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Question: How do you run BiocCheck from a continuous integration service?
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gravatar for richierocks
2.3 years ago by
richierocks10
richierocks10 wrote:

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?

ADD COMMENTlink modified 12 weeks ago by Marcel Ramos ♦♦ 290 • written 2.3 years ago by richierocks10

I've filed issues with R-builder and R-AppVeyor to start the ball rolling.

ADD REPLYlink written 2.3 years ago by richierocks10
1
gravatar for Dan Tenenbaum
2.3 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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.

ADD COMMENTlink written 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k
1
gravatar for Selin Jessa
6 months ago by
Selin Jessa10
McGill University
Selin Jessa10 wrote:

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.

ADD COMMENTlink modified 6 months ago • written 6 months ago by Selin Jessa10
0
gravatar for Marcel Ramos
12 weeks ago by
Marcel Ramos ♦♦ 290
United States
Marcel Ramos ♦♦ 290 wrote:

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

ADD COMMENTlink written 12 weeks ago by Marcel Ramos ♦♦ 290
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