R Under development (unstable) (2025-01-25 r87633 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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
  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: MDS
  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: nMDS
  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: NNMF
  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
  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: tSNE
  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: UMAP
2025-01-26 18:53:40.243854: Isomap START
2025-01-26 18:53:40.244287: constructing knn graph
2025-01-26 18:53:40.247918: calculating geodesic distances
2025-01-26 18:53:40.256476: Classical Scaling
2025-01-26 18:53:40.277062: Isomap START
2025-01-26 18:53:40.27744: constructing knn graph
2025-01-26 18:53:40.28084: calculating geodesic distances
2025-01-26 18:53:40.289573: Classical Scaling
2025-01-26 18:53:40.344738: Calculating kernel PCA
2025-01-26 18:53:40.401415: Trying to calculate reverse
2025-01-26 18:53:40.408708: DONE
2025-01-26 18:53:40.411913: Calculating kernel PCA
2025-01-26 18:53:40.431835: Trying to calculate reverse
2025-01-26 18:53:40.440314: DONE
2025-01-26 18:53:40.443479: Calculating kernel PCA
2025-01-26 18:53:40.462396: Trying to calculate reverse
No inverse function.
2025-01-26 18:53:40.470657: DONE
2025-01-26 18:53:40.474115: Calculating kernel PCA
2025-01-26 18:53:40.50072: Trying to calculate reverse
2025-01-26 18:53:40.505542: DONE
2025-01-26 18:53:40.509077: Calculating kernel PCA
2025-01-26 18:53:40.527461: Trying to calculate reverse
2025-01-26 18:53:40.537306: DONE
2025-01-26 18:53:40.540363: Calculating kernel PCA
2025-01-26 18:53:40.557652: Trying to calculate reverse
2025-01-26 18:53:40.566285: DONE
2025-01-26 18:53:40.56892: Calculating kernel PCA
2025-01-26 18:53:40.597094: Trying to calculate reverse
2025-01-26 18:53:40.617487: DONE
2025-01-26 18:53:40.621113: Calculating kernel PCA
2025-01-26 18:53:40.652573: Trying to calculate reverse
2025-01-26 18:53:40.68123: DONE
2025-01-26 18:53:40.684023: Calculating kernel PCA
2025-01-26 18:53:40.786998: Trying to calculate reverse
No inverse function.
2025-01-26 18:53:41.609237: DONE
2025-01-26 18:53:41.625164: Calculating kernel PCA
2025-01-26 18:53:41.804294: Trying to calculate reverse
No inverse function.
2025-01-26 18:53:42.532114: DONE
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 190 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• umap-learn not available, install with `pip install umap-learn==0.4` (1):
  'test_UMAP.R:12:3'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 190 ]
> 
> proc.time()
   user  system elapsed 
  74.53    3.17  107.64