subset.row not working

[fzhang12]

Hello,

I had a problem with scvelo() when assigning subset.row.

    velo.out <- scvelo(scle.processing, sf.X = scle.processing$sizeFactor.X,
                       mode = "dynamical",
                       subset.row = if.geneSet,
                       use.dimred = "UMAP.X",
                       assay.X = "counts", assay.spliced = "spliced",
                       assay.unspliced = "unspliced",
                       use.theirs = TRUE)

I have different gene sets that I want to use for velocity calculation.
When use.theirs is set to TRUE, scvelo() neglects subset.row and generates identical results.
When use.theirs is set to FALSE, scvelo() reports following error:

Error in py_call_impl(callable, dots$args, dots$keywords) : 
  ValueError: output array is read-only

Detailed traceback:
  File "$HOME/Library/Caches/org.R-project.R/R/basilisk/1.4.0/velociraptor/1.2.0/env/lib/python3.7/site-packages/scvelo/preprocessing/moments.py", line 58, in moments
    normalize_per_cell(adata)
  File "$HOME/Library/Caches/org.R-project.R/R/basilisk/1.4.0/velociraptor/1.2.0/env/lib/python3.7/site-packages/scvelo/preprocessing/utils.py", line 679, in normalize_per_cell
    X /= np.array(counts[:, None])
Calls: scvelo ... <Anonymous> -> do.call -> <Anonymous> -> py_call_impl
Execution halted

Do you have any idea what went wrong? Thank you very much!

Best regards

`sessionInfo()`

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] velociraptor_1.2.0          scater_1.20.1              
 [3] ggplot2_3.3.5               scuttle_1.2.1              
 [5] LoomExperiment_1.10.1       BiocIO_1.2.0               
 [7] rhdf5_2.36.0                SingleCellExperiment_1.14.1
 [9] SummarizedExperiment_1.22.0 Biobase_2.52.0             
[11] GenomicRanges_1.44.0        GenomeInfoDb_1.28.4        
[13] IRanges_2.26.0              MatrixGenerics_1.4.3       
[15] matrixStats_0.60.1          S4Vectors_0.30.0           
[17] BiocGenerics_0.38.0         BiocParallel_1.26.2        

loaded via a namespace (and not attached):
 [1] viridis_0.6.1             edgeR_3.34.1             
 [3] BiocSingular_1.8.1        jsonlite_1.7.2           
 [5] viridisLite_0.4.0         DelayedMatrixStats_1.14.3
 [7] assertthat_0.2.1          statmod_1.4.36           
 [9] dqrng_0.3.0               GenomeInfoDbData_1.2.6   
[11] vipor_0.4.5               pillar_1.6.2             
[13] lattice_0.20-44           limma_3.48.3             
[15] glue_1.4.2                beachmat_2.8.1           
[17] reticulate_1.20           XVector_0.32.0           
[19] colorspace_2.0-2          Matrix_1.3-4             
[21] pkgconfig_2.0.3           zellkonverter_1.2.1      
[23] dir.expiry_1.0.0          zlibbioc_1.38.0          
[25] purrr_0.3.4               scales_1.1.1             
[27] ScaledMatrix_1.0.0        HDF5Array_1.20.0         
[29] batchelor_1.8.1           ResidualMatrix_1.2.0     
[31] tibble_3.1.4              generics_0.1.0           
[33] ellipsis_0.3.2            withr_2.4.2              
[35] magrittr_2.0.1            crayon_1.4.1             
[37] fansi_0.5.0               bluster_1.2.1            
[39] beeswarm_0.4.0            tools_4.1.0              
[41] lifecycle_1.0.0           basilisk.utils_1.4.0     
[43] stringr_1.4.0             Rhdf5lib_1.14.2          
[45] locfit_1.5-9.4            munsell_0.5.0            
[47] cluster_2.1.2             DelayedArray_0.18.0      
[49] irlba_2.3.3               compiler_4.1.0           
[51] rsvd_1.0.5                rlang_0.4.11             
[53] grid_4.1.0                RCurl_1.98-1.4           
[55] rhdf5filters_1.4.0        BiocNeighbors_1.10.0     
[57] igraph_1.2.6              bitops_1.0-7             
[59] basilisk_1.4.0            gtable_0.3.0             
[61] DBI_1.1.1                 R6_2.5.1                 
[63] gridExtra_2.3             dplyr_1.0.7              
[65] utf8_1.2.2                filelock_1.0.2           
[67] metapod_1.0.0             stringi_1.7.4            
[69] ggbeeswarm_0.6.0          Rcpp_1.0.7               
[71] scran_1.20.1              vctrs_0.3.8              
[73] png_0.1-7                 tidyselect_1.1.1         
[75] sparseMatrixStats_1.4.2