Running ‘testthat.R’ [128s/150s]
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
    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
  2022-04-28 07:10:54: Isomap START
  2022-04-28 07:10:54: constructing knn graph
  2022-04-28 07:10:54: calculating geodesic distances
  2022-04-28 07:10:54: Classical Scaling
  2022-04-28 07:10:54: Isomap START
  2022-04-28 07:10:54: constructing knn graph
  2022-04-28 07:10:54: calculating geodesic distances
  2022-04-28 07:10:54: Classical Scaling
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  No inverse function.
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:54: Trying to calculate reverse
  2022-04-28 07:10:54: DONE
  2022-04-28 07:10:54: Calculating kernel PCA
  2022-04-28 07:10:55: Trying to calculate reverse
  No inverse function.
  2022-04-28 07:10:55: DONE
  2022-04-28 07:10:55: Calculating kernel PCA
  2022-04-28 07:10:56: Trying to calculate reverse
  No inverse function.
  2022-04-28 07:10:56: DONE
  [ FAIL 2 | WARN 0 | SKIP 9 | PASS 162 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • NMF not available for testing (3)
  • TensorFlow not available for testing (5)
  • umap-learn not available, install with `pip install umap-learn==0.4` (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_NNMF.R:151:3): Full_rank ────────────────────────────────────────
  Error in `chckpkg("NMF")`: require 'NMF' package, install it using install.packages('NMF')
  Backtrace:
      ▆
   1. ├─dimRed::embed(input_trn, "NNMF", ndim = ncol(input_trn@data)) at test_NNMF.R:151:2
   2. └─dimRed::embed(input_trn, "NNMF", ndim = ncol(input_trn@data))
   3.   └─dimRed .local(.data, ...)
   4.     ├─base::do.call(methodObject@fun, args)
   5.     └─dimRed `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
   6.       └─dimRed:::chckpkg("NMF")
  ── Error (test_high_level_functions.R:21:11): high level functions working? ────
  Error in `chckpkg("NMF")`: require 'NMF' package, install it using install.packages('NMF')
  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("NMF")
  
  [ FAIL 2 | WARN 0 | SKIP 9 | PASS 162 ]
  Error: Test failures
  Execution halted