run_covr_skip_bioc_nstf: Run coverage with skip detection for Bioconductor RUnit-based...

In test.assessr: Assessing Package Test Reliability and Quality

Run coverage with skip detection for Bioconductor RUnit-based packages

Description

'run_covr_skip_bioc_nstf()' orchestrates coverage for packages using the Bioconductor **RUnit** layout, such as **BiocGenerics** and packages that store tests in 'inst/unitTests' or ship a 'tests/run_unitTests.R' wrapper.

Usage

run_covr_skip_bioc_nstf(pkg_source_path, test_pkg_data, cov_env)

Arguments

pkg_source_path	Character scalar. Path to the root of the package source.
test_pkg_data	A list or environment with test metadata (e.g., fields like 'bioc_run_ut_path' (path to 'tests/run_unitTests.R', if present), 'has_BioG_test' (logical flag), etc.).
cov_env	Environment that holds the temporary coverage workspace and shared state for the run.

Details

The function: 1. Builds a source-to-test mapping (using your existing 'get_source_test_mapping_nstf()'). 2. Removes any 'run_unitTests.R' wrapper from the mapping (via 'remove_run_unitTests_mapping()'). 3. Prepares a development environment **before** running RUnit tests: - Detaches commonly attached BioC infrastructure packages ('IRanges', 'S4Vectors', 'BiocGenerics') to avoid namespace/shim conflicts. - Calls 'pkgload::load_all()' to load the package under test. - Clears 'R_TESTS' to avoid R CMD check harness interference when running RUnit programmatically. 4. Identifies problem/skip-able tests via your RUnit-aware 'check_covr_skip_nstf()' (which should use 'RUnit::runTestFile()' + 'RUnit::getErrors()' per file). 5. Builds a list of test files **under 'inst/unitTests'** excluding any that should be skipped. 6. Exposes namespace objects + datasets to a dedicated environment and runs coverage with 'covr::environment_coverage()'.

Use this function **only** for packages that follow the Bioconductor RUnit layout: - tests are located in 'inst/unitTests/', and/or - a 'tests/run_unitTests.R' wrapper exists that calls an internal '.test()' / 'testPackage()' runner.

Value

A 'covr' coverage object on success; 'NULL' on failure (via 'cleanup_and_return_null()').

A covr coverage object, or NULL on failure.

test.assessr documentation built on March 3, 2026, 1:06 a.m.