* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/Nestimate.Rcheck’ * using R Under development (unstable) (2026-07-10 r90234) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-07-11 07:18:07 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘Nestimate/DESCRIPTION’ ... OK * this is package ‘Nestimate’ version ‘0.8.0’ * 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 ‘Nestimate’ can be installed ... [59s/78s] 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 whether startup messages can be suppressed ... 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 ... [147s/195s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [37s/45s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [220s/224s] [220s/225s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Nestimate) > > test_check("Nestimate") Hypergraph: 5 nodes, 3 hyperedges Size distribution: size_2 : 1 size_3 : 2 Hypergraph summary Nodes: 5 Hyperedges: 3 Mean size: 2.67 Max size: 3 Chain structure -- 2 groups: g1, g2 --- g1 --- Chain structure [3 states, 1 communicating classes] irreducible: TRUE aperiodic: FALSE regular: FALSE reversible: FALSE recurrent classes: 1 transient classes: 0 Use summary(x) for the per-state table, plot(x) for the heatmap. --- g2 --- Chain structure [3 states, 1 communicating classes] irreducible: TRUE aperiodic: FALSE regular: FALSE reversible: FALSE recurrent classes: 1 transient classes: 0 Use summary(x) for the per-state table, plot(x) for the heatmap. Dropping 2 single-observation rows (within-person centering). mlVAR result: 12 subjects, 324 observations, 4 variables (lag 1) $temporal 4 x 4 directed (8/16 edges significant at p<0.05) $contemporaneous 4 x 4 undirected $between 4 x 4 undirected Access: fit$temporal, fit$contemporaneous, fit$between (each a netobject); coefs(fit) for tidy coefs. Mixed Markov Model Sequences: 30 | Clusters: 2 | States: 5 ICs: LL = -453.186 | BIC = 1073.032 | AIC = 1004.373 | ICL = 1073.781 Quality: AvePP = 0.988 | Entropy = 0.054 | Class.Err = 0.0% Status: did not converge in 20 iterations Cluster N Mix% AvePP 1 19 (63.3%) 62.8% 0.987 2 11 (36.7%) 37.2% 0.991 --- Cluster 1 (62.8%, n=19) --- A B C D E A 0.174 0.145 0.144 0.076 0.461 B 0.198 0.156 0.384 0.163 0.100 C 0.144 0.315 0.210 0.101 0.230 D 0.119 0.000 0.301 0.347 0.234 E 0.238 0.233 0.267 0.134 0.127 --- Cluster 2 (37.2%, n=11) --- A B C D E A 0.278 0.133 0.135 0.356 0.097 B 0.180 0.197 0.076 0.366 0.180 C 0.453 0.001 0.174 0.194 0.178 D 0.151 0.344 0.047 0.154 0.304 E 0.042 0.173 0.162 0.409 0.214 Mixed Markov Model Sequences: 30 | Clusters: 2 | States: 5 ICs: LL = -453.186 | BIC = 1073.032 | AIC = 1004.373 | ICL = 1073.781 Quality: AvePP = 0.988 | Entropy = 0.054 | Class.Err = 0.0% Status: did not converge in 20 iterations Cluster N Mix% AvePP 1 19 (63.3%) 62.8% 0.987 2 11 (36.7%) 37.2% 0.991 --- Cluster 1 (62.8%, n=19) --- A B C D E A 0.174 0.145 0.144 0.076 0.461 B 0.198 0.156 0.384 0.163 0.100 C 0.144 0.315 0.210 0.101 0.230 D 0.119 0.000 0.301 0.347 0.234 E 0.238 0.233 0.267 0.134 0.127 --- Cluster 2 (37.2%, n=11) --- A B C D E A 0.278 0.133 0.135 0.356 0.097 B 0.180 0.197 0.076 0.366 0.180 C 0.453 0.001 0.174 0.194 0.178 D 0.151 0.344 0.047 0.154 0.304 E 0.042 0.173 0.162 0.409 0.214 Higher-Order Network (HON) Summary Nodes: 18 | Edges: 59 | Trajectories: 40 First-order states: Ask, Delegate, Execute, Explain, Investigate, Plan, Repair, Report Max order observed: 2 (requested: 2) Min frequency: 1 Node order distribution: Order 1: 8 nodes Order 2: 10 nodes Multi-Order Generative Model (MOGen) Summary States: Ask, Delegate, Execute, Explain, Investigate, Plan, Repair, Report Paths: 40 | Observations: 429 Best by AIC: order 2 | Best by BIC: order 0 Selected: order 2 (by aic) HONEM Summary Nodes: 18 | Dimensions: 2 Variance explained: 69.6% Top singular values: 1.853, 1.075 Embedding range: [-0.557, 0.570] centralities computed excluding loops (diagonal). Pass `loops = TRUE` to include self-transitions. centralities computed excluding loops (diagonal). Pass `loops = TRUE` to include self-transitions. centralities computed excluding loops (diagonal). Pass `loops = TRUE` to include self-transitions. centralities computed excluding loops (diagonal). Pass `loops = TRUE` to include self-transitions. Hypergraph: 6 nodes, 8 hyperedges Size distribution: size_2 : 6 size_3 : 2 Method: clique, p = 1.00, include_pairwise = TRUE, max_size = 3 Hypergraph summary Nodes: 6 Hyperedges: 8 Mean size: 2.25 Max size: 3 Hypergraph: 3 nodes, 0 hyperedges Method: clique, p = 1.00, include_pairwise = FALSE, max_size = 3 Hypergraph summary Nodes: 3 Hyperedges: 0 Hypergraph measures: 4 nodes, 2 hyperedges Density: 0.5000 Mean edge size: 3.00 Pairwise participation: 0.8333 Hyperdegree: min=1 med=1.5 max=2 Node strength: min=3.0 med=4.5 max=6.0 Edge sizes: min=3 med=3.0 max=3 Intersection profile (pair counts by overlap size): overlap_2 : 1 Hypergraph measures: 2 nodes, 0 hyperedges Density: 0.0000 Mean edge size: NA Pairwise participation: 0.0000 Hyperdegree: min=0 med=0.0 max=0 Node strength: min=0.0 med=0.0 max=0.0 Metadata aggregated per session: ties resolved by first occurrence in 'code' (99 sessions) magnitude_difference object metric: abs_diff scale: tna_range states (9): adapt, cohesion, consensus, coregulate, discuss, emotion, monitor, plan, synthesis edges: 81 magnitude-difference summary (abs_diff): Min. 1st Qu. Median Mean 3rd Qu. Max. 0.00000 0.01143 0.03002 0.06035 0.06894 0.42910 Mean First Passage Times -- 2 groups: g1, g2 --- g1 --- Mean First Passage Times (3 states) A B C A 3 1 2 B 2 3 1 C 1 2 3 Stationary distribution: A B C 0.3333 0.3333 0.3333 --- g2 --- Mean First Passage Times (3 states) A B C A 3 1 2 B 2 3 1 C 1 2 3 Stationary distribution: A B C 0.3333 0.3333 0.3333 Markov Stability -- 2 groups: g1, g2 --- g1 --- Markov Stability Analysis state persistence stationary_prob return_time sojourn_time avg_time_to_others A 0 0.3333 3 1 1.5 B 0 0.3333 3 1 1.5 C 0 0.3333 3 1 1.5 avg_time_from_others 1.5 1.5 1.5 --- g2 --- Markov Stability Analysis state persistence stationary_prob return_time sojourn_time avg_time_to_others A 0 0.3333 3 1 1.5 B 0 0.3333 3 1 1.5 C 0 0.3333 3 1 1.5 avg_time_from_others 1.5 1.5 1.5 Markov Order Test -- 2 groups: g1, g2 --- g1 --- Markov Order Test [within-w permutation, n_perm = 40, alpha = 0.050] 8 sequences / 144 observations / 4 states Selected order BIC: 1 AIC: 1 permutation-LRT: 1 order loglik AIC BIC df g2 p_permutation p_asymptotic significant 0 -164.72 335.44 344.35 NA NA NA NA NA 1 -137.39 298.78 334.42 9 54.21 0.02439024 1.719176e-08 TRUE 2 -125.66 305.32 385.51 20 23.31 0.19512195 2.736235e-01 FALSE --- g2 --- Markov Order Test [within-w permutation, n_perm = 40, alpha = 0.050] 8 sequences / 144 observations / 4 states Selected order BIC: 0 AIC: 1 permutation-LRT: 1 order loglik AIC BIC df g2 p_permutation p_asymptotic significant 0 -196.50 399.01 407.91 NA NA NA NA NA 1 -176.15 380.31 421.89 9 40.59 0.02439024 5.945574e-06 TRUE 2 -156.20 400.40 531.07 31 39.22 0.43902439 1.476290e-01 FALSE Saving _problems/test-mcml_pc-719.R centralities computed excluding loops (diagonal). Pass `loops = TRUE` to include self-transitions. Metadata aggregated per session: ties resolved by first occurrence in 'timestamp' (2 sessions) Metadata aggregated per session: ties resolved by first occurrence in 'timestamp' (2 sessions) [ FAIL 1 | WARN 70 | SKIP 31 | PASS 4283 ] ══ Skipped tests (31) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test-association_rules.R:1:1', 'test-association_rules_arules.R:1:1', 'test-boot_glasso.R:2:1', 'test-bootstrap_network.R:1:1', 'test-build_clusters.R:1:1', 'test-build_network.R:1:1', 'test-casedrop_reliability.R:3:1', 'test-centrality_stability.R:1:1', 'test-cluster-choice.R:1:1', 'test-cluster-diagnostics.R:1:1', 'test-cograph_network.R:1:1', 'test-estimator_ising.R:1:1', 'test-fix-FIX2.R:1:1', 'test-gimme.R:9:1', 'test-hon.R:1:1', 'test-mlvar.R:1:1', 'test-mmm.R:1:1', 'test-mogen.R:1:1', 'test-network_reliability.R:1:1', 'test-permutation.R:1:1', 'test-persistent_homology.R:1:1', 'test-prepare.R:417:3', 'test-print-cluster.R:1:1', 'test-simplicial.R:1:1' • Source-tree introspection test: hon.R not present in install (1): 'test-fix-FIX5.R:190:3' • Source-tree introspection test: hypa.R not present in install (2): 'test-fix-FIX5.R:47:3', 'test-fix-FIX5.R:77:3' • empty test (3): 'test-hypa.R:340:1', 'test-hypa.R:472:1', 'test-link_prediction.R:432:1' • man/build_hypa.Rd not yet regenerated (orchestrator step) (1): 'test-fix-FIX5.R:106:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-mcml_pc.R:719:3'): lavaan arguments pass through ... verbatim ── Expected `identical(f_wlsmv$loadings$weight, f_ulsmv$loadings$weight)` to be FALSE. Differences: `actual`: TRUE `expected`: FALSE [ FAIL 1 | WARN 70 | SKIP 31 | PASS 4283 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [58s/56s] OK * checking PDF version of manual ... [14s/14s] OK * checking HTML version of manual ... [20s/20s] 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-noLD/Nestimate.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 13:02.58, 642.87 + 23.26