Package conflicts with dependencies

[ayyildizd]

Sorry for re-opening this issue but I am stuck here. If I install SeuratObject 4.1.3 or 4.1.4 I get the error:

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

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
 [1] readxl_1.4.3                yardstick_1.2.0             workflowsets_1.0.1          workflows_1.1.3            
 [5] tune_1.1.2                  rsample_1.2.0               recipes_1.0.8               parsnip_1.1.1              
 [9] modeldata_1.2.0             infer_1.0.5                 dials_1.2.0                 scales_1.3.0               
[13] broom_1.0.5                 tidymodels_1.1.1            gridExtra_2.3               Nebulosa_1.12.0            
[17] tradeSeq_1.16.0             slingshot_2.10.0            TrajectoryUtils_1.10.0      princurve_2.1.6            
[21] viridis_0.6.4               viridisLite_0.4.2           monocle3_1.3.4              UCell_2.6.2                
[25] stringr_1.5.1               DropletUtils_1.22.0         BiocParallel_1.36.0         scDblFinder_1.16.0         
[29] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 GenomicRanges_1.54.1        GenomeInfoDb_1.38.1        
[33] MatrixGenerics_1.14.0       matrixStats_1.1.0           harmony_1.1.0               Rcpp_1.0.11                
[37] easyGgplot2_1.0.0.9000      purrr_1.0.2                 tibble_3.2.1                patchwork_1.1.3            
[41] biomaRt_2.58.0              enrichplot_1.22.0           org.Hs.eg.db_3.18.0         AnnotationDbi_1.64.1       
[45] IRanges_2.36.0              S4Vectors_0.40.2            Biobase_2.62.0              BiocGenerics_0.48.1        
[49] clusterProfiler_4.10.0      magrittr_2.0.3              data.table_1.14.8           scCustomize_1.1.3          
[53] SeuratObject_4.1.4          Seurat_4.4.0                dplyr_1.1.4                 cli_3.6.1                  
[57] tidyr_1.3.0                 ggplot2_3.4.4              

loaded via a namespace (and not attached):
  [1] igraph_1.5.1              ica_1.0-3                 plotly_4.10.3             scater_1.30.0            
  [5] rematch2_2.1.2            zlibbioc_1.48.0           tidyselect_1.2.0          bit_4.0.5                
  [9] GPfit_1.0-8               doParallel_1.0.17         clue_0.3-65               lattice_0.22-5           
 [13] rjson_0.2.21              blob_1.2.4                S4Arrays_1.2.0            parallel_4.3.1           
 [17] png_0.1-8                 ggplotify_0.1.2           goftest_1.2-3             BiocIO_1.12.0            
 [21] bluster_1.12.0            BiocNeighbors_1.20.0      lhs_1.1.6                 uwot_0.1.16              
 [25] shadowtext_0.1.2          curl_5.1.0                mime_0.12                 tidytree_0.4.5           
 [29] leiden_0.4.3.1            ComplexHeatmap_2.18.0     stringi_1.8.2             backports_1.4.1          
 [33] XML_3.99-0.16             lubridate_1.9.3           httpuv_1.6.12             paletteer_1.5.0          
 [37] rappdirs_0.3.3            splines_4.3.1             RcppRoll_0.3.0            mclust_6.0.1             
 [41] prodlim_2023.08.28        ggraph_2.1.0              sctransform_0.4.1         ggbeeswarm_0.7.2         
 [45] DBI_1.1.3                 terra_1.7-55              HDF5Array_1.30.0          withr_2.5.2              
 [49] class_7.3-22              xgboost_1.7.6.1           lmtest_0.9-40             tidygraph_1.2.3          
 [53] rtracklayer_1.62.0        htmlwidgets_1.6.4         fs_1.6.3                  ggrepel_0.9.4            
 [57] SparseArray_1.2.2         cellranger_1.1.0          reticulate_1.34.0         zoo_1.8-12               
 [61] XVector_0.42.0            timechange_0.2.0          foreach_1.5.2             fansi_1.0.5              
 [65] grid_4.3.1                timeDate_4022.108         ggtree_3.10.0             rhdf5_2.46.1             
 [69] R.oo_1.25.0               irlba_2.3.5.1             ggrastr_1.0.2             gridGraphics_0.5-1       
 [73] ellipsis_0.3.2            lazyeval_0.2.2            yaml_2.3.7                survival_3.5-7           
 [77] scattermore_1.2           crayon_1.5.2              RcppAnnoy_0.0.21          RColorBrewer_1.1-3       
 [81] progressr_0.14.0          tweenr_2.0.2              later_1.3.1               ggridges_0.5.4           
 [85] codetools_0.2-19          GlobalOptions_0.1.2       KEGGREST_1.42.0           Rtsne_0.16               
 [89] shape_1.4.6               limma_3.58.1              Rsamtools_2.18.0          filelock_1.0.2           
 [93] DiceDesign_1.9            pkgconfig_2.0.3           xml2_1.3.6                GenomicAlignments_1.38.0 
 [97] aplot_0.2.2               spatstat.sparse_3.0-3     ape_5.7-1                 xtable_1.8-4             
[101] plyr_1.8.9                httr_1.4.7                tools_4.3.1               globals_0.16.2           
[105] hardhat_1.3.0             beeswarm_0.4.0            nlme_3.1-164              HDO.db_0.99.1            
[109] dbplyr_2.4.0              lme4_1.1-35.1             digest_0.6.33             Matrix_1.6-4             
[113] furrr_0.3.1               farver_2.1.1              reshape2_1.4.4            ks_1.14.1                
[117] yulab.utils_0.1.0         rpart_4.1.23              glue_1.6.2                cachem_1.0.8             
[121] BiocFileCache_2.10.1      polyclip_1.10-6           generics_0.1.3            Biostrings_2.70.1        
[125] mvtnorm_1.2-4             parallelly_1.36.0         statmod_1.5.0             R.cache_0.16.0           
[129] ScaledMatrix_1.10.0       minqa_1.2.6               pbapply_1.7-2             spam_2.10-0              
[133] gson_0.1.0                dqrng_0.3.2               utf8_1.2.4                gower_1.0.1              
[137] graphlayouts_1.0.2        shiny_1.8.0               lava_1.7.3                GenomeInfoDbData_1.2.11  
[141] R.utils_2.12.3            rhdf5filters_1.14.1       RCurl_1.98-1.13           memoise_2.0.1            
[145] pheatmap_1.0.12           R.methodsS3_1.8.2         future_1.33.0             RANN_2.6.1               
[149] spatstat.data_3.0-3       rstudioapi_0.15.0         cluster_2.1.6             janitor_2.2.0            
[153] spatstat.utils_3.0-4      hms_1.1.3                 fitdistrplus_1.1-11       munsell_0.5.0            
[157] cowplot_1.1.1             colorspace_2.1-0          rlang_1.1.2               DelayedMatrixStats_1.24.0
[161] sparseMatrixStats_1.14.0  ipred_0.9-14              dotCall64_1.1-1           ggforce_0.4.1            
[165] circlize_0.4.15           scuttle_1.12.0            mgcv_1.9-0                iterators_1.0.14         
[169] abind_1.4-5               GOSemSim_2.28.0           treeio_1.26.0             Rhdf5lib_1.24.0          
[173] bitops_1.0-7              promises_1.2.1            scatterpie_0.2.1          RSQLite_2.3.3            
[177] qvalue_2.34.0             fgsea_1.28.0              DelayedArray_0.28.0       GO.db_3.18.0             
[181] compiler_4.3.1            forcats_1.0.0             prettyunits_1.2.0         boot_1.3-28.1            
[185] beachmat_2.18.0           listenv_0.9.0             edgeR_4.0.2               BiocSingular_1.18.0      
[189] tensor_1.5                MASS_7.3-60               progress_1.2.2            spatstat.random_3.2-2    
[193] R6_2.5.1                  fastmap_1.1.1             fastmatch_1.1-4           vipor_0.4.5              
[197] ROCR_1.0-11               rsvd_1.0.5                nnet_7.3-19               gtable_0.3.4             
[201] KernSmooth_2.23-22        miniUI_0.1.1.1            deldir_2.0-2              htmltools_0.5.7          
[205] bit64_4.0.5               spatstat.explore_3.2-5    lifecycle_1.0.4           ggprism_1.0.4            
[209] nloptr_2.0.3              restfulr_0.0.15           vctrs_0.6.5               spatstat.geom_3.2-7      
[213] snakecase_0.11.1          DOSE_3.28.1               scran_1.30.0              ggfun_0.1.3              
[217] sp_2.1-2                  future.apply_1.11.0       pracma_2.4.4              pillar_1.9.0             
[221] prismatic_1.1.1           metapod_1.10.0            locfit_1.5-9.8            jsonlite_1.8.8           
[225] GetoptLong_1.0.5   

If I update SeuratObject to > version 5.0.0 which is where LayerData function is introduced, I get the same error as above when I run CellColorHeatmap()

Use the HVF to calculate distance metric.
Use 387 features to calculate distance.
Detected query data type: log_normalized_counts
Detected reference data type: log_normalized_counts
Calculate similarity...
Use 'raw' method to find neighbors.
Predict cell type...
Error: No cell overlap between new meta data and Seurat object

And solution seem to be SeuratObject 4.1.4 or 4.1.3 but they don't work as I stated above.