* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/manymome.Rcheck’
* using R Under development (unstable) (2025-12-23 r89222)
* 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 ‘manymome/DESCRIPTION’ ... OK
* this is package ‘manymome’ version ‘0.3.2’
* 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 ‘manymome’ can be installed ... [22s/61s] 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 ... [52s/171s] 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 ... [3m/15m] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11m/21m]
 [11m/21m] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(manymome)
  > 
  > test_check("manymome")
  Starting 2 test processes.
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_cond_indirect_lavaan.R: Stage 1: Simulate estimates
  > test_cond_indirect_lavaan.R: Stage 2: Compute implied statistics
  > test_delta_med_boot.R: Call:
  > test_delta_med_boot.R: delta_med(x = "x", y = "y", m = "m", fit = fit)
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Predictor (x)       : x 
  > test_delta_med_boot.R: Mediator(s) (m)     : m 
  > test_delta_med_boot.R: Outcome variable (y): y 
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Delta_med: 0.230
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Paths removed:
  > test_delta_med_boot.R:  m~x
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Additional information:
  > test_delta_med_boot.R: R-sq: Original                            : 0.351
  > test_delta_med_boot.R: R-sq: Mediator(s) removed                 : 0.121
  > test_delta_med_boot.R: Variance of y                             : 6.273
  > test_delta_med_boot.R: Variance of predicted y                   : 2.203
  > test_delta_med_boot.R: Variance of predicted: mediator(s) removed: 0.759
  > test_delta_med_boot.R: Call:
  > test_delta_med_boot.R: delta_med(x = "x", y = "y", m = "m", fit = fit)
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Predictor (x)       : x 
  > test_delta_med_boot.R: Mediator(s) (m)     : m 
  > test_delta_med_boot.R: Outcome variable (y): y 
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Delta_med: 0.23021
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Paths removed:
  > test_delta_med_boot.R:  m~x
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Additional information:
  > test_delta_med_boot.R: R-sq: Original                            : 0.35122
  > test_delta_med_boot.R: R-sq: Mediator(s) removed                 : 0.12101
  > test_delta_med_boot.R: Variance of y                             : 6.27337
  > test_delta_med_boot.R: Variance of predicted y                   : 2.20333
  > test_delta_med_boot.R: Variance of predicted: mediator(s) removed: 0.75912
  > test_delta_med_boot.R: Call:
  > test_delta_med_boot.R: delta_med(x = "x", y = "y", m = "m", fit = fit, boot_out = boot_out, 
  > test_delta_med_boot.R:     progress = FALSE)
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Predictor (x)       : x 
  > test_delta_med_boot.R: Mediator(s) (m)     : m 
  > test_delta_med_boot.R: Outcome variable (y): y 
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Delta_med                                     :          0.230
  > test_delta_med_boot.R: 95.0% Bootstrap percentile confidence interval: [0.088, 0.316]
  > test_delta_med_boot.R: Number of bootstrap samples                   :            100
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Paths removed:
  > test_delta_med_boot.R:  m~x
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Additional information:
  > test_delta_med_boot.R: R-sq: Original                            : 0.351
  > test_delta_med_boot.R: R-sq: Mediator(s) removed                 : 0.121
  > test_delta_med_boot.R: Variance of y                             : 6.273
  > test_delta_med_boot.R: Variance of predicted y                   : 2.203
  > test_delta_med_boot.R: Variance of predicted: mediator(s) removed: 0.759
  > test_delta_med_boot.R: Call:
  > test_delta_med_boot.R: delta_med(x = "x", y = "y", m = "m", fit = fit, boot_out = boot_out, 
  > test_delta_med_boot.R:     progress = FALSE)
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Predictor (x)       : x 
  > test_delta_med_boot.R: Mediator(s) (m)     : m 
  > test_delta_med_boot.R: Outcome variable (y): y 
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Delta_med                                     :           0.2302
  > test_delta_med_boot.R: 95.0% Bootstrap percentile confidence interval: [0.0882, 0.3159]
  > test_delta_med_boot.R: Number of bootstrap samples                   :              100
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Paths removed:
  > test_delta_med_boot.R:  m~x
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Additional information:
  > test_delta_med_boot.R: R-sq: Original                            : 0.3512
  > test_delta_med_boot.R: R-sq: Mediator(s) removed                 : 0.1210
  > test_delta_med_boot.R: Variance of y                             : 6.2734
  > test_delta_med_boot.R: Variance of predicted y                   : 2.2033
  > test_delta_med_boot.R: Variance of predicted: mediator(s) removed: 0.7591
  > test_delta_med_boot.R: Call:
  > test_delta_med_boot.R: delta_med(x = "x", y = "y", m = "m", fit = fit, boot_out = boot_out, 
  > test_delta_med_boot.R:     progress = FALSE)
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Predictor (x)       : x 
  > test_delta_med_boot.R: Mediator(s) (m)     : m 
  > test_delta_med_boot.R: Outcome variable (y): y 
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Delta_med                                     :           0.2302
  > test_delta_med_boot.R: 80.0% Bootstrap percentile confidence interval: [0.1438, 0.2933]
  > test_delta_med_boot.R: Number of bootstrap samples                   :              100
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Paths removed:
  > test_delta_med_boot.R:  m~x
  > test_delta_med_boot.R: 
  > test_delta_med_boot.R: Additional information:
  > test_delta_med_boot.R: R-sq: Original                            : 0.3512
  > test_delta_med_boot.R: R-sq: Mediator(s) removed                 : 0.1210
  > test_delta_med_boot.R: Variance of y                             : 6.2734
  > test_delta_med_boot.R: Variance of predicted y                   : 2.2033
  > test_delta_med_boot.R: Variance of predicted: mediator(s) removed: 0.7591
  Saving _problems/test_lavaan2lm_list-54.R
  [ FAIL 1 | WARN 0 | SKIP 54 | PASS 583 ]
  
  ══ Skipped tests (54) ══════════════════════════════════════════════════════════
  • Long tests: Test in interactive sections (3):
    'test_cond_indirect_se_print.R:1:1', 'test_compare_boot_mc.R:1:1',
    'test_compare_boot_mc_med_lav.R:1:1'
  • Not used for now (1): 'test_cond_indirect_effects_lm_kway.R:1:1'
  • On CRAN (37): 'test_cond_indirect_effects_to_df.R:1:1',
    'test_cond_indirect_lavaan_mi.R:1:1', 'test_cond_indirect_se.R:1:1',
    'test_all_indirect_paths.R:1:1', 'test_auto_lm2list.R:1:1',
    'test_boot_ci_internal_bc.R:1:1', 'test_do_boot_no_implied.R:1:1',
    'test_do_mc_no_implied.R:1:1',
    'test_fit2boot_out_do_boot_parallel_mini.R:1:1', 'test_get_b_mi.R:1:1',
    'test_get_intercept_mi.R:1:1', 'test_get_prod_mi.R:1:1',
    'test_get_vcov.R:1:1', 'test_index_mome.R:1:1',
    'test_index_mome_complex_models.R:1:1',
    'test_indirect_simple_med_latent_observed.R:169:1', 'test_jn.r:1:1',
    'test_jn_se.r:1:1', 'test_lav_data_used_mi.R:1:1',
    'test_lav_data_used_mi_no_means.R:1:1', 'test_lav_implied_all.R:1:1',
    'test_lm2boot_out_parallel_mini.R:1:1',
    'test_many_indirects_do_sim_once.R:1:1', 'test_mg_boot.R:1:1',
    'test_mi_lavaan_mi_no_means.R:1:1', 'test_mod_only_kway.R:1:1',
    'test_mod_only_kway_cat.R:1:1', 'test_mod_only_plot_vs_w.R:1:1',
    'test_mod_only_not_moderated.R:1:1', 'test_plot_indirect_vs_w.R:1:1',
    'test_proportion.R:1:1', 'test_q_fct_mediation.R:1:1',
    'test_q_fct_mediation_model.R:1:1', 'test_q_fct_mediation_sem.R:1:1',
    'test_q_fct_mediation_sem_lm2lav.R:1:1', 'test_q_fct_mediation_sem_mc.R:1:1',
    'test_total_indirect_simplified.R:1:1'
  • Template for tests for MI (1): 'test_mi_template.R:1:1'
  • Test parallel processing: Test in interactive sections (2):
    'test_fit2boot_out_do_boot_parallel.R:1:1', 'test_lm2boot_out_parallel.R:1:1'
  • To be examined in an interactive session (3):
    'test_cond_indirect_effects_lavaan.R:1:1',
    'test_cond_indirect_effects_lavaan_mi.R:1:1',
    'test_q_fct_mediation_plot_sem.R:1:1'
  • To be run in an interactive section (1): 'test_benchmark_mc.R:1:1'
  • WIP (1): 'test_one_y.R:1:1'
  • empty test (5): , , , ,
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_lavaan2lm_list.R:51:5'): lm_from_lavaan: predict ─────────────
  Expected `predict(fit_list[["y"]], dat[3:5, ])` to equal `predict(lm_y, dat[3:5, ]) - coef(lm_y)[1]`.
  Differences:
    `actual`: 15.544773 15.345507 15.139332
  `expected`: 15.544747 15.345493 15.139317
  
  
  [ FAIL 1 | WARN 0 | SKIP 54 | PASS 583 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [43s/132s] OK
* checking PDF version of manual ... [18s/58s] OK
* checking HTML version of manual ... [22s/61s] 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-OpenBLAS/manymome.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 46:53.11, 1034.86 + 35.23