Package: CalibrationCurves
Check: examples
New result: ERROR
  Running examples in ‘CalibrationCurves-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: val.prob.ci.2
  > ### Title: Calibration performance
  > ### Aliases: val.prob.ci.2
  > 
  > ### ** Examples
  > 
  > 
  > # Load package
  > library(CalibrationCurves)
  > set.seed(1783)
  > 
  > # Simulate training data
  > X      = replicate(4, rnorm(5e2))
  > p0true = binomial()$linkinv(cbind(1, X) %*% c(0.1, 0.5, 1.2, -0.75, 0.8))
  > y      = rbinom(5e2, 1, p0true)
  > Df     = data.frame(y, X)
  > 
  > # Fit logistic model
  > FitLog = lrm(y ~ ., Df)
  > 
  > # Simulate validation data
  > Xval   = replicate(4, rnorm(5e2))
  > p0true = binomial()$linkinv(cbind(1, Xval) %*% c(0.1, 0.5, 1.2, -0.75, 0.8))
  > yval   = rbinom(5e2, 1, p0true)
  > Pred   = binomial()$linkinv(cbind(1, Xval) %*% coef(FitLog))
  > 
  > # Default calibration plot
  > val.prob.ci.2(Pred, yval)
  Error in vcov.rms(object, regcoef.only = regcoef.only, ...) : 
    fit does not have variance-covariance matrix
  Calls: val.prob.ci.2 ... confint.default -> diag -> vcov -> vcov.lrm -> vcov.rms
  Execution halted

Package: CalibrationCurves
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘CalibrationCurves.Rmd’ using rmarkdown
  
  Quitting from lines 177-178 [unnamed-chunk-6] (CalibrationCurves.Rmd)
  Error: processing vignette 'CalibrationCurves.Rmd' failed with diagnostics:
  fit does not have variance-covariance matrix
  --- failed re-building ‘CalibrationCurves.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘CalibrationCurves.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: depigner
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [6s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > # This loads the version being checked, not the version
    > # you have installed
    > library(depigner)
    Welcome to depigner: we are here to un-stress you!
    > 
    > 
    > test_check("depigner")
    v P adjusted with BH method.
    x   The object `x` does not have a P-value column.
        Have you select `test = TRUE` into `summary()`
        and set argument `prtest = "P"` into the
        `print()`, the `summary_interact()`, or
        the `tidy_summary()` function?
    x `x` is returned without changes.
    v Ahh... relaxed!
    * Now, feel free to continue working.
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    Error in solve.default(info, tol = tol) : 
      system is computationally singular: reciprocal condition number = 3.17011e-14
    v Setting active project to
      "/home/hornik/tmp/scratch/RtmpJEpWwa/prj1388aa4168387c".
    v Restoring original working directory: '/home/hornik/tmp/CRAN_recheck/depigner.Rcheck/tests/testthat/'
    v Setting active project to "<no active project>".
    v Deleting temporary project: '/home/hornik/tmp/scratch/RtmpJEpWwa/prj1388aa4168387c/'
    v Setting active project to
      "/home/hornik/tmp/scratch/RtmpJEpWwa/aaa1388aa4f27933c".
    v   Adding 'usethis' to Imports field
        in DESCRIPTION.
    v Writing 'R/utils-depigner.R'.
    v Adding '#\' @importFrom usethis ui_line ui_todo ui_done ui_todo ui_oops ui_info\n#\' @importFrom usethis ui_code_block\n#\' @importFrom usethis ui_stop ui_warn\n#\' @importFrom usethis ui_yeah ui_nope\n#\' @importFrom usethis ui_field ui_value ui_path ui_code' to 'R/utils-depigner.R'
    *   Run `devtools::document()` to update 'NAMESPACE'
    v Restoring original working directory: '/home/hornik/tmp/CRAN_recheck/depigner.Rcheck/tests/testthat/'
    v Setting active project to "<no active project>".
    v Deleting temporary project: '/home/hornik/tmp/scratch/RtmpJEpWwa/aaa1388aa4f27933c/'
    [ FAIL 1 | WARN 3 | SKIP 17 | PASS 88 ]
    
    ══ Skipped tests (17) ══════════════════════════════════════════════════════════
    • !getOption("depigner.dev.test_telegram_bot") is TRUE (7):
      'test-chat_id_from_name.R:6:3', 'test-chat_id_from_name.R:19:3',
      'test-send_to_telegram.R:2:3', 'test-send_to_telegram.R:17:3',
      'test-start_bot_for_chat.R:3:3', 'test-start_bot_for_chat.R:19:3',
      'test-start_bot_for_chat.R:33:3'
    • On CRAN (10): 'test-paired_test_categorical.R:7:3',
      'test-paired_test_categorical.R:14:3', 'test-paired_test_continuous.R:14:3',
      'test-paired_test_continuous.R:21:3', 'test-paired_test_continuous.R:35:3',
      'test-paired_test_continuous.R:48:3', 'test-paired_test_continuous.R:73:3',
      'test-tidy_summary.R:2:3', 'test-tidy_summary.R:29:3', 'test-utils.R:2:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-summary_interact.R:19:3'): expectation class ───────────────────
    <purrr_error_indexed/rlang_error/error/condition>
    Error in `map(.x, .f, ...)`: i In index: 1.
    Caused by error in `dplyr::filter()`:
    i In argument: `Type == 2L`.
    Caused by error:
    ! object 'Type' not found
    
    [ FAIL 1 | WARN 3 | SKIP 17 | PASS 88 ]
    Error: Test failures
    Execution halted

Package: insight
Check: tests
New result: ERROR
    Running ‘testthat.R’ [200s/100s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(insight)
    > test_check("insight")
    Starting 2 test processes
    [ FAIL 18 | WARN 7 | SKIP 73 | PASS 3384 ]
    
    ══ Skipped tests (73) ══════════════════════════════════════════════════════════
    • On CRAN (65): 'test-GLMMadaptive.R:1:1', 'test-averaging.R:3:1',
      'test-brms.R:1:1', 'test-brms_aterms.R:1:1',
      'test-brms_gr_random_effects.R:1:1', 'test-brms_missing.R:1:1',
      'test-blmer.R:249:3', 'test-clean_names.R:103:3',
      'test-clean_parameters.R:2:3', 'test-clean_parameters.R:35:3',
      'test-clmm.R:165:3', 'test-cpglmm.R:145:3', 'test-export_table.R:4:3',
      'test-export_table.R:8:3', 'test-export_table.R:106:3',
      'test-export_table.R:133:3', 'test-export_table.R:164:3',
      'test-export_table.R:193:3', 'test-export_table.R:205:3',
      'test-export_table.R:233:3', 'test-find_smooth.R:31:3',
      'test-find_random.R:27:3', 'test-format_table.R:1:1',
      'test-format_table_ci.R:71:3', 'test-gam.R:1:1', 'test-get_data.R:385:1',
      'test-get_loglikelihood.R:93:3', 'test-get_loglikelihood.R:158:3',
      'test-get_datagrid.R:215:3', 'test-get_datagrid.R:261:3',
      'test-get_predicted.R:2:1', 'test-get_priors.R:3:3',
      'test-get_varcov.R:40:3', 'test-is_converged.R:28:1', 'test-lme.R:34:3',
      'test-lme.R:210:3', 'test-glmmTMB.R:71:3', 'test-glmmTMB.R:755:3',
      'test-glmmTMB.R:787:3', 'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1',
      'test-mipo.R:1:1', 'test-mvrstanarm.R:1:1', 'test-panelr-asym.R:142:3',
      'test-panelr.R:272:3', 'test-phylolm.R:5:1',
      'test-r2_nakagawa_bernoulli.R:1:1', 'test-r2_nakagawa_beta.R:1:1',
      'test-r2_nakagawa_binomial.R:1:1', 'test-r2_nakagawa_gamma.R:1:1',
      'test-r2_nakagawa_linear.R:1:1', 'test-r2_nakagawa_negbin.R:1:1',
      'test-r2_nakagawa_negbin_zi.R:1:1', 'test-r2_nakagawa_ordered_beta.R:1:1',
      'test-r2_nakagawa_poisson.R:1:1', 'test-r2_nakagawa_poisson_zi.R:1:1',
      'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1',
      'test-rlmer.R:259:3', 'test-rqss.R:1:1', 'test-rstanarm.R:1:1',
      'test-spatial.R:1:1', 'test-svylme.R:1:1', 'test-vgam.R:1:1',
      'test-weightit.R:1:1'
    • On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1',
      'test-get_data.R:150:3'
    • Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1'
    • TRUE is TRUE (1): 'test-fixest.R:2:1'
    • bigglm cannot be loaded (1): 'test-model_info.R:24:3'
    • works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-rms.R:7:3'): model_info ──────────────────────────────────────
    model_info(m1)$is_bernoulli is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-rms.R:11:3'): model_info ─────────────────────────────────────
    model_info(m1)$is_ordinal is not FALSE
    
    `actual`:   TRUE 
    `expected`: FALSE
    ── Failure ('test-rms.R:15:3'): find_predictors ────────────────────────────────
    find_predictors(m1) (`actual`) not identical to list(conditional = c("mpg", "gear")) (`expected`).
    
    `actual` is NULL
    `expected` is a list
    ── Failure ('test-rms.R:16:3'): find_predictors ────────────────────────────────
    find_predictors(m1, flatten = TRUE) (`actual`) not identical to c("mpg", "gear") (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('mpg', 'gear')
    ── Failure ('test-rms.R:29:3'): find_response ──────────────────────────────────
    find_response(m1) (`actual`) not identical to "am" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('am')
    ── Failure ('test-rms.R:33:3'): get_response ───────────────────────────────────
    get_response(m1) (`actual`) not identical to mtcars$am (`expected`).
    
    `actual` is NULL
    `expected` is a double vector (1, 1, 1, 0, 0, ...)
    ── Failure ('test-rms.R:37:3'): get_predictors ─────────────────────────────────
    Names of get_predictors(m1) ('') don't match 'mpg', 'gear'
    ── Failure ('test-rms.R:45:3'): get_data ───────────────────────────────────────
    nrow(get_data(m1)) (`actual`) not identical to 32L (`expected`).
    
    `actual` is NULL
    `expected` is an integer vector (32)
    ── Failure ('test-rms.R:46:3'): get_data ───────────────────────────────────────
    Names of get_data(m1) ('') don't match 'am', 'mpg', 'gear'
    ── Failure ('test-rms.R:50:3'): find_formula ───────────────────────────────────
    find_formula(m1) has length 0, not length 1.
    ── Failure ('test-rms.R:51:3'): find_formula ───────────────────────────────────
    find_formula(m1) (`actual`) not equal to list(conditional = as.formula("am ~ mpg + gear")) (`expected`).
    
    `actual` is NULL
    `expected` is a list
    ── Failure ('test-rms.R:59:3'): find_terms ─────────────────────────────────────
    find_terms(m1) (`actual`) not identical to list(response = "am", conditional = c("mpg", "gear")) (`expected`).
    
    `actual` is NULL
    `expected` is a list
    ── Failure ('test-rms.R:63:3'): find_terms ─────────────────────────────────────
    find_terms(m1, flatten = TRUE) (`actual`) not identical to c("am", "mpg", "gear") (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('am', 'mpg', 'gear')
    ── Failure ('test-rms.R:67:3'): n_obs ──────────────────────────────────────────
    n_obs(m1) (`actual`) not identical to 32 (`expected`).
    
    `actual` is NULL
    `expected` is a double vector (32)
    ── Failure ('test-rms.R:79:3'): find_parameters ────────────────────────────────
    find_parameters(m1) (`actual`) not identical to list(conditional = c("Intercept", "mpg", "gear")) (`expected`).
    
    `actual` is length 0
    `expected` is length 1
    
    `names(actual)`:                
    `names(expected)`: "conditional"
    
    `actual$conditional` is absent
    `expected$conditional` is a character vector ('Intercept', 'mpg', 'gear')
    ── Failure ('test-rms.R:83:3'): find_parameters ────────────────────────────────
    nrow(get_parameters(m1)) (`actual`) not identical to 3L (`expected`).
    
      `actual`: 0
    `expected`: 3
    ── Failure ('test-rms.R:84:3'): find_parameters ────────────────────────────────
    get_parameters(m1)$Parameter (`actual`) not identical to c("Intercept", "mpg", "gear") (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('Intercept', 'mpg', 'gear')
    ── Failure ('test-rms.R:95:3'): find_algorithm ─────────────────────────────────
    find_algorithm(m1) (`actual`) not identical to list(algorithm = "ML") (`expected`).
    
    `actual` is NULL
    `expected` is a list
    
    [ FAIL 18 | WARN 7 | SKIP 73 | PASS 3384 ]
    Error: Test failures
    Execution halted