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Fix spectral clustering failure on MKL build #168

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Merged
ms609 merged 4 commits into from
Oct 13, 2025
+12 −4
Merged

Fix spectral clustering failure on MKL build #168

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c50ffaa
Initial plan
Copilot Oct 13, 2025
05fa543
Plan to fix spectral clustering MKL test failure
Copilot Oct 13, 2025
02628b2
Fix spectral clustering test for MKL compatibility
Copilot Oct 13, 2025
2e75bc3
Simpler, more rigorous tests
ms609 Oct 13, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: TreeDist
Type: Package
Title: Calculate and Map Distances Between Phylogenetic Trees
Version: 2.11.0
Version: 2.11.1
Authors@R: c(person("Martin R.", "Smith",
email = "[email protected]",
role = c("aut", "cre", "cph", "prg"),
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5 changes: 5 additions & 0 deletions NEWS.md
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@@ -1,3 +1,8 @@
# TreeDist 2.11.1 (2025-10-13)

- Improve robustness of `SpectralEigens()` tests.


# TreeDist 2.11.0 (2025-09-26)

- `HierarchicalMutualInformation()` calculates the information shared between
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2 changes: 1 addition & 1 deletion R/spectral_clustering.R
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Expand Up @@ -77,5 +77,5 @@ SpectralEigens <- function(D, nn = 10L, nEig = 2L) {
#' @rdname SpectralEigens
SpectralClustering <- function(D, nn = 10L, nEig = 2L) {
.Deprecated("SpectralEigens") # 2021-07
SpectralEigens(D, nn, nEig)
SpectralEigens(D = D, nn = nn, nEig = nEig)
}
7 changes: 5 additions & 2 deletions tests/testthat/test-spectral_clustering.R
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Expand Up @@ -9,7 +9,10 @@ test_that("Spectral clustering works", {
expect_equal(dim(allEig), c(40, 40))
expect_equal(abs(SpectralEigens(d, nEig = 2)), abs(allEig[, 40:39]),
tolerance = sqrt(.Machine[["double.eps"]]))
expect_warning(expect_equal(SpectralClustering(d, nEig = Inf), allEig),

expect_warning(deprecated <- SpectralClustering(d, nEig = Inf),
"'SpectralClustering' is deprecated.")
# Can't check raw equality because signs may flip
expect_true(all.equal(crossprod(deprecated), crossprod(allEig),
tolerance = sqrt(.Machine[["double.eps"]])))
})
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