Seurat v5 gives an error while uploading publicly available GSE dataset

[RajneeshSrivastava]

Hi Team,

I am trying to upgrade to Seurat v5 and want to utilize the BPCells package for handling a large dataset (~2M cells), got errors at very early stage :D. Here I am sharing an example file that I am trying to upload

library(Seurat)
Warning: package ‘Seurat’ was built under R version 4.3.2
library(SeuratObject)
library(BPCells)
library(SeuratDisk)
library(sctransform)
library(glmGamPoi)
library(Matrix)

#data downloaded from #https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4145204
list.files("path/GSE131685/GSM4145204/")  
[1] "barcodes.tsv.gz" "features.tsv.gz" "matrix.mtx.gz"

GSM4145204_data <- Read10X(data.dir = "path/GSE131685/GSM4145204/")  
GSM4145204_object <- CreateSeuratObject(counts = GSM4145204_data)

Error in validObject(.Object) : 
  invalid class “LogMap” object: superclass "mMatrix" not defined in the environment of the object's class

Please note, this snippet was working fine with Seurat 4.3. Please suggest if I am missing any dependencies or required versions of the software.

Here is my session info:

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

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/New_York
tzcode source: internal

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

other attached packages:
[1] Matrix_1.6-2          glmGamPoi_1.14.0      sctransform_0.4.1     SeuratDisk_0.0.0.9021 BPCells_0.1.0        
[6] Seurat_5.0.0          SeuratObject_5.0.0    sp_2.1-1             

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.15.0           jsonlite_1.8.7              magrittr_2.0.3             
  [5] spatstat.utils_3.0-4        zlibbioc_1.48.0             vctrs_0.6.4                 ROCR_1.0-11                
  [9] spatstat.explore_3.2-5      RCurl_1.98-1.13             S4Arrays_1.2.0              htmltools_0.5.7            
 [13] SparseArray_1.2.2           parallelly_1.36.0           KernSmooth_2.23-21          htmlwidgets_1.6.2          
 [17] ica_1.0-3                   plyr_1.8.9                  plotly_4.10.3               zoo_1.8-12                 
 [21] igraph_1.5.1                mime_0.12                   lifecycle_1.0.4             pkgconfig_2.0.3            
 [25] R6_2.5.1                    fastmap_1.1.1               GenomeInfoDbData_1.2.11     MatrixGenerics_1.14.0      
 [29] fitdistrplus_1.1-11         future_1.33.0               shiny_1.7.5.1               digest_0.6.33              
 [33] colorspace_2.1-0            S4Vectors_0.40.1            patchwork_1.1.3             tensor_1.5                 
 [37] RSpectra_0.16-1             irlba_2.3.5.1               GenomicRanges_1.54.1        progressr_0.14.0           
 [41] fansi_1.0.5                 spatstat.sparse_3.0-3       httr_1.4.7                  polyclip_1.10-6            
 [45] abind_1.4-5                 compiler_4.3.1              bit64_4.0.5                 withr_2.5.2                
 [49] fastDummies_1.7.3           MASS_7.3-60                 DelayedArray_0.28.0         tools_4.3.1                
 [53] lmtest_0.9-40               httpuv_1.6.12               future.apply_1.11.0         goftest_1.2-3              
 [57] glue_1.6.2                  nlme_3.1-162                promises_1.2.1              grid_4.3.1                 
 [61] Rtsne_0.16                  cluster_2.1.4               reshape2_1.4.4              generics_0.1.3             
 [65] hdf5r_1.3.8                 gtable_0.3.4                spatstat.data_3.0-3         tidyr_1.3.0                
 [69] data.table_1.14.8           XVector_0.42.0              utf8_1.2.4                  BiocGenerics_0.48.1        
 [73] spatstat.geom_3.2-7         RcppAnnoy_0.0.21            ggrepel_0.9.4               RANN_2.6.1                 
 [77] pillar_1.9.0                stringr_1.5.0               spam_2.10-0                 RcppHNSW_0.5.0             
 [81] later_1.3.1                 splines_4.3.1               dplyr_1.1.3                 lattice_0.21-8             
 [85] renv_1.0.3                  survival_3.5-5              bit_4.0.5                   deldir_1.0-9               
 [89] tidyselect_1.2.0            miniUI_0.1.1.1              pbapply_1.7-2               knitr_1.45                 
 [93] gridExtra_2.3               IRanges_2.36.0              SummarizedExperiment_1.32.0 scattermore_1.2            
 [97] stats4_4.3.1                xfun_0.41                   Biobase_2.62.0              matrixStats_1.1.0          
[101] stringi_1.7.12              lazyeval_0.2.2              yaml_2.3.7                  codetools_0.2-19           
[105] tibble_3.2.1                cli_3.6.1                   uwot_0.1.16                 xtable_1.8-4               
[109] reticulate_1.34.0           munsell_0.5.0               GenomeInfoDb_1.38.1         Rcpp_1.0.11                
[113] globals_0.16.2              spatstat.random_3.2-1       png_0.1-8                   parallel_4.3.1             
[117] ellipsis_0.3.2              ggplot2_3.4.4               dotCall64_1.1-0             bitops_1.0-7               
[121] listenv_0.9.0               viridisLite_0.4.2           scales_1.2.1                ggridges_0.5.4             
[125] leiden_0.4.3                purrr_1.0.2                 crayon_1.5.2                rlang_1.1.2                
[129] cowplot_1.1.1

[longmanz]

Hi,
Thank you for reporting this! At first I was not able to reproduce your error, but after I updated my "Matrix" from "1.6-1.1" to "1.6-2", I suddenly got the same error as you.

I would recommend you to downgrade your "Matrix" back to "1.6-1.1" remotes::install_version("Matrix", version = "1.6-1.1"). If the issue persists, I will reopen this issue for further investigation.