I'd like to know how to set up continuous integration services to run BiocCheck as well as R CMD check. I'm particularly interested in SemaphoreCI and AppVeyor; answers for Travis CI are also likely to be useful to the community.

For AppVeyor and Travis CI, I guess it involves updateing the appveyor.yml/.travis.yml config file.  Adding this line should install the biocCheck package; I'm just not quite sure how to run the check and retrieve the results:

build_script:
 - travis-tool.sh install_bioc BiocCheck

The R Code for a pass is something like:

chk <- BiocCheck::BiocCheck(".")

ok <- with(chk, length(requirements) + length(recommendations) == 0)

How do I set up CI to run BiocCheck?

You get to figure it out! Unless someone else has done it before. What you suggest sounds fine. But you can also run BiocCheck from the OS command line:

R CMD BiocCheck PACKAGE

it will exit with 0 if there are no REQUIREMENTS, or a non-zero exit code otherwise. 

Please report back on what you got to work, I'm sure others will be interested.

One solution for integrating BiocCheck with Travis CI is to run BiocCheck on Travis after a successful R CMD check. Here's what the .travis.yml looks like:

# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r

language: R
r: bioc-devel
sudo: false
warnings_are_errors: true

# BiocCheck
bioc_packages:
  - BiocCheck

after_success:
  - R CMD BiocCheck --new-package --no-check-vignettes [package name]*.tar.gz

And here is a working example. Note that this method means that R CMD BiocCheck will be run, and the results will be recorded in the Travis build log, but a failed BiocCheck won't fail the build, so you will need to check the results manually.

Hi all,

I've looked into the issue and decided to contribute some code to add BiocCheck to the Travis-CI builder.

I was finally able to get my code merged and to run a package check with BiocCheck. Interestingly, my package is producing a false positive with BiocCheck but the build is not erroring out. Based on this thread, I was thinking that Travis will catch any non-zero exit codes. This doesn't seem to be the case?

Essentially, you would have to add

bioc_check: true

to your .travis.yml file.

I will keep you updated on getting this to work for Bioconductor packages.

You can check the build mentioned above here: https://travis-ci.org/waldronlab/MultiAssayExperiment/builds/396569733#L2879

Best regards, Marcel