* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/TreeDist.Rcheck’ * using R Under development (unstable) (2025-10-10 r88914) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘TreeDist/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TreeDist’ version ‘2.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘TreeDistData’ * 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 ‘TreeDist’ can be installed ... [107s/115s] OK * used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * checking C++ specification ... 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 ... [24s/29s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... 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 ‘spelling.R’ Running ‘testthat.R’ [38s/50s] [39s/52s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library("testthat", warn.conflicts = FALSE) > library("TreeDist") > > test_check("TreeDist") Loading required package: ape [ FAIL 1 | WARN 0 | SKIP 7 | PASS 1499 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-HPart.R:67:3', 'test-MSTSegments.R:4:3', 'test-Plot3.R:6:3', 'test-VisualizeMatching.R:21:3', 'test-VisualizeMatching.R:137:3', 'test-plot.R:30:3' • goingQuickly is TRUE (1): 'test-tree_distance_nni.R:25:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-spectral_clustering.R:13:3'): Spectral clustering works ────── SpectralClustering(d, nEig = Inf) (`actual`) not equal to `allEig` (`expected`). actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] - actual[1, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -5.154712e-02 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 5.091990e-01 7.559052e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.563830e-16 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[1, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 6.408770e-02 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 8.852547e-01 0.000000e+00 0.000000e+00 2.134249e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -3.174740e-16 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[2, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 1.151553e-01 0.000000e+00 2.486073e-01 -4.190432e-01 0.000000e+00 0.000000e+00 0.000000e+00 -2.115802e-01 1.191543e-01 0.000000e+00 0.000000e+00 -8.704826e-02 0.000000e+00 2.041259e-01 -1.147019e-01 -1.717954e-01 0.000000e+00 -6.571079e-01 0.000000e+00 0.000000e+00 4.701833e-15 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[2, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 -7.370795e-01 -5.938931e-02 0.000000e+00 0.000000e+00 1.848662e-02 1.711689e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.387658e-01 -1.207545e-01 -7.158372e-02 -2.444797e-01 -5.871108e-02 0.000000e+00 0.000000e+00 3.933197e-01 0.000000e+00 8.212280e-15 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[3, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 -3.109598e-01 0.000000e+00 -5.480230e-01 -1.696803e-01 0.000000e+00 0.000000e+00 0.000000e+00 5.714856e-02 9.571799e-02 0.000000e+00 0.000000e+00 4.200441e-01 0.000000e+00 -4.147262e-01 -1.861241e-01 -1.066787e-01 0.000000e+00 -2.512863e-02 0.000000e+00 0.000000e+00 3.027558e-15 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[3, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 -3.182965e-01 9.680370e-02 0.000000e+00 0.000000e+00 -1.204635e-01 -3.175200e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -2.770617e-01 -1.465257e-01 1.105115e-01 2.150824e-01 -7.756906e-02 0.000000e+00 0.000000e+00 -6.667804e-01 0.000000e+00 1.122504e-15 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[4, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 1.183755e-01 0.000000e+00 -2.527937e-02 -3.504315e-02 0.000000e+00 0.000000e+00 0.000000e+00 1.566063e-01 -1.087534e-01 0.000000e+00 0.000000e+00 -1.888998e-01 0.000000e+00 5.448075e-02 5.429511e-01 -5.886230e-01 0.000000e+00 3.180824e-01 0.000000e+00 0.000000e+00 4.091026e-16 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[4, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 3.461176e-01 4.021624e-01 0.000000e+00 0.000000e+00 -2.234634e-01 -3.267276e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 7.618284e-02 -3.107710e-01 1.211045e-01 -1.659259e-01 4.041843e-01 0.000000e+00 0.000000e+00 2.952446e-01 0.000000e+00 5.504163e-17 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[5, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 -4.348944e-02 0.000000e+00 3.851639e-01 -1.716479e-01 0.000000e+00 0.000000e+00 0.000000e+00 8.243280e-02 -1.297674e-01 0.000000e+00 0.000000e+00 -4.716203e-02 0.000000e+00 1.056828e-01 -5.440578e-01 1.343013e-01 0.000000e+00 5.500584e-01 0.000000e+00 0.000000e+00 -8.791683e-17 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[5, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 3.750467e-01 1.680265e-02 0.000000e+00 0.000000e+00 5.704705e-03 3.755768e-02 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 7.319736e-02 -1.872249e-02 -2.850134e-02 3.968622e-02 -8.158767e-01 0.000000e+00 0.000000e+00 1.311386e-01 0.000000e+00 -4.173006e-15 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[6, ] 0.000000e+00 -1.289944e-01 0.0000000 -0.0140666 0.00000000 -0.13826609 0.000000e+00 2.375951e-02 0.000000e+00 1.209183e-01 0.000000e+00 -6.046891e-02 8.469617e-01 0.000000e+00 0.000000e+00 0.000000e+00 -8.460743e-02 2.364848e-02 0.000000e+00 0.000000e+00 -9.693396e-02 0.000000e+00 5.043668e-02 -2.072662e-01 -2.310937e-02 0.000000e+00 -1.859042e-01 0.000000e+00 0.000000e+00 -6.695165e-15 0.00000000 -0.01988788 0.000000e+00 4.990623e-02 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 + expected[6, ] -1.289944e-01 0.000000e+00 -0.0140666 0.0000000 0.00000000 -0.13826609 2.375951e-02 0.000000e+00 0.000000e+00 2.701239e-01 -4.563794e-01 0.000000e+00 0.000000e+00 3.197356e-01 4.355211e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.108432e-02 -2.884809e-01 -1.315310e-01 1.556369e-01 3.345477e-01 0.000000e+00 0.000000e+00 -1.529225e-01 0.000000e+00 -3.568607e-15 0.00000000 -0.01988788 4.990623e-02 0.000000e+00 0.0000000 -0.1419301 -2.522670e-01 0.000000e+00 -0.2085144 0.0000000 - actual[7, ] 0.000000e+00 1.766599e-01 0.0000000 -0.4941883 0.00000000 0.18919881 0.000000e+00 -4.353399e-01 0.000000e+00 -3.018419e-16 0.000000e+00 -8.187895e-16 4.565792e-15 0.000000e+00 0.000000e+00 0.000000e+00 5.551115e-16 -6.002143e-16 0.000000e+00 0.000000e+00 4.996004e-16 0.000000e+00 -9.228729e-16 -2.386980e-15 1.901257e-15 0.000000e+00 3.219647e-15 0.000000e+00 0.000000e+00 -5.131688e-16 0.00000000 0.39376830 0.000000e+00 -4.777667e-01 0.0000000 0.1307752 -2.258526e-01 0.000000e+00 -0.2186918 0.0000000 + expected[7, ] 1.766599e-01 0.000000e+00 -0.4941883 0.0000000 0.00000000 0.18919881 -4.353399e-01 0.000000e+00 0.000000e+00 -2.969847e-15 -1.127570e-16 0.000000e+00 0.000000e+00 -3.122502e-17 5.620504e-16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.498002e-16 3.469447e-16 -2.949030e-16 -4.787837e-16 -1.394718e-15 0.000000e+00 0.000000e+00 4.163336e-16 0.000000e+00 9.091341e-16 0.00000000 0.39376830 -4.777667e-01 0.000000e+00 0.0000000 0.1307752 -2.258526e-01 0.000000e+00 -0.2186918 0.0000000 - actual[8, ] 0.000000e+00 3.937954e-01 0.0000000 -0.1939950 0.00000000 0.06564936 0.000000e+00 5.063728e-01 0.000000e+00 -1.249001e-16 0.000000e+00 1.040834e-15 -4.884981e-15 0.000000e+00 0.000000e+00 0.000000e+00 -1.075529e-15 8.257284e-16 0.000000e+00 0.000000e+00 1.977585e-16 0.000000e+00 6.522560e-16 -8.326673e-16 3.885781e-16 0.000000e+00 -3.747003e-15 0.000000e+00 0.000000e+00 1.494274e-15 0.00000000 -0.52279241 0.000000e+00 -2.223560e-01 0.0000000 0.3641020 -1.976604e-01 0.000000e+00 -0.2284161 0.0000000 + expected[8, ] 3.937954e-01 0.000000e+00 -0.1939950 0.0000000 0.00000000 0.06564936 5.063728e-01 0.000000e+00 0.000000e+00 2.969847e-15 3.382711e-16 0.000000e+00 0.000000e+00 -3.365364e-16 -1.561251e-15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.096345e-15 -4.440892e-16 5.828671e-16 2.060851e-15 -1.120631e-15 0.000000e+00 0.000000e+00 -3.066991e-15 0.000000e+00 -1.171805e-15 0.00000000 -0.52279241 -2.223560e-01 0.000000e+00 0.0000000 0.3641020 -1.976604e-01 0.000000e+00 -0.2284161 0.0000000 - actual[9, ] 0.000000e+00 4.624706e-01 0.0000000 0.3646738 0.00000000 -0.18404474 0.000000e+00 -2.251193e-01 0.000000e+00 -3.469447e-18 0.000000e+00 3.469447e-17 7.632783e-16 0.000000e+00 0.000000e+00 0.000000e+00 -1.040834e-16 7.285839e-17 0.000000e+00 0.000000e+00 8.326673e-17 0.000000e+00 1.318390e-16 -6.938894e-17 6.938894e-17 0.000000e+00 2.498002e-16 0.000000e+00 0.000000e+00 -1.333140e-15 0.00000000 0.26275291 0.000000e+00 4.553603e-01 0.0000000 0.4556092 -1.675985e-01 0.000000e+00 -0.2377430 0.0000000 + expected[9, ] 4.624706e-01 0.000000e+00 0.3646738 0.0000000 0.00000000 -0.18404474 -2.251193e-01 0.000000e+00 0.000000e+00 -1.276756e-15 -9.540979e-16 0.000000e+00 0.000000e+00 4.163336e-16 1.415534e-15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 3.608225e-16 -6.383782e-16 -4.753142e-16 -9.645063e-16 5.863365e-16 0.000000e+00 0.000000e+00 9.992007e-16 0.000000e+00 5.454002e-16 0.00000000 0.26275291 4.553603e-01 0.000000e+00 0.0000000 0.4556092 -1.675985e-01 0.000000e+00 -0.2377430 0.0000000 - actual[10, ] 0.000000e+00 -8.777701e-16 0.0000000 0.2897752 0.00000000 0.55795738 0.000000e+00 6.838714e-15 0.000000e+00 1.273287e-15 0.000000e+00 -7.147061e-16 -2.553513e-15 0.000000e+00 0.000000e+00 0.000000e+00 -1.186551e-15 1.332268e-15 0.000000e+00 0.000000e+00 4.267420e-16 0.000000e+00 -1.575129e-15 1.804112e-16 -1.942890e-16 0.000000e+00 -1.956768e-15 0.000000e+00 0.000000e+00 -7.071068e-01 0.00000000 -0.01491176 0.000000e+00 -1.613293e-16 0.0000000 -0.1479286 -5.551115e-16 0.000000e+00 -0.2874173 0.0000000 + expected[10, ] 5.438358e-16 0.000000e+00 0.2897752 0.0000000 0.00000000 0.55795738 6.331741e-17 0.000000e+00 0.000000e+00 -7.799317e-15 1.783296e-15 0.000000e+00 0.000000e+00 -1.226449e-15 -1.963707e-15 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.252470e-15 9.714451e-17 7.736867e-16 -9.853229e-16 1.856154e-15 0.000000e+00 0.000000e+00 2.428613e-15 0.000000e+00 -7.071068e-01 0.00000000 -0.01491176 1.006140e-16 0.000000e+00 0.0000000 -0.1479286 -6.383782e-16 0.000000e+00 -0.2874173 0.0000000 and 30 more ... Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-spectral_clustering.R:13:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─testthat::expect_equal(SpectralClustering(d, nEig = Inf), allEig) [ FAIL 1 | WARN 0 | SKIP 7 | PASS 1499 ] Deleting unused snapshots: • Plot3/plotting-order.svg • VisualizeMatching/hidden-edge-labels.svg • VisualizeMatching/jrf-vm-matchzeros-false.svg • VisualizeMatching/rf-collapse-a-node.svg • VisualizeMatching/rf-collapse-and-change.svg • VisualizeMatching/rf-vm-single-splits-plainedges.svg • VisualizeMatching/test-vmr.svg • VisualizeMatching/visualize-mci-matching.svg • VisualizeMatching/vm-one-rooted.svg • plot/test-lc-letters.svg • plot/test-uc-letters.svg • plot/test-without-space.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [172s/225s] OK * checking PDF version of manual ... [11s/13s] OK * checking HTML version of manual ... [6s/10s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-MKL/TreeDist.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 9:06.10, 399.60 + 31.04