igrabski / sc-SHC

Significance analysis for clustering single-cell RNA-sequencing data
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scSHC function Error #1

Closed cutleraging closed 1 year ago

cutleraging commented 1 year ago
> clusters <- scSHC(obj)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘devianceFeatureSelection’ for signature ‘"Seurat"’
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] parallel  grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocNeighbors_1.12.0        dendextend_1.15.2           irlba_2.3.5                 Matrix_1.4-1                sctransform_0.3.3           MASS_7.3-56                
 [7] AER_1.2-10                  survival_3.3-1              sandwich_3.0-1              lmtest_0.9-40               zoo_1.8-10                  car_3.0-12                 
[13] carData_3.0-5               scry_1.6.0                  cluster_2.1.3               sigclust_1.1.0.1            cowplot_1.1.1               gridExtra_2.3              
[19] ggrepel_0.9.1               MultiK_0.1.0                devtools_2.4.3              usethis_2.1.5               clusterProfiler_4.2.2       msigdbr_7.5.1              
[25] scTyper_0.1.0               scater_1.22.0               scuttle_1.4.0               SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0             
[31] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4            BiocGenerics_0.40.0         factoextra_1.0.7           
[37] ROGUE_1.0                   MatrixGenerics_1.6.0        matrixStats_0.62.0          pheatmap_1.0.12             ggplot2_3.3.5               dplyr_1.0.8                
[43] patchwork_1.1.1             nichenetr_1.1.0             scCustomize_0.7.0           SeuratDisk_0.0.0.9019       SeuratObject_4.0.4          Seurat_4.1.0.9004          

loaded via a namespace (and not attached):
  [1] rsvd_1.0.5                Hmisc_4.7-0               ica_1.0-2                 class_7.3-20              ps_1.6.0                  foreach_1.5.2            
  [7] rprojroot_2.0.3           crayon_1.5.1              spatstat.core_2.4-2       dittoSeq_1.7.0            nlme_3.1-157              backports_1.4.1          
 [13] GOSemSim_2.20.0           rlang_1.0.2               XVector_0.34.0            caret_6.0-92              ROCR_1.0-11               callr_3.7.0              
 [19] limma_3.50.3              BiocParallel_1.28.3       rjson_0.2.21              bit64_4.0.5               glue_1.6.2                processx_3.5.3           
 [25] vipor_0.4.5               spatstat.sparse_2.1-1     AnnotationDbi_1.56.2      DOSE_3.20.1               spatstat.geom_2.4-0       tidyselect_1.1.2         
 [31] fitdistrplus_1.1-8        tidyr_1.2.0               ggpubr_0.4.0              xtable_1.8-4              magrittr_2.0.3            evaluate_0.15            
 [37] cli_3.2.0                 zlibbioc_1.40.0           rstudioapi_0.13           miniUI_0.1.1.1            rpart_4.1.16              fastmatch_1.1-3          
 [43] treeio_1.18.1             shiny_1.7.1               BiocSingular_1.10.0       xfun_0.30                 clue_0.3-60               pkgbuild_1.3.1           
 [49] caTools_1.18.2            tidygraph_1.2.1           KEGGREST_1.34.0           tibble_3.1.6              ape_5.6-2                 listenv_0.8.0            
 [55] Biostrings_2.62.0         png_0.1-7                 future_1.24.0             ipred_0.9-12              withr_2.5.0               ggforce_0.3.3            
 [61] bitops_1.0-7              plyr_1.8.7                hardhat_0.2.0             e1071_1.7-9               pROC_1.18.0               pillar_1.7.0             
 [67] GlobalOptions_0.1.2       cachem_1.0.6              fs_1.5.2                  hdf5r_1.3.5               GetoptLong_1.0.5          paletteer_1.4.0          
 [73] DelayedMatrixStats_1.16.0 vctrs_0.4.1               ellipsis_0.3.2            generics_0.1.2            lava_1.6.10               tools_4.1.2              
 [79] foreign_0.8-82            beeswarm_0.4.0            tweenr_1.0.2              munsell_0.5.0             fgsea_1.20.0              proxy_0.4-26             
 [85] DelayedArray_0.20.0       fastmap_1.1.0             compiler_4.1.2            pkgload_1.2.4             abind_1.4-5               httpuv_1.6.5             
 [91] sessioninfo_1.2.2         plotly_4.10.0             GenomeInfoDbData_1.2.7    prodlim_2019.11.13        colorway_0.2.0            lattice_0.20-45          
 [97] deldir_1.0-6              visNetwork_2.1.0          utf8_1.2.2                later_1.3.0               recipes_0.2.0             jsonlite_1.8.0           
[103] scales_1.2.0              ScaledMatrix_1.2.0        tidytree_0.3.9            pbapply_1.5-0             sparseMatrixStats_1.6.0   lazyeval_0.2.2           
[109] promises_1.2.0.1          doParallel_1.0.17         latticeExtra_0.6-29       goftest_1.2-3             spatstat.utils_2.3-0      reticulate_1.25          
[115] checkmate_2.0.0           rmarkdown_2.13            Rtsne_0.16                forcats_0.5.1             downloader_0.4            uwot_0.1.11              
[121] igraph_1.3.0              yaml_2.3.5                htmltools_0.5.2           memoise_2.0.1             fastqcr_0.1.2             graphlayouts_0.8.0       
[127] here_1.0.1                viridisLite_0.4.0         digest_0.6.29             assertthat_0.2.1          mime_0.12                 rappdirs_0.3.3           
[133] RSQLite_2.2.12            yulab.utils_0.0.4         future.apply_1.8.1        remotes_2.4.2             data.table_1.14.2         blob_1.2.3               
[139] DiagrammeR_1.0.9          splines_4.1.2             Formula_1.2-4             labeling_0.4.2            rematch2_2.1.2            RCurl_1.98-1.6           
[145] broom_0.8.0               hms_1.1.1                 colorspace_2.0-3          base64enc_0.1-3           BiocManager_1.30.16       ggbeeswarm_0.6.0         
[151] shape_1.4.6               aplot_0.1.3               ggrastr_1.0.1             nnet_7.3-17               Rcpp_1.0.8.3              RANN_2.6.1               
[157] circlize_0.4.14           enrichplot_1.14.2         fansi_1.0.3               tzdb_0.3.0                brio_1.1.3                parallelly_1.31.0        
[163] ModelMetrics_1.2.2.2      R6_2.5.1                  ggridges_0.5.3            lifecycle_1.0.1           curl_4.3.2                ggsignif_0.6.3           
[169] leiden_0.3.9              testthat_3.1.3            snakecase_0.11.0          DO.db_2.9                 qvalue_2.26.0             desc_1.4.1               
[175] RcppAnnoy_0.0.19          RColorBrewer_1.1-3        iterators_1.0.14          stringr_1.4.0             gower_1.0.0               htmlwidgets_1.5.4        
[181] beachmat_2.10.0           polyclip_1.10-0           purrr_0.3.4               shadowtext_0.1.1          gridGraphics_0.5-1        ComplexHeatmap_2.10.0    
[187] mgcv_1.8-40               globals_0.14.0            htmlTable_2.4.0           spatstat.random_2.2-0     codetools_0.2-18          lubridate_1.8.0          
[193] GO.db_3.14.0              randomForest_4.7-1        prettyunits_1.1.1         RSpectra_0.16-0           gtable_0.3.0              DBI_1.1.2                
[199] ggfun_0.0.6               tensor_1.5                httr_1.4.2                KernSmooth_2.23-20        stringi_1.7.6             reshape2_1.4.4           
[205] farver_2.1.0              viridis_0.6.2             fdrtool_1.2.17            ggtree_3.2.1              timeDate_3043.102         readr_2.1.2              
[211] ggplotify_0.1.0           scattermore_0.8           bit_4.0.4                 scatterpie_0.1.7          jpeg_0.1-9                spatstat.data_2.2-0      
[217] ggraph_2.0.5              janitor_2.1.0             pkgconfig_2.0.3           babelgene_22.3            ggprism_1.0.3.9000        rstatix_0.7.0            
[223] knitr_1.38