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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > > library(testthat) > library(cograph) > > test_check("cograph") ================================================================ CENTRALITY EQUIVALENCE REPORT 100 random connected graphs per measure Sizes: 8, 12, 15, 20 | Densities: 0.3, 0.4, 0.5 Tolerance: 1e-08 ================================================================ radiality: PASS (100.0%, 0 failures, 0 errors) lin: PASS (100.0%, 0 failures, 0 errors) decay: PASS (100.0%, 0 failures, 0 errors) residual_closeness: PASS (100.0%, 0 failures, 0 errors) lobby: PASS (100.0%, 0 failures, 0 errors) barycenter: PASS (100.0%, 0 failures, 0 errors) bottleneck: PASS (100.0%, 0 failures, 0 errors) mnc: PASS (100.0%, 0 failures, 0 errors) average_distance: PASS (100.0%, 0 failures, 0 errors) closeness_vitality: PASS (100.0%, 0 failures, 0 errors) cross_clique: PASS (100.0%, 0 failures, 0 errors) semilocal: PASS (100.0%, 0 failures, 0 errors) clusterrank: PASS (100.0%, 0 failures, 0 errors) entropy: PASS (100.0%, 0 failures, 0 errors) markov: PASS (100.0%, 0 failures, 0 errors) topological_coefficient: PASS (100.0%, 0 failures, 0 errors) leverage: PASS (100.0%, 0 failures, 0 errors) diffusion: PASS (100.0%, 0 failures, 0 errors) laplacian: PASS (100.0%, 0 failures, 0 errors) kreach: PASS (100.0%, 0 failures, 0 errors) salsa (rank vs centiserve): r=-0.016 (n=100) [centiserve returns eigenvalues — bug] leaderrank: PASS (100.0%, 0 failures, 0 errors) stress: PASS (100.0%, 0 failures, 0 errors) flow_betweenness (rank vs sna): r=0.847 (n=100) gilschmidt: PASS (100.0%, 0 failures, 0 errors) load: PASS (100.0%, 0 failures, 0 errors) effective_size: PASS (100.0%, 0 failures, 0 errors) participation: PASS (100.0%, 0 failures, 0 errors) within_module_z: PASS (100.0%, 0 failures) gateway (brainGraph centr=degree): PASS (100.0%, 0 failures) diversity: PASS (100.0%, 0 failures) communicability (tidygraph): ERROR (0.0%, 0 failures) communicability_betweenness (tidygraph): ERROR (0.0%, 0 failures, n=50) integration (tidygraph): ERROR (0.0%, 0 failures) residual_closeness (tidygraph): ERROR (0.0%, 0 failures) dangalchev == residual_closeness: 100/100 passed generalized_closeness == decay(0.7): 100/100 passed communicability >= subgraph_centrality: 100/100 passed harary formula verification: 100/100 passed wiener formula verification: 100/100 passed expected formula verification: 100/100 passed random_walk finite & positive: 100/100 passed communicability_betweenness in [0,1]: 50/50 passed bridging formula verification: 100/100 passed local_bridging formula verification: 100/100 passed dmnc (rank vs centiserve): r=0.182 (n=95) [centiserve vertex ID mapping bug] ================================================================ EQUIVALENCE REPORT SUMMARY ================================================================ MEASURE STATUS PASS% FAIL ERROR MAX_DIFF ------------------------------ -------- ------ -------- -------- ---------- radiality PASS 100.0% 0 0 0 lin PASS 100.0% 0 0 0 decay PASS 100.0% 0 0 0 residual_closeness PASS 100.0% 0 0 0 lobby PASS 100.0% 0 0 0 barycenter PASS 100.0% 0 0 0 bottleneck PASS 100.0% 0 0 0 mnc PASS 100.0% 0 0 0 average_distance PASS 100.0% 0 0 0 closeness_vitality PASS 100.0% 0 0 0 cross_clique PASS 100.0% 0 0 0 semilocal PASS 100.0% 0 0 0 clusterrank PASS 100.0% 0 0 0 entropy PASS 100.0% 0 0 0 markov PASS 100.0% 0 0 0 topological_coefficient PASS 100.0% 0 0 0 leverage PASS 100.0% 0 0 0 diffusion PASS 100.0% 0 0 0 laplacian PASS 100.0% 0 0 0 kreach PASS 100.0% 0 0 0 salsa RANK r=-0.016 0 0 r=-0.016 leaderrank PASS 100.0% 0 0 0 stress PASS 100.0% 0 0 0 flow_betweenness RANK r=0.847 0 0 r=0.847 gilschmidt PASS 100.0% 0 0 0 load PASS 100.0% 0 0 0 effective_size PASS 100.0% 0 0 0 participation PASS 100.0% 0 0 0 within_module_z PASS 100.0% 0 0 0 gateway PASS 100.0% 0 0 0 diversity PASS 100.0% 0 0 0 communicability_tg ERROR 0.0% 0 100 0 comm_betweenness_tg ERROR 0.0% 0 50 0 integration_tg ERROR 0.0% 0 100 0 residual_closeness_tg ERROR 0.0% 0 100 0 dmnc RANK r=0.182 0 0 r=0.182 ------------------------------ -------- ------ -------- -------- ---------- TOTAL PASS 90.1% 0 350 Graphs tested: 100 per measure (3550 total comparisons) Node counts per comparison: 8, 12, 15, 20 ================================================================ centiserve equivalence: 160 tests, 0 failures sna stress equivalence: 20 tests, 0 failures sna gilschmidt equivalence: 20 tests, 0 failures influenceR effective_size equivalence: 20 tests, 0 failures gravity formula: 100/100 passed collective_influence formula: 100/100 passed infection vs betweenness: r=0.548 nonbacktracking vs eigenvector: r=0.909 Zoo batch 2 measures: 12 Cograph Network Summary ====================== Structure: Nodes: 3 Edges: 3 Type: Undirected Edge Statistics: Min weight: 1 Max weight: 1 Mean weight: 1 Node Labels: 1, 2, 3 Layout: not computed Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b424c35f58.svg Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b43a8a564.jpeg Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b41288441b.tiff Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b419ec2a5d.pdf Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b41ff27fb.png Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b453ff239b.png === Cluster Metrics Coverage Tests Complete === Using 'clusters' column for clusters === Cluster Metrics Coverage Tests 41 Complete === === All Community Detection Tests Passed === Community structure (louvain) Nodes: 5 | Communities: 2 | Modularity: 0.1111 Sizes: 3, 2 node community N1 1 N2 1 N3 1 N4 2 N5 2 === All Community Detection Coverage Tests (Series 41) Passed === Cograph network: 3 nodes, 2 edges ( undirected ) Nodes (3): A, B, C Weights: 1 (all equal) Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Nodes (3): A, B, C Weights: 1 (all equal) Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Nodes (3): A, B, C Weights: 1 (all equal) Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Nodes (3): A, B, C Weights: 0.5 to 0.8 Layout: set Cograph network: 3 nodes, 0 edges ( undirected ) Nodes (3): A, B, C Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Source: matrix Nodes (3): A, B, C Weights: 1 (all equal) Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Data: data.frame (3 x 1) Nodes (3): A, B, C Weights: 1 (all equal) Layout: set Cograph network: 3 nodes, 2 edges ( undirected ) Nodes (3): A, B, C Weights: 1 (all equal) Layout: none Using 'layer' column for layers No motifs to plot. Try show_nonsig = TRUE 'tna' package version 1.2.0 ------------------------------------------------------ Tikka, S., López-Pernas, S., and Saqr, M. (2025). tna: An R Package for Transition Network Analysis. Applied Psychological Measurement. https://doi.org/10.1177/01466216251348840 ------------------------------------------------------ Please type 'citation("tna")' for more citation information. See the package website at https://sonsoles.me/tna/ Attaching package: 'tna' The following objects are masked from 'package:cograph': communities, plot_compare The following object is masked from 'package:testthat': compare Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b456112ac1.eps Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b47e5e2e49.ps No edges to display No edges to display No edges to display No edges to display Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b43caa480b.svg Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b46a97d18.jpg Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b47b20a1c.tiff Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Start tag expected, '<' not found Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b456f65f72.png Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b4648b6088.png Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b427bf3edd.png Saved to: D:\temp\2026_04_14_16_55_17_20789\Rtmp827ns0\file183b47df36651.png [ FAIL 0 | WARN 76 | SKIP 103 | PASS 12281 ] ══ Skipped tests (103) ═════════════════════════════════════════════════════════ • Cannot easily test package unavailability (1): 'test-coverage-input-statnet-41.R:46:3' • Cannot test missing ggplot2 when ggplot2 is required for testing (1): 'test-coverage-plot-heatmap-40.R:45:3' • Empty networks require special handling in network_to_igraph (1): 'test-coverage-layout-registry-41.R:524:3' • NetworkX not available (18): 'test-centrality-batch3.R:84:3', 'test-centrality-batch3.R:239:3', 'test-centrality-batch3.R:250:3', 'test-centrality-batch3.R:275:3', 'test-centrality-batch3.R:462:3', 'test-centrality-batch3.R:504:3', 'test-centrality-batch3.R:531:3', 'test-centrality-batch3.R:558:3', 'test-centrality-batch3.R:661:3', 'test-centrality-batch3.R:680:3', 'test-centrality-batch3.R:711:3', 'test-centrality-extended.R:729:3', 'test-centrality-extended.R:751:3', 'test-centrality-extended.R:774:3', 'test-centrality-extended.R:796:3', 'test-centrality-zoo.R:47:3', 'test-centrality-zoo.R:96:3', 'test-centrality-zoo.R:253:3' • On CRAN (54): 'test-assortativity.R:1:1', 'test-build-mcml.R:8:1', 'test-centrality.R:3:1', 'test-cluster-metrics.R:8:1', 'test-disparity.R:3:1', 'test-edge-cases.R:271:3', 'test-edge-cases.R:401:3', 'test-edge-cases.R:411:3', 'test-edge-cases.R:557:3', 'test-edge-cases.R:571:3', 'test-edge-cases.R:589:3', 'test-equiv-assortativity.R:11:1', 'test-equiv-cluster-quality.R:10:1', 'test-equiv-communities.R:11:1', 'test-equiv-disparity.R:13:1', 'test-equiv-edge-centrality.R:11:1', 'test-equiv-network-summary.R:10:1', 'test-equiv-robustness.R:12:1', 'test-equiv-standalone-measures.R:9:1', 'test-from-converters.R:8:1', 'test-integration.R:456:3', 'test-layout-spring-animation.R:8:1', 'test-layouts-extended.R:8:1', 'test-motifs-api.R:4:1', 'test-motifs-equivalence.R:10:1', 'test-network-summary.R:3:1', 'test-overlay-communities.R:4:1', 'test-palettes.R:8:1', 'test-plot-chord.R:1:1', 'test-plot-compare.R:385:3', 'test-plot-forest.R:1:1', 'test-plot-mixed-network.R:313:3', 'test-plot-simplicial.R:7:1', 'test-qgraph-args.R:8:1', 'test-rich-club-equivalence.R:8:1', 'test-robustness.R:9:1', 'test-shapes.R:1:1', 'test-simplify.R:3:1', 'test-sn-edges.R:8:1', 'test-sn-nodes.R:8:1', 'test-sn-save.R:31:3', 'test-sn-save.R:89:3', 'test-sn-save.R:113:3', 'test-sn-save.R:492:3', 'test-soplot.R:8:1', 'test-splot.R:627:3', 'test-splot.R:725:3', 'test-themes-extended.R:8:1', 'test-tier2-cross-package.R:14:1', 'test-tier2-equivalence.R:9:1', 'test-tier2-features.R:4:1', 'test-tna-integration.R:4:1', 'test-tna-temporal.R:273:3', 'test-validate-nestimate-bootstrap-permutation.R:10:1' • PS device not available (1): 'test-coverage-100pct.R:440:13' • Package availability guards — untestable when packages installed (1): 'test-coverage-round7.R:832:3' • PostScript device has font issues on this system (4): 'test-coverage-output-save-41.R:82:3', 'test-coverage-output-save-41.R:106:3', 'test-coverage-output-save-41.R:134:3', 'test-coverage-output-save-41.R:158:3' • Real TNA bootstrap objects have different structure - covered by mock tests (9): 'test-coverage-plot-bootstrap-40.R:500:3', 'test-coverage-plot-bootstrap-40.R:505:3', 'test-coverage-plot-bootstrap-40.R:510:3', 'test-coverage-plot-bootstrap-40.R:515:3', 'test-coverage-plot-bootstrap-40.R:520:3', 'test-coverage-plot-bootstrap-40.R:525:3', 'test-coverage-plot-bootstrap-40.R:530:3', 'test-coverage-plot-bootstrap-40.R:535:3', 'test-coverage-plot-bootstrap-40.R:834:3' • Skipping - themes may be registered by other tests with different classes (1): 'test-coverage-zzz-41.R:360:3' • cograph does not support 0-node networks (1): 'test-coverage-methods-plot-42.R:271:5' • digest is always available — lines 202-203 are package guards (1): 'test-coverage-round7.R:507:3' • empty test (3): 'test-coverage-motifs-40.R:363:1', 'test-coverage-motifs-40.R:545:1', 'test-coverage-round5.R:1972:1' • grImport2 cannot parse this SVG - skipping gTree test (1): 'test-coverage-shapes-svg-41.R:599:5' • grImport2 is installed - skipping missing package test (1): 'test-coverage-shapes-svg-41.R:354:5' • grImport2 is installed - testing fallback behavior (1): 'test-coverage-shapes-svg-41.R:442:5' • plot method requires splot integration testing (1): 'test-coverage-communities-40.R:721:3' • requireNamespace("network", quietly = TRUE) is TRUE (1): 'test-coverage-network-utils-40.R:593:3' • rsvg is installed - testing fallback behavior (1): 'test-coverage-shapes-svg-41.R:664:5' • {svglite} is not installed (1): 'test-coverage-output-save-43.R:240:3' [ FAIL 0 | WARN 76 | SKIP 103 | PASS 12281 ] > > proc.time() user system elapsed 833.17 99.98 965.64