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floundeR Dependency Assessment

Source: DEPENDENCIES.md

This file records the current R dependency posture for the revival build. It is generated from the declared DESCRIPTION dependency surface and should be refreshed when dependencies are added, removed, or moved between Imports and Suggests.

Container Baseline

The development Docker image builds from rocker/r-ver:4.6.0 and installs the declared CRAN and Bioconductor dependency set through scripts/bootstrap-r-dependencies.R --install.

Verified on 2026-06-13:

  • R: 4.6.0
  • Bioconductor: 3.23
  • Image tag: flounder-dev:latest
  • Build result: passed
  • Notable native dependency coverage: Rsamtools and ShortRead built successfully from source with the system libraries declared in Dockerfile.

The image is intentionally a development/check image. It includes Cargo and rustc so source package checks can build the embedded Rust extension. It does not include private Grammateus runtime assets, downloaded POD5 files, or derived large example data.

Version Snapshot

The following versions were reported by scripts/audit-r-dependencies.R inside the clean container after dependency installation.

Package Declared In Channel Version Support Posture
BiocGenerics Imports Bioconductor 0.58.1 Manage through BiocManager for the active R/Bioconductor release.
Biostrings Imports Bioconductor 2.80.1 Supported Bioconductor sequence infrastructure; retained for FASTA/FASTQ and sequence evidence while modern Rust-backed paths are added.
GenomeInfoDb Imports Bioconductor 1.48.0 Supported Bioconductor genome metadata infrastructure; review necessity as core QC contracts narrow.
GenomicRanges Imports Bioconductor 1.64.0 Supported Bioconductor ranges infrastructure; review necessity as BAM/POD5 Rust bindings mature.
IRanges Imports Bioconductor 2.46.0 Supported Bioconductor ranges infrastructure; dependency burden should remain justified by active code.
Rsamtools Imports Bioconductor 2.28.0 Supported but native-heavy; keep only until curated Bamana-backed BAM QC can replace or narrow its role.
ShortRead Imports Bioconductor 1.70.0 Supported but native-heavy and legacy-oriented; retain only for existing FASTQ/FASTA paths until lighter QC wrappers exist.
aws.s3 Imports CRAN 0.3.22 Retained for anonymous ONT open-data access; network tests remain opt-in.
cli Imports CRAN 3.6.6 Supported CRAN diagnostics dependency.
dplyr Imports CRAN 1.2.1 Supported tidy data dependency; should remain if public QC outputs stay tidy.
emojifont Imports CRAN 0.6.0 Legacy presentation dependency; candidate for removal unless active report styling still requires it.
ggplot2 Imports CRAN 4.0.3 Supported plotting dependency; central for R plot handoff into Grammateus.
ggsci Imports CRAN 5.0.0 Palette dependency; review against Mnemosyne/Grammateus branding before retaining.
jsonlite Imports CRAN 2.0.0 Supported JSON dependency; required for Synoptikon QC payload writing and schema-facing tests.
knitr Suggests CRAN 1.51 Standard R package vignette builder; not used as the production QC report renderer.
lubridate Imports CRAN 1.9.5 Supported timestamp handling dependency.
magick Imports CRAN 2.9.1 Native image dependency; review once Grammateus asset rendering owns report images.
magrittr Imports CRAN 2.0.5 Pipe dependency used by legacy API style; review after modernisation.
purrr Imports CRAN 1.2.2 Supported tidy iteration dependency.
R6 Imports CRAN 2.6.1 Legacy object model dependency; retain while existing classes remain exported.
RColorBrewer Imports CRAN 1.1-3 Palette dependency; review against current branding.
readr Imports CRAN 2.2.0 Supported table parser; central to sequencing-summary modernisation.
reshape2 Imports CRAN 1.4.5 Legacy reshape dependency; candidate for replacement with tidyr/dplyr patterns.
rlang Imports CRAN 1.2.0 Supported tidy error/programming dependency.
rmarkdown Suggests CRAN 2.31 Standard R package vignette engine only; Grammateus remains the strategic HTML/PDF QC report renderer.
stringdist Imports CRAN 0.9.17 Supported fuzzy matching dependency; likely relevant to kit/adapter evidence.
stringr Imports CRAN 1.6.0 Supported string handling dependency.
testthat Suggests CRAN 3.3.2 Supported test framework dependency.
tibble Imports CRAN 3.3.1 Supported tidy return-value dependency.
tidyr Imports CRAN 1.3.2 Supported tidy reshaping dependency.
tidyselect Imports CRAN 1.2.1 Supported tidy selection dependency.

Current Check Findings

After the container dependency build, R CMD check --no-manual --no-build-vignettes . progressed beyond dependency validation. The remaining issues are package-quality tasks, not missing dependency blockers:

  • Blast examples/tests fail because flnDr("drosophila_uniref100.blastx.gz") resolves to NA under check.
  • The POD5 manifest fixture has at least one sha256 value that is not 64 characters.
  • Legacy vignettes fail during direct source-tree check execution.
  • Direct source-tree checks report expected notes/warnings for hidden development files; release checks should be run on an R CMD build tarball.
  • Several declared imports are currently unused by static analysis and should be removed, moved, or justified during API modernisation.

Commands

Build the dependency image:

docker build -t flounder-dev .

Audit dependencies in the image:

docker run --rm flounder-dev Rscript scripts/audit-r-dependencies.R

Run the source-tree package check in the image:

docker run --rm flounder-dev R CMD check --no-manual --no-build-vignettes .