Running 'testthat.R' [131s]
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
    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
  Saving _problems/test_isomap-14.R
  2026-06-05 08:35:47.756582: Isomap START
  2026-06-05 08:35:47.757258: constructing knn graph
  2026-06-05 08:35:47.764154: calculating geodesic distances
  2026-06-05 08:35:47.774354: Classical Scaling
  2026-06-05 08:35:47.835909: Calculating kernel PCA
  2026-06-05 08:35:47.915821: Trying to calculate reverse
  2026-06-05 08:35:47.926924: DONE
  2026-06-05 08:35:47.932392: Calculating kernel PCA
  2026-06-05 08:35:47.959804: Trying to calculate reverse
  2026-06-05 08:35:47.972177: DONE
  2026-06-05 08:35:47.977902: Calculating kernel PCA
  2026-06-05 08:35:48.000602: Trying to calculate reverse
  No inverse function.
  2026-06-05 08:35:48.011296: DONE
  2026-06-05 08:35:48.014453: Calculating kernel PCA
  2026-06-05 08:35:48.027707: Trying to calculate reverse
  2026-06-05 08:35:48.035717: DONE
  2026-06-05 08:35:48.041002: Calculating kernel PCA
  2026-06-05 08:35:48.073242: Trying to calculate reverse
  2026-06-05 08:35:48.088832: DONE
  2026-06-05 08:35:48.093747: Calculating kernel PCA
  2026-06-05 08:35:48.126772: Trying to calculate reverse
  2026-06-05 08:35:48.143129: DONE
  2026-06-05 08:35:48.148704: Calculating kernel PCA
  2026-06-05 08:35:48.188779: Trying to calculate reverse
  2026-06-05 08:35:48.21394: DONE
  2026-06-05 08:35:48.219262: Calculating kernel PCA
  2026-06-05 08:35:48.262781: Trying to calculate reverse
  2026-06-05 08:35:48.316722: DONE
  2026-06-05 08:35:48.321967: Calculating kernel PCA
  2026-06-05 08:35:48.438429: Trying to calculate reverse
  No inverse function.
  2026-06-05 08:35:49.169713: DONE
  2026-06-05 08:35:49.190351: Calculating kernel PCA
  2026-06-05 08:35:49.448031: Trying to calculate reverse
  No inverse function.
  2026-06-05 08:35:50.138016: DONE
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 185 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_NNMF.R:65:3'
  • umap-learn not available, install with `pip install umap-learn==0.4` (1):
    'test_UMAP.R:12:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_isomap.R:14:3'): check vs vegan isomap ─────────────────────────
  Error in `isomapdist(dist, ...)`: data are fragmented
  Backtrace:
      ▆
   1. └─vegan::isomap(dist(getData(a)), k = 8, ndim = 2) at test_isomap.R:14:3
   2.   └─vegan::isomapdist(dist, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 185 ]
  Error:
  ! Test failures.
  Execution halted