Running ‘testthat.R’ [76s/95s]
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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: reconstruction_rmse
  2024-11-02 14:03:58.496056: Calculating kernel PCA
  2024-11-02 14:03:58.555293: Trying to calculate reverse
  2024-11-02 14:03:58.562641: DONE
  2024-11-02 14:03:58.566367: Calculating kernel PCA
  2024-11-02 14:03:58.590664: Trying to calculate reverse
  2024-11-02 14:03:58.605952: DONE
  2024-11-02 14:03:58.615871: Calculating kernel PCA
  2024-11-02 14:03:58.647088: Trying to calculate reverse
  No inverse function.
  2024-11-02 14:03:58.653391: DONE
  2024-11-02 14:03:58.657067: Calculating kernel PCA
  2024-11-02 14:03:58.671142: Trying to calculate reverse
  2024-11-02 14:03:58.676447: DONE
  2024-11-02 14:03:58.68: Calculating kernel PCA
  2024-11-02 14:03:58.702631: Trying to calculate reverse
  2024-11-02 14:03:58.717721: DONE
  2024-11-02 14:03:58.725685: Calculating kernel PCA
  2024-11-02 14:03:58.788968: Trying to calculate reverse
  2024-11-02 14:03:58.80705: DONE
  2024-11-02 14:03:58.815172: Calculating kernel PCA
  2024-11-02 14:03:58.87081: Trying to calculate reverse
  2024-11-02 14:03:58.89353: DONE
  2024-11-02 14:03:58.89716: Calculating kernel PCA
  2024-11-02 14:03:58.941127: Trying to calculate reverse
  2024-11-02 14:03:58.988605: DONE
  2024-11-02 14:03:58.996317: Calculating kernel PCA
  2024-11-02 14:03:59.153155: Trying to calculate reverse
  No inverse function.
  2024-11-02 14:03:59.548406: DONE
  2024-11-02 14:03:59.583222: Calculating kernel PCA
  2024-11-02 14:03:59.855458: Trying to calculate reverse
  No inverse function.
  2024-11-02 14:04:00.331123: DONE
  [ FAIL 1 | WARN 9 | SKIP 15 | PASS 145 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • FastICA not available (1): 'test_fastICA.R:2:3'
  • NMF not available for testing (4): 'test_NNMF.R:16:3', 'test_NNMF.R:64:3',
    'test_NNMF.R:138:3', 'test_NNMF.R:151:3'
  • Not all required packages for isomap tests installed (1):
    'test_isomap.R:45:5'
  • Rtsne not available (1): 'test_misc_functions.R:40:3'
  • TensorFlow not available for testing (5): 'test_autoencoder.R:15:3',
    'test_autoencoder.R:39:3', 'test_autoencoder.R:57:5',
    'test_autoencoder.R:140:5', 'test_autoencoder.R:168:3'
  • empty test (1): 'test_HLLE.R:1:1'
  • umap not available (2): 'test_UMAP.R:9:5', 'test_UMAP.R:43:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_isomap.R:17:3'): check vs vegan isomap ─────────────────────────
  Error in `chckpkg("RSpectra")`: require 'RSpectra' package, install it using install.packages('RSpectra')
  Backtrace:
      ▆
   1. ├─dimRed::embed(a, "Isomap", knn = 8, ndim = 2) at test_isomap.R:17:3
   2. └─dimRed::embed(a, "Isomap", knn = 8, ndim = 2)
   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.       └─dimRed:::chckpkg("RSpectra")
  
  [ FAIL 1 | WARN 9 | SKIP 15 | PASS 145 ]
  Error: Test failures
  Execution halted