[bug] Error while running perform_de() function

[vd4mmind]

Describe the bug
Error while running the perform_de() function

To Reproduce
Steps to reproduce the behavior:

1. In R:

# Performing differential expression analysis following by impacted pathway analysis

sce_subset <- sce[, sce$clusters == 1]

#DE
result_de <- perform_de(
  sce_subset,
  mast_method = "glmer",
  min_counts = 1,
  min_cells_pc = 0.25,
  dependent_var = "diagnosis",
  ref_class = "Controls",
  confounding_vars = c("cngeneson"),
  random_effects_var = "manifest",
  ensembl_mapping_file = ensembl_fp,
  nAGQ = 0)

3. See error:
   ── Starting Differential Gene Expression ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────

── Pre-processing SingleCellExperiment ──

Selected 2284 from 9902 genes with >1 count(s) in >25% of cells.
→ Rescaling numeric variables

── Calculating variance explained by individual ──

→ Normalizing counts
→ Calculating variance explained by individual for 2284 genes
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Expected behavior
What is the workaround here? Not sure why this is happening. It seems like a specific issue with related to the data but not sure what it is. Any suggestion?

System

R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DT_0.32                     plotly_4.10.4.9000          ggplot2_3.5.0               KernSmooth_2.23-20          fields_15.2                
 [6] viridisLite_0.4.2           spam_2.10-0                 dplyr_1.1.4                 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0              S4Vectors_0.36.2           
[16] BiocGenerics_0.44.0         MatrixGenerics_1.10.0       matrixStats_1.2.0           scFlow_0.7.4                DoubletFinder_2.0.4        
[21] EWCE_1.6.0                  RNOmni_1.0.1.2              apcluster_1.4.11            lme4_1.1-35.1               Seurat_5.0.2               
[26] SeuratObject_5.0.1          sp_2.1-3                    irlba_2.3.5.1               Matrix_1.6-5               

loaded via a namespace (and not attached):
  [1] rsvd_1.0.5                    ica_1.0-3                     svglite_2.1.3                 foreach_1.5.2                 lmtest_0.9-40                
  [6] crayon_1.5.2                  MASS_7.3-58.2                 rhdf5filters_1.10.1           MAST_1.24.1                   WriteXLS_6.5.0               
 [11] nlme_3.1-162                  backports_1.4.1               monocle3_1.3.5                rlang_1.1.3                   XVector_0.38.0               
 [16] bib2df_1.1.2.0                ROCR_1.0-11                   nloptr_2.0.3                  limma_3.54.2                  scater_1.26.1                
 [21] filelock_1.0.3                stringfish_0.16.0             qs_0.25.7                     BiocParallel_1.32.6           rjson_0.2.21                 
 [26] bit64_4.0.5                   glue_1.7.0                    rngtools_1.5.2                sctransform_0.4.1             parallel_4.2.3               
 [31] vipor_0.4.7                   spatstat.sparse_3.0-3         AnnotationDbi_1.60.2          UpSetR_1.4.0                  HGNChelper_0.8.1             
 [36] dotCall64_1.1-1               spatstat.geom_3.2-9           tidyselect_1.2.0              fitdistrplus_1.1-11           XML_3.99-0.16.1              
 [41] tidyr_1.3.1                   zoo_1.8-12                    ggpubr_0.6.0                  formattable_0.2.1             xtable_1.8-4                 
 [46] RcppHNSW_0.6.0                magrittr_2.0.3                evaluate_0.23                 scuttle_1.8.4                 cli_3.6.2                    
 [51] zlibbioc_1.44.0               rstudioapi_0.15.0             doRNG_1.8.6                   miniUI_0.1.1.1                whisker_0.4.1                
 [56] bslib_0.6.1                   treeio_1.22.0                 rliger_1.0.1                  fastDummies_1.7.3             maps_3.4.2                   
 [61] shiny_1.8.0                   xfun_0.42                     BiocSingular_1.14.0           cluster_2.1.4                 KEGGREST_1.38.0              
 [66] tibble_3.2.1                  interactiveDisplayBase_1.36.0 ggrepel_0.9.5                 threejs_0.3.3                 ape_5.7-1                    
 [71] listenv_0.9.1                 Biostrings_2.66.0             png_0.1-8                     future_1.33.1                 withr_3.0.0                  
 [76] bitops_1.0-7                  plyr_1.8.9                    dqrng_0.3.2                   RcppParallel_5.1.7            pillar_1.9.0                 
 [81] cachem_1.0.8                  fs_1.6.3                      hdf5r_1.3.9                   paletteer_1.6.0               DelayedMatrixStats_1.20.0    
 [86] vctrs_0.6.5                   ellipsis_0.3.2                generics_0.1.3                RApiSerialize_0.1.2           tools_4.2.3                  
 [91] beeswarm_0.4.0                munsell_0.5.0                 DelayedArray_0.24.0           fastmap_1.1.1                 compiler_4.2.3               
 [96] abind_1.4-5                   httpuv_1.6.14                 ExperimentHub_2.6.0           ewceData_1.6.0                GenomeInfoDbData_1.2.9       
[101] gridExtra_2.3                 enrichR_3.2                   edgeR_3.40.2                  lattice_0.20-45               deldir_2.0-4                 
[106] utf8_1.2.4                    later_1.3.2                   prismatic_1.1.1               BiocFileCache_2.6.1           humaniformat_0.6.0           
[111] jsonlite_1.8.8                kBET_0.99.6                   scales_1.3.0                  ScaledMatrix_1.6.0            tidytree_0.4.6               
[116] pbapply_1.7-2                 carData_3.0-5                 sparseMatrixStats_1.10.0      lazyeval_0.2.2                promises_1.2.1               
[121] car_3.1-2                     doParallel_1.0.17             R.utils_2.12.3                goftest_1.2-3                 spatstat.utils_3.0-4         
[126] reticulate_1.35.0             rmarkdown_2.25                sandwich_3.1-0                cowplot_1.1.3                 Rtsne_0.17                   
[131] forcats_1.0.0                 uwot_0.1.16.9000              igraph_2.0.2                  HDF5Array_1.26.0              survival_3.5-3               
[136] yaml_2.3.8                    systemfonts_1.0.5             htmltools_0.5.7               memoise_2.0.1                 locfit_1.5-9.8               
[141] digest_0.6.34                 assertthat_0.2.1              mime_0.12                     rappdirs_0.3.3                RSQLite_2.3.5                
[146] yulab.utils_0.1.4             future.apply_1.11.1           orthogene_1.4.2               data.table_1.15.2             blob_1.2.4                   
[151] R.oo_1.26.0                   preprocessCore_1.60.2         labeling_0.4.3                splines_4.2.3                 Formula_1.2-5                
[156] rematch2_2.1.2                Rhdf5lib_1.20.0               AnnotationHub_3.6.0           RCurl_1.98-1.14               broom_1.0.5                  
[161] hms_1.1.3                     gprofiler2_0.2.3              base64enc_0.1-3               rhdf5_2.42.1                  colorspace_2.1-0             
[166] DropletUtils_1.18.1           BiocManager_1.30.22           WebGestaltR_0.4.6             ggbeeswarm_0.7.2              aplot_0.2.2                  
[171] maxLik_1.5-2                  sass_0.4.8                    mclust_6.1                    Rcpp_1.0.12                   RANN_2.6.1                   
[176] fansi_1.0.6                   tzdb_0.4.0                    parallelly_1.37.1             R6_2.5.1                      grid_4.2.3                   
[181] ggridges_0.5.6                lifecycle_1.0.4               miscTools_0.6-28              curl_5.2.0                    ggsignif_0.6.4               
[186] minqa_1.2.6                   jquerylib_0.1.4               leaflet_2.2.1                 leiden_0.4.3.1                RcppAnnoy_0.0.22             
[191] RColorBrewer_1.1-3            iterators_1.0.14              spatstat.explore_3.2-6        stringr_1.5.1                 htmlwidgets_1.6.4            
[196] beachmat_2.14.2               polyclip_1.10-6               biomaRt_2.54.1                purrr_1.0.2                   crosstalk_1.2.1              
[201] DirichletReg_0.7-1            gridGraphics_0.5-1            globals_0.16.2                patchwork_1.2.0               spatstat.random_3.2-3        
[206] progressr_0.14.0              codetools_0.2-19              FNN_1.1.4                     prettyunits_1.2.0             dbplyr_2.4.0                 
[211] RSpectra_0.16-1               R.methodsS3_1.8.2             gtable_0.3.4                  DBI_1.2.2                     highr_0.10                   
[216] ggfun_0.1.4                   tensor_1.5                    httr_1.4.7                    stringi_1.8.3                 progress_1.2.3               
[221] farver_2.1.1                  reshape2_1.4.4                english_1.2-6                 viridis_0.6.5                 ggtree_3.6.2                 
[226] xml2_1.3.6                    ggdendro_0.2.0                boot_1.3-28.1                 grr_0.9.5                     BiocNeighbors_1.16.0         
[231] readr_2.1.5                   ggplotify_0.1.2               homologene_1.4.68.19.3.27     scattermore_1.2               BiocVersion_3.16.0           
[236] bit_4.0.5                     spatstat.data_3.0-4           pkgconfig_2.0.3               babelgene_22.9                rstatix_0.7.2                
[241] knitr_1.45

Additional context
Add any other context about the problem here.