LoadVizgen function not found

[wdg118]

Hi,
I'm trying to work through the vignette here (https://satijalab.org/seurat/articles/spatial_vignette_2.html) but when I try to load my vizgen data it says 'could not find function "LoadVizgen" '

This is the code I used:

library(remotes)
library(Seurat)
library(future)
plan("multisession", workers = 10)
vizgen.obj <- LoadVizgen(data.dir = "directory_to_my_file", fov = "276")

Thanks,

Will

[AustinHartman]

Make sure you have installed the correct branch of Seurat with devtools::install_github("satijalab/seurat", "feat/imaging") and that you are loading that version of Seurat when you call LoadVizgen

[sdwien]

Dear Seurat Team,

I seem to have a problem when installing this particular branch of Seurat from guthub.

I tried both:

library(remotes)
remotes::install_github("satijalab/seurat", "feat/imaging")

and:

devtools::install_github("satijalab/seurat", "feat/imaging")

and the message I am getting in both cases is:

Downloading GitHub repo satijalab/seurat@feat/imaging
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                          
2: CRAN packages only                           
3: None                                         
4: SeuratObject (4.1.0 -> 6bdcdda14...) [GitHub]

Enter one or more numbers, or an empty line to skip updates: 1
SeuratObject (4.1.0 -> 6bdcdda14...) [GitHub]
Downloading GitHub repo mojaveazure/seurat-object@develop
Error: Failed to install 'Seurat' from GitHub:
  Failed to install 'SeuratObject' from GitHub:
  lazy-load database '/project/R/x86_64-pc-linux-gnu-library/4.2/crayon/R/crayon.rdb' is corrupt
In addition: Warning messages:
1: In compiler_flags(debug = FALSE) :
  restarting interrupted promise evaluation
2: In compiler_flags(debug = FALSE) : internal error -3 in R_decompress1

Here goes my session info:

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] remotes_2.4.2      sp_1.5-0           SeuratObject_4.1.0 Seurat_4.1.1      

loaded via a namespace (and not attached):
  [1] plyr_1.8.7                  igraph_1.3.5               
  [3] lazyeval_0.2.2              splines_4.2.1              
  [5] listenv_0.8.0               scattermore_0.8            
  [7] usethis_2.1.6               GenomeInfoDb_1.32.2        
  [9] ggplot2_3.3.6               digest_0.6.30              
 [11] htmltools_0.5.3             fansi_1.0.3                
 [13] magrittr_2.0.3              memoise_2.0.1              
 [15] tensor_1.5                  cluster_2.1.4              
 [17] ROCR_1.0-11                 globals_0.16.1             
 [19] matrixStats_0.62.0          spatstat.sparse_3.0-0      
 [21] prettyunits_1.1.1           colorspace_2.0-3           
 [23] ggrepel_0.9.1               dplyr_1.0.10               
 [25] callr_3.7.1                 crayon_1.5.2               
 [27] RCurl_1.98-1.8              jsonlite_1.8.3             
 [29] progressr_0.11.0            spatstat.data_3.0-0        
 [31] survival_3.4-0              zoo_1.8-11                 
 [33] glue_1.6.2                  polyclip_1.10-4            
 [35] gtable_0.3.1                zlibbioc_1.42.0            
 [37] XVector_0.36.0              leiden_0.4.3               
 [39] DelayedArray_0.22.0         pkgbuild_1.3.1             
 [41] future.apply_1.9.1          BiocGenerics_0.42.0        
 [43] abind_1.4-5                 scales_1.2.1               
 [45] DBI_1.1.3                   spatstat.random_3.0-0      
 [47] miniUI_0.1.1.1              Rcpp_1.0.9                 
 [49] viridisLite_0.4.1           xtable_1.8-4               
 [51] reticulate_1.26             spatstat.core_2.4-4        
 [53] stats4_4.2.1                profvis_0.3.7              
 [55] htmlwidgets_1.5.4           httr_1.4.4                 
 [57] RColorBrewer_1.1-3          ellipsis_0.3.2             
 [59] ica_1.0-3                   urlchecker_1.0.1           
 [61] pkgconfig_2.0.3             uwot_0.1.14                
 [63] deldir_1.0-6                utf8_1.2.2                 
 [65] tidyselect_1.2.0            rlang_1.0.6                
 [67] reshape2_1.4.4              later_1.3.0                
 [69] munsell_0.5.0               tools_4.2.1                
 [71] cachem_1.0.6                cli_3.4.1                  
 [73] generics_0.1.3              devtools_2.4.5             
 [75] ggridges_0.5.4              stringr_1.4.1              
 [77] fastmap_1.1.0               goftest_1.2-3              
 [79] processx_3.7.0              fs_1.5.2                   
 [81] fitdistrplus_1.1-8          purrr_0.3.5                
 [83] RANN_2.6.1                  pbapply_1.5-0              
 [85] future_1.28.0               nlme_3.1-160               
 [87] mime_0.12                   compiler_4.2.1             
 [89] plotly_4.10.0               curl_4.3.3                 
 [91] png_0.1-7                   spatstat.utils_3.0-1       
 [93] tibble_3.1.8                stringi_1.7.8              
 [95] ps_1.7.1                    rgeos_0.5-9                
 [97] lattice_0.20-45             Matrix_1.5-1               
 [99] vctrs_0.5.0                 pillar_1.8.1               
[101] lifecycle_1.0.3             spatstat.geom_3.0-3        
[103] lmtest_0.9-40               RcppAnnoy_0.0.20           
[105] data.table_1.14.4           cowplot_1.1.1              
[107] bitops_1.0-7                irlba_2.3.5.1              
[109] httpuv_1.6.6                patchwork_1.1.2            
[111] GenomicRanges_1.48.0        R6_2.5.1                   
[113] promises_1.2.0.1            KernSmooth_2.23-20         
[115] gridExtra_2.3               IRanges_2.30.0             
[117] parallelly_1.32.1           sessioninfo_1.2.2          
[119] codetools_0.2-18            MASS_7.3-58                
[121] assertthat_0.2.1            pkgload_1.3.0              
[123] SummarizedExperiment_1.26.1 rprojroot_2.0.3            
[125] withr_2.5.0                 sctransform_0.3.5          
[127] S4Vectors_0.34.0            GenomeInfoDbData_1.2.8     
[129] mgcv_1.8-40                 parallel_4.2.1             
[131] grid_4.2.1                  rpart_4.1.16               
[133] tidyr_1.2.1                 MatrixGenerics_1.8.1       
[135] Rtsne_0.16                  Biobase_2.56.0             
[137] shiny_1.7.3  

Any ideas what is missing / not working here?

Many thanks,
best,
Sophia

[sdwien]

Update to my previous post:
After restarting R, the installation from the github repository worked, and after that, I loaded Seurat:

library(Seurat)

and was able to access the LoadVizgen function:

?LoadVizgen

Best,
Sophia

PS.: Just a remark, in the usage page, in the first line and in the usage example, it says "ReadVizgen" ...