Error while subsetting Seurat Object : object 'CRsparse_rowSums' not found

[KshitijDeoghar]

I am trying to do Motif Enrichment analysis for an immune-cell scATAC-seq dataset.
Since I was getting errors with FindMarkers for the Motif Enrichment step, I just tried to extract the standard chromosomes. Earlier, it used to work fine, but I am running into this error

DefaultAssay(Granulocytes) <- "peaks"

features.keep <- as.character(seqnames(granges(Granulocytes))) %in% standardChromosomes(granges(Granulocytes))

Granulocytes <- Granulocytes[features.keep, ]

After this line of code, I am getting the error -
Error in .local(x, na.rm, dims, ...) :
object 'CRsparse_rowSums' not found

Any help would be appreciated.

sessionInfo()

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets
[7] methods base

other attached packages:
[1] lubridate_1.9.4
[2] forcats_1.0.0
[3] stringr_1.5.1
[4] purrr_1.0.2
[5] readr_2.1.5
[6] tidyr_1.3.1
[7] tibble_3.2.1
[8] tidyverse_2.0.0
[9] dplyr_1.1.4
[10] harmony_1.2.3
[11] Rcpp_1.0.13-1
[12] ggplot2_3.5.1
[13] EnsDb.Mmusculus.v79_2.99.0
[14] ensembldb_2.26.0
[15] AnnotationFilter_1.26.0
[16] GenomicFeatures_1.54.4
[17] AnnotationDbi_1.64.1
[18] Biobase_2.62.0
[19] hdf5r_1.3.11
[20] Signac_1.14.0
[21] Seurat_5.1.0
[22] chromVAR_1.24.0
[23] motifmatchr_1.24.0
[24] patchwork_1.3.0
[25] BSgenome.Mmusculus.UCSC.mm10_1.4.3
[26] BSgenome_1.70.2
[27] rtracklayer_1.62.0
[28] BiocIO_1.12.0
[29] Biostrings_2.70.3
[30] XVector_0.42.0
[31] GenomicRanges_1.54.1
[32] GenomeInfoDb_1.38.8
[33] IRanges_2.36.0
[34] S4Vectors_0.40.2
[35] BiocGenerics_0.48.1
[36] TFBSTools_1.40.0
[37] JASPAR2020_0.99.10
[38] SeuratObject_5.0.2
[39] sp_2.1-4

loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 matrixStats_1.4.1
[3] spatstat.sparse_3.1-0 bitops_1.0-9
[5] DirichletMultinomial_1.44.0 httr_1.4.7
[7] RColorBrewer_1.1-3 tools_4.3.3
[9] sctransform_0.4.1 R6_2.5.1
[11] DT_0.33 lazyeval_0.2.2
[13] uwot_0.2.2 withr_3.0.2
[15] prettyunits_1.2.0 gridExtra_2.3
[17] progressr_0.15.1 cli_3.6.3
[19] spatstat.explore_3.3-3 fastDummies_1.7.4
[21] spatstat.data_3.1-4 ggridges_0.5.6
[23] pbapply_1.7-2 Rsamtools_2.18.0
[25] R.utils_2.12.3 parallelly_1.41.0
[27] rstudioapi_0.17.1 RSQLite_2.3.9
[29] generics_0.1.3 gtools_3.9.5
[31] ica_1.0-3 spatstat.random_3.3-2
[33] GO.db_3.18.0 Matrix_1.6-5
[35] abind_1.4-8 R.methodsS3_1.8.2
[37] lifecycle_1.0.4 yaml_2.3.10
[39] SummarizedExperiment_1.32.0 SparseArray_1.2.4
[41] BiocFileCache_2.10.2 Rtsne_0.17
[43] grid_4.3.3 blob_1.2.4
[45] promises_1.3.2 crayon_1.5.3
[47] miniUI_0.1.1.1 lattice_0.22-5
[49] cowplot_1.1.3 annotate_1.80.0
[51] KEGGREST_1.42.0 pillar_1.10.1
[53] rjson_0.2.23 future.apply_1.11.3
[55] codetools_0.2-19 fastmatch_1.1-6
[57] leiden_0.4.3.1 glue_1.8.0
[59] spatstat.univar_3.1-1 data.table_1.16.4
[61] vctrs_0.6.5 png_0.1-8
[63] spam_2.11-0 gtable_0.3.6
[65] poweRlaw_0.80.0 cachem_1.1.0
[67] S4Arrays_1.2.1 mime_0.12
[69] pracma_2.4.4 survival_3.5-8
[71] RcppRoll_0.3.1 fitdistrplus_1.2-2
[73] ROCR_1.0-11 nlme_3.1-164
[75] bit64_4.5.2 progress_1.2.3
[77] filelock_1.0.3 RcppAnnoy_0.0.22
[79] irlba_2.3.5.1 KernSmooth_2.23-22
[81] colorspace_2.1-1 seqLogo_1.68.0
[83] DBI_1.2.3 tidyselect_1.2.1
[85] bit_4.5.0.1 compiler_4.3.3
[87] curl_6.0.1 xml2_1.3.6
[89] DelayedArray_0.28.0 plotly_4.10.4
[91] scales_1.3.0 caTools_1.18.3
[93] lmtest_0.9-40 rappdirs_0.3.3
[95] digest_0.6.37 goftest_1.2-3
[97] spatstat.utils_3.1-1 htmltools_0.5.8.1
[99] pkgconfig_2.0.3 MatrixGenerics_1.14.0
[101] dbplyr_2.5.0 fastmap_1.2.0
[103] rlang_1.1.4 htmlwidgets_1.6.4
[105] shiny_1.10.0 farver_2.1.2
[107] zoo_1.8-12 jsonlite_1.8.9
[109] BiocParallel_1.36.0 R.oo_1.27.0
[111] RCurl_1.98-1.16 magrittr_2.0.3
[113] GenomeInfoDbData_1.2.11 dotCall64_1.2
[115] munsell_0.5.1 reticulate_1.40.0
[117] stringi_1.8.4 zlibbioc_1.48.2
[119] MASS_7.3-60.0.1 plyr_1.8.9
[121] parallel_4.3.3 listenv_0.9.1
[123] ggrepel_0.9.6 deldir_2.0-4
[125] CNEr_1.38.0 splines_4.3.3
[127] tensor_1.5 hms_1.1.3
[129] igraph_2.1.2 spatstat.geom_3.3-4
[131] RcppHNSW_0.6.0 reshape2_1.4.4
[133] biomaRt_2.58.2 TFMPvalue_0.0.9
[135] XML_3.99-0.18 BiocManager_1.30.25
[137] tzdb_0.4.0 httpuv_1.6.15
[139] RANN_2.6.2 polyclip_1.10-7
[141] future_1.34.0 scattermore_1.2
[143] xtable_1.8-4 restfulr_0.0.15
[145] RSpectra_0.16-2 later_1.4.1
[147] viridisLite_0.4.2 memoise_2.0.1
[149] GenomicAlignments_1.38.2 cluster_2.1.6
[151] timechange_0.3.0 globals_0.16.3

[timoast]

Please see here: #1596