JRaviLab · epbrenner · Jul 28, 2026 · Jul 28, 2026 · Jul 29, 2026 · Jul 29, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,5 +53,6 @@ biocViews: GenomeAssembly, Annotation, Sequencing
 VignetteBuilder: knitr
 Suggests:
     rmarkdown,
+    writexl,
     testthat (>= 3.0.0)
 Config/roxygen2/version: 8.0.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(CDHIT2duckdb)
 export(buildClusterFeatureMap)
 export(cleanData)
 export(cleanMetaData)
+export(exportProcessedData)
 export(generatePlots)
 export(generateSummary)
 export(prepareGenomes)

diff --git a/R/data_curation.R b/R/data_curation.R
diff --git a/R/data_processing.R b/R/data_processing.R
diff --git a/README.Rmd b/README.Rmd
@@ -270,6 +270,8 @@ Processing times vary by species and isolate count:
 - These numbers will all vary greatly based on isolate number, genome complexity, and available hardware.
 - Parallelization significantly reduces processing time when multiple cores are available.
 - If a `future::multisession` error occurs mid-run (e.g. while testing via `devtools::load_all()` before installing the package), restart your R session fully before retrying. An orphaned background worker process can leave a stale lock on the local DuckDB caches (e.g. `data/bvbrc/bvbrcData.duckdb`), which can produce inconsistent results on the next run that look like a data or QC bug but are actually just leftover session state.
+- If a `furrr`/`future::multisession` worker fails with `could not find function ".xxx"` for an internal amRdata helper, your installed copy of amRdata is stale relative to the source you're editing. `future::multisession` workers are fresh R processes that resolve `amRdata` by loading the *installed* package from `.libPaths()` — they do not see changes made only via `devtools::load_all()` in your interactive session. Run `devtools::install()` (or `pkgbuild::compile_dll(); devtools::document(); devtools::install()`) before exercising any function that runs work via `future`/`furrr`, or temporarily set `future::plan(future::sequential)` while iterating with `load_all()` alone.
+- `runDataProcessing()`/`runPanaroo2Duckdb()` default `panaroo_refind_mode` to `"off"` rather than Panaroo's own default. Refinding recovers gene calls that annotation tools missed, but its search can take substantially longer (or in rare cases fail to complete within hours) when a genome carries a cluster of CDS with internal stop codons — a condition existing genome-quality metadata (CheckM completeness/contamination, consistency scores, quality flags) does not flag. This default trades some gene-recovery accuracy for predictable runtime until a QC step upstream can screen out affected genomes; set `panaroo_refind_mode = "default"` to restore Panaroo's normal behavior.
 
 ### Integration with amR suite
 

diff --git a/README.md b/README.md
@@ -291,6 +291,30 @@ Processing times vary by species and isolate count:
   results on the next run that look like a data or QC bug but are
   actually just leftover session state.
 
+- If a `furrr`/`future::multisession` worker fails with
+  `could not find function ".xxx"` for an internal amRdata helper,
+  your installed copy of amRdata is stale relative to the source
+  you're editing. `future::multisession` workers are fresh R
+  processes that resolve `amRdata` by loading the *installed* package
+  from `.libPaths()` — they do not see changes made only via
+  `devtools::load_all()` in your interactive session. Run
+  `devtools::install()` before exercising any function that runs work
+  via `future`/`furrr`, or temporarily set
+  `future::plan(future::sequential)` while iterating with `load_all()`
+  alone.
+
+- `runDataProcessing()`/`runPanaroo2Duckdb()` default
+  `panaroo_refind_mode` to `"off"` rather than Panaroo's own default.
+  Refinding recovers gene calls that annotation tools missed, but its
+  search can take substantially longer (or in rare cases fail to
+  complete within hours) when a genome carries a cluster of CDS with
+  internal stop codons — a condition existing genome-quality metadata
+  (CheckM completeness/contamination, consistency scores, quality
+  flags) does not flag. This default trades some gene-recovery
+  accuracy for predictable runtime until a QC step upstream can screen
+  out affected genomes; set `panaroo_refind_mode = "default"` to
+  restore Panaroo's normal behavior.
+
 ### Integration with amR suite
 
 amRdata is designed to work seamlessly with other amR packages:

diff --git a/inst/extdata/Campy_testdata.zip b/inst/extdata/Campy_testdata.zip
diff --git a/man/dot-apply_metadata_qc.Rd b/man/dot-apply_metadata_qc.Rd
diff --git a/man/dot-ftpes_download_two_pass.Rd b/man/dot-ftpes_download_two_pass.Rd
diff --git a/man/dot-ftpes_download_one.Rd → man/dot-ftps_download_one.Rd b/man/dot-ftpes_download_one.Rd → man/dot-ftps_download_one.Rd
diff --git a/man/dot-ftps_download_two_pass.Rd b/man/dot-ftps_download_two_pass.Rd
diff --git a/man/dot-parse_bvbrc_tsv.Rd b/man/dot-parse_bvbrc_tsv.Rd
diff --git a/man/dot-processPanaroo.Rd b/man/dot-processPanaroo.Rd
diff --git a/man/dot-runPanaroo.Rd b/man/dot-runPanaroo.Rd
diff --git a/man/exportProcessedData.Rd b/man/exportProcessedData.Rd
diff --git a/man/exportTables.Rd b/man/exportTables.Rd
diff --git a/man/genomeList.Rd b/man/genomeList.Rd
diff --git a/man/prepareGenomes.Rd b/man/prepareGenomes.Rd