NEWS
phruta 0.1.4
- 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.
phruta 0.1.3
- Version accepted in ROpenSci
salphycon released (v. 0.1)