Closed alexvpickering closed 5 months ago
Following the vignette I keep getting error Error in .subset2(x, i, exact = exact) : subscript out of bounds:
Error in .subset2(x, i, exact = exact) : subscript out of bounds
library(Seurat) library(SeuratData) options(Seurat.object.assay.version = "v5") pbmc3k <- LoadData("pbmc3k") class(pbmc3k[["RNA"]]) # [1] "Assay5" # attr(,"package") # [1] "SeuratObject" as(object = pbmc3k[["RNA"]], Class = "Assay") Warning: No layers found matching search pattern provided Warning: No layers found matching search pattern provided Error in .subset2(x, i, exact = exact) : subscript out of bounds In addition: Warning message: Layer ‘scale.data’ is empty
Have tried with a few different datasets and getting the same error.
sessionInfo() R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 [6] LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C time zone: America/Vancouver tzcode source: system (glibc) 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_5.1.0 SeuratObject_5.0.2 sp_2.1-4 loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 remotes_2.5.0 rlang_1.1.3 magrittr_2.0.3 [7] RcppAnnoy_0.0.22 matrixStats_1.3.0 ggridges_0.5.6 compiler_4.4.0 spatstat.geom_3.2-9 png_0.1-8 [13] vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1 crayon_1.5.2 pkgconfig_2.0.3 fastmap_1.2.0 [19] utf8_1.2.4 promises_1.3.0 purrr_1.0.2 jsonlite_1.8.8 goftest_1.2-3 later_1.3.2 [25] spatstat.utils_3.0-4 irlba_2.3.5.1 parallel_4.4.0 cluster_2.1.6 R6_2.5.1 ica_1.0-3 [31] stringi_1.8.4 RColorBrewer_1.1-3 spatstat.data_3.0-4 reticulate_1.36.1 parallelly_1.37.1 lmtest_0.9-40 [37] scattermore_1.2 Rcpp_1.0.12 tensor_1.5 future.apply_1.11.2 zoo_1.8-12 sctransform_0.4.1 [43] httpuv_1.6.15 Matrix_1.6-5 splines_4.4.0 igraph_2.0.3 tidyselect_1.2.1 abind_1.4-5 [49] spatstat.random_3.2-3 codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.2-7 curl_5.2.1 listenv_0.9.1 [55] lattice_0.22-5 tibble_3.2.1 plyr_1.8.9 shiny_1.8.1.1 ROCR_1.0-11 Rtsne_0.17 [61] future_1.33.2 fastDummies_1.7.3 survival_3.5-8 polyclip_1.10-6 fitdistrplus_1.1-11 pillar_1.9.0 [67] KernSmooth_2.23-22 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 ggplot2_3.5.1 munsell_0.5.1 [73] scales_1.3.0 globals_0.16.3 xtable_1.8-4 glue_1.7.0 lazyeval_0.2.2 tools_4.4.0 [79] data.table_1.15.4 RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1 dotCall64_1.1-1 cowplot_1.1.3 [85] grid_4.4.0 tidyr_1.3.1 colorspace_2.1-0 nlme_3.1-163 patchwork_1.2.0 cli_3.6.2 [91] rappdirs_0.3.3 spatstat.sparse_3.0-3 spam_2.10-0 fansi_1.0.6 viridisLite_0.4.2 dplyr_1.1.4 [97] uwot_0.2.2 gtable_0.3.5 digest_0.6.35 progressr_0.14.0 ggrepel_0.9.5 htmlwidgets_1.6.4 [103] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12 MASS_7.3-60 >
Sorry wrong repo
alexvpickering
commented
5 months ago alexvpickering
commented
5 months ago
Following the vignette I keep getting error
Error in .subset2(x, i, exact = exact) : subscript out of bounds:Have tried with a few different datasets and getting the same error.