CreateSeuratObject() error: Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found

[Dazcam]

Hi there,

I've recently upgraded to Seurat 5 and I'm now receiving the above error when trying to run CreateSeuratObject() on a script that perviously ran without error. This script downloads publicly available data from a repository and runs the basic Seurat process. It worked previously when using Seurat versions 3 and 4.

However, this error also arises when running CreateSeuratObject() using the gene expression matrix and meta data extracted from the pbmc3k dataset:

library(Seurat)
library(SeuratData)

BiocManager::version()
#> [1] '3.18'

unloadNamespace('Azimuth', 'TFBSTools')

InstallData("pbmc3k")
data("pbmc3k")
#> Error: Please run UpdateSeuratObject on your object

pbmc3k <- UpdateSeuratObject(pbmc3k)
#> Validating object structure
#> Updating object slots
#> Ensuring keys are in the proper structure
#> Warning: Assay RNA changing from Assay to Assay
#> Ensuring keys are in the proper structure
#> Ensuring feature names don't have underscores or pipes
#> Updating slots in RNA
#> Validating object structure for Assay 'RNA'
#> Object representation is consistent with the most current Seurat version

pbmc3k
#> An object of class Seurat 
#> 13714 features across 2700 samples within 1 assay 
#> Active assay: RNA (13714 features, 0 variable features)
#> 2 layers present: counts, data

mat <- pbmc3k@assays$RNA@counts
meta <- pbmc3k@meta.data

test <- CreateSeuratObject(counts = mat, meta.data = meta)
#> Error in .local(x, na.rm, dims, ...) : 
#>  object 'CRsparse_colSums' not found

I have seen other posts recently on this issue and have tried to implement the following suggested 'solutions':

• Upgraded Bioconductor manager to 3.18 (and updated packages accordingly)
• Tried removing the Azimuth and TFBSTools packages using unloadNamespace()

I appreciate this may be an ongoing issue, but thought I'd start a new thread as the other threads imply this has been resolved.

Any help you could offer would be greatly appreciated.

---

Here is my sessionInfo():

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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: Europe/London
tzcode source: internal

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

other attached packages:
[1] pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2.9001   Seurat_5.0.1            SeuratObject_5.0.1      sp_2.1-2               
[6] shinyBS_0.61.1         

loaded via a namespace (and not attached):
  [1] fs_1.6.3                          ProtGenerics_1.34.0               matrixStats_1.2.0                
  [4] spatstat.sparse_3.0-3             bitops_1.0-7                      DirichletMultinomial_1.44.0      
  [7] lubridate_1.9.3                   TFBSTools_1.40.0                  httr_1.4.7                       
 [10] RColorBrewer_1.1-3                tools_4.3.1                       sctransform_0.4.1                
 [13] utf8_1.2.4                        R6_2.5.1                          DT_0.31                          
 [16] lazyeval_0.2.2                    uwot_0.1.16                       rhdf5filters_1.14.1              
 [19] withr_2.5.2                       scCustomize_2.0.1                 prettyunits_1.2.0                
 [22] gridExtra_2.3                     progressr_0.14.0                  cli_3.6.2                        
 [25] Biobase_2.62.0                    spatstat.explore_3.2-5            fastDummies_1.7.3                
 [28] EnsDb.Hsapiens.v86_2.99.0         shinyjs_2.1.0                     spatstat.data_3.0-3              
 [31] readr_2.1.4                       ggridges_0.5.5                    pbapply_1.7-2                    
 [34] Rsamtools_2.18.0                  R.utils_2.12.3                    parallelly_1.36.0                
 [37] BSgenome_1.70.1                   readxl_1.4.3                      rstudioapi_0.15.0                
 [40] RSQLite_2.3.4                     shape_1.4.6                       generics_0.1.3                   
 [43] BiocIO_1.12.0                     gtools_3.9.5                      ica_1.0-3                        
 [46] spatstat.random_3.2-2             googlesheets4_1.1.1               dplyr_1.1.4                      
 [49] GO.db_3.18.0                      Matrix_1.6-4                      ggbeeswarm_0.7.2                 
 [52] fansi_1.0.6                       S4Vectors_0.40.2                  abind_1.4-5                      
 [55] R.methodsS3_1.8.2                 lifecycle_1.0.4                   yaml_2.3.8                       
 [58] snakecase_0.11.1                  SummarizedExperiment_1.32.0       rhdf5_2.46.1                     
 [61] SparseArray_1.2.2                 BiocFileCache_2.10.1              Rtsne_0.17                       
 [64] paletteer_1.5.0                   grid_4.3.1                        blob_1.2.4                       
 [67] promises_1.2.1                    shinydashboard_0.7.2              crayon_1.5.2                     
 [70] Require_0.3.1                     miniUI_0.1.1.1                    lattice_0.22-5                   
 [73] cowplot_1.1.2                     GenomicFeatures_1.54.1            annotate_1.80.0                  
 [76] KEGGREST_1.42.0                   knitr_1.45                        pillar_1.9.0                     
 [79] GenomicRanges_1.54.1              rjson_0.2.21                      future.apply_1.11.0              
 [82] codetools_0.2-19                  fastmatch_1.1-4                   leiden_0.4.3.1                   
 [85] glue_1.6.2                        data.table_1.14.10                vctrs_0.6.5                      
 [88] png_0.1-8                         spam_2.10-0                       cellranger_1.1.0                 
 [91] gtable_0.3.4                      poweRlaw_0.70.6                   rematch2_2.1.2                   
 [94] cachem_1.0.8                      xfun_0.41                         Signac_1.12.0                    
 [97] S4Arrays_1.2.0                    mime_0.12                         pracma_2.4.4                     
[100] survival_3.5-7                    gargle_1.5.2                      RcppRoll_0.3.0                   
[103] ellipsis_0.3.2                    fitdistrplus_1.1-11               ROCR_1.0-11                      
[106] nlme_3.1-164                      bit64_4.0.5                       progress_1.2.3                   
[109] filelock_1.0.3                    RcppAnnoy_0.0.21                  GenomeInfoDb_1.38.2              
[112] irlba_2.3.5.1                     vipor_0.4.5                       KernSmooth_2.23-22               
[115] SeuratDisk_0.0.0.9021             colorspace_2.1-0                  seqLogo_1.68.0                   
[118] BiocGenerics_0.48.1               DBI_1.1.3                         ggrastr_1.0.2                    
[121] tidyselect_1.2.0                  bit_4.0.5                         compiler_4.3.1                   
[124] curl_5.2.0                        hdf5r_1.3.8                       xml2_1.3.6                       
[127] DelayedArray_0.28.0               plotly_4.10.3                     rtracklayer_1.62.0               
[130] scales_1.3.0                      caTools_1.18.2                    lmtest_0.9-40                    
[133] rappdirs_0.3.3                    stringr_1.5.1                     digest_0.6.33                    
[136] goftest_1.2-3                     presto_1.0.0                      spatstat.utils_3.0-4             
[139] rmarkdown_2.25                    XVector_0.42.0                    htmltools_0.5.7                  
[142] pkgconfig_2.0.3                   MatrixGenerics_1.14.0             dbplyr_2.4.0                     
[145] fastmap_1.1.1                     ensembldb_2.26.0                  GlobalOptions_0.1.2              
[148] rlang_1.1.2                       htmlwidgets_1.6.4                 shiny_1.8.0                      
[151] zoo_1.8-12                        jsonlite_1.8.8                    BiocParallel_1.36.0              
[154] R.oo_1.25.0                       RCurl_1.98-1.13                   magrittr_2.0.3                   
[157] GenomeInfoDbData_1.2.11           dotCall64_1.1-1                   patchwork_1.1.3                  
[160] Rhdf5lib_1.24.1                   munsell_0.5.0                     Rcpp_1.0.11                      
[163] reticulate_1.34.0                 stringi_1.8.3                     zlibbioc_1.48.0                  
[166] MASS_7.3-60                       plyr_1.8.9                        parallel_4.3.1                   
[169] listenv_0.9.0                     ggrepel_0.9.4                     forcats_1.0.0                    
[172] deldir_2.0-2                      CNEr_1.38.0                       Biostrings_2.70.1                
[175] splines_4.3.1                     tensor_1.5                        circlize_0.4.15                  
[178] hms_1.1.3                         BSgenome.Hsapiens.UCSC.hg38_1.4.5 igraph_1.6.0                     
[181] spatstat.geom_3.2-7               RcppHNSW_0.5.0                    reshape2_1.4.4                   
[184] biomaRt_2.58.0                    stats4_4.3.1                      TFMPvalue_0.0.9                  
[187] XML_3.99-0.16                     evaluate_0.23                     ggprism_1.0.4                    
[190] JASPAR2020_0.99.10                tzdb_0.4.0                        httpuv_1.6.13                    
[193] RANN_2.6.1                        tidyr_1.3.0                       purrr_1.0.2                      
[196] polyclip_1.10-6                   future_1.33.0                     scattermore_1.2                  
[199] ggplot2_3.4.4                     janitor_2.2.0                     xtable_1.8-4                     
[202] restfulr_0.0.15                   AnnotationFilter_1.26.0           RSpectra_0.16-1                  
[205] later_1.3.2                       googledrive_2.1.1                 viridisLite_0.4.2                
[208] tibble_3.2.1                      Azimuth_0.5.0                     beeswarm_0.4.0                   
[211] memoise_2.0.1                     AnnotationDbi_1.64.1              GenomicAlignments_1.38.0         
[214] IRanges_2.36.0                    cluster_2.1.6                     timechange_0.2.0   

[dcollins15]

A solution is available here.