[R-pkg-team] Bug#1125224: r-cran-mice: autopkgtest needs update for new version of lme4

[Paul Gevers]

Source: r-cran-mice
Version: 3.17.0-1
Severity: serious
X-Debbugs-CC: lme4 at packages.debian.org
Tags: sid forky
User: debian-ci at lists.debian.org
Usertags: needs-update
Control: affects -1 src:lme4

Dear maintainer(s),

With a recent upload of lme4 the autopkgtest of r-cran-mice fails in 
testing when that autopkgtest is run with the binary packages of lme4 
from unstable. It passes when run with only packages from testing. In 
tabular form:

                        pass            fail
lme4                   from testing    1.1-38-1
r-cran-mice            from testing    3.17.0-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of lme4 to testing 
[1]. Of course, lme4 shouldn't just break your autopkgtest (or even 
worse, your package), but it is my understanding that the r ecosystem 
does good testing itself and r-cran-mice is outdated, so I'm suspecting 
the issue lies with r-cran-mice.

If this is a real problem in your package (and not only in your 
autopkgtest), the right binary package(s) from lme4 could add a 
versioned Breaks on the unfixed version of (one of your) package(s). 
Note: the Breaks is nice even if the issue is only in the autopkgtest as 
it helps the migration software to figure out the right versions to 
combine in the tests.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=lme4

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-mice/67653839/log.gz

  65s BEGIN TEST testthat.R
  65s  65s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
  65s Copyright (C) 2025 The R Foundation for Statistical Computing
  65s Platform: x86_64-pc-linux-gnu
  65s  65s R is free software and comes with ABSOLUTELY NO WARRANTY.
  65s You are welcome to redistribute it under certain conditions.
  65s Type 'license()' or 'licence()' for distribution details.
  65s  65s R is a collaborative project with many contributors.
  65s Type 'contributors()' for more information and
  65s 'citation()' on how to cite R or R packages in publications.
  65s  65s Type 'demo()' for some demos, 'help()' for on-line help, or
  65s 'help.start()' for an HTML browser interface to help.
  65s Type 'q()' to quit R.
  65s  65s > library(testthat)
  65s > library(mice)
  66s  66s Attaching package: ‘mice’
  66s  66s The following object is masked from ‘package:stats’:
  66s  66s     filter
  66s  66s The following objects are masked from ‘package:base’:
  66s  66s     cbind, rbind
  66s  66s >  66s > test_check("mice")
112s [ FAIL 1 | WARN 0 | SKIP 0 | PASS 377 ]
112s 112s ══ Failed tests 
════════════════════════════════════════════════════════════════
112s ── Error ('test-mice.impute.2l.bin.R:30:1'): (code run outside of 
`test_that()`) ──
112s Error: object 'ID' not found
112s Backtrace:
112s     ▆
112s  1. ├─... %>% dplyr::select(-month) at test-mice.impute.2l.bin.R:30:1
112s  2. ├─dplyr::select(., -month)
112s  3. ├─tidyr::fill(., treatment)
112s  4. ├─tidyr::complete(toenail, ID, visit)
112s  5. └─tidyr:::complete.data.frame(toenail, ID, visit)
112s  6.   ├─tidyr::expand(data, ...)
112s  7.   └─tidyr:::expand.data.frame(data, ...)
112s  8.     └─tidyr:::grid_dots(..., `_data` = data)
112s  9.       └─rlang::eval_tidy(dot, data = mask)
112s 112s [ FAIL 1 | WARN 0 | SKIP 0 | PASS 377 ]
112s Error: Test failures
112s Execution halted
113s autopkgtest [11:12:27]: test run-unit-test

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