Bioconductor pre-review#10
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fixing makevars build issue on windows
Error in [.default(tb, cl, cl): subscript out of bounds Fix is build the confusion matrix over the union of actual and predicted labels via shared factor levels
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1. Windows linker failure (Build R-release/devel/oldrel for Windows)
BLAS/LAPACK symbols (dgemm_, ddot_, etc.) were undefined because src/Makevars and src/Makevars.win never set PKG_LIBS.
Fix: added PKG_LIBS =$(LAPACK_LIBS) $ (BLAS_LIBS) $(FLIBS) to both.
2. R-devel/Linux arm64 test failure (Error in [.default(tb, cl, cl): subscript out of bounds)
In
swarmbHIVE.R, the classification metrics built table(actual_labels, predicted_labels), whose columns only contain classes the model actually predicted. Indexing tb[cl, cl] over the actual class names blew up whenever the model never predicted some class — an RNG-dependent condition, which is why only R-devel arm64 tripped it while R-release passed.Fix: build the confusion matrix over the union of actual and predicted labels via shared factor levels, so it's always square. Never-predicted classes now correctly score F1 = 0 instead of erroring. Same fix hardens balanced_accuracy and kappa, where the non-square table also silently misaligned diag().
Per run at: Bioconductor/BiocContributions#41