Running ‘testthat.R’ [24s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(supernova)
  > 
  > test_check("supernova")
  Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
  Downloading GitHub repo UCLATALL/JMRData@HEAD
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘/home/hornik/tmp/scratch/Rtmp7PXWcd/remotes32bb1f2ec51385/UCLATALL-JMRData-0b78ebe/DESCRIPTION’ ... OK
  * preparing ‘JMRData’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘JMRData_0.1.0.tar.gz’
  
  Installing package into '/home/hornik/tmp/scratch/RtmpUqyxjM/RLIBS_3247f15d35e4ac'
  (as 'lib' is unspecified)
  * installing *source* package ‘JMRData’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (JMRData)
  [ FAIL 23 | WARN 0 | SKIP 15 | PASS 173 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-generate_models.R:222:3', 'test-listwise_delete.R:23:3',
    'test-listwise_delete.R:29:3', 'test-listwise_delete.R:33:3',
    'test-number.R:15:3', 'test-number.R:19:3', 'test-number.R:23:3',
    'test-pairwise.R:18:3', 'test-pairwise.R:99:3', 'test-pairwise.R:113:3',
    'test-supernova.r:321:3', 'test-supernova.r:333:3', 'test-supernova.r:338:3',
    'test-supernova.r:343:3', 'test-supernova.r:348:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-supernova.lmerMod.R:25:3'): cannot compute SS types other than Type III for lmerMod ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9) at test-supernova.lmerMod.R:25:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:34:3'): there is no verbose print for lmerMod (warn and switch off) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9) at test-supernova.lmerMod.R:34:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:45:3'): supernova object has table, fit, and models ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9) at test-supernova.lmerMod.R:45:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:71:3'): supernova works when lmer() is piped in ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
       ▆
    1. ├─... %>% expect_s3_class("supernova") at test-supernova.lmerMod.R:71:3
    2. ├─testthat::expect_s3_class(., "supernova")
    3. │ └─testthat::quasi_label(enquo(object), arg = "object")
    4. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    5. ├─supernova::supernova(.)
    6. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9)
    7. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base (local) withOneRestart(expr, restarts[[1L]])
   10.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:80:3'): supernova works when data is piped into lmer() is piped in ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
       ▆
    1. ├─... %>% expect_s3_class("supernova") at test-supernova.lmerMod.R:80:3
    2. ├─testthat::expect_s3_class(., "supernova")
    3. │ └─testthat::quasi_label(enquo(object), arg = "object")
    4. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    5. ├─supernova::supernova(.)
    6. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), data = .)
    7. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base (local) withOneRestart(expr, restarts[[1L]])
   10.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:90:3'): supernova can test simple nested designs ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(value ~ instructions + (1 | group), test_jmr_ex11.1) at test-supernova.lmerMod.R:90:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:103:3'): supernova can test simple crossed designs ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9) at test-supernova.lmerMod.R:103:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:116:3'): supernova can test multiple crossed designs ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(...) at test-supernova.lmerMod.R:116:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:129:3'): supernova can test mixed designs ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(...) at test-supernova.lmerMod.R:129:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:145:3'): nested repeated measures tables are beautifully formatted ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(value ~ instructions + (1 | group), test_jmr_ex11.1) at test-supernova.lmerMod.R:145:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.lmerMod.R:159:3'): crossed repeated measures tables are beautifully formatted ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(...) at test-supernova.lmerMod.R:159:3
   2. └─base::loadNamespace(x) at test-supernova.lmerMod.R:11:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.r:252:5'): supernova calculates ANOVAs properly (including different SS types) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'car'
  Backtrace:
       ▆
    1. ├─base::lapply(models_to_test, anova_tester_type_2) at test-supernova.r:259:3
    2. │ └─supernova (local) FUN(X[[i]], ...)
    3. │   └─supernova (local) anova_tester(model, type = 2) at test-supernova.r:258:26
    4. │     └─supernova (local) expect_supernova(obj, type) at test-supernova.r:252:5
    5. │       └─supernova (local) expect_partials(object, type, ...) at test-supernova.r:73:5
    6. │         └─supernova (local) get_partials(object$fit, type = type) at test-supernova.r:123:3
    7. │           └─base::suppressMessages(car::Anova) at test-supernova.r:18:5
    8. │             └─base::withCallingHandlers(...)
    9. └─base::loadNamespace(x)
   10.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.     └─base (local) withOneRestart(expr, restarts[[1L]])
   12.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.r:305:3'): supernova uses listwise deletion for missing data ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'car'
  Backtrace:
      ▆
   1. ├─supernova (local) expect_supernova(two_way) at test-supernova.r:305:3
   2. │ └─supernova (local) expect_partials(object, type, ...) at test-supernova.r:73:5
   3. │   └─supernova (local) get_partials(object$fit, type = type) at test-supernova.r:123:3
   4. │     └─base::suppressMessages(car::Anova) at test-supernova.r:18:5
   5. │       └─base::withCallingHandlers(...)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-supernova.r:314:3'): supernova makes correct calculations for unbalanced data ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'car'
  Backtrace:
      ▆
   1. ├─supernova (local) expect_supernova(two_way) at test-supernova.r:314:3
   2. │ └─supernova (local) expect_partials(object, type, ...) at test-supernova.r:73:5
   3. │   └─supernova (local) get_partials(object$fit, type = type) at test-supernova.r:123:3
   4. │     └─base::suppressMessages(car::Anova) at test-supernova.r:18:5
   5. │       └─base::withCallingHandlers(...)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-utils-formula.R:69:3'): frm_fixed_terms only extracts non-random terms from the formula ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-utils-formula.R:69:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─supernova:::frm_fixed_terms(y ~ a + (1 | group))
    5. │ ├─base::setdiff(frm_terms(frm), frm_random_terms(frm))
    6. │ │ └─base::as.vector(y)
    7. │ └─supernova:::frm_random_terms(frm)
    8. └─base::loadNamespace(x)
    9.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   10.     └─base (local) withOneRestart(expr, restarts[[1L]])
   11.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-utils-formula.R:73:3'): frm_random_terms only extracts random terms from the formula ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-utils-formula.R:73:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─supernova:::frm_random_terms(y ~ a + (1 | group))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-utils-formula.R:81:3'): frm_fixed_vars extracts only the variables used in fixed terms ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-utils-formula.R:81:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─supernova:::frm_fixed_vars(y ~ a + a:b + b:c + (1 | group))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-utils-formula.R:85:3'): frm_random_vars extracts only the variables used in random terms ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-utils-formula.R:85:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─supernova:::frm_random_vars(y ~ a + a:b + b:c + (1 | group))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-variables.R:117:3'): variables are extracted from simple nested models ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(value ~ instructions + (1 | group), test_jmr_ex11.1) at test-variables.R:117:3
   2. └─base::loadNamespace(x) at test-variables.R:4:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-variables.R:136:3'): variables are extracted from simple crossed models ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(puzzles_completed ~ condition + (1 | subject), test_jmr_ex11.9) at test-variables.R:136:3
   2. └─base::loadNamespace(x) at test-variables.R:4:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-variables.R:155:3'): variables are extracted from simple crossed models with interactions ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(recall ~ type * time + (1 | subject), test_jmr_ex11.17) at test-variables.R:155:3
   2. └─base::loadNamespace(x) at test-variables.R:4:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-variables.R:174:3'): variables are extracted from models with multiple crossed variables ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(...) at test-variables.R:174:3
   2. └─base::loadNamespace(x) at test-variables.R:4:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-variables.R:192:3'): variables are extracted from mixed models with interactions ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. ├─supernova (local) fit_lmer(...) at test-variables.R:192:3
   2. └─base::loadNamespace(x) at test-variables.R:4:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 23 | WARN 0 | SKIP 15 | PASS 173 ]
  Deleting unused snapshots:
  • pairwise/bonferroni-one-variable.svg
  • pairwise/multiple-plots-term-factor-am.svg
  • pairwise/multiple-plots-term-factor-cyl-factor-am.svg
  • pairwise/t-test-one-variable.svg
  Error: Test failures
  Execution halted