Open neuhausi opened 6 months ago
library(Seurat) library(ggplot2) library(sctransform) library(SeuratData) ... InstallData("pbmc3k") ... data("pbmc3k") pbmc3k Error: Please run UpdateSeuratObject on your object Error during wrapup: no slot of name "images" for this object of class "Seurat" Error: no more error handlers available (recursive errors?); invoking 'abort' restart .... pbmc3k = UpdateSeuratObject(pbmc3k) ... 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 pbmc <- CreateSeuratObject(counts = pbmc3k) Warning: Data is of class Seurat. Coercing to dgCMatrix. Error in UseMethod(generic = "as.sparse", object = x) : no applicable method for 'as.sparse' applied to an object of class "Seurat" .... sessionInfo() R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.4.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 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: America/New_York tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] cbmc.SeuratData_3.1.4 pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2.9001 sctransform_0.4.1 ggplot2_3.5.1 [6] Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-4 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3 spatstat.utils_3.0-4 rmarkdown_2.26 [7] fs_1.6.4 vctrs_0.6.5 ROCR_1.0-11 memoise_2.0.1 spatstat.explore_3.2-7 usethis_2.2.3 [13] htmltools_0.5.8.1 curl_5.2.1 parallelly_1.37.1 KernSmooth_2.23-22 desc_1.4.3 htmlwidgets_1.6.4 [19] ica_1.0-3 plyr_1.8.9 plotly_4.10.4 zoo_1.8-12 cachem_1.0.8 igraph_2.0.3 [25] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0 R6_2.5.1 fastmap_1.1.1 [31] fitdistrplus_1.1-11 future_1.33.2 shiny_1.8.1.1 digest_0.6.35 colorspace_2.1-0 ps_1.7.6 [37] patchwork_1.2.0 tensor_1.5 RSpectra_0.16-1 irlba_2.3.5.1 pkgload_1.3.4 progressr_0.14.0 [43] fansi_1.0.6 spatstat.sparse_3.0-3 httr_1.4.7 polyclip_1.10-6 abind_1.4-5 compiler_4.4.0 [49] remotes_2.5.0 withr_3.0.0 fastDummies_1.7.3 pkgbuild_1.4.4 MASS_7.3-60.2 canvasXpress_1.43.7 [55] rappdirs_0.3.3 sessioninfo_1.2.2 tools_4.4.0 lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.2 [61] goftest_1.2-3 glue_1.7.0 callr_3.7.6 nlme_3.1-164 promises_1.3.0 grid_4.4.0 [67] Rtsne_0.17 cluster_2.1.6 reshape2_1.4.4 generics_0.1.3 gtable_0.3.5 spatstat.data_3.0-4 [73] tidyr_1.3.1 data.table_1.15.4 utf8_1.2.4 spatstat.geom_3.2-9 RcppAnnoy_0.0.22 ggrepel_0.9.5 [79] RANN_2.6.1 pillar_1.9.0 stringr_1.5.1 spam_2.10-0 RcppHNSW_0.6.0 later_1.3.2 [85] splines_4.4.0 dplyr_1.1.4 lattice_0.22-6 survival_3.5-8 deldir_2.0-4 tidyselect_1.2.1 [91] miniUI_0.1.1.1 pbapply_1.7-2 knitr_1.46 gridExtra_2.3 scattermore_1.2 xfun_0.43 [97] devtools_2.4.5 matrixStats_1.3.0 stringi_1.8.3 lazyeval_0.2.2 yaml_2.3.8 evaluate_0.23 [103] codetools_0.2-20 tibble_3.2.1 cli_3.6.2 uwot_0.2.2 xtable_1.8-4 reticulate_1.36.1 [109] processx_3.8.4 munsell_0.5.1 Rcpp_1.0.12 globals_0.16.3 spatstat.random_3.2-3 png_0.1-8 [115] parallel_4.4.0 ellipsis_0.3.2 dotCall64_1.1-1 profvis_0.3.8 urlchecker_1.0.1 listenv_0.9.1 [121] viridisLite_0.4.2 scales_1.3.0 ggridges_0.5.6 crayon_1.5.2 leiden_0.4.3.1 purrr_1.0.2 [127] rlang_1.1.3 cowplot_1.1.3
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