Issue with class_df in create.RCTD

[Jiayi-Zheng]

Hello, the package was running smoothly when I use all default setting. Until I checked the manual of create.RCTD hoping to adjust arguments for better model fitting. I saw that there is this class_df that when not set to NULL can return me with confidence score on classification. So I used RCTD <- create.RCTD(query, reference, max_cores = 8,class_df=T), which it told me below error message after getting all the DEGs.

Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) : attempt to set 'colnames' on an object with less than two dimensions

Below is my sessioninfo

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Ventura 13.6.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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: Asia/Hong_Kong
tzcode source: internal

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

other attached packages:
[1] spacexr_2.2.1         scCustomize_2.1.2     SeuratDisk_0.0.0.9021 clustree_0.5.1       
[5] ggraph_2.2.1          ggplot2_3.5.1         Seurat_5.0.0          SeuratObject_5.0.2   
[9] sp_2.1-4             

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.1               later_1.3.2                
  [4] tibble_3.2.1                polyclip_1.10-6             janitor_2.2.0              
  [7] fastDummies_1.7.3           lifecycle_1.0.4             doParallel_1.0.17          
 [10] globals_0.16.3              lattice_0.22-6              hdf5r_1.3.10               
 [13] MASS_7.3-60.2               MAST_1.30.0                 backports_1.5.0            
 [16] magrittr_2.0.3              plotly_4.10.4               remotes_2.5.0              
 [19] httpuv_1.6.15               sctransform_0.4.1           spam_2.10-0                
 [22] sessioninfo_1.2.2           pkgbuild_1.4.4              spatstat.sparse_3.1-0      
 [25] reticulate_1.38.0           cowplot_1.1.3               pbapply_1.7-2              
 [28] RColorBrewer_1.1-3          lubridate_1.9.3             pkgload_1.3.4              
 [31] abind_1.4-5                 zlibbioc_1.50.0             quadprog_1.5-8             
 [34] Rtsne_0.17                  GenomicRanges_1.56.1        purrr_1.0.2                
 [37] BiocGenerics_0.50.0         tweenr_2.0.3                circlize_0.4.16            
 [40] GenomeInfoDbData_1.2.12     IRanges_2.38.0              S4Vectors_0.42.0           
 [43] ggrepel_0.9.5               irlba_2.3.5.1               listenv_0.9.1              
 [46] spatstat.utils_3.0-5        goftest_1.2-3               RSpectra_0.16-1            
 [49] spatstat.random_3.2-3       fitdistrplus_1.1-11         parallelly_1.37.1          
 [52] leiden_0.4.3.1              codetools_0.2-20            DelayedArray_0.30.1        
 [55] ggforce_0.4.2               shape_1.4.6.1               tidyselect_1.2.1           
 [58] UCSC.utils_1.0.0            farver_2.1.2                viridis_0.6.5              
 [61] matrixStats_1.3.0           stats4_4.4.1                spatstat.explore_3.2-7     
 [64] jsonlite_1.8.8              ellipsis_0.3.2              tidygraph_1.3.1            
 [67] progressr_0.14.0            iterators_1.0.14            ggridges_0.5.6             
 [70] survival_3.6-4              systemfonts_1.1.0           foreach_1.5.2              
 [73] tools_4.4.1                 progress_1.2.3              ragg_1.3.2                 
 [76] ica_1.0-3                   Rcpp_1.0.12                 glue_1.7.0                 
 [79] gridExtra_2.3               SparseArray_1.4.8           usethis_2.2.3              
 [82] MatrixGenerics_1.16.0       GenomeInfoDb_1.40.1         dplyr_1.1.4                
 [85] withr_3.0.0                 fastmap_1.2.0               fansi_1.0.6                
 [88] digest_0.6.36               timechange_0.3.0            R6_2.5.1                   
 [91] mime_0.12                   textshaping_0.4.0           ggprism_1.0.5              
 [94] colorspace_2.1-0            scattermore_1.2             tensor_1.5                 
 [97] spatstat.data_3.1-2         utf8_1.2.4                  tidyr_1.3.1                
[100] generics_0.1.3              data.table_1.15.4           prettyunits_1.2.0          
[103] graphlayouts_1.1.1          httr_1.4.7                  htmlwidgets_1.6.4          
[106] S4Arrays_1.4.1              uwot_0.2.2                  pkgconfig_2.0.3            
[109] gtable_0.3.5                lmtest_0.9-40               SingleCellExperiment_1.26.0
[112] XVector_0.44.0              htmltools_0.5.8.1           profvis_0.3.8              
[115] dotCall64_1.1-1             scales_1.3.0                Biobase_2.64.0             
[118] png_0.1-8                   snakecase_0.11.1            rstudioapi_0.16.0          
[121] reshape2_1.4.4              curl_5.2.1                  checkmate_2.3.1            
[124] nlme_3.1-164                GlobalOptions_0.1.2         cachem_1.1.0               
[127] zoo_1.8-12                  stringr_1.5.1               KernSmooth_2.23-24         
[130] parallel_4.4.1              miniUI_0.1.1.1              vipor_0.4.7                
[133] ggrastr_1.0.2               pillar_1.9.0                grid_4.4.1                 
[136] vctrs_0.6.5                 RANN_2.6.1                  urlchecker_1.0.1           
[139] promises_1.3.0              xtable_1.8-4                cluster_2.1.6              
[142] paletteer_1.6.0             beeswarm_0.4.0              cli_3.6.3                  
[145] compiler_4.4.1              rlang_1.1.4                 crayon_1.5.3               
[148] future.apply_1.11.2         labeling_0.4.3              rematch2_2.1.2             
[151] fs_1.6.4                    forcats_1.0.0               plyr_1.8.9                 
[154] ggbeeswarm_0.7.2            stringi_1.8.4               viridisLite_0.4.2          
[157] deldir_2.0-4                munsell_0.5.1               lazyeval_0.2.2             
[160] devtools_2.4.5              spatstat.geom_3.2-9         Matrix_1.7-0               
[163] RcppHNSW_0.6.0              hms_1.1.3                   patchwork_1.2.0            
[166] bit64_4.0.5                 future_1.33.2               shiny_1.8.1.1              
[169] SummarizedExperiment_1.34.0 ROCR_1.0-11                 igraph_2.0.3               
[172] memoise_2.0.1               bit_4.0.5```

Thank you for your help and appreciate this conveniently-used and computationally undemanding package you created!