Fixed a bug in sq.retrieve.direct() where a failed sequence search (caught by tryCatch) could crash the function with an “argument is of length zero” error instead of just skipping that search.
Fixed a bug in acc.retrieve() where running on an operating system other than macOS, Linux, or Windows left the results object unassigned instead of falling back to a working code path.
Removed the duplicated curation logic in sq.curate(). The function now shares one internal implementation between its file-based and object-based modes, so a fix only needs to be made once going forward.
Removed a broken Release job from the R-CMD-check GitHub Action workflow. It referenced a job id that didn’t exist and called scripts (deploy.sh, a Docker Hub webhook) that aren’t part of this repository.
Added a Bioconductor install step to the R-CMD-check GitHub Action so Biostrings, msa, odseq, and DECIPHER install correctly on CI. These are Bioconductor packages and were never reliably resolved by remotes::install_deps() alone.
Updated actions/checkout, actions/cache, and actions/upload-artifact in the R-CMD-check GitHub Action to v4. GitHub deprecated actions/cache v1/v2 and started failing runs that use them, and actions/upload-artifact was pinned to the floating @main tag, which can change without warning.
Applied the same actions/checkout/actions/cache v4 update to the pkgdown and test-coverage GitHub Actions, and added a matching Bioconductor install step to both, since both install the package and need Biostrings, msa, odseq, and DECIPHER to do so.
Fixed a malformed tag trigger in the pkgdown workflow (-'*' instead of - '*'), which is invalid YAML list syntax and likely meant the release-tag trigger was never actually firing.
Confirmed Remotes: in DESCRIPTION still needs cran/ips, since ips was archived on CRAN in November 2025. Rogue needs no remote, it remains on CRAN.
