Package or namespace load failed for ‘SCP’

[Streisenberg]

Hello Hao,

I am experiencing an issue while trying to load the package. The error message I'm receiving is as follows:

Error: package or namespace load failed for ‘SCP’:
 object ‘LayerData<-’ is not exported by 'namespace:SeuratObject'

I attempted to troubleshoot this issue from the Seurat/SeuratObject end but I haven't been successful yet. Any assistance you could provide would be greatly appreciated!

To help reproduce the issue, here is my session info:

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.5

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] slingshot_2.6.0             TrajectoryUtils_1.6.0       SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
 [5] Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0             
 [9] S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0       matrixStats_1.0.0          
[13] princurve_2.1.6             ggthemes_4.2.4              RColorBrewer_1.1-3          patchwork_1.1.2            
[17] lubridate_1.9.2             forcats_1.0.0               stringr_1.5.0               dplyr_1.1.2                
[21] purrr_1.0.1                 readr_2.1.4                 tidyr_1.3.0                 tibble_3.2.1               
[25] ggplot2_3.4.2               tidyverse_2.0.0             SCpubr_1.1.2.9000           harmony_0.1.1              
[29] Rcpp_1.0.11                 data.table_1.14.8           SeuratObject_4.1.3          Seurat_4.3.0               
[33] CytoTRACE_0.3.3            

loaded via a namespace (and not attached):
  [1] scattermore_1.1           R.methodsS3_1.8.2         ragg_1.2.5                bit64_4.0.5              
  [5] irlba_2.3.5.1             DelayedArray_0.24.0       R.utils_2.12.2            KEGGREST_1.38.0          
  [9] RCurl_1.98-1.12           doParallel_1.0.17         generics_0.1.3            callr_3.7.3              
 [13] cowplot_1.1.1             usethis_2.1.6             RSQLite_2.3.1             RANN_2.6.1               
 [17] future_1.32.0             bit_4.0.5                 tzdb_0.4.0                HiClimR_2.2.1            
 [21] spatstat.data_3.0-1       httpuv_1.6.11             hms_1.1.3                 promises_1.2.0.1         
 [25] DEoptimR_1.1-0            fansi_1.0.4               igraph_1.5.0              DBI_1.1.3                
 [29] htmlwidgets_1.6.2         spacexr_2.2.1             spatstat.geom_3.2-1       ellipsis_0.3.2           
 [33] annotate_1.76.0           sparseMatrixStats_1.10.0  deldir_1.0-9              vctrs_0.6.3              
 [37] remotes_2.4.2             here_1.0.1                ROCR_1.0-11               abind_1.4-5              
 [41] cachem_1.0.8              withr_2.5.0               robustbase_0.99-0         progressr_0.13.0         
 [45] sctransform_0.3.5         prettyunits_1.1.1         goftest_1.2-3             cluster_2.1.4            
 [49] lazyeval_0.2.2            crayon_1.5.2              genefilter_1.80.3         spatstat.explore_3.2-1   
 [53] edgeR_3.40.2              pkgconfig_2.0.3           labeling_0.4.2            nlme_3.1-162             
 [57] pkgload_1.3.2.1           devtools_2.4.5            rlang_1.1.1               globals_0.16.2           
 [61] lifecycle_1.0.3           miniUI_0.1.1.1            rsvd_1.0.5                rprojroot_2.0.3          
 [65] polyclip_1.10-4           lmtest_0.9-40             Matrix_1.5-4              zoo_1.8-12               
 [69] ggridges_0.5.4            GlobalOptions_0.1.2       processx_3.8.2            png_0.1-8                
 [73] viridisLite_0.4.2         rjson_0.2.21              bitops_1.0-7              R.oo_1.25.0              
 [77] KernSmooth_2.23-21        Biostrings_2.66.0         DelayedMatrixStats_1.20.0 blob_1.2.4               
 [81] shape_1.4.6               parallelly_1.36.0         spatstat.random_3.1-5     R.cache_0.16.0           
 [85] scales_1.2.1              memoise_2.0.1             magrittr_2.0.3            plyr_1.8.8               
 [89] ica_1.0-3                 zlibbioc_1.44.0           compiler_4.2.2            clue_0.3-64              
 [93] fitdistrplus_1.1-11       Rsamtools_2.14.0          cli_3.6.1                 XVector_0.38.0           
 [97] urlchecker_1.0.1          SeuratWrappers_0.3.1      listenv_0.9.0             pbapply_1.7-0            
[101] ps_1.7.5                  MASS_7.3-60               mgcv_1.8-42               tidyselect_1.2.0         
[105] stringi_1.7.12            textshaping_0.3.6         locfit_1.5-9.7            ggrepel_0.9.3            
[109] grid_4.2.2                tools_4.2.2               timechange_0.2.0          future.apply_1.11.0      
[113] parallel_4.2.2            circlize_0.4.15           rstudioapi_0.14           ccaPP_0.3.3              
[117] foreach_1.5.2             gridExtra_2.3             farver_2.1.1              Rtsne_0.16               
[121] digest_0.6.33             BiocManager_1.30.20       shiny_1.7.4.1             later_1.3.1              
[125] RcppAnnoy_0.0.20          ncdf4_1.21                httr_1.4.6                AnnotationDbi_1.60.2     
[129] ComplexHeatmap_2.15.4     colorspace_2.1-0          XML_3.99-0.14             fs_1.6.2                 
[133] tensor_1.5                reticulate_1.30           splines_4.2.2             uwot_0.1.14              
[137] RcppRoll_0.3.0            spatstat.utils_3.0-3      sp_1.6-1                  plotly_4.10.2            
[141] sessioninfo_1.2.2         systemfonts_1.0.4         xtable_1.8-4              jsonlite_1.8.7           
[145] R6_2.5.1                  profvis_0.3.8             pillar_1.9.0              htmltools_0.5.5          
[149] mime_0.12                 nnls_1.4                  glue_1.6.2                fastmap_1.1.1            
[153] BiocParallel_1.32.6       codetools_0.2-19          pkgbuild_1.4.0            pcaPP_2.0-3              
[157] mvtnorm_1.2-2             utf8_1.2.3                lattice_0.21-8            spatstat.sparse_3.0-1    
[161] sva_3.46.0                curl_5.0.1                leiden_0.4.3              survival_3.5-5           
[165] limma_3.54.2              munsell_0.5.0             GetoptLong_1.0.5          GenomeInfoDbData_1.2.9   
[169] iterators_1.0.14          reshape2_1.4.4            gtable_0.3.3 

Also I have the following versions of the "SCP", "Seurat" and "SeuratObject" packages installed:

> packageVersion("SCP")
[1] ‘0.4.7.9000’
> packageVersion("Seurat")
[1] ‘4.3.0’
> packageVersion("SeuratObject")
[1] ‘4.1.3’

Thank you in advance for any help!

[zhanghao-njmu]

Strange. In Seurat v4 or SeuratObject v4, there should not be a function called LayerData. This function is only exported in version 5. Therefore, please double-check if the version of Seurat in your environment is indeed v4.

https://github.com/satijalab/seurat/blob/727d26176d87c96c36ccd79d51219e66c9f0da37/NAMESPACE#L517C26-L517C35 https://github.com/mojaveazure/seurat-object/blob/89fe70b832602dd5dc4f846ccd086223a3129fa5/NAMESPACE#L36

[Sinejune]

I had the same problem, you can try upgrading matrix to 1.6.1.1 and seuratobject to version 5.0, hope this helps!

[kli28]

Same with this problem. When I installed SCP following the instructions, it installed seurat v5.0 by default. And then I just changed it to Seurat 4.4.0. Then I met the problem. But I think upgrading seuratobject to version 5.0 is not a good idea? Because most of the tools in SCP may be supported by Seurat 4 ? So is it possible to be forced to install Seurat 4?

[kli28]

@Streisenberg Hi, Have you solved this problem in other ways instead of changing seuratobject to version 5.0?

[Jaimelan]

I also have this problem with seurat 4.4.0

[xiaodiYan]

I also have this problem with seurat 4.4.0