Error when displaying object in Quarto website with `df-print:paged`: arguments imply differing number of rows

[isaactpetersen]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

I receive an error when trying to display an object in Quarto via GitHub Actions on Linux using df-print:paged. Specifically, the object is pooled results from a lm() fit to multiply imputed data (imputed using the mice package). I receive the error when pooling results using mice::pool() in Quarto (when running on GitHub Actions). Oddly enough, I don't receive an error when running the code in a .R file locally on my PC (or even when running the code in a .R file on Linux GitHub Actions). However, I do receive the error locally on my PC when using Quarto. Interestingly, I seem to receive the error when I specify df-print:paged in the _quarto.yml file. I do not receive the error when I remove df-print:paged in the _quarto.yml file. I had previously posted the bug in amices/mice#733, but it seems it may be a Quarto bug.

Here is the error I receive:

Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 1 has 1 row to replace 0 rows
Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 2 has 1 row to replace 0 rows

Error:
! arguments imply differing number of rows: 1, 0

The error seems related to the following issue: rstudio/rstudio#15459.

In summary:

• it works when running it locally on my PC: https://isaactpetersen.github.io/QuartoReprexForEdit/#sec-pc
• it works when running the code via a .R file on Linux (via GitHub Actions): https://isaactpetersen.github.io/QuartoReprexForEdit/#sec-linux
• it works when running the code on Quarto (via GitHub Actions on Linux) when NOT specifying df-print:paged
• it doesn't work when run on Quarto (via GitHub Actions on Linux) when specifying df-print:paged: https://isaactpetersen.github.io/QuartoReprexForEdit/#sec-quarto

Steps to reproduce

Here is a link to a reproducible example:
https://isaactpetersen.github.io/QuartoReprexForEdit/ (archived at https://perma.cc/Q5ZS-BP4E)

Here is the code that generates the reproducible example:
https://github.com/isaactpetersen/QuartoReprexForEdit/blob/main/index.qmd

Here is the output:

# Load libraries
library("mice")
#> 
#> Attaching package: 'mice'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> The following objects are masked from 'package:base':
#> 
#>     cbind, rbind

# Impute data
imp <- mice::mice(
  nhanes,
  maxit = 2,
  m = 2)
#> 
#>  iter imp variable
#>   1   1  bmi  hyp  chl
#>   1   2  bmi  hyp  chl
#>   2   1  bmi  hyp  chl
#>   2   2  bmi  hyp  chl

# Fit regression model to multiply imputed data
fit <- with(
  data = imp,
  exp = lm(bmi ~ hyp + chl))

# Pool results across models
fit_pooled <- mice::pool(fit)

# Summarize pooled results
fit_pooled

Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 1 has 1 row to replace 0 rows
Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 2 has 1 row to replace 0 rows
Error:
! arguments imply differing number of rows: 1, 0

summary(fit_pooled)
#>          term   estimate  std.error statistic        df      p.value
#> 1 (Intercept) 23.5653619 4.58749728  5.136867 20.222496 4.858105e-05
#> 2         hyp -2.6735267 2.23416369 -1.196657  9.102038 2.616789e-01
#> 3         chl  0.0350338 0.02406278  1.455933 18.483798 1.621871e-01

# Session Info
sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] mice_3.19.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] generics_0.1.4     tidyr_1.3.2        shape_1.4.6.1      lattice_0.22-7    
#>  [5] lme4_1.1-38        digest_0.6.39      magrittr_2.0.4     mitml_0.4-5       
#>  [9] evaluate_1.0.5     grid_4.5.2         iterators_1.0.14   fastmap_1.2.0     
#> [13] foreach_1.5.2      jomo_2.7-6         glmnet_4.1-10      Matrix_1.7-4      
#> [17] nnet_7.3-20        backports_1.5.0    survival_3.8-3     purrr_1.2.0       
#> [21] codetools_0.2-20   reformulas_0.4.3.1 Rdpack_2.6.4       cli_3.6.5         
#> [25] rlang_1.1.6        rbibutils_2.4      splines_4.5.2      reprex_2.1.1      
#> [29] withr_3.0.2        yaml_2.3.12        pan_1.9            tools_4.5.2       
#> [33] nloptr_2.2.1       minqa_1.2.8        dplyr_1.1.4        boot_1.3-32       
#> [37] broom_1.0.11       vctrs_0.6.5        R6_2.6.1           rpart_4.1.24      
#> [41] lifecycle_1.0.5    fs_1.6.6           MASS_7.3-65        pkgconfig_2.0.3   
#> [45] pillar_1.11.1      glue_1.8.0         Rcpp_1.1.0         xfun_0.55         
#> [49] tibble_3.3.0       tidyselect_1.2.1   knitr_1.51         htmltools_0.5.9   
#> [53] nlme_3.1-168       rmarkdown_2.30     compiler_4.5.2

Actual behavior

Error:

Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 1 has 1 row to replace 0 rows
Warning in `[<-.data.frame`(`*tmp*`, is_list, value = list(`3` = "<df[,11] [0 ×
11]>", : replacement element 2 has 1 row to replace 0 rows

Error:
! arguments imply differing number of rows: 1, 0

Expected behavior

Display the object without error

Your environment

• IDE: none used for GitHub Actions
• OS: Ubuntu 24.04.3 LTS

Quarto check output

quarto --version
  quarto check
  shell: /usr/bin/bash -e {0}
  env:
    BUNDLE_EXT: linux-amd64.deb
1.8.26
Quarto 1.8.26

[✓] Checking environment information...
      Quarto cache location: /home/runner/.cache/quarto

[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK

[✓] Checking versions of quarto dependencies......OK

[✓] Checking Quarto installation......OK
      Version: 1.8.26
      Path: /opt/quarto/bin


[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)


[✓] Checking LaTeX....................OK
      Tex:  (not detected)


[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/google-chrome
      Source: PATH


(|) Checking basic markdown render....
[✓] Checking basic markdown render....OK


(|) Checking Python 3 installation....
[✓] Checking Python 3 installation....OK
      Version: 3.12.3
      Path: /usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

      There is a requirements.txt file in this directory. Is this for a venv that you need to restore?


[✓] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/

[mcanouil]

Are you sure you are running the same thing?
For instance, I don't see any renv.lock to ensure you are using the exact same dependency tree in the different environments.
CI/CD runs on the very latest while you might not.

[isaactpetersen]

Thanks for the quetsion. I edited my original message to clarify that I receive the error when using Quarto and df-print:paged, whether running it via GitHub Actions on Linux or running it locally on my PC. I do not receive the error when running it via a .R file (instead of via Quarto). The PC is running the same environment for both the (local) .R file and the (local) .qmd file, so a different environment does not appear to explain the error. It appears to be an issue with df-print:paged in Quarto.

[mcanouil]

An R script is not the same thing because you don't apply the extra R tool you've requested from Quarto (https://pkgs.rstudio.com/rmarkdown/reference/paged_table.html).

rmarkdown::paged_table(fit_pooled)

The issue will exhibit without Quarto.

The issue is that rmarkdown::paged_table is for data.frame but fit_pooled is not really a data.frame. It's a list with heterogenous content (including data.frame).

The object has a print method which is used by default and display one of the data.frame from the object, but when you change the df-print option, you ask to apply another transformation on it.
Unfortunately, those methods don't know and can't know that fit_pooled is not a data.frame.

You can try knitr::kable(fit_pooled) or anything that assumes a real rectangular data.frame.

In the end, the issue in on mice maintainers/developers.