vignette throws error?

[vjcitn]

processing file: scdneySpatial.Rmd
  |....................................        |  81% [kontextOutcome]         Error in elem_list_rect(fill = contextColours) : 
  could not find function "elem_list_rect"

@almahmoud did you run across this?

Quitting from lines 987-1003 [kontextOutcome] (scdneySpatial.Rmd)
                                                                                                                    
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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: America/New_York
tzcode source: internal

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

other attached packages:
 [1] scdneySpatialBiocAsia2024_2.0.1 knitr_1.48                     
 [3] glmnet_4.1-8                    Matrix_1.7-1                   
 [5] scater_1.34.0                   scuttle_1.15.5                 
 [7] cytomapper_1.18.0               EBImage_4.47.1                 
 [9] lubridate_1.9.3                 forcats_1.0.0                  
[11] stringr_1.5.1                   purrr_1.0.2                    
[13] readr_2.1.5                     tibble_3.2.1                   
[15] tidyverse_2.0.0                 ggplot2_3.5.1                  
[17] ttservice_0.4.1                 tidyr_1.3.1                    
[19] dplyr_1.1.4                     tidySingleCellExperiment_1.16.0
[21] ClassifyR_3.9.5                 survival_3.7-0                 
[23] BiocParallel_1.40.0             MultiAssayExperiment_1.32.0    
[25] generics_0.1.3                  Statial_1.8.0                  
[27] spicyR_1.17.8                   lisaClust_1.13.3               
[29] FuseSOM_1.8.0                   simpleSeg_1.8.0                
[31] SpatialDatasets_1.4.0           SpatialExperiment_1.16.0       
[33] SingleCellExperiment_1.28.0     SummarizedExperiment_1.36.0    
[35] GenomicRanges_1.58.0            GenomeInfoDb_1.42.0            
[37] IRanges_2.40.0                  S4Vectors_0.44.0               
[39] MatrixGenerics_1.18.0           matrixStats_1.4.1              
[41] ExperimentHub_2.14.0            AnnotationHub_3.14.0           
[43] BiocFileCache_2.14.0            dbplyr_2.5.0                   
[45] Biobase_2.66.0                  BiocGenerics_0.52.0            
[47] rmarkdown_2.28                 

loaded via a namespace (and not attached):
  [1] tiff_0.1-12                 FCPS_1.3.4                 
  [3] nnet_7.3-19                 goftest_1.2-3              
  [5] Biostrings_2.74.0           HDF5Array_1.34.0           
  [7] TH.data_1.1-2               vctrs_0.6.5                
  [9] spatstat.random_3.3-2       digest_0.6.37              
 [11] png_0.1-8                   shape_1.4.6.1              
 [13] proxy_0.4-27                ggrepel_0.9.6              
 [15] deldir_2.0-4                permute_0.9-7              
 [17] magick_2.8.5                MASS_7.3-61                
 [19] reshape2_1.4.4              httpuv_1.6.15              
 [21] foreach_1.5.2               withr_3.0.2                
 [23] ggfun_0.1.7                 psych_2.4.6.26             
 [25] xfun_0.48                   ggpubr_0.6.0               
 [27] ellipsis_0.3.2              memoise_2.0.1              
 [29] ggbeeswarm_0.7.2            RProtoBufLib_2.17.0        
 [31] diptest_0.77-1              princurve_2.1.6            
 [33] systemfonts_1.1.0           tidytree_0.4.6             
 [35] zoo_1.8-12                  GlobalOptions_0.1.2        
 [37] V8_6.0.0                    DEoptimR_1.1-3             
 [39] Formula_1.2-5               prabclus_2.3-4             
 [41] KEGGREST_1.46.0             promises_1.3.0             
 [43] httr_1.4.7                  rstatix_0.7.2              
 [45] rhdf5filters_1.17.0         fpc_2.2-13                 
 [47] rhdf5_2.49.0                UCSC.utils_1.2.0           
 [49] concaveman_1.1.0            curl_5.2.3                 
 [51] zlibbioc_1.52.0             ScaledMatrix_1.14.0        
 [53] analogue_0.17-7             polyclip_1.10-7            
 [55] GenomeInfoDbData_1.2.13     SparseArray_1.6.0          
 [57] fftwtools_0.9-11            doParallel_1.0.17          
 [59] xtable_1.8-4                evaluate_1.0.1             
 [61] S4Arrays_1.6.0              hms_1.1.3                  
 [63] irlba_2.3.5.1               colorspace_2.1-1           
 [65] filelock_1.0.3              spatstat.data_3.1-2        
 [67] flexmix_2.3-19              magrittr_2.0.3             
 [69] ggtree_3.14.0               later_1.3.2                
 [71] viridis_0.6.5               modeltools_0.2-23          
 [73] lattice_0.22-6              robustbase_0.99-4-1        
 [75] spatstat.geom_3.3-3         XML_3.99-0.17              
 [77] cowplot_1.1.3               RcppAnnoy_0.0.22           
 [79] ggupset_0.4.0               class_7.3-22               
 [81] svgPanZoom_0.3.4            pillar_1.9.0               
 [83] nlme_3.1-166                iterators_1.0.14           
 [85] compiler_4.4.1              beachmat_2.22.0            
 [87] stringi_1.8.4               tensor_1.5                 
 [89] minqa_1.2.8                 plyr_1.8.9                 
 [91] treekoR_1.13.0              crayon_1.5.3               
 [93] abind_1.4-8                 gridGraphics_0.5-1         
 [95] locfit_1.5-9.10             sp_2.1-4                   
 [97] bit_4.5.0                   terra_1.7-78               
 [99] sandwich_3.1-1              multcomp_1.4-26            
[101] fastcluster_1.2.6           codetools_0.2-20           
[103] BiocSingular_1.22.0         bslib_0.8.0                
[105] coop_0.6-3                  GetoptLong_1.0.5           
[107] plotly_4.10.4               mime_0.12                  
[109] splines_4.4.1               circlize_0.4.16            
[111] Rcpp_1.0.13-1               profileModel_0.6.1         
[113] blob_1.2.4                  utf8_1.2.4                 
[115] clue_0.3-65                 BiocVersion_3.20.0         
[117] lme4_1.1-35.5               fs_1.6.5                   
[119] nnls_1.6                    ggsignif_0.6.4             
[121] ggplotify_0.1.2             scam_1.2-17                
[123] statmod_1.5.0               tzdb_0.4.0                 
[125] svglite_2.1.3               tweenr_2.0.3               
[127] pkgconfig_2.0.3             pheatmap_1.0.12            
[129] tools_4.4.1                 cachem_1.1.0               
[131] RSQLite_2.3.7               viridisLite_0.4.2          
[133] DBI_1.2.3                   numDeriv_2016.8-1.1        
[135] fastmap_1.2.0               scales_1.3.0               
[137] grid_4.4.1                  shinydashboard_0.7.2       
[139] broom_1.0.7                 sass_0.4.9                 
[141] patchwork_1.3.0             brglm_0.7.2                
[143] BiocManager_1.30.25         carData_3.0-5              
[145] farver_2.1.2                mgcv_1.9-1                 
[147] yaml_2.3.10                 ggthemes_5.1.0             
[149] cli_3.6.3                   hopach_2.66.0              
[151] lifecycle_1.0.4             uwot_0.2.2                 
[153] mvtnorm_1.3-1               kernlab_0.9-33             
[155] startup_0.22.0              backports_1.5.0            
[157] cytolib_2.17.0              timechange_0.3.0           
[159] gtable_0.3.6                rjson_0.2.23               
[161] ape_5.8                     parallel_4.4.1             
[163] limma_3.62.0                edgeR_4.4.0                
[165] jsonlite_1.8.9              bitops_1.0-9               
[167] bit64_4.5.2                 Rtsne_0.17                 
[169] FlowSOM_2.13.0              yulab.utils_0.1.7          
[171] vegan_2.6-8                 spatstat.utils_3.1-0       
[173] BiocNeighbors_2.0.0         ranger_0.16.0              
[175] flowCore_2.17.0             bdsmatrix_1.3-7            
[177] jquerylib_0.1.4             highr_0.11                 
[179] spatstat.univar_3.0-1       lazyeval_0.2.2             
[181] ConsensusClusterPlus_1.70.0 shiny_1.9.1                
[183] diffcyt_1.25.0              htmltools_0.5.8.1          
[185] rappdirs_0.3.3              glue_1.8.0                 
[187] XVector_0.46.0              RCurl_1.98-1.16            
[189] treeio_1.30.0               mclust_6.1.1               
[191] mnormt_2.1.1                coxme_2.2-22               
[193] jpeg_0.1-10                 gridExtra_2.3              
[195] boot_1.3-31                 igraph_2.1.1               
[197] R6_2.5.1                    ggiraph_0.8.10             
[199] labeling_0.4.3              ggh4x_0.2.8                
[201] cluster_2.1.6               Rhdf5lib_1.27.0            
[203] aplot_0.2.3                 nloptr_2.1.1               
[205] DelayedArray_0.32.0         tidyselect_1.2.1           
[207] vipor_0.4.7                 ggforce_0.4.2              
[209] raster_3.6-30               car_3.1-3                  
[211] AnnotationDbi_1.68.0        rsvd_1.0.5                 
[213] munsell_0.5.1               DataVisualizations_1.3.2   
[215] data.table_1.16.2           ComplexHeatmap_2.22.0      
[217] htmlwidgets_1.6.4           RColorBrewer_1.1-3         
[219] rlang_1.1.4                 spatstat.sparse_3.1-0      
[221] spatstat.explore_3.3-3      colorRamps_2.3.4           
[223] uuid_1.2-1                  lmerTest_3.1-3             
[225] ggnewscale_0.5.0            fansi_1.0.6                
[227] beeswarm_0.4.0             
> 

[vjcitn]

might come from ggh4x?

[vjcitn]

processing file: scdneySpatial.Rmd
  |....................................        |  81% [kontextOutcome]         Error in new_scale("fill") : could not find function "new_scale"
Selection: 

need ggnewscale?

[fame2827]

You might need to update spicyR to 1.18.0

[vjcitn]

Indeed that seems to be sufficient.