Hello everyone,
After having had to revert versions of a set of packages recently, ggplot2 is not working anymore. However, I am unable to identify the dependencies that really cause the issue. Any suggestion or hint would be more than appreciated. Many thanks in advance.
library(tidyverse)
ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point()
Warning: Incompatible methods ("Ops.S7_object", "+.gg") for "+"Error in ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point() :
sessioninfo::session_info()
#> ─ Session info ───────────────
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os Red Hat Enterprise Linux 8.10 (Ootpa)
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Copenhagen
#> date 2025-09-18
#> pandoc 2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
#> quarto 1.2.269 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.2.2)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.2)
#> evaluate 1.0.5 2025-08-27 [1] CRAN (R 4.2.2)
#> fastmap 1.1.1 2023-02-24 [3] CRAN (R 4.2.2)
#> fs 1.6.3 2023-07-20 [3] CRAN (R 4.2.2)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.2.2)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.2.2)
#> knitr 1.46 2024-04-06 [1] CRAN (R 4.2.2)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.2)
#> reprex 2.1.1 2024-07-06 [1] CRAN (R 4.2.2)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.2)
#> rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.2.2)
#> rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.2.2)
#> sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.2.2)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.2.2)
#> xfun 0.43 2024-03-25 [1] CRAN (R 4.2.2)
#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.2.2)
#>
#> [1] .../bin/Rpackages
#> [2] .../software/R/4.2.2/lib64/R/library
#> [3] .../software/R-packages/4.2.2
margusl
September 18, 2025, 10:18am
2
Welcome! Your session_info() seems to be from a different session where ggplot2 and many of its dependencies were not loaded. It would help if you could edit your post and include a reprex from:
reprex::reprex({
library(tidyverse)
ggplot(data = mtcars, aes(x = wt, y = mpg)) + geom_point()
sessioninfo::session_info()
})
Thanks a ton for the reply @margusl . Indeed, when I tried to run reprex in exactly the way, you outlined, I get yet another error:
This reprex appears to crash R.
Quitting from lines at lines 20-23 [unnamed-chunk-2] (cushy-kitty_reprex.spin.Rmd)
Error in xfun::upload_imgur(file, key, ..., include_xml = TRUE) :
Failed to upload cushy-kitty_reprex_files/figure-gfm/unnamed-chunk-2-1.png (reason: 1025)
However, here is the output from sessioninfo::session_info(). Many thanks for any advice!
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 (2022-10-31)
os Red Hat Enterprise Linux 8.10 (Ootpa)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Copenhagen
date 2025-09-18
rstudio 2022.12.0+353 Elsbeth Geranium (server)
pandoc 2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
quarto 1.2.269 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.2.2)
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aplot 0.2.9 2025-09-12 [1] CRAN (R 4.2.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.2)
backports 1.5.0 2024-05-23 [1] CRAN (R 4.2.2)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.2)
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.2.2)
Biobase 2.58.0 2022-11-01 [3] Bioconductor
BiocFileCache 2.6.1 2023-02-17 [3] Bioconductor
BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor
BiocIO 1.8.0 2022-11-01 [3] Bioconductor
BiocManager 1.30.26 2025-06-05 [1] CRAN (R 4.2.2)
BiocParallel 1.32.6 2023-03-17 [3] Bioconductor
biomaRt 2.54.1 2023-03-20 [3] Bioconductor
Biostrings 2.66.0 2022-11-01 [3] Bioconductor
biovizBase 1.46.0 2022-11-01 [3] Bioconductor
bit 4.6.0 2025-03-06 [1] CRAN (R 4.2.2)
bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.2.2)
bitops 1.0-9 2024-10-03 [1] CRAN (R 4.2.2)
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clusterProfiler 4.6.2 2023-03-05 [3] Bioconductor
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VP dbplyr 2.3.3 2025-09-10 [3] CRAN (R 4.2.2) (on disk 2.5.1)
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VP evaluate 0.21 2025-08-27 [3] CRAN (R 4.2.2) (on disk 1.0.5)
factoextra 1.0.7 2020-04-01 [1] CRAN (R 4.2.2)
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farver 2.1.1 2022-07-06 [3] CRAN (R 4.2.2)
fastmap 1.1.1 2023-02-24 [3] CRAN (R 4.2.2)
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fgsea 1.24.0 2022-11-01 [3] Bioconductor
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Formula 1.2-5 2023-02-24 [3] CRAN (R 4.2.2)
fs 1.6.3 2023-07-20 [3] CRAN (R 4.2.2)
future 1.67.0 2025-07-29 [1] CRAN (R 4.2.2)
future.apply 1.20.0 2025-06-06 [1] CRAN (R 4.2.2)
VP generics 0.1.3 2025-05-09 [3] CRAN (R 4.2.2) (on disk 0.1.4)
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GenomeInfoDbData 1.2.11 2024-04-11 [1] Bioconductor
GenomicAlignments 1.34.1 2023-03-09 [3] Bioconductor
GenomicFeatures 1.50.4 2023-01-24 [3] Bioconductor
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GGally 2.2.1 2024-02-14 [1] CRAN (R 4.2.2)
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ggbio 1.46.0 2022-11-01 [1] Bioconductor
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ggfun 0.2.0 2025-07-15 [1] CRAN (R 4.2.2)
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GOSemSim 2.24.0 2022-11-01 [3] Bioconductor
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graphlayouts 1.0.0 2023-05-01 [3] CRAN (R 4.2.2)
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gridGraphics 0.5-1 2020-12-13 [3] CRAN (R 4.2.2)
gson 0.1.0 2023-03-07 [3] CRAN (R 4.2.2)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.2.2)
Gviz 1.42.1 2023-02-17 [3] Bioconductor
HDO.db 0.99.1 2023-04-18 [3] Bioconductor
here 1.0.2 2025-09-15 [1] CRAN (R 4.2.2)
Hmisc 5.2-3 2025-03-16 [1] CRAN (R 4.2.2)
hms 1.1.3 2023-03-21 [3] CRAN (R 4.2.2)
htmlTable 2.4.3 2024-07-21 [1] CRAN (R 4.2.2)
VP htmltools 0.5.5 2024-04-04 [3] CRAN (R 4.2.2) (on disk 0.5.8.1)
VP htmlwidgets 1.6.2 2023-12-06 [3] CRAN (R 4.2.2) (on disk 1.6.4)
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RANN 2.6.1 2019-01-08 [3] CRAN (R 4.2.2)
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RColorBrewer 1.1-3 2022-04-03 [3] CRAN (R 4.2.2)
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VP rlang 1.1.1 2024-01-10 [3] CRAN (R 4.2.2) (on disk 1.1.3)
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ROCR 1.0-11 2020-05-02 [3] CRAN (R 4.2.2)
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[1] /maps/projects/ralab/people/pbr316/bin/Rpackages
[2] /maps/direct/software/R/4.2.2/lib64/R/library
[3] /maps/projects/scarball/apps/Modules/software/R-packages/4.2.2
* ── Packages attached to the search path.
V ── Loaded and on-disk version mismatch.
P ── Loaded and on-disk path mismatch.
─────────────────────────────────────────────────────────────
margusl
September 18, 2025, 10:58am
4
I'm afraid that this session_info()is also from different session -- that simple tidyverse + ggplot() snippet in your first post can't load all those Bioconductor , gg* , spatial, etc packages. Though the fact that reprex() had something to upload to Imgur hints that ggplot might actually work in a clean R session. Have you tried restarting R?
If you do need to fiddle with package versions, I'd start with ggplot2 , reverting it to pre-4.0 version (e.g to 3.5.2) should clear S7 dependencies
But you do have quite a mix there. For example that xfun from 2024 includes Imgur API key that's not valid anymore and it's the reason of reprex error. Updating xfun to at least 0.51 should fix this.
Once again, many thanks for the quick reply and help @margusl as reverting ggplot back to v3.5.2 did the trick. Good incentive to get familiar with S7 objects.
1 Like
system
September 26, 2025, 5:40am
6
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