Publish

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: followupTable
> ### Title: Summary tables for a given followup time point.
> ### Aliases: followupTable
> 
> ### ** Examples
> 
> library(survival)
> data(pbc)
> pbc$edema <- factor(pbc$edema,levels=c("0","0.5","1"),labels=c("0","0.5","1"))
> pbc$sex <- factor(pbc$sex,levels=c("m","f"),labels=c("m","f"))
> followupTable(Hist(time,status)~age+edema+sex,data=pbc,followup.time=1000)
Error in a$specials[[i]] : subscript out of bounds
Calls: followupTable ... specialFrame -> <Anonymous> -> delete.response -> off
Execution halted

Running ‘testthat.R’ [5s/7s]
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Publish)
  Loading required package: prodlim
  > 
  > test_check("Publish")
  [1] "Outcome variable(s): X8"
  [1] "Passive variables: "
  [1] "Partially obs. variables: X3,X6"
  [1] "Fully obs. substantive model variables: X4,X7"
  [1] "Imputation  1"
  [1] "Imputing:  X3  using  X6,X4,X7  plus outcome"
  [1] "Imputing:  X6  using  X3,X4,X7  plus outcome"
  [1] "Imputation  2"
  [1] "Imputation  3"
            Variable Units Imputed (3) Coefficient         CI.95   p-value 
         (Intercept)                         -
...[truncated]...
ate table with groups and missing values and labels with special characters ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─Publish::univariateTable(...) at test-univariateTable.R:40:5
   2.   └─Publish::specialFrame(...)
   3.     └─prodlim::model.design(...)
   4.       └─stats::delete.response(terms)
   5.         └─stats (local) off(a$specials[[i]])
  ── Error ('test-univariateTable.R:56:5'): Univariate table with row percent ────
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─base::summary(...) at test-univariateTable.R:56:5
   2. └─Publish::univariateTable(...)
   3.   └─Publish::specialFrame(...)
   4.     └─prodlim::model.design(...)
   5.       └─stats::delete.response(terms)
   6.         └─stats (local) off(a$specials[[i]])
  
  [ FAIL 2 | WARN 1 | SKIP 3 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted