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Error in cliDef@subclasses : no applicable method for @ applied to an object of class "NULL" #755

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Ramelanson opened this issue May 6, 2025 · 1 comment
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@Ramelanson
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** If this is a question and not a bug report or enhancement request, please post to our google group at https://groups.google.com/forum/#!forum/monocle-3-users**

Describe the bug
When trying to download Monocle3 using R v=4.5, I encounter an error with the command line interface syntax.

Error in cliDef@subclasses :
no applicable method for @ applied to an object of class "NULL"
Error in setClass("cell_data_set", contains = c("SingleCellExperiment"), :
error in contained classes ("SingleCellExperiment") for class “cell_data_set”; class definition removed from ‘monocle3’
Error: unable to load R code in package ‘monocle3’
Execution halted

To Reproduce
devtools::install_github('cole-trapnell-lab/monocle3')

traceback()
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traceback()
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Expected behavior
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sessionInfo():
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R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] miniUI_0.1.2 compiler_4.5.0 BiocManager_1.30.25 promises_1.3.2
[5] Rcpp_1.0.14 callr_3.7.6 later_1.4.2 fastmap_1.2.0
[9] mime_0.13 R6_2.6.1 curl_6.2.2 htmlwidgets_1.6.4
[13] desc_1.4.3 profvis_0.4.0 shiny_1.10.0 rlang_1.1.6
[17] cachem_1.1.0 httpuv_1.6.16 fs_1.6.6 pkgload_1.4.0
[21] memoise_2.0.1 cli_3.6.5 magrittr_2.0.3 ps_1.9.1
[25] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 xtable_1.8-4
[29] remotes_2.5.0 devtools_2.4.5 lifecycle_1.0.4 vctrs_0.6.5
[33] glue_1.8.0 urlchecker_1.0.1 sessioninfo_1.2.3 pkgbuild_1.4.7
[37] purrr_1.0.4 tools_4.5.0 usethis_3.1.0 ellipsis_0.3.2
[41] htmltools_0.5.8.1

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@Ramelanson Ramelanson added the bug Something isn't working label May 6, 2025
@AndrewLyon
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Experiencing this issue as well. I also force reinstall SingleCellExperiment as well.

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