Error in LinkPeaks: Deprecated Sparse Matrix Conversion ('dgTMatrix') in Matrix Package

[ahdee]

Hi I'm encountering an error while using the LinkPeaks function in the Signac package. The warning message is as follows: Error: (converted from warning) 'as(<dgCMatrix>, "dgTMatrix")' is deprecated. Use 'as(., "TsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated"). This issue seems to be related to the internal conversion of sparse matrices in the Matrix package, as dgTMatrix is now deprecated and is advised to be replaced with TsparseMatrix.

After reviewing the LinkPeaks code, I suspect the issue may arise during the construction of sparse matrices with sparseMatrix or potentially in the correlation methods (corSparse or SparseSpearmanCor)?

Session:

 [1] Matrix_1.6-1.1                    Signac_1.9.0.9000                 pathfindR_2.3.0.9001              pathfindR.data_2.0.0             
 [5] presto_1.0.0                      data.table_1.14.8                 limma_3.58.1                      fgsea_1.29.1                     
 [9] ggrastr_1.0.2                     monocle3_1.3.4                    SingleCellExperiment_1.24.0       SummarizedExperiment_1.32.0      
[13] MatrixGenerics_1.14.0             matrixStats_1.0.0                 kableExtra_1.4.0                  ggrepel_0.9.4                    
[17] TFBSTools_1.31.2                  JASPAR2020_0.99.10                openxlsx_4.2.5.2                  randomcoloR_1.1.0.1              
[21] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1                   rtracklayer_1.62.0                BiocIO_1.12.0                    
[25] Biostrings_2.70.1                 XVector_0.42.0                    EnsDb.Hsapiens.v86_2.99.0         ensembldb_2.26.0                 
[29] AnnotationFilter_1.26.0           GenomicFeatures_1.54.1            AnnotationDbi_1.64.1              Biobase_2.62.0                   
[33] GenomicRanges_1.54.1              GenomeInfoDb_1.38.0               IRanges_2.36.0                    S4Vectors_0.40.1                 
[37] BiocGenerics_0.48.1               lubridate_1.9.3                   forcats_1.0.0                     stringr_1.5.0                    
[41] purrr_1.0.2                       readr_2.1.4                       tidyr_1.3.0                       tibble_3.2.1                     
[45] tidyverse_2.0.0                   dplyr_1.1.3                       patchwork_1.1.3.9000              ggpubr_0.6.0                     
[49] ggplot2_3.4.4                     RColorBrewer_1.1-3                scales_1.2.1                      HGNChelper_0.8.1                 
[53] harmony_1.1.0                     Rcpp_1.0.11                       Seurat_5.0.0                      SeuratObject_5.0.0               
[57] sp_2.1-1                         ```

[timoast]

Please update to the latest release