* using log directory ‘/Users/ripley/R/packages/tests-devel/dimRed.Rcheck’ * using R Under development (unstable) (2024-03-27 r86215) * using platform: aarch64-apple-darwin23.4.0 * R was compiled by Apple clang version 15.0.0 (clang-1500.3.9.4) GNU Fortran (GCC) 12.2.0 * running under: macOS Sonoma 14.4.1 * 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 code 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 ... NOTE checkRd: (-1) DRR-class.Rd:79: Lost braces; missing escapes or markup? 79 | n^{1/3} up to sacrificing some accuracy, for details see | ^ * 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’ [29s/29s] [29s/29s] 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 2024-03-27 14:02:31.418346: Isomap START 2024-03-27 14:02:31.418496: constructing knn graph 2024-03-27 14:02:31.419653: calculating geodesic distances 2024-03-27 14:02:31.424605: Classical Scaling 2024-03-27 14:02:31.429973: Isomap START 2024-03-27 14:02:31.430093: constructing knn graph 2024-03-27 14:02:31.431257: calculating geodesic distances 2024-03-27 14:02:31.436914: Classical Scaling 2024-03-27 14:02:31.447422: Calculating kernel PCA 2024-03-27 14:02:31.462894: Trying to calculate reverse 2024-03-27 14:02:31.465256: DONE 2024-03-27 14:02:31.466197: Calculating kernel PCA 2024-03-27 14:02:31.473578: Trying to calculate reverse 2024-03-27 14:02:31.476359: DONE 2024-03-27 14:02:31.477344: Calculating kernel PCA 2024-03-27 14:02:31.483477: Trying to calculate reverse No inverse function. 2024-03-27 14:02:31.485723: DONE 2024-03-27 14:02:31.486564: Calculating kernel PCA 2024-03-27 14:02:31.496151: Trying to calculate reverse 2024-03-27 14:02:31.497869: DONE 2024-03-27 14:02:31.498779: Calculating kernel PCA 2024-03-27 14:02:31.508428: Trying to calculate reverse 2024-03-27 14:02:31.513234: DONE 2024-03-27 14:02:31.514104: Calculating kernel PCA 2024-03-27 14:02:31.52324: Trying to calculate reverse 2024-03-27 14:02:31.528042: DONE 2024-03-27 14:02:31.528964: Calculating kernel PCA 2024-03-27 14:02:31.539882: Trying to calculate reverse 2024-03-27 14:02:31.546021: DONE 2024-03-27 14:02:31.546961: Calculating kernel PCA 2024-03-27 14:02:31.55986: Trying to calculate reverse 2024-03-27 14:02:31.572045: DONE 2024-03-27 14:02:31.572934: Calculating kernel PCA 2024-03-27 14:02:31.609545: Trying to calculate reverse No inverse function. 2024-03-27 14:02:31.766113: DONE 2024-03-27 14:02:31.770642: Calculating kernel PCA 2024-03-27 14:02:31.818447: Trying to calculate reverse No inverse function. 2024-03-27 14:02:31.946252: 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 ... 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, 1 NOTE See ‘/Users/ripley/R/packages/tests-devel/dimRed.Rcheck/00check.log’ for details. 71.69 real 63.98 user 5.18 sys