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
