Running 'testthat.R' [213s]
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: 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: 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
  2023-03-20 01:11:23: Isomap START
  2023-03-20 01:11:23: constructing knn graph
  2023-03-20 01:11:23: calculating geodesic distances
  2023-03-20 01:11:23: Classical Scaling
  2023-03-20 01:11:23: Isomap START
  2023-03-20 01:11:23: constructing knn graph
  2023-03-20 01:11:23: calculating geodesic distances
  2023-03-20 01:11:24: Classical Scaling
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  No inverse function.
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  2023-03-20 01:11:24: DONE
  2023-03-20 01:11:24: Calculating kernel PCA
  2023-03-20 01:11:24: Trying to calculate reverse
  No inverse function.
  2023-03-20 01:11:25: DONE
  2023-03-20 01:11:25: Calculating kernel PCA
  2023-03-20 01:11:25: Trying to calculate reverse
  No inverse function.
  2023-03-20 01:11:26: DONE
  [ FAIL 1 | WARN 8 | SKIP 7 | PASS 185 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • FastICA not available (1)
  • TensorFlow not available for testing (5)
  • umap-learn not available, install with `pip install umap-learn==0.4` (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_isomap.R:49:3'): check other.data ──────────────────────────────
  <std::runtime_error/C++Error/error/condition>
  Error: TridiagEigen: eigen decomposition failed
  Backtrace:
      ▆
   1. ├─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE) at test_isomap.R:49:2
   2. └─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE)
   3.   └─dimRed (local) .local(.data, ...)
   4.     ├─base::do.call(methodObject@fun, args)
   5.     └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
   6.       ├─RSpectra::eigs_sym(k, pars$ndim, which = "LA", opts = list(retvec = TRUE))
   7.       └─RSpectra:::eigs_sym.matrix(k, pars$ndim, which = "LA", opts = list(retvec = TRUE))
   8.         └─RSpectra:::eigs_real_sym(...)
   9.           └─base::do.call(.Call, args = dot_call_args)
  
  [ FAIL 1 | WARN 8 | SKIP 7 | PASS 185 ]
  Error: Test failures
  Execution halted