Running ‘testthat.R’ [112s/177s]
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
    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: Isomap
    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: kPCA
    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: PCA_L1
    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: LaplacianEigenmaps
    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: LLE
  2022-06-24 19:32:38: Isomap START
  2022-06-24 19:32:38: constructing knn graph
  2022-06-24 19:32:38: calculating geodesic distances
  2022-06-24 19:32:38: Classical Scaling
  2022-06-24 19:32:38: Isomap START
  2022-06-24 19:32:38: constructing knn graph
  2022-06-24 19:32:38: calculating geodesic distances
  2022-06-24 19:32:38: Classical Scaling
  2022-06-24 19:32:38: Calculating kernel PCA
  2022-06-24 19:32:38: Trying to calculate reverse
  2022-06-24 19:32:38: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  No inverse function.
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  2022-06-24 19:32:39: DONE
  2022-06-24 19:32:39: Calculating kernel PCA
  2022-06-24 19:32:39: Trying to calculate reverse
  No inverse function.
  2022-06-24 19:32:40: DONE
  2022-06-24 19:32:40: Calculating kernel PCA
  2022-06-24 19:32:40: Trying to calculate reverse
  No inverse function.
  2022-06-24 19:32:41: DONE
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • 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:21:11): high level functions working? ────
  Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
   2. │ └─base::withCallingHandlers(...)
   3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
   4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
   5.   └─dimRed .local(.data, ...)
   6.     ├─base::do.call(methodObject@fun, args)
   7.     └─dimRed `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
   8.       └─dimRed:::chckpkg("lle")
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
  Error: Test failures
  Execution halted