSE) in .Rprofile too – Biodegradable

Answer 4

I use the ~/.Rprofile solution suggested by Dirk, but I just wanted to point out that

chooseCRANmirror(graphics=FALSE)

seems to be the sensible thing to do instead of

chooseCRANmirror(81)

, which may work, but which involves the magic number 81 (or maybe this is subtle way to promote tourism to 81 = UK (Bristol) :-) )

Connote

Answer 5

Repository selection screen cannot be shown on your system (OS X), since OS X no longer includes X11. R tries to show you the prompt through X11. Install X11 from http://xquartz.macosforge.org/landing/. Then run the install command. The repo selection prompt will be shown.

Tillo

This should be the accepted answer. The Apple support article about X11 support in OS X is at support.apple.com/kb/HT5293?viewlocale=en_US&locale=en_US – Armenian

The problem is likely that the window doesn't show because of X11, but arguably, chooseCRANmirror()/repos parameter are much simpler solutions. – Retroversion

Answer 6

I used

chooseCRANmirror(81)

it gives you a prompt to select the country. Then you can do a selection by typing the country mirror code specified there.

Yellowgreen

chooseCRANmirror(ind=81) – Spirochete

Answer 7

If you need to set the mirror in a non-interactive way (for example doing an rbundler install in a deploy script) you can do it in this way:

First manually run:

chooseCRANmirror()

Pick the mirror number that is best for you and remember it. Then to automate the selection:

R -e 'chooseCRANmirror(graphics=FALSE, ind=87);library(rbundler);bundle()'

Where 87 is the number of the mirror you would like to use. This snippet also installs the rbundle for you. You can omit that if you like.

Downtrodden

Answer 8

You could also disable all graphical menus by running this or placing it in your Rprofile

options(menu.graphics = FALSE)

Forsythia

Answer 9

A drop down menu should pop up for you to select from (or you will get a bunch of numbers to choose from), whether you are using R in the terminal or an IDE such as RStudio. This is supported on Windows, Mac OS, and most Linux systems. However, it may require additional configuration or dependencies such as X-windows.

To enable X-windows when using remote access use the following -XY flags:

ssh -XY [email protected]

There is often a default repo but this can be specified if you have any issue, such as running scripts or Rmarkdown/knitr. You can use the repo opset the mirror or repository for CRAN each time you install with:

install.packages("package", repo="<your.nearest.mirror>")

It is advisable to use the nearest mirror to your location for faster downloads. For example:

install.packages("RMySQL", repos="https://cran.stat.auckland.ac.nz/")

You can also set the repos option in your session so you only need to it once per interactive session (or script). You can check whether repos is configured with:

options(repos)

If you get "Error in options(repos) : object 'repos' not found" then you can set the repository option. For example:

options(repos = "https://cran.stat.auckland.ac.nz/")

Then it should work to install packages like usual. For Example:

install.packages("RMySQL")

As mentioned by others, you can configure the repository in your .Rprofile file and have this work across all of your scripts. It's up to you whether your prefer these "global" options on your system or "local" options in your session or script. These "local" options take more time to use each session but have the benefit of making others able to use your scripts if they don't have your .Rprofile.

Astound

Answer 10

Add into ~/.Rprofile

local({r <- getOption("repos")
    r["CRAN"] <- "mirror_site"  #for example, https://mirrors.ustc.edu.cn/CRAN/
    options(repos=r)
    options(BioC_mirror="bioc_mirror_site") #if using biocLite
})

Baptistry

Answer 11

I had, on macOS, the exact thing that you say: A 'please select' prompt and then nothing more.

After I opened (and updated; don't know if that was relevant) X-Quartz, and then restarted R and tried again, I got an X-window list of mirrors to choose from after a few seconds. It was faster the third time onwards.

Lisk