Can't connect to CRAN mirror from RStudio - r

This is my first post in the stack though this has been my go to option for any coding related issue for a long time. So recently my machine was reconfigured and I had to reinstall with the IT support all my IDEs including R and RStudio. Since then I am getting this vexing issue of installing any new R package and even existing R packages keep throwing error that it's not installed or can't connect to CRAN mirror
> .libPaths()
[1] "H:/My Documents/R/R-3.3.2" "H:/My Documents/R/R-3.3.2/library" "C:/R/R-3.5.3/library"
> .libPaths("C:/R/R-3.5.3/library")
> install.packages("DBI",repos="https://cran.rstudio.com/")
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://cran.rstudio.com/src/contrib:
cannot open URL 'http://cran.rstudio.com/src/contrib/PACKAGES'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning in install.packages :
package ‘DBI’ is not available (for R version 3.5.3)
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
I saw this was posted in another thread here:
R - cannot access urls for package installation
I tried all recommendations in here, still couldn't get it fixed. Any idea what else could be broken. Much appreciate your reponse. BTW, I am not an R pro either, just a little bit hands on.

Related

Rstudio not connecting to CRAN

I get this error
Installing package into ‘C:/Users/XXXXX/Downloads/RPackages’
(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: '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'
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.rstudio.com/bin/windows/contrib/3.4/shinythemes_1.1.1.zip'
Content type 'application/zip' length 999652 bytes (976 KB)
downloaded 976 KB
That is, Rstudio keeps trying to connect to other URLs and only succeeds when it connects to https://cran.rstudio.com/bin/windows/contrib/3.4/shinythemes_1.1.1.zip
Why is this the case?
I set my GLOBAL (CDN) Rstudio, Secure HTTP method and using Internet Explorer Proxy Settings for HTTP method.
It seems an index server crashed. You should use RGUI instead of RStudio to install package(s), set option firstly.

Why install.packages and download.file aren't working while RCurl::getURL is?

I have trouble with installing packages from internet:
> install.packages("qualV")
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://mirror.ibcp.fr/pub/CRAN/src/contrib
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://mirror.ibcp.fr/pub/CRAN/src/contrib
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib
Warning in install.packages :
package ‘qualV’ is not available (for R version 3.2.2)
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://mirror.ibcp.fr/pub/CRAN/bin/windows/contrib/3.2
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2
I've checked the repositories, proxy and set debug info:
> options(internet.info = 0)
> options()$repos
CRAN CRANextra
"https://mirror.ibcp.fr/pub/CRAN/" "http://www.stats.ox.ac.uk/pub/RWin"
attr(,"RStudio")
[1] TRUE
>
> Sys.getenv("http_proxy")
[1] ""
> Sys.getenv("https_proxy")
[1] ""
I've unchecked: R-studio->Tools->Global Options->Use Internet Explorer library/proxy for HTTP (I've also tried pure R without R-studio with same results)
Seems the problem is with internet access:
> url.link <- "https://stat.ethz.ch/R-manual/R-devel/library/utils/html/download.file.html"
> content <- download.file(url.link, destfile = "download.file.html")
trying URL 'https://stat.ethz.ch/R-manual/R-devel/library/utils/html/download.file.html'
Error in download.file(url.link, destfile = "download.file.html") :
cannot open URL 'https://stat.ethz.ch/R-manual/R-devel/library/utils/html/download.file.html'
In addition: Warning message:
In download.file(url.link, destfile = "download.file.html") :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Here comes interesting part, seems that the problem is not with internet access:
> library(RCurl)
> content <- getURL(url.link)
> nchar(content)
[1] 13537
Why install.packages and download.file aren't working while getURL is working?
PS: OS is Windows 7 running on corporate notebook so there are AV/FW installed that I cannot disable (I'm not admininstrator).
This is a guess.
I think you have a new version of RStudio but an old version of R. In my experience you can install the package if you just use R, i.e. not through RStudio. I would recommend updating both R and RStudio to the latest versions.
I think the issue arises because RStudio enforces https, which is only introduced in a later version of R.

R - cannot access urls for package installation

I recently installed R Studio (Version 0.99.892) on a personal computer (windows 8) and am trying to install, among others, the following packages:
ggplot2;
dplyr;
rmarkdown;
tidyr.
Neither R nor R Studio is able to install any of these packages. Each time I attempt to install a package, I get the set of warnings I include at the bottom of this post.
I have used the install.packages command as well as the built-in package installation tool. I have tried several different mirrors.
I have tried a public university internet source, my own private internet source, and a phone tether. I have tried to connect through a VPN. I have added R Studio to my Windows Firewall exception list and have also completely disabled the Windows Firewall. I am running no other firewalls.
I have toggled the various connection options in the "Packages" tab in Global Options.
I can access the URLs in a browser.
Here are the warnings from R Studio:
> install.packages("devtools")
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://cran.fhcrc.org/src/contrib:
cannot open URL 'https://cran.fhcrc.org/src/contrib/PACKAGES'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
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/Nikhailovich/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://cran.fhcrc.org/src/contrib:
cannot open URL 'https://cran.fhcrc.org/src/contrib/PACKAGES'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
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 :
package ‘devtools’ is not available (for R version 3.2.3)
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository https://cran.fhcrc.org/bin/windows/contrib/3.2:
cannot open URL 'https://cran.fhcrc.org/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2/PACKAGES'
Here are the warnings from R (3.2.3):
> install.packages("ggplot2")
Installing package into ‘C:/Users/Nikhailovich/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error in download.file(url, destfile = f, quiet = TRUE) :
cannot open URL 'https://cran.r-project.org/CRAN_mirrors.csv'
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning: unable to access index for repository https://dirichlet.mat.puc.cl/src/contrib:
cannot open URL 'https://dirichlet.mat.puc.cl/src/contrib/PACKAGES'
Warning: 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: unable to access index for repository https://dirichlet.mat.puc.cl/bin/windows/contrib/3.2:
cannot open URL 'https://dirichlet.mat.puc.cl/bin/windows/contrib/3.2/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2/PACKAGES'
Warning message:
package ‘ggplot2’ is not available (for R version 3.2.3)
There are several stackexchange posts on package installation in R and R Studio, but I was not able to find any that answered my particular situation. Thanks in advance to anyone that knows what's going on
Run this command:
options(repos="https://CRAN.R-project.org")
after that try install.packages;it should work.Tested on my system.
This has happened to me before. Try explicitly specifying the location:
install.packages("devtools", repos="https://cran.rstudio.com/")
You can indeed specify the location when using the install.packages() function with the argument repos=, but you can also choose your favorite repository which will be used each time you download a package.
options(repos="my_favorite_CRAN_mirror")
You can see a list of all availables mirrors on the CRAN website. Juste copy/paste the adress of the closest CRAN repository to you.
You should be able after this step to retry install.packages('ggplot2')
You should try following code:
install.packages("ggbiplot",dependencies = TRUE, repos = 'http://cran.rstudio.com/')
It will help you to install the packages for the error:
package is not available for this version
Run the following command in R terminal-
options(repos="https://CRAN.R-project.org")
then-
use-install.packages('library')
I want to add that I had this issue, but the fix was not in R, but in our system. Our IT guy said: For some unknown reason, the DNS resolver service was unable to resolve hostnames. I’ve restarted the resolvd service. The server can now resolve hostnames.
The error on his end was: Temporary failure in name resolution
I was having a similar error while trying to install the packages dplyr, tidyr packages.
I solved the issue by checking my R.version and downloading a new version of base R. (3.3.3)
Try this...
Tools-->Global Option--> Package
Change "Primary CRAN Repository" to htpps Location
This method fixed my issue

Strange Error Trying to Install Certain Packages in R

I'm trying to install the dplyr package in R.
When I do it I get the following error:
> install.packages("dplyr")
Warning in install.packages :
InternetOpenUrl failed: ''
Warning in install.packages :
InternetOpenUrl failed: ''
Warning in install.packages :
unable to access index for repository https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib
Installing package into ‘C:/Users/Matt/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
InternetOpenUrl failed: ''
Warning in install.packages :
InternetOpenUrl failed: ''
Warning in install.packages :
unable to access index for repository https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib
Warning in install.packages :
package ‘dplyr’ is not available (for R version 3.2.2)
Warning in install.packages :
InternetOpenUrl failed: ''
Warning in install.packages
InternetOpenUrl failed: ''
Warning in install.packages :
unable to access index for repository https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/3.2
I am able to install some packages and not others where I get this error. I have changed the mirror. Also I have uninstalled R and R studio and reinstalled. No luck.
Can anyone help?
Thank you.
I have an answer - but it isn't what I'd consider "good". I just kept trying to load the package and finally it worked. I know that my connection was good which suggests to me it was a problem at the CRAN mirror. However, that doesn't make complete sense because I manually changed mirrors and had the same problem. So unless the mirrors are somehow really tied together in real time I'm not sure how that could be the problem. So - my "not good" advice is to just keep trying to load the package over an extended period of time and it (hopefully) should work.

Dependency error in installing packages in R

Hi I am relatively new user of R. Installed R on win8. Now I am trying to install packages but i getting following error:
install.packages("C:/Users/Owner/Downloads/pROC_1.5.4.tar.gz", repos = NULL, type = "source")
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://cran.rstudio.com/bin/windows/contrib/3.0
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
InternetOpenUrl failed: 'The server name or address could not be resolved'
Warning in install.packages :
unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.0
Warning in install.packages :
package ‘C:/Users/Owner/Downloads/pROC_1.5.4.tar.gz’ is not available (for R version 3.0.1)
Installing package into ‘C:/Users/Owner/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
ERROR: dependency 'plyr' is not available for package 'pROC'
* removing 'C:/Users/Owner/Documents/R/win-library/3.0/pROC'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-30~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Owner\Documents\R\win-library\3.0" "C:/Users/Owner/Downloads/pROC_1.5.4.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/Owner/Downloads/pROC_1.5.4.tar.gz’ had non-zero exit status
Installing the plyr package won't make a lot of difference since pROC is not supported for your R distribution.
Also since you use Rstudio you might find it easier to install packages via
Tools>Install Packages
and then set
Install from:
to
Repository(CRAN).
That way you don't have to manually download them.
As an alternative to pROC you can maybe use ROCR.
Also this might be of interest if you were planning to use pROC to calculate the area under the curve, anyway I'm digressing.
it would appear that the immediate problem is the fact that you are using forward slashes instead of backslashes, were you to change that it would look like this:
install.packages("C:\\Users\\Owner\\Downloads\\pROC_1.5.4.tar.gz", repos = NULL, type = "source")
Good luck!

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