Mysterious error message: Error in .rowStats_SVT

[yls2g13]

I'm receiving this weird error message. I can't use traceback() and nothing comes up on Google.

I've tried with both celda and decontX versions of decontX() to no avail. I find that this behaviour happens when I load library(celda) and/or library(decontX) - appreciate some help here.

I do find that in a new session if I just call decontX::decontX(sce) it does work. After some testing I find that Azimuth is the offending package. However, using detach("package:Azimuth", unload = TRUE) doesn't reverse the offense and I find i have to restart my R again to get it working.

I'm not sure if this is the right platform to report it but I thought this might help anyone facing this issue.

Error message:

> sce <- celda::decontX(sce) 
-------------------------------------------------- Starting DecontX -------------------------------------------------- 
Fri Feb  7 12:07:52 2025 .. Analyzing all cells 
Fri Feb  7 12:07:53 2025 .... Generating UMAP and estimating cell types 
Error in .rowStats_SVT("sum", x, na.rm = na.rm, dims = dims) :    could not find function ".rowStats_SVT" 

> sce <- decontX::decontX(sce) 
-------------------------------------------------- Starting DecontX -------------------------------------------------- 
Fri Feb  7 12:08:08 2025 .. Analyzing all cells 
Fri Feb  7 12:08:08 2025 .... Generating UMAP and estimating cell types 
Error in .rowStats_SVT("sum", x, na.rm = na.rm, dims = dims) :    could not find function ".rowStats_SVT"

sessionInfo():

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.4 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  LAPACK version 3.9.0

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

time zone: Australia/Melbourne
tzcode source: system (glibc)

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

other attached packages:
 [1] celda_1.22.0                Matrix_1.7-0                scGate_1.6.2                SeuratData_0.2.2.9001       ggpubr_0.6.0               
 [6] dittoSeq_1.18.0             scDblFinder_1.20.0          scater_1.34.0               scuttle_1.16.0              cowplot_1.1.3              
[11] patchwork_1.3.0             decontX_1.4.0               lubridate_1.9.4             forcats_1.0.0               stringr_1.5.1              
[16] dplyr_1.1.4                 purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
[21] ggplot2_3.5.1               tidyverse_2.0.0             SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 Biobase_2.62.0             
[26] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8         IRanges_2.36.0              S4Vectors_0.44.0            BiocGenerics_0.52.0        
[31] MatrixGenerics_1.14.0       matrixStats_1.5.0           Seurat_5.2.1                SeuratObject_5.0.2          sp_2.1-4                   

loaded via a namespace (and not attached):
  [1] spatstat.sparse_3.1-0    bitops_1.0-9             doParallel_1.0.17        httr_1.4.7               RColorBrewer_1.1-3      
  [6] tools_4.4.1              sctransform_0.4.1        backports_1.5.0          R6_2.5.1                 lazyeval_0.2.2          
 [11] uwot_0.2.2               withr_3.0.2              gridExtra_2.3            progressr_0.15.1         cli_3.6.3               
 [16] spatstat.explore_3.3-4   fastDummies_1.7.5        enrichR_3.2              spatstat.data_3.1-4      ggridges_0.5.6          
 [21] pbapply_1.7-2            QuickJSR_1.4.0           Rsamtools_2.18.0         StanHeaders_2.32.10      dbscan_1.2-0            
 [26] WriteXLS_6.7.0           parallelly_1.41.0        limma_3.62.1             rstudioapi_0.17.1        FNN_1.1.4.1             
 [31] generics_0.1.3           BiocIO_1.12.0            combinat_0.0-8           ica_1.0-3                spatstat.random_3.3-2   
 [36] car_3.1-3                inline_0.3.20            loo_2.8.0                ggbeeswarm_0.7.2         abind_1.4-8             
 [41] lifecycle_1.0.4          yaml_2.3.10              edgeR_4.4.1              carData_3.0-5            SparseArray_1.6.1       
 [46] Rtsne_0.17               grid_4.4.1               promises_1.3.2           dqrng_0.4.1              crayon_1.5.3            
 [51] miniUI_0.1.1.1           lattice_0.22-6           beachmat_2.22.0          pillar_1.10.1            knitr_1.49              
 [56] metapod_1.14.0           rjson_0.2.23             xgboost_1.7.8.1          future.apply_1.11.3      codetools_0.2-20        
 [61] glue_1.8.0               V8_6.0.0                 spatstat.univar_3.1-1    data.table_1.16.4        vctrs_0.6.5             
 [66] png_0.1-8                spam_2.11-1              gtable_0.3.6             xfun_0.50                S4Arrays_1.6.0          
 [71] mime_0.12                RcppEigen_0.3.4.0.2      survival_3.6-4           pheatmap_1.0.12          iterators_1.0.14        
 [76] statmod_1.5.0            bluster_1.16.0           fitdistrplus_1.2-2       ROCR_1.0-11              nlme_3.1-164            
 [81] RcppAnnoy_0.0.22         rstan_2.32.6             irlba_2.3.5.1            vipor_0.4.7              KernSmooth_2.23-24      
 [86] colorspace_2.1-1         UCell_2.10.1             tidyselect_1.2.1         compiler_4.4.1           curl_6.2.0              
 [91] BiocNeighbors_2.0.0      DelayedArray_0.32.0      plotly_4.10.4            rtracklayer_1.62.0       scales_1.3.0            
 [96] lmtest_0.9-40            rappdirs_0.3.3           digest_0.6.37            goftest_1.2-3            spatstat.utils_3.1-2    
[101] rmarkdown_2.29           XVector_0.42.0           htmltools_0.5.8.1        pkgconfig_2.0.3          fastmap_1.2.0           
[106] rlang_1.1.5              htmlwidgets_1.6.4        shiny_1.10.0             farver_2.1.2             zoo_1.8-12              
[111] jsonlite_1.8.9           BiocParallel_1.36.0      BiocSingular_1.22.0      RCurl_1.98-1.16          magrittr_2.0.3          
[116] Formula_1.2-5            GenomeInfoDbData_1.2.11  dotCall64_1.2            munsell_0.5.1            Rcpp_1.0.14             
[121] viridis_0.6.5            reticulate_1.40.0        stringi_1.8.4            MCMCprecision_0.4.0      zlibbioc_1.48.2         
[126] MASS_7.3-60.2            plyr_1.8.9               pkgbuild_1.4.5           parallel_4.4.1           listenv_0.9.1           
[131] ggrepel_0.9.6            deldir_2.0-4             Biostrings_2.70.3        splines_4.4.1            tensor_1.5              
[136] hms_1.1.3                locfit_1.5-9.10          igraph_2.1.4             spatstat.geom_3.3-5      ggsignif_0.6.4          
[141] RcppHNSW_0.6.0           reshape2_1.4.4           ScaledMatrix_1.14.0      rstantools_2.4.0         XML_3.99-0.17           
[146] evaluate_1.0.3           RcppParallel_5.1.10      scran_1.34.0             foreach_1.5.2            tzdb_0.4.0              
[151] httpuv_1.6.15            RANN_2.6.2               polyclip_1.10-7          future_1.34.0            scattermore_1.2         
[156] rsvd_1.0.5               broom_1.0.7              xtable_1.8-4             restfulr_0.0.15          RSpectra_0.16-2         
[161] rstatix_0.7.2            later_1.4.1              viridisLite_0.4.2        beeswarm_0.4.0           GenomicAlignments_1.38.2
[166] cluster_2.1.6            timechange_0.3.0         globals_0.16.3

[joshua-d-campbell]

Hi @yls2g13, thanks for posting this. It is strange behavior. This function doesn't come from our code. We use some other Bioconductor tools to quickly generate a UMAP, mainly the "calculateUMAP" function from scater. I wonder if attaching the Azimuth package somehow interferes with functions from that package although I'm not sure how that would happen. I guess the easiest way to get around this is not load Azimuth until after decontX is run for now.

As this isn't really a bug with our code, I will move it to a Discussion so others can still see it in the future.