Error in .GetSeuratCompat() : no".GetSeuratCompat" function.

[asmlgkj]

rm(list = ls())
library(SeuratData)
── Installed datasets ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── SeuratData v0.2.1 ──
✔ ifnb 3.0.0 ✔ ssHippo 3.1.4
✔ panc8 3.0.2 ✔ stxBrain 0.1.1
✔ pbmc3k 3.1.4

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── Key ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ Dataset loaded successfully
❯ Dataset built with a newer version of Seurat than installed
❓ Unknown version of Seurat installed

library(Seurat)
Attaching SeuratObject
brain <- LoadData("stxBrain", type = "anterior1")
brain <- SCTransform(brain, assay = "Spatial", verbose = FALSE)
Error in .GetSeuratCompat() : no".GetSeuratCompat" function. -->

other attached packages:
[1] SeuratObject_4.1.4 Seurat_4.4.0
[3] stxBrain.SeuratData_0.1.1 ssHippo.SeuratData_3.1.4
[5] pbmc3k.SeuratData_3.1.4 panc8.SeuratData_3.0.2
[7] ifnb.SeuratData_3.0.0 SeuratData_0.2.1

loaded via a namespace (and not attached):
[1] Rtsne_0.17 colorspace_2.1-0 deldir_2.0-2
[4] ellipsis_0.3.2 ggridges_0.5.4 spatstat.data_3.0-3
[7] leiden_0.4.3.1 listenv_0.9.0 remotes_2.4.2.1
[10] ggrepel_0.9.5 fansi_1.0.6 codetools_0.2-19
[13] splines_4.2.3 polyclip_1.10-6 spam_2.10-0
[16] jsonlite_1.8.8 ica_1.0-3 cluster_2.1.6
[19] png_0.1-8 uwot_0.1.16 shiny_1.8.0
[22] sctransform_0.4.0 spatstat.sparse_3.0-3 compiler_4.2.3
[25] httr_1.4.7 Matrix_1.6-5 fastmap_1.1.1
[28] lazyeval_0.2.2 cli_3.6.2 later_1.3.2
[31] htmltools_0.5.7 tools_4.2.3 igraph_1.6.0
[34] dotCall64_1.1-1 gtable_0.3.4 glue_1.6.2
[37] RANN_2.6.1 reshape2_1.4.4 dplyr_1.1.4
[40] rappdirs_0.3.3 Rcpp_1.0.11 scattermore_1.2
[43] vctrs_0.6.5 spatstat.explore_3.2-5 nlme_3.1-164
[46] progressr_0.14.0 lmtest_0.9-40 spatstat.random_3.2-2
[49] stringr_1.5.1 ps_1.7.5 globals_0.16.2
[52] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.4
[55] irlba_2.3.5.1 goftest_1.2-3 future_1.33.1
[58] MASS_7.3-60 zoo_1.8-12 scales_1.3.0
[61] promises_1.2.1 spatstat.utils_3.0-4 parallel_4.2.3
[64] RColorBrewer_1.1-3 reticulate_1.34.0 pbapply_1.7-2
[67] gridExtra_2.3 ggplot2_3.4.4 stringi_1.8.3
[70] pkgbuild_1.4.3 rlang_1.1.2 pkgconfig_2.0.3
[73] matrixStats_1.2.0 lattice_0.22-5 ROCR_1.0-11
[76] purrr_1.0.2 tensor_1.5 patchwork_1.2.0
[79] htmlwidgets_1.6.4 processx_3.8.3 cowplot_1.1.1
[82] tidyselect_1.2.0 parallelly_1.36.0 RcppAnnoy_0.0.21
[85] plyr_1.8.9 magrittr_2.0.3 R6_2.5.1
[88] generics_0.1.3 pillar_1.9.0 fitdistrplus_1.1-11
[91] survival_3.5-7 abind_1.4-5 sp_2.1-2
[94] tibble_3.2.1 future.apply_1.11.1 crayon_1.5.2
[97] KernSmooth_2.23-22 utf8_1.2.4 spatstat.geom_3.2-7
[100] plotly_4.10.3 grid_4.2.3 data.table_1.14.10
[103] callr_3.7.3 digest_0.6.33 xtable_1.8-4
[106] tidyr_1.3.0 httpuv_1.6.13 munsell_0.5.0
[109] viridisLite_0.4.2 tcltk_4.2.3

rm(list = ls())
library(SeuratData)
library(Seurat)
brain <- LoadData("stxBrain", type = "anterior1")
brain <- SCTransform(brain, assay = "Spatial", verbose = FALSE)

[lgaspardboulinc31]

Hi ! I add same issue but found a fix here by following the advices. satijalab/seurat-object#165

[jjccco]

I just made it work successfully! Please uninstall and then install these packages with a particular version——SeuratObject(4.1.3), sctransform(0.3.5) and Seurat(4.3.0)

[AlonsoOga]

Hi @jjccco could you provide guidance on how to install previous versions of sctransform? I am only able to get sctransform0.4.1 and SCTransform only when I update BiocManager.

[dbtsshome]

@AlonsoOga library(devtools) ; install_version("Seurat",version='4.4.0.0')