loadGiotto() in updated Giotto package can't load the data saved using the older version of Giotto

[MomenehForoutan]

Hi team,
I had previously used Giotto v3.1 to save my processed CosMx data through saveGiotto() function. Now, I have updated the package to v3.3.1, and I get an Error when trying to read the data using loadGiotto().

Thanks!
Sepideh

fov_join <- loadGiotto(paste0(outPath, "GiottoDir_proc_ann2"))
1. read Giotto object
2. read Giotto feature information
[1] "Path/to/GiottoDir_proc_ann2/Features/rna_feature_spatVector.shp"
Error in if (input == "" || length(grep("\\n|\\r", input))) { : 
  missing value where TRUE/FALSE needed

Looking at the output folder for features, in older versions of Giotto we would have files for the rna slot (see the screenshot below):

However, in the new version, we get different set of files for rna and age_probe slots due to handling them separately in the new workflow (see this screenshot):

So I think loadGiotto() expects a different data structure now for loading the data? But in general, it would be good to be able to load the data generated using the older versions. Any help with this will be highly appreciated!

Many thanks!
Sepideh

Here is my session info:

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.7 (Ootpa)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Giotto_3.3.1       smfishHmrf_0.1     fs_1.6.3           pracma_2.4.2       singscore_1.18.0  
 [6] InSituType_0.99.4  data.table_1.14.8  qs_0.25.5          dplyr_1.1.3        patchwork_1.1.3   
[11] viridis_0.6.4      viridisLite_0.4.2  ggplot2_3.4.4      RColorBrewer_1.1-3

loaded via a namespace (and not attached):
  [1] utf8_1.2.4                  reticulate_1.34.0           sccomp_1.2.1               
  [4] tidyselect_1.2.0            RSQLite_2.3.1               AnnotationDbi_1.60.2       
  [7] htmlwidgets_1.6.2           grid_4.2.0                  devtools_2.4.5             
 [10] flowCore_2.10.0             munsell_0.5.0               codetools_0.2-19           
 [13] umap_0.2.10.0               future_1.33.0               miniUI_0.1.1.1             
 [16] withr_2.5.2                 colorspace_2.1-0            progressr_0.14.0           
 [19] Biobase_2.58.0              knitr_1.45                  rstudioapi_0.15.0          
 [22] stats4_4.2.0                SingleCellExperiment_1.20.1 listenv_0.9.0              
 [25] MatrixGenerics_1.10.0       Rdpack_2.5                  rstan_2.26.23              
 [28] GenomeInfoDbData_1.2.9      bit64_4.0.5                 parallelly_1.36.0          
 [31] vctrs_0.6.4                 generics_0.1.3              xfun_0.41                  
 [34] timechange_0.2.0            lsa_0.73.3                  R6_2.5.1                   
 [37] doParallel_1.0.17           GenomeInfoDb_1.34.9         clue_0.3-65                
 [40] locfit_1.5-9.8              bitops_1.0-7                cachem_1.0.8               
 [43] DelayedArray_0.24.0         promises_1.2.1              scales_1.2.1               
 [46] gtable_0.3.4                globals_0.16.2              processx_3.8.2             
 [49] RProtoBufLib_2.10.0         rlang_1.1.2                 GlobalOptions_0.1.2        
 [52] inline_0.3.19               yaml_2.3.7                  reshape2_1.4.4             
 [55] httpuv_1.6.11               tools_4.2.0                 usethis_2.2.2              
 [58] ellipsis_0.3.2              BiocGenerics_0.44.0         sessioninfo_1.2.2          
 [61] Rcpp_1.0.11                 plyr_1.8.9                  zlibbioc_1.44.0            
 [64] purrr_1.0.2                 RCurl_1.98-1.12             ps_1.7.5                   
 [67] prettyunits_1.2.0           openssl_2.1.1               GetoptLong_1.0.5           
 [70] urlchecker_1.0.1            S4Vectors_0.36.2            SeuratObject_4.1.4         
 [73] SummarizedExperiment_1.28.0 ggrepel_0.9.4               cluster_2.1.4              
 [76] magrittr_2.0.3              RSpectra_0.16-1             SparseM_1.81               
 [79] circlize_0.4.15             SnowballC_0.7.1             matrixStats_1.1.0          
 [82] pkgload_1.3.3               stringfish_0.15.8           hms_1.1.3                  
 [85] mime_0.12                   evaluate_0.23               xtable_1.8-4               
 [88] XML_3.99-0.14               mclust_6.0.0                IRanges_2.32.0             
 [91] gridExtra_2.3               shape_1.4.6                 rstantools_2.3.1.1         
 [94] compiler_4.2.0              tibble_3.2.1                crayon_1.5.2               
 [97] StanHeaders_2.26.28         htmltools_0.5.7             later_1.3.1                
[100] tzdb_0.4.0                  tidyr_1.3.0                 RcppParallel_5.1.7         
[103] lubridate_1.9.3             DBI_1.1.3                   RApiSerialize_0.1.2        
[106] ComplexHeatmap_2.14.0       rappdirs_0.3.3              boot_1.3-28.1              
[109] Matrix_1.6-1.1              readr_2.1.4                 cli_3.6.1                  
[112] rbibutils_2.2.15            parallel_4.2.0              GenomicRanges_1.50.2       
[115] forcats_1.0.0               pkgconfig_2.0.3             sp_2.1-1                   
[118] terra_1.7-55                foreach_1.5.2               annotate_1.76.0            
[121] QuickJSR_1.0.6              XVector_0.38.0              stringr_1.5.0              
[124] callr_3.7.3                 digest_0.6.33               RcppAnnoy_0.0.21           
[127] graph_1.76.0                Biostrings_2.66.0           rmarkdown_2.25             
[130] edgeR_3.40.2                GSEABase_1.60.0             shiny_1.7.5                
[133] rjson_0.2.21                lifecycle_1.0.4             jsonlite_1.8.7             
[136] askpass_1.2.0               limma_3.54.2                fansi_1.0.5                
[139] pillar_1.9.0                lattice_0.21-9              loo_2.6.0                  
[142] KEGGREST_1.38.0             fastmap_1.1.1               httr_1.4.7                 
[145] pkgbuild_1.4.2              glue_1.6.2                  remotes_2.4.2.1            
[148] png_0.1-8                   iterators_1.0.14            bit_4.0.5                  
[151] stringi_1.8.1               profvis_0.3.8               blob_1.2.4                 
[154] memoise_2.0.1               cytolib_2.10.1              irlba_2.3.5.1              
[157] future.apply_1.11.0