Error when trying to run PhEMD with data_model = "negbinomial_sz"

[VladimirShitov]

When I am trying to run the PhEMD pipeline with my data, I get the following error during the execution of function embedCells():

Error in if (isSparseMatrix(counts)) { : the condition has length > 1

According to the traceback, the problem is that isSparseMatrix(counts) returns vector "FALSE FALSE" instead of a single value. According to the comment here you are aware of this problem. Do you have any plans to fix it or workarounds to run the code? Currently, it is impossible to run PhEMD with data_model = "negbinomial_sz" on the latest versions of R.

Session info:

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] tidyr_1.3.0         phemd_1.12.0        SeuratObject_4.1.3  Seurat_4.3.0        monocle_2.24.1     
 [6] DDRTree_0.1.5       irlba_2.3.5.1       VGAM_1.1-7          ggplot2_3.4.0       Biobase_2.56.0     
[11] BiocGenerics_0.42.0 Matrix_1.5-3