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

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?

Pomegranate

Does your package modify options('repose') at all? If not, this seems like something strange about your setup rather than the package, so I would think it would be accepted by CRAN. You can always put the package on GitHub and run it through travis and/or appveyor and see if the note goes away on those platforms. – Cracker

I have exactly the same problem. When I run it through devtools::check(cran = TRUE), I get rid of the NOTE though. What exactly is the difference? – Avenge

I am having almost the exact same problem. – Thagard

My guess is that something on my local machine is not set properly....when I ran my package through the winbilder (win-builder.r-project.org) the message disappeared. CRAN accepted the package I was originally posting about without complaint. – Pomegranate

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.

Emulous