quadGate.tmix vignette example broken

[rwbaer]

Describe the bug
I am trying to run the self-contained example code for quadGate.tmix in
https://www.bioconductor.org/packages/devel/bioc/vignettes/openCyto/inst/doc/HowToAutoGating.html
I get an error that seems related to an S4 slot issue.

To Reproduce
Steps to reproduce the behavior:
Run this code snippet

# example code
gs <- load_gs(system.file("extdata/gs_DC_auto", package = "flowWorkspaceData"))
fr <- gh_pop_get_data(gs[[2]], "HLADR+", returnType = "flowFrame")
chnl <- c("CD11c", "CD123")
p <- autoplot(fr, chnl[1], chnl[2])
g <- openCyto:::.quadGate.tmix(fr, channels = chnl, K = 3, usePrior = "no")
p + geom_gate(g)

The snippet results in the following

> # example code
> gs <- load_gs(system.file("extdata/gs_DC_auto", package = "flowWorkspaceData"))
> fr <- gh_pop_get_data(gs[[2]], "HLADR+", returnType = "flowFrame")
> chnl <- c("CD11c", "CD123")
> p <- autoplot(fr, chnl[1], chnl[2])
> g <- openCyto:::.quadGate.tmix(fr, channels = chnl, K = 3, usePrior = "no")
Error in UseMethod("filter") : 
  no applicable method for 'filter' applied to an object of class "flowFrame"
Error in object@lambda : 
  no applicable method for `@` applied to an object of class "try-error"

Expected behavior
I expect the graph shown in th vignette.

SessionInfo:

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 27744)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] shiny_1.9.1          patchwork_1.3.0      lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1        dplyr_1.1.4         
 [7] purrr_1.0.2          readr_2.1.5          tidyr_1.3.1          tibble_3.2.1         tidyverse_2.0.0      CytoML_2.16.0       
[13] ggcyto_1.32.0        ncdfFlow_2.50.0      BH_1.84.0-0          ggplot2_3.5.1        cytoverse_0.0.0.9000 CytoExploreR_1.1.0  
[19] openCyto_2.16.1      flowWorkspace_4.16.0 flowCore_2.16.0     

loaded via a namespace (and not attached):
 [1] RBGL_1.80.0         gridExtra_2.3       rlang_1.1.4         magrittr_2.0.3      matrixStats_1.4.1   compiler_4.4.1     
 [7] png_0.1-8           vctrs_0.6.5         reshape2_1.4.4      pkgconfig_2.0.3     crayon_1.5.3        fastmap_1.2.0      
[13] labeling_0.4.3      utf8_1.2.4          promises_1.3.0      rmarkdown_2.28      tzdb_0.4.0          graph_1.82.0       
[19] xfun_0.48           zlibbioc_1.50.0     cachem_1.1.0        jsonlite_1.8.9      later_1.3.2         parallel_4.4.1     
[25] R6_2.5.1            bslib_0.8.0         stringi_1.8.4       RColorBrewer_1.1-3  reticulate_1.39.0   pkgload_1.4.0      
[31] jquerylib_0.1.4     Rcpp_1.0.13         knitr_1.48          zoo_1.8-12          timechange_0.3.0    httpuv_1.6.15      
[37] Matrix_1.7-0        tidyselect_1.2.1    rstudioapi_0.17.1   yaml_2.3.10         lattice_0.22-6      plyr_1.8.9         
[43] Biobase_2.64.0      withr_3.0.1         askpass_1.2.1       evaluate_1.0.1      Rtsne_0.17          EmbedSOM_2.1.2     
[49] pillar_1.9.0        flowAI_1.34.0       stats4_4.4.1        generics_0.1.3      S4Vectors_0.42.1    hms_1.1.3          
[55] munsell_0.5.1       scales_1.3.0        xtable_1.8-4        glue_1.8.0          changepoint_2.2.4   tools_4.4.1        
[61] hexbin_1.28.4       robustbase_0.99-4-1 data.table_1.16.2   RSpectra_0.16-2     fs_1.6.4            visNetwork_2.1.2   
[67] XML_3.99-0.17       grid_4.4.1          flowClust_3.42.0    RProtoBufLib_2.16.0 umap_0.2.10.0       colorspace_2.1-1   
[73] cli_3.6.3           rsvd_1.0.5          rhandsontable_0.3.8 fansi_1.0.6         cytolib_2.16.0      Rgraphviz_2.48.0   
[79] gtable_0.3.6        DEoptimR_1.1-3      sass_0.4.9          digest_0.6.37       BiocGenerics_0.50.0 farver_2.1.2       
[85] htmlwidgets_1.6.4   memoise_2.0.1       htmltools_0.5.8.1   lifecycle_1.0.4     mime_0.12           openssl_2.2.2      
[91] MASS_7.3-60.2    

Additional context
Before getting the error with the vignette code I got a similar error with my own gating set.