Running ‘testthat.R’ [100s/144s]
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: AutoEncoder
  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
    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: DrL
    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: FruchtermanReingold
    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: HLLE
  2023-09-08 20:15:39.947663: Isomap START
  2023-09-08 20:15:39.948095: constructing knn graph
  2023-09-08 20:15:39.952255: calculating geodesic distances
  2023-09-08 20:15:39.964891: Classical Scaling
  2023-09-08 20:15:40.012672: Isomap START
  2023-09-08 20:15:40.013107: constructing knn graph
  2023-09-08 20:15:40.016414: calculating geodesic distances
  2023-09-08 20:15:40.044962: Classical Scaling
  2023-09-08 20:15:40.114425: Calculating kernel PCA
  2023-09-08 20:15:40.174529: Trying to calculate reverse
  2023-09-08 20:15:40.208414: DONE
  2023-09-08 20:15:40.212239: Calculating kernel PCA
  2023-09-08 20:15:40.336488: Trying to calculate reverse
  2023-09-08 20:15:40.360445: DONE
  2023-09-08 20:15:40.364317: Calculating kernel PCA
  2023-09-08 20:15:40.397044: Trying to calculate reverse
  No inverse function.
  2023-09-08 20:15:40.404132: DONE
  2023-09-08 20:15:40.424116: Calculating kernel PCA
  2023-09-08 20:15:40.438817: Trying to calculate reverse
  2023-09-08 20:15:40.460315: DONE
  2023-09-08 20:15:40.464045: Calculating kernel PCA
  2023-09-08 20:15:40.489033: Trying to calculate reverse
  2023-09-08 20:15:40.498676: DONE
  2023-09-08 20:15:40.502495: Calculating kernel PCA
  2023-09-08 20:15:40.523913: Trying to calculate reverse
  2023-09-08 20:15:40.534212: DONE
  2023-09-08 20:15:40.537978: Calculating kernel PCA
  2023-09-08 20:15:40.586519: Trying to calculate reverse
  2023-09-08 20:15:40.605091: DONE
  2023-09-08 20:15:40.609573: Calculating kernel PCA
  2023-09-08 20:15:40.641747: Trying to calculate reverse
  2023-09-08 20:15:40.689554: DONE
  2023-09-08 20:15:40.693861: Calculating kernel PCA
  2023-09-08 20:15:40.864527: Trying to calculate reverse
  No inverse function.
  2023-09-08 20:15:41.351969: DONE
  2023-09-08 20:15:41.363601: Calculating kernel PCA
  2023-09-08 20:15:41.968739: Trying to calculate reverse
  No inverse function.
  2023-09-08 20:15:42.439623: DONE
  [ FAIL 1 | WARN 10 | SKIP 7 | PASS 168 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • FastICA not available (1): 'test_fastICA.R:2:3'
  • TensorFlow not available for testing (5): 'test_autoencoder.R:15:3',
    'test_autoencoder.R:39:3', 'test_autoencoder.R:57:5',
    'test_autoencoder.R:140:5', 'test_autoencoder.R:168:3'
  • umap-learn not available, install with `pip install umap-learn==0.4` (1):
    'test_UMAP.R:12:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_high_level_functions.R:20:11'): high level functions working? ──
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  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.       └─methods::as(...)
   9.         └─methods:::.class1(object)
  
  [ FAIL 1 | WARN 10 | SKIP 7 | PASS 168 ]
  Error: Test failures
  Execution halted