Appendices

Covers: the key actionable point of each appendix (A-H) in the Bioconductor package development guide.

Appendix A - Using Devel Bioconductor

Develop against Bioconductor devel so your package is ready when devel becomes the next release. The R version you pair with devel depends on the time of year (R releases once a year in mid-April; Bioconductor releases twice a year, mid-April and mid-October):

Mid-April to mid-October: use R-release (the current released R) with Bioconductor devel.
Mid-October to mid-April: use R-devel (daily build) with Bioconductor devel, because a new R is coming in April.

Rule of thumb: target the R version that users will have when the current devel branch becomes the release branch.

Install/switch to devel:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::valid()   # check all packages are the correct devel versions

BiocManager::install(version = "devel") flips the active version to devel; BiocManager::valid() reports any out-of-date or “too new” packages. For the mid-October to mid-April window, first install R-devel (source from stat.ethz.ch/R/daily, macOS from mac.r-project.org, Windows rdevel from CRAN) and run the same commands in that R.

Appendix B - Advanced Build Options

Skip unsupported platforms via Config/Bioconductor/UnsupportedPlatforms in DESCRIPTION (or legacy UnsupportedPlatforms: in .BBSoptions); platforms are win, mac, etc.
Long tests (>40 min): put them in a longtests/ dir and set RunLongTests: TRUE in .BBSoptions; they run weekly (Saturdays, up to 6 hours) and their failures do not block propagation. Keep normal tests/ under 40 minutes.
GPU packages: declare GPU_reliance: required or optional in .BBSoptions.

Appendix C - Querying Web Resources

Keep downloads reasonably sized so R CMD check finishes well under 10 minutes.
Never use unbounded while() retries; set an explicit max number of attempts (e.g. an N.TRIES loop wrapped in tryCatch()) and fail with a clear message that includes the URL and error.
Respect getOption("timeout") and check HTTP status from httr::GET() / download.file().

Appendix D - C and Fortran

Follow the “System and foreign language interfaces” section of Writing R Extensions.
Use R’s internal facilities (R_alloc, R’s RNG) instead of system equivalents; register native routines.
Add R_CheckUserInterrupt() in long C-level loops.
Use Makevars/Makefile sparingly. During development enable all warnings and disable optimization, e.g. gcc -Wall -Wextra -pedantic -O0 -ggdb, clang -Weverything -O0 -g (put user Makevars in ~/.R/).

Appendix E - C++/Mavericks Best Practices

Prefer Rcpp for C++ integration; use BH for Boost instead of bundling it.
Define R_NO_REMAP and use fully-qualified names (Rf_length(), std::map); never using namespace std; (especially in headers).
Keep R headers out of extern "C" blocks.
Avoid dereferencing/incrementing past-the-end iterators (segfaults). Regenerate old SWIG code with a C++11-capable SWIG.

Appendix F - Man Page Links

\linkS4class{} cross-references (e.g. to SummarizedExperiment) can trigger check warnings. To resolve: put the target package in Depends: (not just Imports:), add #' @import <pkg> in roxygen, and run devtools::document() so NAMESPACE gets the import() entry.

Appendix G - Book News

Changelog for the guidelines. 1.0.0 (2021-06-02) initial release; 1.0.1 (2021-08-19) added the package-naming section. Tracks when new guidance was added.

Appendix H - References

Bibliography. Key citation: Soneson et al. (2025), “Eleven Quick Tips for Writing a Bioconductor Package,” PLoS Computational Biology 21(3):e1012856.

Source: Using devel Bioconductor , Advanced build options , Querying web resources , C and Fortran code , C++ Mavericks best practices , Links in man pages , Book news , References Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).