BUG: Error in LeverageScore(): ! too slow -- only after upgrading to Seurat 5.3.0

[lhoranportelance]

Issue Description

Running SketchData on my data no longer works after upgrading from Seurat 5.2.1 to 5.3.0. The same code (see below) ran fine on 5.2.1 but is now producing an error on 5.3.0.

Reproducing Code Example

seurat[["RNA"]] <- split(seurat[["RNA"]], f = seurat$dataset_region)
seurat <- NormalizeData(seurat)
seurat <- FindVariableFeatures(seurat)
seurat_sketched <- SketchData(object = seurat, ncells = 10000, method = "LeverageScore", sketched.assay = "sketch")

Error Message

Error in `LeverageScore()`:
! too slow

Additional Comments

No response

Session Info

R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/2022.1.2.146/mkl/2022.0.2/lib/intel64/libmkl_rt.so.2;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
 [1] harmony_1.2.3      Rcpp_1.0.14        lubridate_1.9.4    forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4        purrr_1.0.4       
 [8] readr_2.1.5        tidyr_1.3.1        tibble_3.2.1       ggplot2_3.5.1      tidyverse_2.0.0    scCustomize_3.0.1  Seurat_5.3.0      
[15] SeuratObject_5.1.0 sp_2.2-0          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.17.1      jsonlite_2.0.0         shape_1.4.6.1          magrittr_2.0.3         spatstat.utils_3.1-3  
  [7] ggbeeswarm_0.7.2       farver_2.1.2           GlobalOptions_0.1.2    vctrs_0.6.5            ROCR_1.0-11            spatstat.explore_3.4-2
 [13] paletteer_1.6.0        janitor_2.2.1          htmltools_0.5.8.1      sctransform_0.4.1      parallelly_1.43.0      KernSmooth_2.23-26    
 [19] htmlwidgets_1.6.4      ica_1.0-3              plyr_1.8.9             plotly_4.10.4          zoo_1.8-13             igraph_2.1.4          
 [25] mime_0.13              lifecycle_1.0.4        pkgconfig_2.0.3        Matrix_1.7-2           R6_2.6.1               fastmap_1.2.0         
 [31] fitdistrplus_1.2-2     future_1.34.0          shiny_1.10.0           snakecase_0.11.1       digest_0.6.37          colorspace_2.1-1      
 [37] rematch2_2.1.2         patchwork_1.3.0        tensor_1.5             RSpectra_0.16-2        irlba_2.3.5.1          progressr_0.15.1      
 [43] spatstat.sparse_3.1-0  timechange_0.3.0       httr_1.4.7             polyclip_1.10-7        abind_1.4-8            compiler_4.4.3        
 [49] withr_3.0.2            fastDummies_1.7.5      MASS_7.3-65            tools_4.4.3            vipor_0.4.7            lmtest_0.9-40         
 [55] beeswarm_0.4.0         httpuv_1.6.15          future.apply_1.11.3    goftest_1.2-3          glue_1.8.0             nlme_3.1-167          
 [61] promises_1.3.2         grid_4.4.3             Rtsne_0.17             cluster_2.1.8          reshape2_1.4.4         generics_0.1.3        
 [67] gtable_0.3.6           spatstat.data_3.1-6    tzdb_0.5.0             hms_1.1.3              data.table_1.17.0      spatstat.geom_3.3-6   
 [73] RcppAnnoy_0.0.22       ggrepel_0.9.6          RANN_2.6.2             pillar_1.10.1          spam_2.11-1            RcppHNSW_0.6.0        
 [79] ggprism_1.0.5          later_1.4.1            circlize_0.4.16        splines_4.4.3          lattice_0.22-6         survival_3.8-3        
 [85] deldir_2.0-4           tidyselect_1.2.1       miniUI_0.1.1.1         pbapply_1.7-2          gridExtra_2.3          scattermore_1.2       
 [91] matrixStats_1.5.0      stringi_1.8.4          lazyeval_0.2.2         codetools_0.2-20       cli_3.6.4              uwot_0.2.3            
 [97] xtable_1.8-4           reticulate_1.40.0      munsell_0.5.1          globals_0.16.3         spatstat.random_3.3-3  png_0.1-8             
[103] ggrastr_1.0.2          spatstat.univar_3.1-1  parallel_4.4.3         dotCall64_1.2          listenv_0.9.1          viridisLite_0.4.2     
[109] scales_1.3.0           ggridges_0.5.6         crayon_1.5.3           rlang_1.1.4            cowplot_1.1.3

[lima1]

#7171

[lhoranportelance]

#7171

Already looked at this when troubleshooting. I just downgraded from 5.3.0 back to 5.2.1 and the exact same code seen above works. It is a version issue.

[lima1]

Try adding features = VariableFeatures(object) to SketchData() as a workaround. Looks like a bug.

[lhoranportelance]

Try adding features = VariableFeatures(object) to SketchData() as a workaround. Looks like a bug.

Tried this too -- doesn't work on 5.3.0

[lima1]

FWIW, I encountered this bug after upgrading to 5.3.0 and explicitely specifying the features solved it for me, but I'm gonna shut up now since I'm not involved with Seurat.