Troubleshooting¶

This page collects common setup and runtime issues for online-fdr.

`rpy2` and R Parity Issues¶

Parity tests require:

rpy2 installed in the active environment
R available on PATH
Bioconductor onlineFDR pinned to 2.18.0
R 4.5.x (for Bioconductor 3.22)

Symptom: `R` or `Rscript` not found¶

Check runtime availability:

R --version
Rscript --version

If unavailable, install R and ensure executables are on PATH.

Install the Python parity dependency group:

uv sync --group dev --group parity

Symptom: Bioconductor/R version mismatch¶

Example error:

Bioconductor version '3.22' requires R version '4.5'

Fix by upgrading to R 4.5.x, then reinstalling:

Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org')); if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')"
Rscript -e "BiocManager::install(version = '3.22', ask = FALSE, update = FALSE)"
Rscript -e "BiocManager::install('onlineFDR', version = '3.22', ask = FALSE, update = FALSE)"
Rscript -e "stopifnot(as.character(utils::packageVersion('onlineFDR')) == '2.18.0')"

Symptom: Linux build error with missing `tirpc`¶

If rpy2 build fails with linker errors such as cannot find -ltirpc, install:

sudo apt-get update
sudo apt-get install -y libtirpc-dev

Then reinstall dependencies.

Import Errors¶

Symptom: `ModuleNotFoundError: No module named 'online_fdr'`¶

Install package dependencies and run from repository root:

uv sync --group dev
uv run python -c "import online_fdr; print(online_fdr.__version__)"

Test Selection Problems¶

Symptom: R parity setup is incomplete¶

The default test command excludes live R parity through the live_r_parity pytest marker, so local development can run without R:

uv run python -m pytest -q

After R setup is complete, run:

uv run python -m pytest -m live_r_parity tests/test_onlinefdr_parity.py tests/test_async_methods.py -q

Documentation Build Issues¶

Symptom: `mkdocs` command not found¶

Install docs dependencies:

uv sync --group docs --no-dev

Then run:

uv run mkdocs build --strict

Troubleshooting¶

rpy2 and R Parity Issues¶

Symptom: R or Rscript not found¶