broom

Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glance.survfit
> ### Title: Glance at a(n) survfit object
> ### Aliases: glance.survfit
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed(c("survival", "ggplot2"))) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ 
+ # load libraries for models and data
+ library(survival)
+ 
+ # fit model
+ cfit <- coxph(Surv(time, status) ~ age + sex, lung)
+ sfit <- survfit(cfit)
+ 
+ # summarize model fit with tidiers + visualization
+ tidy(sfit)
+ glance(sfit)
+ 
+ library(ggplot2)
+ 
+ ggplot(tidy(sfit), aes(time, estimate)) +
+   geom_line() +
+   geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25)
+ 
+ # multi-state
+ fitCI <- survfit(Surv(stop, status * as.numeric(event), type = "mstate") ~ 1,
+   data = mgus1, subset = (start == 0)
+ )
+ 
+ td_multi <- tidy(fitCI)
+ 
+ td_multi
+ 
+ ggplot(td_multi, aes(time, estimate, group = state)) +
+   geom_line(aes(color = state)) +
+   geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25)
+ ## Don't show: 
+ }) # examplesIf
> library(survival)
> cfit <- coxph(Surv(time, status) ~ age + sex, lung)
> sfit <- survfit(cfit)
Error in a$specials[[i]] : subscript out of bounds
Calls: withAutoprint ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [14s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(broom)
  > 
  > test_check("broom")
  
  Attaching package: 'modeldata'
  
  The following object is masked from 'package:datasets':
  
      penguins
  
  Multiple parameters; naming those columns ndf and ddf.
  Saving _problems/test-survival-coxph-84.R
  Saving _problems/test-survival-coxph-84.R
  [ FAIL 2 | WARN 1 | SKIP 99 | PASS 934 ]
  
  ══ Skipped tests (99) ══════════════════════════════════════════════════════════
  • On CRAN (99): 'test-aer.R:1:1', 'test-a
...[truncated]...
)) == head(results(newdata))
  Backtrace:
      ▆
   1. └─modeltests::check_augment_function(...) at test-survival-coxph.R:79:3
   2.   └─modeltests:::check_augment_data_specification(...)
   3.     └─testthat::expect_equal(...)
  ── Error ('test-survival-coxph.R:79:3'): augment.coxph ─────────────────────────
  Error in `data.frame(..., check.names = FALSE)`: arguments imply differing number of rows: 229, 228
  Backtrace:
      ▆
   1. └─modeltests::check_augment_function(...) at test-survival-coxph.R:79:3
   2.   └─modeltests:::check_augment_data_specification(...)
   3.     └─broom (local) aug(model, data = dl$tibble, newdata = new_dl$tibble)
   4.       └─broom::augment_columns(...)
   5.         ├─tibble::as_tibble(cbind(original, ret))
   6.         └─base::cbind(original, ret)
   7.           └─base::cbind(deparse.level, ...)
   8.             └─base::data.frame(..., check.names = FALSE)
  
  [ FAIL 2 | WARN 1 | SKIP 99 | PASS 934 ]
  Error:
  ! Test failures.
  Execution halted

Installation failed.
See ‘/data/localhost/ripley/R/packages/tests-clang/broom.Rcheck/00install.out’ for details.