Error "no 'dimnames' attribute for array" when running scTyper on an Integerated data set

[moutazhelal]

Dear Authors,

Thank your for reading my message.
I have encountered an Error while trying to run scTyper. I am running scTyper function on a Integrated data set I integrated 4 data set using Seurat's Integration pipeline I have encountered This Error:

[[2022-06-24 10:40:51]] Run Cell typing using average expression value--------
Error in expr[a, ] : no 'dimnames' attribute for array

I am running :

celltyped.seurat= scTyper(seurat.object= MM.combined, marker="Jerby_Arnon.2018.MEL", wd = getwd(), output.name = "scTyper.output", pheno.fn = "Sample.csv", qc = FALSE, run.cellranger=FALSE, norm.seurat=FALSE, cell.typing.method="Average", level="cell", run.inferCNV=FALSE, proj.name = "scTyper", report.mode=TRUE, mc.cores = 5)

`R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

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

other attached packages:
[1] colorspace_2.0-3 pander_0.6.5 kableExtra_1.3.4 knitr_1.39 png_0.1-7 circlize_0.4.15 ComplexHeatmap_2.12.0
[8] gridExtra_2.3 ggplot2_3.3.6 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0 limma_3.52.1
[15] reshape2_1.4.4 Biobase_2.56.0 BiocGenerics_0.42.0 perm_1.0-0.2 rmarkdown_2.14 gProfileR_0.7.0 fastqcr_0.1.2
[22] infercnv_1.12.0 scTyper_0.1.0 patchwork_1.1.1 SeuratData_0.2.2 sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.1

loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.25 tidyselect_1.1.2 htmlwidgets_1.5.4 Rtsne_0.16 munsell_0.5.0
[7] codetools_0.2-18 ica_1.0-2 future_1.26.1 miniUI_0.1.1.1 withr_2.5.0 argparse_2.1.5
[13] spatstat.random_2.2-0 progressr_0.10.1 rstudioapi_0.13 SingleCellExperiment_1.18.0 ROCR_1.0-11 tensor_1.5
[19] listenv_0.8.0 MatrixGenerics_1.8.0 GenomeInfoDbData_1.2.8 polyclip_1.10-0 coda_0.19-4 parallelly_1.32.0
[25] vctrs_0.4.1 generics_0.1.2 TH.data_1.1-1 lambda.r_1.2.4 xfun_0.31 fastcluster_1.2.3
[31] R6_2.5.1 doParallel_1.0.17 clue_0.3-61 locfit_1.5-9.5 bitops_1.0-7 spatstat.utils_2.3-1
[37] reshape_0.8.9 DelayedArray_0.22.0 assertthat_0.2.1 promises_1.2.0.1 scales_1.2.0 multcomp_1.4-19
[43] rgeos_0.5-9 gtable_0.3.0 globals_0.15.0 goftest_1.2-3 sandwich_3.0-2 rlang_1.0.2
[49] systemfonts_1.0.4 GlobalOptions_0.1.2 splines_4.2.0 lazyeval_0.2.2 rjags_4-13 spatstat.geom_2.4-0
[55] yaml_2.3.5 abind_1.4-5 httpuv_1.6.5 tools_4.2.0 ellipsis_0.3.2 gplots_3.1.3
[61] spatstat.core_2.4-4 jquerylib_0.1.4 RColorBrewer_1.1-3 phyclust_0.1-30 ggridges_0.5.3 Rcpp_1.0.8.3
[67] plyr_1.8.7 zlibbioc_1.42.0 purrr_0.3.4 RCurl_1.98-1.6 rpart_4.1.16 deldir_1.0-6
[73] pbapply_1.5-0 GetoptLong_1.0.5 cowplot_1.1.1 zoo_1.8-10 SummarizedExperiment_1.26.1 ggrepel_0.9.1
[79] cluster_2.1.3 magrittr_2.0.3 data.table_1.14.2 futile.options_1.0.1 scattermore_0.8 lmtest_0.9-40
[85] RANN_2.6.1 mvtnorm_1.1-3 parallelDist_0.2.6 fitdistrplus_1.1-8 matrixStats_0.62.0 mime_0.12
[91] evaluate_0.15 xtable_1.8-4 shape_1.4.6 compiler_4.2.0 tibble_3.1.7 KernSmooth_2.23-20
[97] crayon_1.5.1 htmltools_0.5.2 mgcv_1.8-40 later_1.3.0 tidyr_1.2.0 libcoin_1.0-9
[103] RcppParallel_5.1.5 DBI_1.1.3 formatR_1.12 MASS_7.3-56 rappdirs_0.3.3 Matrix_1.4-1
[109] cli_3.3.0 igraph_1.3.1 pkgconfig_2.0.3 coin_1.4-2 plotly_4.10.0 spatstat.sparse_2.1-1
[115] xml2_1.3.3 foreach_1.5.2 svglite_2.1.0 bslib_0.3.1 webshot_0.5.3 XVector_0.36.0
[121] rvest_1.0.2 stringr_1.4.0 digest_0.6.29 sctransform_0.3.3 RcppAnnoy_0.0.19 spatstat.data_2.2-0
[127] leiden_0.4.2 uwot_0.1.11 edgeR_3.38.1 shiny_1.7.1 gtools_3.9.2.1 modeltools_0.2-23
[133] rjson_0.2.21 lifecycle_1.0.1 nlme_3.1-157 jsonlite_1.8.0 futile.logger_1.4.3 viridisLite_0.4.0
[139] fansi_1.0.3 pillar_1.7.0 lattice_0.20-45 fastmap_1.1.0 httr_1.4.3 survival_3.3-1
[145] glue_1.6.2 iterators_1.0.14 sass_0.4.1 stringi_1.7.6 caTools_1.18.2 dplyr_1.0.9
[151] irlba_2.3.5 future.apply_1.9.0 ape_5.6-2 `