I got this error with default settings. Any suggestions? Thank you very much in advance!
sds <- slingshot(rd, # input
dist.method = "slingshot", # this is default; see createClusterMST for details. c("simple", "scaled.full", "scaled.diag", "slingshot", "mnn")
df$cl)
top_res <- topologyTest(sds = sds, # slingshot results, asuming all conditions the same
conditions = df$conditions)
## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux
##
## Matrix products: default
## BLAS: /usr/lib64/libblas.so.3.4.2
## LAPACK: /usr/lib64/liblapack.so.3.4.2
##
## 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] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] caret_6.0-92 lattice_0.20-45
## [3] viridis_0.6.2 viridisLite_0.4.1
## [5] RColorBrewer_1.1-3 ggplot2_3.4.1
## [7] readxl_1.4.0 writexl_1.4.0
## [9] knitr_1.41 tidyr_1.2.1
## [11] dplyr_1.0.10 SeuratObject_4.1.3
## [13] Seurat_4.3.0 slingshot_2.4.0
## [15] TrajectoryUtils_1.4.0 SingleCellExperiment_1.20.1
## [17] SummarizedExperiment_1.28.0 Biobase_2.58.0
## [19] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
## [21] IRanges_2.32.0 S4Vectors_0.36.2
## [23] BiocGenerics_0.44.0 MatrixGenerics_1.10.0
## [25] matrixStats_0.63.0 princurve_2.1.6
## [27] condiments_1.4.0
##
## loaded via a namespace (and not attached):
## [1] pacman_0.5.1 utf8_1.2.3
## [3] spatstat.explore_3.0-5 reticulate_1.26
## [5] tidyselect_1.2.0 htmlwidgets_1.5.4
## [7] grid_4.2.0 BiocParallel_1.30.4
## [9] Rtsne_0.16 pROC_1.18.0
## [11] munsell_0.5.0 ScaledMatrix_1.6.0
## [13] ragg_1.2.2 codetools_0.2-18
## [15] ica_1.0-3 future_1.29.0
## [17] miniUI_0.1.1.1 withr_2.5.0
## [19] spatstat.random_3.0-1 colorspace_2.1-0
## [21] progressr_0.11.0 highr_0.9
## [23] ROCR_1.0-11 tensor_1.5
## [25] listenv_0.8.0 labeling_0.4.2
## [27] GenomeInfoDbData_1.2.9 polyclip_1.10-4
## [29] farver_2.1.1 distinct_1.8.0
## [31] parallelly_1.32.1 vctrs_0.5.1
## [33] generics_0.1.3 ipred_0.9-12
## [35] xfun_0.35 Ecume_0.9.2
## [37] timechange_0.1.1 randomForest_4.7-1
## [39] R6_2.5.1 doParallel_1.0.17
## [41] ggbeeswarm_0.6.0 rsvd_1.0.5
## [43] spatstat.univar_3.0-1 bitops_1.0-7
## [45] spatstat.utils_3.1-0 cachem_1.0.6
## [47] DelayedArray_0.24.0 assertthat_0.2.1
## [49] promises_1.2.0.1 scales_1.2.1
## [51] nnet_7.3-17 beeswarm_0.4.0
## [53] gtable_0.3.1 beachmat_2.14.0
## [55] globals_0.16.2 goftest_1.2-3
## [57] timeDate_3043.102 rlang_1.0.6
## [59] systemfonts_1.0.4 splines_4.2.0
## [61] lazyeval_0.2.2 ModelMetrics_1.2.2.2
## [63] spatstat.geom_3.0-3 abind_1.4-5
## [65] yaml_2.3.6 reshape2_1.4.4
## [67] httpuv_1.6.6 tools_4.2.0
## [69] lava_1.6.10 ellipsis_0.3.2
## [71] jquerylib_0.1.4 proxy_0.4-26
## [73] ggridges_0.5.4 Rcpp_1.0.10
## [75] plyr_1.8.8 sparseMatrixStats_1.10.0
## [77] zlibbioc_1.44.0 purrr_1.0.1
## [79] RCurl_1.98-1.8 deldir_1.0-6
## [81] rpart_4.1.16 pbapply_1.6-0
## [83] cowplot_1.1.1 zoo_1.8-11
## [85] ggrepel_0.9.3 cluster_2.1.3
## [87] magrittr_2.0.3 data.table_1.14.8
## [89] scattermore_0.8 lmtest_0.9-40
## [91] RANN_2.6.1 fitdistrplus_1.1-8
## [93] patchwork_1.1.2 mime_0.12
## [95] evaluate_0.18 xtable_1.8-4
## [97] gridExtra_2.3 compiler_4.2.0
## [99] transport_0.15-4 scater_1.24.0
## [101] tibble_3.2.1 KernSmooth_2.23-20
## [103] htmltools_0.5.6.1 mgcv_1.8-40
## [105] later_1.3.0 lubridate_1.9.0
## [107] DBI_1.1.3 MASS_7.3-57
## [109] Matrix_1.5-3 cli_3.4.1
## [111] parallel_4.2.0 gower_1.0.0
## [113] igraph_1.4.1 pkgconfig_2.0.3
## [115] sp_1.5-1 spatstat.sparse_3.0-0
## [117] plotly_4.10.1 scuttle_1.8.4
## [119] recipes_0.2.0 foreach_1.5.2
## [121] vipor_0.4.5 bslib_0.4.1
## [123] hardhat_0.2.0 rngtools_1.5.2
## [125] XVector_0.38.0 prodlim_2019.11.13
## [127] doRNG_1.8.2 stringr_1.5.0
## [129] digest_0.6.31 sctransform_0.3.5
## [131] RcppAnnoy_0.0.20 spatstat.data_3.0-0
## [133] cellranger_1.1.0 rmarkdown_2.18
## [135] leiden_0.4.3 uwot_0.1.14
## [137] DelayedMatrixStats_1.20.0 kernlab_0.9-31
## [139] shiny_1.7.3 lifecycle_1.0.3
## [141] nlme_3.1-157 jsonlite_1.8.4
## [143] BiocNeighbors_1.16.0 limma_3.54.2
## [145] fansi_1.0.4 pillar_1.9.0
## [147] fastmap_1.1.0 httr_1.4.4
## [149] survival_3.3-1 glue_1.6.2
## [151] png_0.1-7 iterators_1.0.14
## [153] class_7.3-20 stringi_1.7.12
## [155] sass_0.4.4 textshaping_0.3.6
## [157] BiocSingular_1.14.0 irlba_2.3.5.1
## [159] e1071_1.7-9 future.apply_1.10.0
Hello
I got this error with default settings. Any suggestions? Thank you very much in advance!
Here is the code:
Here is the seesionInfo: