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Bioconductor Packages: Development, Maintenance, and Peer Review

B Long Tests

B.1 What are they

Code in the tests subdirectory of all Bioconductor software packages is run by R CMD check on a daily basis as part of the Bioconductor nightly builds. The maximum amount of time that R CMD check is allowed to spend on each package is 40 min.

Package developers who wish to implement tests that will be too long to run in the context of the nightly builds can set up “long tests” in their package and add the package to the Bioconductor Long Tests builds.

B.2 Setup

4 steps:

  • Put the code for the “long tests” in the longtests subdirectory of your package. Like for the code in the tests directory, this code will typically (but not necessarily) run unit tests.

  • Add your package to the Long Tests builds by adding a .BBSoptions file to its top-level directory with the following line in it:

    RunLongTests: TRUE

  • The code in the longtests subdirectory will be run once a week (every Saturday) as part of the Long Tests builds and will be allowed to run for a maximum of 6 hours before a TIMEOUT is raised.

  • Check the latest Long Tests report for BioC devel. The next time the report is updated (normally every Saturday), your package should be included in it.

Note that we also run the Long Tests builds for the current release branch once a week (every Saturday). The latest report for these builds is here.

B.3 “Short tests” vs “long tests”

The Long Tests setup forces developers to split the testing code in their package between “short tests” and “long tests”. The former go in the tests subdirectory and must be able to run in less than 40 min (this limit is actually for the full R CMD check command which runs other possibly time-consuming things in addition to the code in tests). The latter go in the longtests subdirectory and must be able to run in less than 6 hours.

Note that, unlike with “short tests” failures, “long tests” failures don’t prevent a package from propagating after a version bump. In other words, even if a package is included in the Long Tests builds, propagation is still determined by the results of the nightly builds.

B.4 Need help?

Ask on the bioc-devel mailing list if you have questions or need help with the Long Tests builds.