Running 'testthat.R' [98s]
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 09:27:33.890687: Isomap START
  2023-09-08 09:27:33.891029: constructing knn graph
  2023-09-08 09:27:33.894067: calculating geodesic distances
  2023-09-08 09:27:33.902422: Classical Scaling
  2023-09-08 09:27:33.916934: Isomap START
  2023-09-08 09:27:33.917177: constructing knn graph
  2023-09-08 09:27:33.919297: calculating geodesic distances
  2023-09-08 09:27:33.927285: Classical Scaling
  2023-09-08 09:27:33.956654: Calculating kernel PCA
  2023-09-08 09:27:33.974272: Trying to calculate reverse
  2023-09-08 09:27:33.995284: DONE
  2023-09-08 09:27:33.997231: Calculating kernel PCA
  2023-09-08 09:27:34.028375: Trying to calculate reverse
  2023-09-08 09:27:34.033881: DONE
  2023-09-08 09:27:34.035778: Calculating kernel PCA
  2023-09-08 09:27:34.047321: Trying to calculate reverse
  No inverse function.
  2023-09-08 09:27:34.051978: DONE
  2023-09-08 09:27:34.053818: Calculating kernel PCA
  2023-09-08 09:27:34.063136: Trying to calculate reverse
  2023-09-08 09:27:34.06612: DONE
  2023-09-08 09:27:34.067908: Calculating kernel PCA
  2023-09-08 09:27:34.083626: Trying to calculate reverse
  2023-09-08 09:27:34.091186: DONE
  2023-09-08 09:27:34.093086: Calculating kernel PCA
  2023-09-08 09:27:34.10791: Trying to calculate reverse
  2023-09-08 09:27:34.115108: DONE
  2023-09-08 09:27:34.11703: Calculating kernel PCA
  2023-09-08 09:27:34.136299: Trying to calculate reverse
  2023-09-08 09:27:34.148131: DONE
  2023-09-08 09:27:34.150046: Calculating kernel PCA
  2023-09-08 09:27:34.171813: Trying to calculate reverse
  2023-09-08 09:27:34.191323: DONE
  2023-09-08 09:27:34.193224: Calculating kernel PCA
  2023-09-08 09:27:34.271054: Trying to calculate reverse
  No inverse function.
  2023-09-08 09:27:34.698843: DONE
  2023-09-08 09:27:34.708857: Calculating kernel PCA
  2023-09-08 09:27:34.896614: Trying to calculate reverse
  No inverse function.
  2023-09-08 09:27:35.454915: 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