NOTE in R CRAN check ---No repository set, so cyclic dependency check skipped

Question

I have read NOTE in R CRAN Check: No repository set, so cyclic dependency check skipped and to the best of my knowledge followed the suggestions. Specifically I have an .Rprofile file in ~/ with the line options(repos = c(CRAN=\"http://cran.r-project.org\"). I ran the bash script at the bottom of the page and still have two notes instead of the one I would expect about a New submission.

bash-3.2$ ${R} CMD check --as-cran ${name}
* using log directory ‘/private/tmp/deptest.Rcheck’
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘deptest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deptest’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘John Doe <[email protected]>’
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK

Any suggestions how to eliminate the second note about No repository set, so cyclic dependency check skipped when running R CMD check --as-cran would be most welcome. I get the same two notes when trying to create a much larger package as well. The same two notes appear when I try to build a package using RStudio as the editor for what that is worth.

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.1.2

To verify the contents of .Rprofile I entered:

ip-152010130116:~ alan$ pwd
/Users/alan
ip-152010130116:~ alan$ open -a TextEdit .Rprofile

and the single line in .Rprofile is

options(repos = c(CRAN = "http://cran.r-project.org"))

Thanks in advance

What is the likelihood CRAN will accept a package with the NOTE No repository set, so cyclic dependency check skipped?

Answer 1

I had your problem too, and fixed it by adding the following to .Rprofile:

 local({r <- getOption("repos"); r["CRAN"] <- "http://ftp.ussg.iu.edu/CRAN/";   options(repos = r)})

I think your issue is because you're not pointing to a specific CRAN mirror. You will want to change the repository to reflect the mirror nearest you.