Mat::submat(): indices out of bounds or incorrectly used

[YanCheer]

When I run CHOIR, it reported an error as Mat::submat(): indices out of bounds or incorrectly used.
I have tried CHOIR with data layer of the RNA assay without countsplitting, or count_log layer of the RNA assay after countsplitting, or scale.data layer of the integrated layer. ALL of these three data that were fed into CHOIR reported this error.
However, it is strange that another dataset of mine could be successfully run without such an error and smothly resulted in an output.
So, I wonder if it were a bug of CHOIR, or some mistakes that were hidden in my datasets?

The comands are like this:

seurat_E19_merged <- CHOIR(seurat_E19_merged,
                use_assay = "RNA",
		countsplit = FALSE, 
		batch_correction_method = "Harmony", 
		batch_labels = "Sample",
                n_cores = 100
)

seurat_E19_merged <- CHOIR(seurat_E19_merged,
                use_assay = "RNA",
		use_slot  = "counts_log",
		countsplit = TRUE, 
		batch_correction_method = "Harmony", 
		batch_labels = "Sample",
                n_cores = 100
)

seurat_E19_merged <- CHOIR(seurat_E19_merged,
                use_assay = "integrated",
                use_slot  = "scale.data",
                batch_correction_method = "Harmony",
                batch_labels = "Sample",
                n_cores = 100
)

And the running log is just like this:

----------------------------------------
- CHOIR - Part 1: Build clustering tree
 ----------------------------------------
2025-05-24 12时48分09秒 : (Step 1/7) Checking inputs and preparing object..

Input data:
 - Object type: Seurat (v5)
 - # of cells: 18289
 - # of batches: 3
 - # of modalities: 1
 - ATAC data: FALSE
 - Countsplitting: TRUE
 - Assay: RNA
 - Layer used to build tree: counts_log_1
 - Layer used to prune tree: counts_log_2

Proceeding with the following parameters:
 - Intermediate data stored under key: CHOIR
 - Alpha: 0.05
 - Multiple comparison adjustment: bonferroni
 - Features to train RF: var
 - # of excluded features: 0
 - # of permutations: 100
 - # of RF trees: 50
 - Use variance: TRUE
 - Minimum accuracy: 0.5
 - Minimum connections: 1
 - Maximum repeated errors: 20
 - Maximum cells sampled: Inf
 - Downsampling rate: 0.6768
 - Minimum reads: >0 reads
 - Maximum clusters: auto
 - Minimum cluster depth: 2000
 - Normalization method: none
 - Subtree dimensionality reductions: TRUE
 - Dimensionality reduction method: Default
 - Dimensionality reduction parameters provided: No
 - # of variable features: Default
 - Batch correction method: Harmony
 - Batch correction parameters provided: No
 - Metadata column containing batch information: Sample
 - Maximum # of batches used per permutation test: Inf
 - Nearest neighbor parameters provided: 
     - verbose: FALSE
 - Clustering parameters provided: 
     - algorithm: 1
     - group.singletons: TRUE
     - verbose: FALSE
 - # of cores: 100
 - Random seed: 1

2025-05-24 12时48分10秒 : (Step 2/7) Running initial dimensionality reduction..
2025-05-24 12时48分10秒 : Preparing matrix using 'RNA' assay and 'counts_log_1' slot..
2025-05-24 12时48分13秒 : Running PCA with 2000 variable features..
2025-05-24 12时48分36秒 : Running Harmony batch correction using column 'Sample'..
Transposing data matrix
2025-05-24 12时49分30秒 : (Step 3/7) Generating initial nearest neighbors graph..
2025-05-24 12时49分37秒 : (Step 4/7) Identify starting clustering resolution..
2025-05-24 12时50分07秒 : Starting resolution: 0.01
2025-05-24 12时50分07秒 : (Step 5/7) Building root clustering tree..
2025-05-24 12时51分26秒 : Identified resolution with maximum silhouette.
2025-05-24 12时51分26秒 : Running MRtree..

                      
                      Identified 11 clusters in root tree.
2025-05-24 12时51分43秒 : (Step 6/7) Subclustering root tree..
Transposing data matrix
2025-05-24 12时52分15秒 : 3% (Subtree 1/11, 5704 cells), 11 total clusters.
2025-05-24 12时53分33秒 : 12% (Subtree 1/11, 5704 cells), 23 total clusters.
2025-05-24 12时54分08秒 : 21% (Subtree 1/11, 5704 cells), 28 total clusters.
2025-05-24 12时55分40秒 : 31% (Subtree 1/11, 5704 cells), 34 total clusters.
Transposing data matrix
2025-05-24 12时56分16秒 : 35% (Subtree 2/11, 6889 cells), 34 total clusters.
2025-05-24 12时57分49秒 : 42% (Subtree 2/11, 6889 cells), 46 total clusters.
2025-05-24 12时58分56秒 : 50% (Subtree 2/11, 6889 cells), 54 total clusters.
2025-05-24 13时00分08秒 : 61% (Subtree 2/11, 6889 cells), 62 total clusters.
Transposing data matrix
2025-05-24 13时00分44秒 : 69% (Subtree 3/11, 486 cells), 65 total clusters.
2025-05-24 13时00分58秒 : 71% (Subtree 3/11, 486 cells), 67 total clusters.
Transposing data matrix
2025-05-24 13时01分08秒 : 72% (Subtree 4/11, 480 cells), 67 total clusters.
Transposing data matrix
2025-05-24 13时02分11秒 : 76% (Subtree 5/11, 2496 cells), 71 total clusters.
2025-05-24 13时02分34秒 : 82% (Subtree 5/11, 2496 cells), 74 total clusters.
Transposing data matrix
2025-05-24 13时03分26秒 : 88% (Subtree 6/11, 456 cells), 77 total clusters.
2025-05-24 13时04分10秒 : 90% (Subtree 6/11, 456 cells), 81 total clusters.
Transposing data matrix
2025-05-24 13时04分15秒 : 91% (Subtree 7/11, 611 cells), 81 total clusters.
Transposing data matrix
ERROR: Mat::submat(): indices out of bounds or incorrectly used