Running ‘testthat.R’ [125s/154s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dimRed)
  Loading required package: DRR
  Loading required package: kernlab
  Loading required package: CVST
  Loading required package: Matrix
  
  Attaching package: 'dimRed'
  
  The following object is masked from 'package:stats':
  
      embed
  
  The following object is masked from 'package:base':
  
      as.data.frame
  
  > 
  > test_check("dimRed")
  embedding: DiffusionMaps
    quality: Q_local
    quality: Q_global
    quality: mean_R_NX
    quality: AUC_lnK_R_NX
    quality: total_correlation
    quality: cophenetic_correlation
    quality: distance_correlation
    quality: reconstruction_rmse
  embedding: DRR
    quality: Q_local
    quality: Q_global
    quality: mean_R_NX
    quality: AUC_lnK_R_NX
    quality: total_correlation
    quality: cophenetic_correlation
    quality: distance_correlation
    quality: reconstruction_rmse
  embedding: FastICA
    quality: Q_local
    quality: Q_global
    quality: mean_R_NX
    quality: AUC_lnK_R_NX
    quality: total_correlation
    quality: cophenetic_correlation
    quality: distance_correlation
    quality: reconstruction_rmse
  embedding: KamadaKawai
  2023-03-20 23:59:41.423827: Isomap START
  2023-03-20 23:59:41.424504: constructing knn graph
  2023-03-20 23:59:41.432396: calculating geodesic distances
  2023-03-20 23:59:41.45191: Classical Scaling
  2023-03-20 23:59:41.477469: Isomap START
  2023-03-20 23:59:41.478103: constructing knn graph
  2023-03-20 23:59:41.482291: calculating geodesic distances
  2023-03-20 23:59:41.497389: Classical Scaling
  2023-03-20 23:59:41.538582: Calculating kernel PCA
  2023-03-20 23:59:41.574366: Trying to calculate reverse
  2023-03-20 23:59:41.596865: DONE
  2023-03-20 23:59:41.601929: Calculating kernel PCA
  2023-03-20 23:59:41.685804: Trying to calculate reverse
  2023-03-20 23:59:41.696437: DONE
  2023-03-20 23:59:41.701644: Calculating kernel PCA
  2023-03-20 23:59:41.723509: Trying to calculate reverse
  No inverse function.
  2023-03-20 23:59:41.732281: DONE
  2023-03-20 23:59:41.737601: Calculating kernel PCA
  2023-03-20 23:59:41.756327: Trying to calculate reverse
  2023-03-20 23:59:41.776013: DONE
  2023-03-20 23:59:41.781188: Calculating kernel PCA
  2023-03-20 23:59:41.814512: Trying to calculate reverse
  2023-03-20 23:59:41.830446: DONE
  2023-03-20 23:59:41.835765: Calculating kernel PCA
  2023-03-20 23:59:41.866993: Trying to calculate reverse
  2023-03-20 23:59:41.882757: DONE
  2023-03-20 23:59:41.888099: Calculating kernel PCA
  2023-03-20 23:59:41.927112: Trying to calculate reverse
  2023-03-20 23:59:41.951876: DONE
  2023-03-20 23:59:41.956843: Calculating kernel PCA
  2023-03-20 23:59:41.999711: Trying to calculate reverse
  2023-03-20 23:59:42.03754: DONE
  2023-03-20 23:59:42.042441: Calculating kernel PCA
  2023-03-20 23:59:42.217513: Trying to calculate reverse
  No inverse function.
  2023-03-20 23:59:42.808307: DONE
  2023-03-20 23:59:42.841017: Calculating kernel PCA
  2023-03-20 23:59:43.294487: Trying to calculate reverse
  No inverse function.
  2023-03-20 23:59:43.809424: DONE
  [ FAIL 4 | WARN 0 | SKIP 7 | PASS 154 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • FastICA not available (1)
  • TensorFlow not available for testing (5)
  • umap-learn not available, install with `pip install umap-learn==0.4` (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_high_level_functions.R:20:11'): high level functions working? ──
  Error in `rankmatrix_C(dX)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_high_level_functions.R:20:10
    2. │ └─base::withCallingHandlers(...)
    3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
    4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
    5.   └─dimRed (local) .local(.data, ...)
    6.     ├─base::do.call(methodObject@fun, args)
    7.     └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
    8.       └─dimRed:::em_graph_layout(...)
    9.         └─dimRed:::construct_knn_graph(data.dist, knn)
   10.           └─coRanking::rankmatrix(data.dist, input = "dist")
   11.             └─coRanking:::rankmatrix_C(dX)
  ── Error ('test_quality.R:8:5'): quality ───────────────────────────────────────
  Error in `euclidean_C(X)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_true(is.numeric(Q_local(resPCA))) at test_quality.R:8:4
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─dimRed::Q_local(resPCA)
    5. └─dimRed::Q_local(resPCA)
    6.   └─dimRed (local) .local(object, ...)
    7.     └─coRanking::coranking(...)
    8.       └─coRanking::rankmatrix(Xi, input = input_Xi, use = use)
    9.         └─coRanking:::euclidean(as.matrix(X), use)
   10.           └─coRanking:::euclidean_C(X)
  ── Error ('test_quality.R:47:3'): Q_local ndim ─────────────────────────────────
  Error in `euclidean_C(X)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─base::sapply(1:4, function(x) quality(resPCA, "Q_local", ndim = x)) at test_quality.R:47:2
    2.   └─base::lapply(X = X, FUN = FUN, ...)
    3.     └─dimRed (local) FUN(X[[i]], ...)
    4.       ├─dimRed::quality(resPCA, "Q_local", ndim = x) at test_quality.R:47:21
    5.       └─dimRed::quality(resPCA, "Q_local", ndim = x)
    6.         └─dimRed (local) .local(.data, ...)
    7.           ├─base::do.call(methodFunction, args)
    8.           ├─dimRed (local) `<stndrdGn>`(object = `<dmRdRslt>`, ndim = 1L)
    9.           └─dimRed (local) `<stndrdGn>`(object = `<dmRdRslt>`, ndim = 1L)
   10.             └─dimRed (local) .local(object, ...)
   11.               └─coRanking::coranking(...)
   12.                 └─coRanking::rankmatrix(Xi, input = input_Xi, use = use)
   13.                   └─coRanking:::euclidean(as.matrix(X), use)
   14.                     └─coRanking:::euclidean_C(X)
  ── Error ('test_quality.R:91:3'): AUC_lnK_R_NX ─────────────────────────────────
  Error in `euclidean_C(X)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_true(...) at test_quality.R:91:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─dimRed::AUC_lnK_R_NX(resPCA, weight = "inv")
    5. └─dimRed::AUC_lnK_R_NX(resPCA, weight = "inv")
    6.   └─dimRed (local) .local(object, ...)
    7.     ├─dimRed::R_NX(object)
    8.     └─dimRed::R_NX(object)
    9.       └─dimRed (local) .local(object, ...)
   10.         └─coRanking::coranking(...)
   11.           └─coRanking::rankmatrix(Xi, input = input_Xi, use = use)
   12.             └─coRanking:::euclidean(as.matrix(X), use)
   13.               └─coRanking:::euclidean_C(X)
  
  [ FAIL 4 | WARN 0 | SKIP 7 | PASS 154 ]
  Error: Test failures
  Execution halted