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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

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7
  • 1
    it should come up with a list of numbers from 1 - 100 coresponding to the mirror , try typing 84 and hit enter
    – pyCthon
    Commented Jul 14, 2012 at 23:28
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    also add what OS you are using , and which version of R
    – pyCthon
    Commented Jul 14, 2012 at 23:29
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    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?
    – sayhey69
    Commented Jul 14, 2012 at 23:29
  • @pyCthon I typed 84, but nothing is returned.
    – Jim Johnson
    Commented Jul 14, 2012 at 23:31
  • @sayhey69 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.
    – Jim Johnson
    Commented Jul 14, 2012 at 23:32

11 Answers 11

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354

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.

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    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!
    – MichaelChirico
    Commented Oct 6, 2016 at 22:22
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    And here are some mirrors to chose from, to be kind to cran: cran.r-project.org/mirrors.html
    – hobs
    Commented Apr 20, 2017 at 19:12
  • 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.
    – Steven C. Howell
    Commented Jul 16, 2018 at 20:56
126

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.

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    I think this should be the accepted answer. It Just Works(tm), in all cases, including on headless systems (servers, IoT, etc.). Thanks, Dirk.
    – Jesse Adelman
    Commented Oct 7, 2018 at 22:45
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    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.
    – Dirk is no longer here
    Commented Oct 7, 2018 at 22:51
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    I hope you don't mind, Dirk, but I just edited your post to reflect your suggestion.
    – Jesse Adelman
    Commented Oct 8, 2018 at 3:05
  • 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.
    – Dirk is no longer here
    Commented Oct 8, 2018 at 3:08
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    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: stackoverflow.com/a/48152179/8400969
    – Michael Roswell
    Commented Nov 22, 2022 at 14:48
77

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.

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    Oops, do chooseCRANmirror(81) and it brings up a prompt for you to enter a number. All in the console.
    – Jared
    Commented Apr 4, 2013 at 3:09
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    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.)
    – Darren Cook
    Commented Jun 10, 2013 at 2:48
  • @DarrenCook You might be right but I find a lot of people can be intimidated by those files. I know I was.
    – Jared
    Commented Jun 14, 2013 at 22:48
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    chooseCRANmirror(ind=81) is what Jared probably meant. It will bypass the prompt.
    – Casey Watson
    Commented Feb 19, 2014 at 20:54
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    Can set options(menu.graphics = FALSE) in .Rprofile too
    – Andy Barbour
    Commented May 27, 2016 at 16:54
32

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) :-) )

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13

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.

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10

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.

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    chooseCRANmirror(ind=81)
    – zabala
    Commented Dec 14, 2022 at 22:01
4

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.

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3

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

options(menu.graphics = FALSE)
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3

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.

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2

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
})
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0

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.

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