topologyTest error Error in pcurves[[l.ind]] : subscript out of bounds

[jiw181]

Hello

I got this error with default settings. Any suggestions? Thank you very much in advance!

Here is the code:

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)

Here is the seesionInfo:

## 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

[yujia-zhu]

Hey, I am facing the same error. Were you able to resolve it?

[HectorRDB]

Are all conditions present in all lineages ?