"checking CRAN incoming feasibility" is shown locally but not in Travis

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1

Hi all, I’m having trouble with some log lines from R CMD check not appearing in my build logs, where check warnings weren’t showing while the build was failing. The build is now passing, because I changed the error detection code, but the output is still missing. Unfortunately this is probably going to be difficult to reproduce outside of its original context. The repository in question is:

with the .travis.yml file:

I’m using a custom script to work around testthat output getting hidden while avoiding building and testing more than once. The most recent CI build that shows this problem:

https://travis-ci.org/Mouse-Imaging-Centre/RMINC/jobs/656426972#L3331

The issue occurs in

* using log directory ‘/home/travis/build/Mouse-Imaging-Centre/RMINC/RMINC.Rcheck’
* using R version 3.6.2 (2017-01-27)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-install --as-cran’
* checking for file ‘RMINC/DESCRIPTION’ ... OK
* this is package ‘RMINC’ version ‘1.5.2.2’
* checking if this is a source package ... OK

where when I run locally I get

* using log directory ‘/hpf/largeprojects/MICe/chammill/RMINC/RMINC.Rcheck’
* using R version 3.5.1 (2018-07-02)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-install --as-cran’
* checking for file ‘RMINC/DESCRIPTION’ ... OK
* this is package ‘RMINC’ version ‘1.5.2.2’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Chris Hammill <cfhammill@gmail.com>’

New submission

Availability using Additional_repositories specification:
  ?   ?   http://bioconductor.org/packages/3.10/bioc

Found the following (possibly) invalid URLs:
  URL: http://www.bic.mni.mcgill.ca/ServicesSoftware/QualityControlCIVET12
    From: man/civet.readQC.Rd
    Status: Error
    Message: libcurl error code 7:
      	Failed to connect to www.bic.mni.mcgill.ca port 80: Connection timed out

The Date field is over a month old.

Size of tarball: 32910511 bytes
* checking if this is a source package ... OK

Previously I used a case insensitive grep for the term ERROR, which caused this to flag my builds as failing (due to the libcurl error). But it didn’t show up in the log output.

Does anyone know why this isn’t showing up in the output?

3

The 1st in Google on "incoming feasibility" site:github.com:

And stuff it links to

https://cran.r-project.org/doc/manuals/R-ints.html#Tools

Suggest that this check is disabled by default since R 3.4.0 except when run from release() and you need to set envvar _R_CHECK_CRAN_INCOMING_=TRUE to enable it.

4

Thanks. Unfortunately in my custom script I’m not using devtools for the check phase. In my local machine case I’m using R 3.5.1 so R CMD check --as-cran shows this note at least that late. It’s possible that the travis R build sets _R_CHECK_CRAN_INCOMING=FALSE and that explains the difference.

Note: The case insensitive grep difference is explained by the term “syntax errors” appearing in the R CMD check output.

5

I confirm that Travis sets _R_CHECK_CRAN_INCOMING_=false.

This is actually documented at

You’ll need to set it to true before R CMD check runs.

But since it’s false by default, you’d need to do it anyway.
If it’s true in your local environment, this means you set it there.

6

Thanks! It’s unset in my local environment which defaults to True as far as I can tell (the default setting you posted above is for devtools which modifies the environment variable before running R CMD check).

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