[R-pkg-team] Bug#1039640: r-bioc-scater: autopkgtest failure with r-base (4.3.1-1)

[Bas Couwenberg]

Source: r-bioc-scater
Version: 1.26.1+ds-1
Severity: serious
Justification: autopkgtest failure

Dear Maintainer,

The autopkgtest of your package fails with r-base (4.3.1-1):

 168s [ FAIL 6 | WARN 4 | SKIP 0 | PASS 505 ]
 168s 
 168s ══ Failed tests ════════════════════════════════════════════════════════════════
 168s ── Error ('test-plot-dimred.R:84'): we can produce UMAP plots ──────────────────
 168s Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
 168s Backtrace:
 168s      ▆
 168s   1. └─scater::runUMAP(example_sce, ncomponents = 4) at test-plot-dimred.R:84:4
 168s   2.   ├─scater::calculateUMAP(y, ...)
 168s   3.   └─scater::calculateUMAP(y, ...)
 168s   4.     └─scater (local) .local(x, ...)
 168s   5.       └─scater:::.calculate_umap(...)
 168s   6.         ├─base::do.call(uwot::umap, args)
 168s   7.         └─uwot (local) `<fn>`(...)
 168s   8.           └─uwot:::uwot(...)
 168s   9.             └─uwot:::data2set(...)
 168s  10.               └─uwot:::x2set(...)
 168s  11.                 └─uwot:::x2nn(...)
 168s  12.                   └─uwot:::find_nn(...)
 168s  13.                     └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  14.                       └─FNN::get.knn(X, k)
 168s ── Error ('test-red-dim.R:290'): runUMAP works as expected ─────────────────────
 168s Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
 168s Backtrace:
 168s      ▆
 168s   1. └─scater::runUMAP(normed, ncomponents = 3) at test-red-dim.R:290:4
 168s   2.   ├─scater::calculateUMAP(y, ...)
 168s   3.   └─scater::calculateUMAP(y, ...)
 168s   4.     └─scater (local) .local(x, ...)
 168s   5.       └─scater:::.calculate_umap(...)
 168s   6.         ├─base::do.call(uwot::umap, args)
 168s   7.         └─uwot (local) `<fn>`(...)
 168s   8.           └─uwot:::uwot(...)
 168s   9.             └─uwot:::data2set(...)
 168s  10.               └─uwot:::x2set(...)
 168s  11.                 └─uwot:::x2nn(...)
 168s  12.                   └─uwot:::find_nn(...)
 168s  13.                     └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  14.                       └─FNN::get.knn(X, k)
 168s ── Error ('test-red-dim.R:324'): runUMAP on existing reduced dimension results works as expected ──
 168s Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
 168s Backtrace:
 168s      ▆
 168s   1. └─scater::runUMAP(normedP, dimred = "PCA") at test-red-dim.R:324:4
 168s   2.   ├─scater::calculateUMAP(y, ...)
 168s   3.   └─scater::calculateUMAP(y, ...)
 168s   4.     └─scater (local) .local(x, ...)
 168s   5.       └─scater:::.calculate_umap(...)
 168s   6.         ├─base::do.call(uwot::umap, args)
 168s   7.         └─uwot (local) `<fn>`(X = `<dbl[,4]>`, n_components = 2, n_neighbors = 15, pca = 4L)
 168s   8.           └─uwot:::uwot(...)
 168s   9.             └─uwot:::data2set(...)
 168s  10.               └─uwot:::x2set(...)
 168s  11.                 └─uwot:::x2nn(...)
 168s  12.                   └─uwot:::find_nn(...)
 168s  13.                     └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  14.                       └─FNN::get.knn(X, k)
 168s ── Error ('test-red-dim.R:405'): multi-modal UMAP works as expected ────────────
 168s Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
 168s Backtrace:
 168s      ▆
 168s   1. ├─scater::calculateMultiUMAP(things) at test-red-dim.R:405:4
 168s   2. └─scater::calculateMultiUMAP(things)
 168s   3.   └─scater (local) .local(x, ...)
 168s   4.     └─uwot::umap(combined, metric = mult.metrics, ...)
 168s   5.       └─uwot:::uwot(...)
 168s   6.         └─uwot:::data2set(...)
 168s   7.           └─uwot:::x2set(...)
 168s   8.             └─uwot:::x2nn(...)
 168s   9.               └─uwot:::find_nn(...)
 168s  10.                 └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  11.                   └─FNN::get.knn(X, k)
 168s ── Failure ('test-red-dim.R:531'): run* functions work with sparse matrices ────
 168s `runUMAP(normed)` threw an error.
 168s Message: DLL requires the use of native symbols
 168s Class:   simpleError/error/condition
 168s Backtrace:
 168s      ▆
 168s   1. ├─testthat::expect_error(runUMAP(normed), NA) at test-red-dim.R:531:4
 168s   2. │ └─testthat:::quasi_capture(...)
 168s   3. │   ├─testthat (local) .capture(...)
 168s   4. │   │ └─base::withCallingHandlers(...)
 168s   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 168s   6. └─scater::runUMAP(normed)
 168s   7.   ├─scater::calculateUMAP(y, ...)
 168s   8.   └─scater::calculateUMAP(y, ...)
 168s   9.     └─scater (local) .local(x, ...)
 168s  10.       └─scater:::.calculate_umap(...)
 168s  11.         ├─base::do.call(uwot::umap, args)
 168s  12.         └─uwot (local) `<fn>`(...)
 168s  13.           └─uwot:::uwot(...)
 168s  14.             └─uwot:::data2set(...)
 168s  15.               └─uwot:::x2set(...)
 168s  16.                 └─uwot:::x2nn(...)
 168s  17.                   └─uwot:::find_nn(...)
 168s  18.                     └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  19.                       └─FNN::get.knn(X, k)
 168s ── Error ('test-red-dim.R:539'): projectReducedDim works as expected ───────────
 168s Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
 168s Backtrace:
 168s      ▆
 168s   1. └─scater::runUMAP(example_sce) at test-red-dim.R:539:4
 168s   2.   ├─scater::calculateUMAP(y, ...)
 168s   3.   └─scater::calculateUMAP(y, ...)
 168s   4.     └─scater (local) .local(x, ...)
 168s   5.       └─scater:::.calculate_umap(...)
 168s   6.         ├─base::do.call(uwot::umap, args)
 168s   7.         └─uwot (local) `<fn>`(...)
 168s   8.           └─uwot:::uwot(...)
 168s   9.             └─uwot:::data2set(...)
 168s  10.               └─uwot:::x2set(...)
 168s  11.                 └─uwot:::x2nn(...)
 168s  12.                   └─uwot:::find_nn(...)
 168s  13.                     └─uwot:::FNN_nn(X, k = k, include_self = include_self)
 168s  14.                       └─FNN::get.knn(X, k)
 168s 
 168s [ FAIL 6 | WARN 4 | SKIP 0 | PASS 505 ]

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-scater/34918494/log.gz