Running ‘testthat.R’ [97s/49s]
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
  > test_q_fct_indicators_reliability.R: 
  > test_q_fct_indicators_reliability.R: Attaching package: 'psych'
  > test_q_fct_indicators_reliability.R: 
  > test_q_fct_indicators_reliability.R: The following object is masked from 'package:lavaan':
  > test_q_fct_indicators_reliability.R: 
  > test_q_fct_indicators_reliability.R:     cor2cov
  > test_q_fct_indicators_reliability.R: 
  > test_q_fct_indicators_reliability.R: The following object is masked from 'package:testthat':
  > test_q_fct_indicators_reliability.R: 
  > test_q_fct_indicators_reliability.R:     describe
  > test_q_fct_indicators_reliability.R: 
  Saving _problems/test_sam_q_mediation-179.R
  [ FAIL 1 | WARN 0 | SKIP 71 | PASS 679 ]
  
  ══ Skipped tests (71) ══════════════════════════════════════════════════════════
  • 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 (1): 'test_sam.R:24:1'
  • Not used for now (1): 'test_cond_indirect_effects_lm_kway.R:1:1'
  • On CRAN (52): '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_empty_cases.R:1:1',
    'test_do_boot_implied_lv_means.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_mi_lavaan_mi_no_means.R:1:1',
    'test_mg_boot.R:1:1', 'test_mod_only_kway.R:1:1',
    'test_mod_only_kway_cat.R:1:1', 'test_mod_only_not_moderated.R:1:1',
    'test_mod_only_plot_vs_w.R:1:1', 'test_plot_indirect_vs_w.R:1:1',
    'test_proportion.R:1:1', 'test_q_fct_get_fit.R:1:1',
    'test_q_fct_mediation.R:1:1',
    'test_q_fct_mediation_lm_indicators_scale_scores_reverse.R:1:1',
    'test_q_fct_mediation_model.R:1:1', 'test_q_fct_mediation_sem.R:1:1',
    'test_q_fct_mediation_sem_fixedx_FALSE.R:1:1',
    'test_q_fct_mediation_sem_indicators_measurement_reverse.R:1:1',
    'test_q_fct_mediation_sem_indicators_sam_reverse.R:1:1',
    'test_q_fct_mediation_sem_indicators_scale_scores.R:1:1',
    'test_q_fct_mediation_sem_indicators_scale_scores_reverse.R:1:1',
    'test_q_fct_mediation_sem_indicators_measurement.R:204:1',
    'test_q_fct_mediation_sem_listwise.R:1:1',
    'test_q_fct_mediation_sem_lm2lav.R:1:1', 'test_q_fct_mediation_sem_mc.R:1:1',
    'test_sam_do_boot.R:1:1', 'test_sam_do_boot_mod.R:1:1',
    'test_sam_update.R:1:1', 'test_sam_q_mediation.R:192:1',
    '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 (2): 'test_one_y.R:1:1', 'test_sam_update_internal.R:1:1'
  • empty test (5): , , , ,
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_sam_q_mediation.R:178:1'): q function: mediation with indicators: SAM ──
  Expected `out_simple$loadings[names(get_loadings(fit))]` to equal `get_loadings(fit)`.
  Differences:
    `actual$m`: 0.287224483 0.055765990 0.391292751
  `expected$m`: 0.287224476 0.055765974 0.391292747
  
  
  [ FAIL 1 | WARN 0 | SKIP 71 | PASS 679 ]
  Error:
  ! Test failures.
  Execution halted