* using log directory ‘/Users/ripley/R/packages/tests-Accelerate/dimRed.Rcheck’ * using R Under development (unstable) (2023-09-15 r85152) * using platform: aarch64-apple-darwin22.6.0 * R was compiled by Apple clang version 15.0.0 (clang-1500.0.40.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.5.2 * 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’ [32s/32s] [32s/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 2023-09-16 05:51:49.579567: Isomap START 2023-09-16 05:51:49.579726: constructing knn graph 2023-09-16 05:51:49.580954: calculating geodesic distances 2023-09-16 05:51:49.586841: Classical Scaling 2023-09-16 05:51:49.592692: Isomap START 2023-09-16 05:51:49.592849: constructing knn graph 2023-09-16 05:51:49.594169: calculating geodesic distances 2023-09-16 05:51:49.600439: Classical Scaling 2023-09-16 05:51:49.610847: Calculating kernel PCA 2023-09-16 05:51:49.623642: Trying to calculate reverse 2023-09-16 05:51:49.625311: DONE 2023-09-16 05:51:49.626182: Calculating kernel PCA 2023-09-16 05:51:49.631073: Trying to calculate reverse 2023-09-16 05:51:49.63284: DONE 2023-09-16 05:51:49.633697: Calculating kernel PCA 2023-09-16 05:51:49.638212: Trying to calculate reverse No inverse function. 2023-09-16 05:51:49.639941: DONE 2023-09-16 05:51:49.64077: Calculating kernel PCA 2023-09-16 05:51:49.649477: Trying to calculate reverse 2023-09-16 05:51:49.650885: DONE 2023-09-16 05:51:49.651755: Calculating kernel PCA 2023-09-16 05:51:49.659017: Trying to calculate reverse 2023-09-16 05:51:49.662571: DONE 2023-09-16 05:51:49.663506: Calculating kernel PCA 2023-09-16 05:51:49.670958: Trying to calculate reverse 2023-09-16 05:51:49.674438: DONE 2023-09-16 05:51:49.675364: Calculating kernel PCA 2023-09-16 05:51:49.684833: Trying to calculate reverse 2023-09-16 05:51:49.691301: DONE 2023-09-16 05:51:49.692208: Calculating kernel PCA 2023-09-16 05:51:49.703044: Trying to calculate reverse 2023-09-16 05:51:49.714888: DONE 2023-09-16 05:51:49.715908: Calculating kernel PCA 2023-09-16 05:51:49.741212: Trying to calculate reverse No inverse function. 2023-09-16 05:51:49.899368: DONE 2023-09-16 05:51:49.902049: Calculating kernel PCA 2023-09-16 05:51:49.94829: Trying to calculate reverse No inverse function. 2023-09-16 05:51:50.072606: 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, ] 2.220446e-16 2.220446e-16 28.13975 + expected[1, ] 1.162495e+01 2.220446e-16 22.40198 - actual[2, ] 3.648156e+01 1.882895e+01 37.68898 + expected[2, ] 3.125542e+01 3.643579e+01 42.10810 - actual[3, ] 7.296311e+01 3.765791e+01 47.23820 + expected[3, ] 5.088589e+01 7.287158e+01 61.81422 - actual[4, ] 1.094447e+02 5.648686e+01 56.78742 + expected[4, ] 7.051636e+01 1.093074e+02 81.52034 - actual[5, ] 1.459262e+02 7.531581e+01 66.33665 + expected[5, ] 9.014683e+01 1.457432e+02 101.22646 ── 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, ] 3.165063e-01 0.44895533 2.220446e-16 + expected[1, ] 2.220446e-16 0.54891084 2.220446e-16 - actual[2, ] 3.297361e-01 0.38727671 7.107383e-02 + expected[2, ] 7.317427e-02 0.48173830 5.130585e-02 - actual[3, ] 3.575894e-01 0.29726475 1.421477e-01 + expected[3, ] 1.948635e-01 0.40204353 7.743607e-02 - actual[4, ] 2.902082e-01 0.39177181 2.132215e-01 + expected[4, ] 5.022464e-01 0.27441923 7.205177e-03 - actual[5, ] 3.350848e-01 0.26877673 2.842953e-01 + expected[5, ] 5.575179e-01 0.21186758 6.780121e-02 - actual[6, ] 4.040365e-01 0.09913555 3.553692e-01 + expected[6, ] 1.972195e-01 0.25657899 3.440469e-01 - actual[7, ] 1.306261e-02 0.82061151 4.264430e-01 + expected[7, ] 8.607848e-02 0.23698021 4.909986e-01 - actual[8, ] 3.479180e-01 0.13577555 4.975168e-01 + expected[8, ] 1.590949e-01 0.16984841 5.423864e-01 - actual[9, ] 3.377478e-01 0.11943506 5.685907e-01 + expected[9, ] 1.036687e-01 0.13586905 6.604263e-01 - actual[10, ] 2.574806e-01 0.23890904 6.396645e-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, ] 0.4255589 0.2196405 0.03553692 + expected[1, ] 0.1187305 0.4941225 -0.01697331 - actual[2, ] 0.4108683 0.2120584 0.10661075 + expected[2, ] 0.1440807 0.4392939 0.05914963 - actual[3, ] 0.3961777 0.2044762 0.17768458 + expected[3, ] 0.1694309 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, ] 0.4255589 0.2196405 0.03553692 + expected[1, ] 0.1187305 0.4941225 -0.01697331 - actual[2, ] 0.4108683 0.2120584 0.10661075 + expected[2, ] 0.1440807 0.4392939 0.05914963 - actual[3, ] 0.3961777 0.2044762 0.17768458 + expected[3, ] 0.1694309 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-Accelerate/dimRed.Rcheck/00check.log’ for details. 72.18 real 65.64 user 5.45 sys