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:
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 ‘126.96.36.199’ * 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 ‘188.8.131.52’ * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Chris Hammill <email@example.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?