R: install.packages error

Question

I'm just trying to simply install a package, and the whole thing is FUBAR. Worked fine earlier this week. Haven't touched firewall settings or anything, and have tried to install both "readxl" and "dplyr" (dplyr just to test if the problem was the readxl package) on two separate machines on two separate networks, with the problem persisting. Tried my home internet (both wifi and hardwire) as well as a mobile hotspot on my cell phone. How do I get it to go back to normal, with downloading and installing packages fast and easy?

> install.packages("readxl")
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Installing package into ‘C:/Users/grant/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES'
trying URL 'http://cran.mtu.edu/bin/windows/contrib/3.4/readxl_1.0.0.zip'
Content type 'application/zip' length 1461628 bytes (1.4 MB)
downloaded 1.4 MB

package ‘readxl’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\grant\AppData\Local\Temp\Rtmpwb6TUN\downloaded_packages

@Kevin, I selected the CRAN mirror in Michigan using chooseCRANmirror, but install.packages still defaulted to the original, bad mirror.

> chooseCRANmirror(local.only = TRUE)
Secure CRAN mirrors 

 1: 0-Cloud [https]                 2: Australia (Canberra) [https]    3: Australia (Melbourne) [https]
 4: Australia (Perth) [https]       5: Austria [https]                 6: Belgium (Ghent) [https]      
 7: Brazil (RJ) [https]             8: Brazil (SP 1) [https]           9: Bulgaria [https]             
10: Chile 1 [https]                11: China (Lanzhou) [https]        12: Colombia (Cali) [https]      
13: Czech Republic [https]         14: Denmark [https]                15: France (Lyon 1) [https]      
16: France (Lyon 2) [https]        17: France (Marseille) [https]     18: France (Montpellier) [https] 
19: France (Paris 2) [https]       20: Germany (Münster) [https]      21: Iceland [https]              
22: Indonesia (Jakarta) [https]    23: Ireland [https]                24: Italy (Padua) [https]        
25: Japan (Tokyo) [https]          26: Malaysia [https]               27: Mexico (Mexico City) [https] 
28: Norway [https]                 29: Philippines [https]            30: Russia (Moscow) [https]      
31: Spain (A Coruña) [https]       32: Spain (Madrid) [https]         33: Sweden [https]               
34: Switzerland [https]            35: UK (Bristol) [https]           36: UK (Cambridge) [https]       
37: UK (London 1) [https]          38: USA (CA 1) [https]             39: USA (KS) [https]             
40: USA (MI 1) [https]             41: USA (TN) [https]               42: USA (TX 1) [https]           
43: USA (TX 2) [https]             44: (other mirrors)                

Selection: 40
> install.packages("dplyr")
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Installing package into ‘C:/Users/grant/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  InternetOpenUrl failed: 'The operation timed out'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning in install.packages :
  unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES'
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.4/dplyr_0.7.1.zip'
Content type 'application/zip' length 2881930 bytes (2.7 MB)
downloaded 2.7 MB

package ‘dplyr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\grant\AppData\Local\Temp\RtmpQXhfjF\downloaded_packages

My default CRAN mirror has been updated as well, but doesn't seem to have an effect even after restarting RStudio.

***** Temporary Fix ***** This code must be run: a) after switching the default CRAN mirror and b) at the start of every session.

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

Try a different download mirror. This one looks like it has moved or is down — Kevin, Jul 15 '17 at 05:13
Thanks. How do I do that in a particular session? I tried changing my Rprofile CRAN setting to a mirror in Michigan, restarting R, then running "repos = getOption("repos")" with install.packages, but I'm still experiencing the error. It looks like it is still pointing towards the original mirror. Am I supposed to do something else? Sorry, not very familiar with the back end setup options. Thanks again. — CurlyW, Jul 15 '17 at 06:20
Try running `chooseCRANmirror() and selecting the one nearest. — Kevin, Jul 15 '17 at 19:49
Updated OP with a temp solution. Looks like it's a bug, with a CRANextra mirror baked into RStudio options, pointing to an unstable destination. RStudio is reportedly aware of the issue, confirms it's a bug, and will fix on next release. Temp solution must still be run at the beginning of every session. Related posts: https://stackoverflow.com/questions/45108484/warning-unable-to-access-index-for-repository-https-www-stats-ox-ac-uk-pub-rw?rq=1 https://stackoverflow.com/questions/45115975/problems-with-installation-r-packages Thanks for your help in narrowing the issue, Kevin. — CurlyW, Jul 16 '17 at 05:08
Glad I could help, but you did all the work. I up-voted the question since it was very intriguing. I checked my "repositories" in the /etc directory and it is indeed baked into RStudio. Nice catch! — Kevin, Jul 16 '17 at 05:15

score 2 · Answer 1 · answered Jul 15 '17 at 22:53

2

I ran into the same problem and have been working on it all day. I tried several different CRAN mirrors and finally this one worked:

install.packages('readxl', dependencies=TRUE, repos='https://ftp.ussg.iu.edu/CRAN/')

Downloads occurred instantly.

answered Jul 15 '17 at 22:53

mack13

21
1

Hi Mack, thanks for the suggestion. Unfortunately for me, it still defaults to the original, bad CRAN mirror first, then only checks the provided repos after multiple fails for the first one nearly 2 minutes in. – CurlyW Jul 16 '17 at 04:53
It's an RStudio bug. Thanks for the input. – CurlyW Jul 16 '17 at 05:09

score 1 · Answer 2 · answered Feb 28 '21 at 00:43

1

Try increasing the time out limit (maybe 300 will work instead of 100)

options(timeout=300)

answered Feb 28 '21 at 00:43

Marco Ramos

11
1

score 0 · Answer 3 · answered Jul 16 '17 at 05:12

Looks like it's a bug, with a CRANextra mirror baked into the RStudio options, pointing to an unstable destination. RStudio is reportedly aware of the issue, confirms it's a bug, and will fix on next release.

Default CRAN mirror must be changed first, then temp solution must still be run at the beginning of every session.

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

R: install.packages error

3 Answers3