* using log directory ‘/Users/ripley/R/packages/tests-devel/dimRed.Rcheck’
* using R Under development (unstable) (2023-09-28 r85227)
* using platform: aarch64-apple-darwin23.0.0
* R was compiled by
    Apple clang version 15.0.0 (clang-1500.0.40.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.0
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dimRed/DESCRIPTION’ ... OK
* this is package ‘dimRed’ version ‘0.2.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dimRed’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [31s/32s]
 [31s/32s] ERROR
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: 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
  2023-09-28 17:22:56.973544: Isomap START
  2023-09-28 17:22:56.973713: constructing knn graph
  2023-09-28 17:22:56.974935: calculating geodesic distances
  2023-09-28 17:22:56.980724: Classical Scaling
  2023-09-28 17:22:56.986097: Isomap START
  2023-09-28 17:22:56.986239: constructing knn graph
  2023-09-28 17:22:56.987388: calculating geodesic distances
  2023-09-28 17:22:56.993343: Classical Scaling
  2023-09-28 17:22:57.005142: Calculating kernel PCA
  2023-09-28 17:22:57.021255: Trying to calculate reverse
  2023-09-28 17:22:57.023578: DONE
  2023-09-28 17:22:57.024489: Calculating kernel PCA
  2023-09-28 17:22:57.03194: Trying to calculate reverse
  2023-09-28 17:22:57.034698: DONE
  2023-09-28 17:22:57.035703: Calculating kernel PCA
  2023-09-28 17:22:57.048855: Trying to calculate reverse
  No inverse function.
  2023-09-28 17:22:57.05135: DONE
  2023-09-28 17:22:57.05229: Calculating kernel PCA
  2023-09-28 17:22:57.063268: Trying to calculate reverse
  2023-09-28 17:22:57.06505: DONE
  2023-09-28 17:22:57.065938: Calculating kernel PCA
  2023-09-28 17:22:57.075793: Trying to calculate reverse
  2023-09-28 17:22:57.085385: DONE
  2023-09-28 17:22:57.086381: Calculating kernel PCA
  2023-09-28 17:22:57.09556: Trying to calculate reverse
  2023-09-28 17:22:57.100202: DONE
  2023-09-28 17:22:57.101096: Calculating kernel PCA
  2023-09-28 17:22:57.111949: Trying to calculate reverse
  2023-09-28 17:22:57.117871: DONE
  2023-09-28 17:22:57.118772: Calculating kernel PCA
  2023-09-28 17:22:57.131362: Trying to calculate reverse
  2023-09-28 17:22:57.143397: DONE
  2023-09-28 17:22:57.144253: Calculating kernel PCA
  2023-09-28 17:22:57.172502: Trying to calculate reverse
  No inverse function.
  2023-09-28 17:22:57.324417: DONE
  2023-09-28 17:22:57.327168: Calculating kernel PCA
  2023-09-28 17:22:57.377082: Trying to calculate reverse
  No inverse function.
  2023-09-28 17:22:57.502714: DONE
  [ FAIL 4 | WARN 11 | SKIP 7 | PASS 182 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • FastICA not available (1): 'test_fastICA.R:2:3'
  • 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'
  • umap-learn not available, install with `pip install umap-learn==0.4` (1):
    'test_UMAP.R:12:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_NNMF.R:105:3'): other arguments ──────────────────────────────
  dim_3_args@other.data$w (`actual`) not equal to `dim_3_rot` (`expected`).
  
  actual vs expected
                      [,1]         [,2]         [,3]
  - actual[1, ]   33.86881 2.220446e-16 2.220446e-16
  + expected[1, ] 11.62495 2.220446e-16 2.240198e+01
  - actual[2, ]   37.52666 2.958845e+01 1.976184e+01
  + expected[2, ] 31.25542 3.643579e+01 4.210810e+01
  - actual[3, ]   38.97432 5.482087e+01 4.372093e+01
  + expected[3, ] 50.88589 7.287158e+01 6.181422e+01
  - actual[4, ]   69.27110 1.369114e+02 1.289431e+01
  + expected[4, ] 70.51636 1.093074e+02 8.152034e+01
  - actual[5, ]   29.33830 8.058796e+01 1.154367e+02
  + expected[5, ] 90.14683 1.457432e+02 1.012265e+02
  ── Failure ('test_NNMF.R:106:3'): other arguments ──────────────────────────────
  getData(getDimRedData(dim_3_args)) (`actual`) not equal to `dim_3_pred` (`expected`).
  
  actual vs expected
                           [,1]       [,2]         [,3]
  - actual[1, ]    2.220446e-16 0.39921880 4.143205e-01
  + expected[1, ]  2.220446e-16 0.54891084 2.220446e-16
  - actual[2, ]    5.905139e-02 0.38264119 4.282111e-01
  + expected[2, ]  7.317427e-02 0.48173830 5.130585e-02
  - actual[3, ]    1.181028e-01 0.36606358 4.421018e-01
  + expected[3, ]  1.948635e-01 0.40204353 7.743607e-02
  - actual[4, ]    1.771542e-01 0.34948596 4.559924e-01
  + expected[4, ]  5.022464e-01 0.27441923 7.205177e-03
  - actual[5, ]    2.362056e-01 0.33290835 4.698830e-01
  + expected[5, ]  5.575179e-01 0.21186758 6.780121e-02
  - actual[6, ]    2.952569e-01 0.31633074 4.837737e-01
  + expected[6, ]  1.972195e-01 0.25657899 3.440469e-01
  - actual[7, ]    3.543083e-01 0.29975313 4.976643e-01
  + expected[7, ]  8.607848e-02 0.23698021 4.909986e-01
  - actual[8, ]    4.133597e-01 0.28317552 5.115549e-01
  + expected[8, ]  1.590949e-01 0.16984841 5.423864e-01
  - actual[9, ]    4.724111e-01 0.26659790 5.254456e-01
  + expected[9, ]  1.036687e-01 0.13586905 6.604263e-01
  - actual[10, ]   5.314625e-01 0.25002029 5.393362e-01
  + expected[10, ] 2.164839e-01 0.05846474 6.911614e-01
  ── Failure ('test_NNMF.R:132:3'): other arguments ──────────────────────────────
  `dim_3_apply` (`actual`) not equal to `dim_3_exp` (`expected`).
  
  actual vs expected
                        [,1]      [,2]        [,3]
  - actual[1, ]   0.02952569 0.3909300  0.42126582
  + expected[1, ] 0.11873045 0.4941225 -0.01697331
  - actual[2, ]   0.08857708 0.3743524  0.43515645
  + expected[2, ] 0.14408070 0.4392939  0.05914963
  - actual[3, ]   0.14762847 0.3577748  0.44904709
  + expected[3, ] 0.16943094 0.3844652  0.13527257
  ── Failure ('test_NNMF.R:133:3'): other arguments ──────────────────────────────
  `dim_3_pred` (`actual`) not equal to `dim_3_exp` (`expected`).
  
  actual vs expected
                        [,1]      [,2]        [,3]
  - actual[1, ]   0.02952569 0.3909300  0.42126582
  + expected[1, ] 0.11873045 0.4941225 -0.01697331
  - actual[2, ]   0.08857708 0.3743524  0.43515645
  + expected[2, ] 0.14408070 0.4392939  0.05914963
  - actual[3, ]   0.14762847 0.3577748  0.44904709
  + expected[3, ] 0.16943094 0.3844652  0.13527257
  
  [ FAIL 4 | WARN 11 | SKIP 7 | PASS 182 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/dimRed.Rcheck/00check.log’
for details.

       73.13 real        65.38 user         5.97 sys