Bioconductor Basilisk

basilisk

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.24.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: reticulate
• Imports: dir.expiry
• Install: BiocManager::install("basilisk")

When to Use

• Developing Bioconductor packages that require a reliable, self-contained Python environment using BasiliskEnvironment to freeze dependencies.
• Executing Python-based calculations (e.g., scikit-learn's TruncatedSVD) on R matrices safely in an isolated process via basiliskRun.
• Managing multiple, isolated Python environments within a single R session using createLocalBasiliskEnv and basiliskRun to prevent dependency clashes.

When NOT to Use

• For interactive, ad-hoc Python development where you want to use your pre-existing global environment, use reticulate directly because basilisk is primarily intended for package developers to freeze dependencies.
• For simple R-native tasks, use native R implementations because provisioning custom Python virtual environments adds installation overhead.

Data Requirements

• Input format: Pure R objects (e.g., matrices like matrix(rnorm(1000), ncol=10)) that are amenable to serialization.
• Structure: Variables must be explicitly passed as arguments to the function supplied to basiliskRun.
• Normalization state: Not explicitly constrained by basilisk; depends entirely on the downstream Python module being called.

Key Parameters

• envname (no default): The unique name of the basilisk environment to create or load in BasiliskEnvironment.
• pkgname (no default): The name of the client package defining the environment in BasiliskEnvironment.
• packages (no default): A character vector of Python packages (with explicit version constraints like "pandas==2.2.3") to install.
• fun (no default): The R function containing the Python code to execute inside the isolated environment via basiliskRun.
• persist (FALSE): Logical indicating whether to persist variables across multiple calls to basiliskRun by passing a store environment.
• obsolete.only (TRUE): Logical in clearExternalDir to remove only obsolete environments.

Best Practices

• Always specify exact version numbers for all Python packages (e.g., "scikit-learn==1.6.1") in BasiliskEnvironment to future-proof the installation.
• Use basiliskStart and basiliskStop (via on.exit()) to manage the process context when executing basiliskRun.
• Ensure the return value of the function passed to basiliskRun is a pure R object, not a reticulate binding or pointer to external memory.
• Explicitly import non-base R functions via their namespace (using ::) inside the function passed to basiliskRun.

Common Pitfalls

• Relying on closures capturing the R environment in which the function was defined causes failures; fix this by explicitly passing variables as arguments to the function in basiliskRun.
• Returning reticulate bindings to Python objects causes invalid pointer errors when transferred back to the parent process; fix this by returning only pure R objects.
• Deeply nested directories on Windows exceeding the 260-character file path limit cause installation to silently fail; fix this by setting the BASILISK_EXTERNAL_DIR environment variable to a shorter path.
• Low disk usage quotas causing incomplete installations; fix this by running clearExternalDir to forcibly clear obsolete environments.

Alternatives

• reticulate: The underlying framework for R-to-Python interoperability, suitable for interactive use but lacks the Bioconductor-managed freezing of Python versions.
• renv: Manages R package dependencies and Python virtualenvs at the project level rather than the package level.
• herper: Manages Conda environments from R but does not isolate execution in a separate process like basilisk.

Citations

• Lun A (2025). Freezing Python versions inside Bioconductor packages. Package basilisk vignette.

References

• Homepage: https://bioconductor.org/packages/basilisk
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html

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