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Bioconductor Policy Posture

Source: BIOCONDUCTOR_POLICY.md

This document records the Bioconductor-facing policy check for floundeR before any future submission. It was verified against official Bioconductor package guidance on 2026-06-14. Bioconductor documentation cited here was last built on 2026-06-09.

floundeR is not being submitted to Bioconductor in this slice. This is a readiness posture for later release planning.

Sources Checked

Policy Conclusions

Private Grammateus Runtime Assets

Bioconductor-facing floundeR must not require private Grammateus source or private Grammateus runtime downloads for installation, package load, examples, vignettes, tests, R CMD check, or BiocCheck.

The public package may document that governed HTML/PDF rendering is enhanced by an optional private runtime, but that runtime must remain outside the Bioconductor package and outside default checks. Core QC, report-contract creation, plot/figure preparation, and Synoptikon payload generation must continue to work without Grammateus assets.

Required floundeR posture:

  • Keep Grammateus runtime support optional and explicit.
  • Keep runtime downloads out of package code, examples, README-evaluated code, vignettes, and tests.
  • Keep private runtime integration tests opt-in through environment variables and an explicit GRAMMATEUS_HOME.
  • Keep public tests asserting that core QC works when Grammateus is absent.
  • Do not include private Grammateus source, runtime archives, extracted runtime assets, credentials, or private release URLs in the submitted package.

External System Requirements

Bioconductor permits external software requirements when they are documented in SystemRequirements, but package code must not install system dependencies for users. Non-trivial installation steps should be described in a top-level INSTALL file and user-facing documentation.

Required floundeR posture:

  • Keep Rust/Cargo requirements in SystemRequirements.
  • Add or maintain a top-level INSTALL file before submission, covering Linux, macOS, and Windows source-install requirements.
  • Do not install Rust, Cargo, system libraries, private runtimes, or external applications from R code, tests, examples, vignettes, or README-evaluated chunks.
  • Prefer open, trusted, easy-to-install system requirements.
  • Treat Grammateus runtime assets as optional external artifacts, not required system software.

R Package Dependencies

Bioconductor package dependencies must be available through Bioconductor or CRAN. The Remotes: field is not supported for Bioconductor builds.

Required floundeR posture:

  • Do not depend on GitHub-only R packages for any Bioconductor-facing build.
  • Keep optional developer-only tools out of mandatory dependency fields.
  • Ensure all Imports, Depends, and Suggests packages are available from CRAN or Bioconductor before submission.
  • Do not encode private Grammateus source as an R package dependency.

Downloads, Web Resources, And Caching

Bioconductor allows web-resource access when it is robust, bounded, clear on failure, and does not make checks slow or unreliable. Downloaded files should use Bioconductor-friendly caching, preferably BiocFileCache, or standard cache locations such as tools::R_user_dir() when appropriate. Package code must not download or write files to a user’s home directory, working directory, or installed package directory by default.

Required floundeR posture:

  • Keep ONT S3 examples and POD5 downloads opt-in.
  • Keep network tests skipped by default.
  • Keep default package checks runnable without network access.
  • Cache external files outside the repository and outside the installed package directory.
  • Prefer BiocFileCache for Bioconductor-facing download helpers, or document why tools::R_user_dir("floundeR", "cache") is used for a specific cache.
  • Fail quickly and clearly when web resources are unavailable.
  • Keep default examples and vignettes under reasonable check-time limits.

Large Data And POD5 Examples

Bioconductor does not support git-lfs for package data, and large datasets should be routed through ExperimentHub or AnnotationHub where appropriate. Smaller raw data fixtures may live under inst/extdata when documented with source/provenance scripts.

Required floundeR posture:

  • Do not commit downloaded ONT POD5 files or large derived POD5 artifacts.
  • Keep the ONT Zymo fecal POD5 source as opt-in real-data documentation, not a default package fixture.
  • Before submission, decide whether any real POD5 example should be represented by a tiny documented fixture, an ExperimentHub/AnnotationHub-backed resource, or a non-running opt-in example.
  • Keep source object keys, sizes, timestamps, checksums, and derivation provenance for any example data workflow.

Tests And Checks

Bioconductor expects packages to build, check, and pass BiocCheck without errors. Unit tests are part of the standard build/check process.

Required floundeR posture:

  • Run R CMD build, R CMD check, and BiocCheck against the current Bioconductor devel environment before submission.
  • Keep tests offline by default.
  • Keep private Grammateus tests behind explicit opt-in flags and runtime paths.
  • Keep tests for missing optional runtime behavior in the public test suite.
  • Reassess long-running or network-sensitive tests before submission.

Current floundeR Readiness Assessment

Current posture is directionally compatible with a future Bioconductor track because:

  • Grammateus remains optional and private.
  • Core QC APIs are designed to work without Grammateus runtime assets.
  • ONT POD5 real-data usage is opt-in and cache-oriented.
  • GitHub Actions are currently disabled, but disabled templates separate public runtime-free checks from private credentialed runtime checks.

Known submission blockers or follow-up work:

  • Add a top-level INSTALL file for source-install system requirements.
  • Add biocViews before any formal submission.
  • Confirm all package dependencies are CRAN/Bioconductor-available and remove any GitHub-only dependency assumptions.
  • Prefer or support BiocFileCache for Bioconductor-facing external file caching.
  • Run BiocCheck in a current Bioconductor devel environment.
  • Resolve current local dependency gaps that prevent full R CMD check in this host library.
  • Keep private Grammateus runtime assets, credentials, URLs, and workflows out of the public package build path.