Issue Running ArchR2Signac()

[shamer3]

I am currently trying to convert 5 samples contained within an ArchR project into Signal/Seurat object. I have managed to set up okay however once I try and run ArchR2Signac() I am met with the following error:

Error in `separate()`:
! Can't extract columns that don't exist.
✖ Column `ranges` doesn't exist.

The process begins but then stop and generates this error message. The steps that do run are as follows:

[1] "In Progress:"
[1] "Prepare Seurat list for each sample"
[1] "POT"
[1] 24919  5510

My R.sessionInfo is as follows:

R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

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: Europe/London
tzcode source: internal

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

other attached packages:
 [1] ArchRtoSignac_1.0.4         EnsDb.Hsapiens.v86_2.99.0   ensembldb_2.26.0            AnnotationFilter_1.26.0    
 [5] GenomicFeatures_1.54.4      AnnotationDbi_1.64.1        Signac_1.12.0               biovizBase_1.50.0          
 [9] patchwork_1.2.0             hues_0.2.0                  Seurat_5.0.3                SeuratObject_5.0.1         
[13] sp_2.1-3                    Cairo_1.6-2                 ggrastr_1.0.2               rhdf5_2.46.1               
[17] SummarizedExperiment_1.32.0 Biobase_2.62.0              MatrixGenerics_1.14.0       Rcpp_1.0.12                
[21] Matrix_1.6-5                GenomicRanges_1.54.1        GenomeInfoDb_1.38.8         IRanges_2.36.0             
[25] S4Vectors_0.40.2            BiocGenerics_0.48.1         matrixStats_1.2.0           data.table_1.15.2          
[29] stringr_1.5.1               plyr_1.8.9                  magrittr_2.0.3              ggplot2_3.4.2              
[33] gtable_0.3.4                gtools_3.9.5                gridExtra_2.3               ArchR_1.0.2                

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.34.0               fs_1.6.3                          spatstat.sparse_3.0-3            
  [4] bitops_1.0-7                      devtools_2.4.5                    httr_1.4.7                       
  [7] RColorBrewer_1.1-3                doParallel_1.0.17                 profvis_0.3.8                    
 [10] tools_4.3.2                       sctransform_0.4.1                 backports_1.4.1                  
 [13] utf8_1.2.4                        R6_2.5.1                          lazyeval_0.2.2                   
 [16] uwot_0.1.16                       rhdf5filters_1.14.1               GetoptLong_1.0.5                 
 [19] urlchecker_1.0.1                  withr_3.0.0                       prettyunits_1.2.0                
 [22] progressr_0.14.0                  cli_3.6.2                         spatstat.explore_3.2-7           
 [25] fastDummies_1.7.3                 spatstat.data_3.0-4               ggridges_0.5.6                   
 [28] pbapply_1.7-2                     Rsamtools_2.18.0                  foreign_0.8-86                   
 [31] harmony_1.2.0                     dichromat_2.0-0.1                 parallelly_1.37.1                
 [34] sessioninfo_1.2.2                 BSgenome_1.70.2                   maps_3.4.2                       
 [37] RSQLite_2.3.5                     rstudioapi_0.16.0                 pals_1.8                         
 [40] BiocIO_1.12.0                     generics_0.1.3                    shape_1.4.6.1                    
 [43] ica_1.0-3                         spatstat.random_3.2-3             dplyr_1.1.4                      
 [46] ggbeeswarm_0.7.2                  fansi_1.0.6                       abind_1.4-5                      
 [49] lifecycle_1.0.4                   yaml_2.3.8                        BiocFileCache_2.10.1             
 [52] SparseArray_1.2.4                 Rtsne_0.17                        blob_1.2.4                       
 [55] promises_1.2.1                    crayon_1.5.2                      miniUI_0.1.1.1                   
 [58] lattice_0.22-6                    cowplot_1.1.3                     KEGGREST_1.42.0                  
 [61] mapproj_1.2.11                    pillar_1.9.0                      knitr_1.45                       
 [64] ComplexHeatmap_2.18.0             rjson_0.2.21                      future.apply_1.11.1              
 [67] codetools_0.2-19                  fastmatch_1.1-4                   leiden_0.4.3.1                   
 [70] glue_1.7.0                        remotes_2.5.0                     vctrs_0.6.5                      
 [73] png_0.1-8                         spam_2.10-0                       cachem_1.0.8                     
 [76] xfun_0.42                         S4Arrays_1.2.1                    mime_0.12                        
 [79] survival_3.5-7                    RcppRoll_0.3.0                    pheatmap_1.0.12                  
 [82] iterators_1.0.14                  shinythemes_1.2.0                 ellipsis_0.3.2                   
 [85] fitdistrplus_1.1-11               ROCR_1.0-11                       nlme_3.1-164                     
 [88] usethis_2.2.3                     bit64_4.0.5                       filelock_1.0.3                   
 [91] progress_1.2.3                    RcppAnnoy_0.0.22                  irlba_2.3.5.1                    
 [94] vipor_0.4.7                       KernSmooth_2.23-22                rpart_4.1.23                     
 [97] colorspace_2.1-0                  DBI_1.2.2                         Hmisc_5.1-2                      
[100] nnet_7.3-19                       processx_3.8.4                    tidyselect_1.2.1                 
[103] bit_4.0.5                         compiler_4.3.2                    curl_5.2.1                       
[106] htmlTable_2.4.2                   xml2_1.3.6                        desc_1.4.3                       
[109] rhandsontable_0.3.8               DelayedArray_0.28.0               plotly_4.10.4                    
[112] rtracklayer_1.62.0                checkmate_2.3.1                   scales_1.3.0                     
[115] lmtest_0.9-40                     callr_3.7.5                       rappdirs_0.3.3                   
[118] digest_0.6.35                     goftest_1.2-3                     spatstat.utils_3.0-4             
[121] presto_1.0.0                      rmarkdown_2.26                    XVector_0.42.0                   
[124] htmltools_0.5.7                   pkgconfig_2.0.3                   base64enc_0.1-3                  
[127] dbplyr_2.5.0                      fastmap_1.1.1                     rlang_1.1.3                      
[130] GlobalOptions_0.1.2               htmlwidgets_1.6.4                 shiny_1.8.0                      
[133] zoo_1.8-12                        jsonlite_1.8.8                    BiocParallel_1.36.0              
[136] VariantAnnotation_1.48.1          RCurl_1.98-1.14                   Formula_1.2-5                    
[139] GenomeInfoDbData_1.2.11           dotCall64_1.1-1                   Rhdf5lib_1.24.2                  
[142] munsell_0.5.0                     reticulate_1.35.0                 stringi_1.8.3                    
[145] zlibbioc_1.48.2                   MASS_7.3-60                       pkgbuild_1.4.4                   
[148] listenv_0.9.1                     ggrepel_0.9.5                     deldir_2.0-4                     
[151] Biostrings_2.70.3                 splines_4.3.2                     tensor_1.5                       
[154] hms_1.1.3                         circlize_0.4.16                   BSgenome.Hsapiens.UCSC.hg38_1.4.5
[157] ps_1.7.6                          igraph_2.0.3                      spatstat.geom_3.2-9              
[160] RcppHNSW_0.6.0                    biomaRt_2.58.2                    reshape2_1.4.4                   
[163] pkgload_1.3.4                     XML_3.99-0.16.1                   evaluate_0.23                    
[166] BiocManager_1.30.22               foreach_1.5.2                     httpuv_1.6.14                    
[169] RANN_2.6.1                        tidyr_1.3.1                       purrr_1.0.2                      
[172] polyclip_1.10-6                   future_1.33.1                     clue_0.3-65                      
[175] scattermore_1.2                   xtable_1.8-4                      restfulr_0.0.15                  
[178] RSpectra_0.16-1                   later_1.3.2                       viridisLite_0.4.2                
[181] tibble_3.2.1                      memoise_2.0.1                     beeswarm_0.4.0                   
[184] GenomicAlignments_1.38.2          cluster_2.1.6                     globals_0.16.3 

[rootze]

@shamer3 Thanks for using the ArchRtoSignac package. I am not really familiar with this error. But I can try to help.

In order to better help you dissect the error, I would like to ask you the following questions. Firstly, what data matrix do you have in your ArchrPorject? You can use getAvailableMatrices() to get the data matrix. Secondly, were you able to call peaks on your ArchRProject? It would be best if you have a peak matrix to make this data conversion work. Thirdly, I am aware of the recent update on Seurat and SeuratObject to Version 5. However, I have yet to get a chance to test it on this new Seurat version. So I don't know what it looks like. Please let me know if it works on version 5 or not.

[rootze]

Package Update V1.0.5 -- fix the problem