Your message dated Fri, 18 Aug 2023 08:24:42 +0200 with message-id <[email protected]> and subject line Closing has caused the Debian Bug report #1039640, regarding r-bioc-scater: autopkgtest failure with r-base (4.3.1-1) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 1039640: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1039640 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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
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--- Begin Message ---This issue was fixed with recent upload but not mentioned in changelog -- http://fam-tille.de
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