Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > pkg_name <- "tern.gee"
  > library(pkg_name, character.only = TRUE)
  Loading required package: tern
  Loading required package: rtables
  Loading required package: formatters
  
  Attaching package: 'formatters'
  
  The following object is masked from 'package:base':
  
      %||%
  
  Loading required package: magrittr
  
  Attaching package: 'rtables'
  
  The following object is masked from 'package:utils':
  
      str
  
  > testthat::test_check(pkg_name)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:magrittr':
  
      equals, is_less_than, not
  
  [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-tabulate_gee.R:32:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ──────────────
  Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, 
      "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected
  Backtrace:
      ▆
   1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3
   2. └─tern.gee:::lsmeans.tern_gee_logistic(model)
   3.   ├─base::cbind(...)
   4.   ├─...[]
   5.   └─base::`[.data.frame`(...)
  ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ──
  Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, 
      "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected
  Backtrace:
      ▆
   1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3
   2. ├─tern.gee::lsmeans(model)
   3. └─tern.gee:::lsmeans.tern_gee_logistic(model)
   4.   ├─base::cbind(...)
   5.   ├─...[]
   6.   └─base::`[.data.frame`(...)
  ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ──
  Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, 
      "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected
  Backtrace:
      ▆
   1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3
   2. ├─tern.gee::lsmeans(model)
   3. └─tern.gee:::lsmeans.tern_gee_logistic(model)
   4.   ├─base::cbind(...)
   5.   ├─...[]
   6.   └─base::`[.data.frame`(...)
  ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ──
  Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, 
      "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected
  Backtrace:
       ▆
    1. ├─... %>% ... at test-tabulate_gee.R:64:3
    2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl)
    3. │ ├─rtables:::set_def_child_ord(lyt, df)
    4. │ └─rtables:::set_def_child_ord(lyt, df)
    5. │   ├─rtables:::set_def_child_ord(clayout(lyt), df)
    6. │   └─rtables:::set_def_child_ord(clayout(lyt), df)
    7. │     └─base::lapply(lyt, set_def_child_ord, df = df)
    8. │       ├─rtables (local) FUN(X[[i]], ...)
    9. │       └─rtables (local) FUN(X[[i]], ...)
   10. │         └─base::lapply(lyt, set_def_child_ord, df = df)
   11. │           ├─rtables (local) FUN(X[[i]], ...)
   12. │           └─rtables (local) FUN(X[[i]], ...)
   13. ├─tern.gee::lsmeans(model)
   14. └─tern.gee:::lsmeans.tern_gee_logistic(model)
   15.   ├─base::cbind(...)
   16.   ├─...[]
   17.   └─base::`[.data.frame`(...)
  ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ──
  Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, 
      "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected
  Backtrace:
       ▆
    1. ├─... %>% ... at test-tabulate_gee.R:89:3
    2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl)
    3. │ ├─rtables:::set_def_child_ord(lyt, df)
    4. │ └─rtables:::set_def_child_ord(lyt, df)
    5. │   ├─rtables:::set_def_child_ord(clayout(lyt), df)
    6. │   └─rtables:::set_def_child_ord(clayout(lyt), df)
    7. │     └─base::lapply(lyt, set_def_child_ord, df = df)
    8. │       ├─rtables (local) FUN(X[[i]], ...)
    9. │       └─rtables (local) FUN(X[[i]], ...)
   10. │         └─base::lapply(lyt, set_def_child_ord, df = df)
   11. │           ├─rtables (local) FUN(X[[i]], ...)
   12. │           └─rtables (local) FUN(X[[i]], ...)
   13. ├─tern.gee::lsmeans(model)
   14. └─tern.gee:::lsmeans.tern_gee_logistic(model)
   15.   ├─base::cbind(...)
   16.   ├─...[]
   17.   └─base::`[.data.frame`(...)
  
  [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ]
  Error: Test failures
  Execution halted