NEWS

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ClinicalVariantR 0.99.3 (2026-07-22)

• NAMESPACE: use selective @importFrom only (no wholesale import(shiny), import(DT), or import(jsonlite)) so loading no longer warns about replacing renderDataTable, dataTableOutput, or validate.
• .Rbuildignore: exclude duplicate R/shiny_* / R/ui_* helpers; the app runs from inst/shinyapp/ and attaches only shiny + bslib at launch.
• Align app/engine version strings (APP_VERSION, ACMG_PRO_ENGINE) with package DESCRIPTION version 0.99.3.
• Vignettes: Bioconductor vs GitHub install/reinstall paths and app step summary.
• Check NOTES: ignore LICENSE.md; ship only ClinicalVariantR*.Rmd vignettes.
• Remove unused crosstalk dependency; keep dependency bootstrap only under scripts/ (not shipped in the Bioconductor tarball).
• Fix package Rd wording that broke PDF manual generation; keep DESCRIPTION free of blank lines between fields.
• BiocCheck: drop inst/CITATION until a preprint/publication DOI exists; expand Description to three sentences; avoid paste in a condition message.

ClinicalVariantR 0.99.2 (2026-07-20)

• Fix analysis crash on variants with pathogenic VEP CLIN_SIG in CSQ: rbind failed when merging ClinVar protein DB (extra source column) with the CSQ catalog (numbers of columns of arguments do not match).
• R CMD check: .Rbuildignore now uses ^data/ (and similar) so development non-R assets under data/ are excluded; package samples remain in inst/extdata/. Roxygen @importFrom tags keep NAMESPACE Imports wired.

ClinicalVariantR 0.99.1 (2026-07-17)

• R CMD check / R-universe WARNING cleanup:
  • Ship non-R assets under inst/extdata/ (and ignore package-root data/).
  • ASCII-only package R/ sources (em/en dashes and similar replaced).
  • Declare digest / openssl Imports used by auth storage.
  • Wire NAMESPACE imports for bslib, VariantAnnotation, and methods.
  • Declare optional shinyjs in Suggests (Group B run-button enable/disable).
  • Add .Rbuildignore for development-only root Shiny/config/scripts trees.

ClinicalVariantR 0.99.0 (2026-07-08)

• Initial Bioconductor submission scaffold (x.99.y versioning).
• Interactive Shiny platform for ACMG/AMP germline variant classification from VEP / SnpEff / ANNOVAR-annotated VCFs.
• Three workflows: full clinical (Group A), automated rapid (Group B), and gene-panel (Group C).
• Streaming whole-VCF analysis with optional bcftools acceleration.
• Structured criterion-level evidence export and reproducibility metadata.
• Package entry points: ClinicalVariantR() / ClinicalVariantRApp() return a Shiny app object (user launches with shiny::runApp()).
• Vignettes: introduction and run/test guide covering app launch, sample data, UI checks, and CLI/unit tests.