Error in ComplexUpset after ggplot2 4.0.0 update

[abichat]

Description

A major update to ggplot2 (version 4.0.0) is expected around mid-to-late July 2025.

Unfortunately, using it will break ComplexUpset::upset(), I will show it with the first vignette example.

Behaviors

With ggplot2 3.5.2 (runs fine)

# pak::pak("tidyverse/ggplot2@v3.5.2")
library(ComplexUpset)

packageVersion("ggplot2")
#> [1] '3.5.2'
packageVersion("ComplexUpset")
#> [1] '1.3.6'

movies <- as.data.frame(ggplot2movies::movies)
genres <- colnames(movies)[18:24]

upset(movies, genres, name = "genre", width_ratio = 0.1)

^{Created on 2025-07-09 with reprex v2.1.1}

With ggplot2 4.0.0 (warnings and error)

# pak::pak("tidyverse/ggplot2")
library(ComplexUpset)

packageVersion("ggplot2")
#> [1] '3.5.2.9001'
packageVersion("ComplexUpset")
#> [1] '1.3.6'

movies <- as.data.frame(ggplot2movies::movies)
genres <- colnames(movies)[18:24]

upset(movies, genres, name = "genre", width_ratio = 0.1)
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ComplexUpset package.
#>   Please report the issue at
#>   <https://github.com/krassowski/complex-upset/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.
#> Error in `plot_theme()`:
#> ! The `axis.title.x` theme element must be a <element_text> object.

^{Created on 2025-07-09 with reprex v2.1.1}

The first warning is due to the change from size to linewidth in aesthetic for lines (since ggplot2 3.4.0, but only soft deprecated then).
The following ones are likely due to stricter class checks with the S7 implementation in 4.0.0.

See this post: Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare

Conclusion

Do you think a patch will be available soon? It would be greatly appreciated.
Huge thanks for maintaining this package, I use it a lot!

Context

ComplexUpset 1.3.6

R session information

> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11)
 os       macOS Sequoia 15.5
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Paris
 date     2025-07-09
 pandoc   NA
 quarto   1.7.29 @ /usr/local/bin/quarto

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────
 package       * version    date (UTC) lib source
 cli             3.6.5      2025-04-23 [1] CRAN (R 4.5.0)
 colorspace      2.1-1      2024-07-26 [1] CRAN (R 4.5.0)
 ComplexUpset  * 1.3.6      2025-07-09 [1] Github (krassowski/complex-upset@db1e099)
 crayon          1.5.3      2024-06-20 [1] CRAN (R 4.5.0)
 dplyr           1.1.4      2023-11-17 [1] CRAN (R 4.5.0)
 farver          2.1.2      2024-05-13 [1] CRAN (R 4.5.0)
 generics        0.1.4      2025-05-09 [1] CRAN (R 4.5.0)
 ggplot2         3.5.2.9001 2025-07-09 [1] Github (tidyverse/ggplot2@f666daf)
 ggplot2movies   0.0.1      2015-08-25 [1] CRAN (R 4.5.0)
 glue            1.8.0      2024-09-30 [1] CRAN (R 4.5.0)
 gtable          0.3.6      2024-10-25 [1] CRAN (R 4.5.0)
 labeling        0.4.3      2023-08-29 [1] CRAN (R 4.5.0)
 lifecycle       1.0.4      2023-11-07 [1] CRAN (R 4.5.0)
 magrittr        2.0.3      2022-03-30 [1] CRAN (R 4.5.0)
 patchwork       1.3.0      2024-09-16 [1] CRAN (R 4.5.0)
 pillar          1.10.2     2025-04-05 [1] CRAN (R 4.5.0)
 pkgconfig       2.0.3      2019-09-22 [1] CRAN (R 4.5.0)
 R6              2.6.1      2025-02-15 [1] CRAN (R 4.5.0)
 ragg            1.4.0      2025-04-10 [1] CRAN (R 4.5.0)
 RColorBrewer    1.1-3      2022-04-03 [1] CRAN (R 4.5.0)
 rlang           1.1.6      2025-04-11 [1] CRAN (R 4.5.0)
 S7              0.2.0      2024-11-07 [1] CRAN (R 4.5.0)
 scales          1.4.0      2025-04-24 [1] CRAN (R 4.5.0)
 sessioninfo     1.2.3      2025-02-05 [1] CRAN (R 4.5.0)
 systemfonts     1.2.3      2025-04-30 [1] CRAN (R 4.5.0)
 textshaping     1.0.1      2025-05-01 [1] CRAN (R 4.5.0)
 tibble          3.3.0      2025-06-08 [1] CRAN (R 4.5.0)
 tidyselect      1.2.1      2024-03-11 [1] CRAN (R 4.5.0)
 vctrs           0.6.5      2023-12-01 [1] CRAN (R 4.5.0)
 withr           3.0.2      2024-10-28 [1] CRAN (R 4.5.0)

[lisiarend]

Any news on this?

[federicomarini]

Hey Mike @krassowski I hope all is good on your side...

I have seen that #212 went merged in and the github version works fine.
Is there a timeline for a possible submission anytime soon to CRAN? My package GeneTonic is still failing in its checks because of this version still not being propagated.

Can't say I have the skills and the bandwidth to take over some maintenance because that would be a half lie (a well-intending one, but still a lie...)

Federico

[mitraak]

Hey all, circling back here with the same issue that @federicomarini mentioned above. The PR is merged but the tests are not passing since R CMD check throws an error that vdiffr package not available, which is odd as this is a testthat extension. Maybe that's the reason for the hold up?

[krassowski]

PRs to fix CI, making submission to CRAN possible welcome!

[federicomarini]

You mean simply fixing the current GHA? I think it is possibly solved in a glance by updating the R versions.
Trying that now on my fork

[federicomarini]

master...federicomarini:complex-upset:master was the only thing I changed.

And yes, confirmed, at least it triggers another error but this time is due to a simple test.
https://github.com/federicomarini/complex-upset/actions/runs/18569380062/job/52939039108
Can that maybe safely be skipped? I am not too familiar with vdiffr but maybe others can jump on and we can fix it quickly.

[sebastian-gregoricchio]

My package DEprot also imports ComplexUpset. Any update on the date/possibility of a CRAN version update?

[vanderleidebastiani]

PRs to fix CI, making submission to CRAN possible welcome!

See pull #217

[pascalnoser]

Apologies for adding yet another comment asking about this, but I'm also working on a package that imports ComplexUpset and was wondering if there is any chance that the CRAN version will be updated?

[krassowski]

Does the version from main work well or would you need #217 in too?

I am happy to try submitting a new version over the weekend, though with test suite out of commission I do not feel confident without users testing it first and with previous submissions being rejected I suspect there may be more changes needed.