Update to Bioc 3.23/R 4.6, resolve R CMD check warnings, and fix BiocCheck errors - #146

Merged

jpflores-13 merged 9 commits into

PhanstielLab:develfrom

jpflores-13:fix-bioc-badges

Jun 12, 2026

Commits on Jun 12, 2026

Skip readCool test when offline to prevent CI timeout on large file download

JP Flores
authored and
JP Flores
committed
Skip readCool test on CI to prevent timeout on large file download

JP Flores
authored and
JP Flores
committed
Fix \itemize -> \describe in roxygen docs to resolve R 4.6 checkRd warnings

JP Flores
authored and
JP Flores
committed
Fix remaining checkRd warnings: bad markup in segments docs, missed \itemize conversions, and suppress global variable NOTEs

JP Flores
authored and
JP Flores
committed
Bump R dependency to >= 4.2.0 for pipe placeholder syntax in readCool.R

JP Flores
authored and
JP Flores
committed
Fix C++ boolean operator warnings and remaining \itemize in annoDomains

JP Flores
authored and
JP Flores
committed
Fix BiocCheck errors: Authors@R in DESCRIPTION, \value sections in docs, suppress devel version number check

JP Flores
authored and
JP Flores
committed
Fix Authors@R: only one cre allowed, remove duplicate from Phanstiel

JP Flores
authored and
JP Flores
committed
Fix double-escaped backslashes in \value sections

JP Flores
authored and
JP Flores
committed