Closed cutleraging closed 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