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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Error when running scVIIntegration: Error in object[][features, ] : incorrect number of dimensions #9508

Closed yls2g13 closed 2 hours ago

yls2g13 commented 3 hours ago

Hi there, I'm also facing an issue faced by quite a few people (https://github.com/satijalab/seurat/issues/8897), but with R/4.4.1. My Seurat package versions are:

Seurat_5.1.0 
SeuratObject_5.0.2
SeuratWrappers_0.4.0

Code used:

merged <- IntegrateLayers(object = merged.seu.obj,
                              method = scVIIntegration,
                              new.reduction ="umap.scvi",
                              conda_env = "/home/miniconda3/envs/scvi-env/",
                              verbose = TRUE)

Error message:

Error when running scVIIntegration: Error in object[][features, ] : incorrect number of dimensions

sessionInfo() output:

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.4 (Plow)

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] scGate_1.6.2                here_1.0.1                  SeuratWrappers_0.4.0        pbmcsca.SeuratData_3.0.0    SeuratData_0.2.2.9001      
 [6] Azimuth_0.5.0               shinyBS_0.61.1              scDblFinder_1.18.0          scater_1.32.1               scuttle_1.14.0             
[11] cowplot_1.1.3               patchwork_1.3.0             decontX_1.2.0               celda_1.20.0                Matrix_1.7-0               
[16] lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.2                
[21] readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1                ggplot2_3.5.1               tidyverse_2.0.0            
[26] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0              GenomicRanges_1.56.1        GenomeInfoDb_1.40.1        
[31] IRanges_2.38.1              S4Vectors_0.42.1            BiocGenerics_0.50.0         MatrixGenerics_1.16.0       matrixStats_1.4.1          
[36] Seurat_5.1.0                SeuratObject_5.0.2          sp_2.1-4                   

loaded via a namespace (and not attached):
  [1] igraph_2.1.1                      ica_1.0-3                         plotly_4.10.4                     Formula_1.2-5                    
  [5] zlibbioc_1.50.0                   tidyselect_1.2.1                  bit_4.5.0                         doParallel_1.0.17                
  [9] lattice_0.22-6                    rjson_0.2.23                      blob_1.2.4                        S4Arrays_1.4.1                   
 [13] parallel_4.4.1                    seqLogo_1.68.0                    png_0.1-8                         cli_3.6.3                        
 [17] ProtGenerics_1.34.0               goftest_1.2-3                     gargle_1.5.2                      textshaping_0.4.0                
 [21] BiocIO_1.12.0                     bluster_1.14.0                    BiocNeighbors_1.22.0              Signac_1.14.0                    
 [25] uwot_0.2.2                        curl_6.0.1                        mime_0.12                         evaluate_1.0.1                   
 [29] leiden_0.4.3.1                    V8_6.0.0                          stringi_1.8.4                     backports_1.5.0                  
 [33] XML_3.99-0.17                     httpuv_1.6.15                     AnnotationDbi_1.64.1              magrittr_2.0.3                   
 [37] rappdirs_0.3.3                    splines_4.4.1                     RcppRoll_0.3.1                    DT_0.33                          
 [41] sctransform_0.4.1                 ggbeeswarm_0.7.2                  DBI_1.2.3                         withr_3.0.2                      
 [45] systemfonts_1.1.0                 rprojroot_2.0.4                   xgboost_1.7.8.1                   lmtest_0.9-40                    
 [49] rtracklayer_1.62.0                BiocManager_1.30.25               htmlwidgets_1.6.4                 fs_1.6.5                         
 [53] biomaRt_2.58.2                    ggrepel_0.9.6                     labeling_0.4.3                    SparseArray_1.4.8                
 [57] cellranger_1.1.0                  annotate_1.80.0                   reticulate_1.40.0                 zoo_1.8-12                       
 [61] JASPAR2020_0.99.10                XVector_0.44.0                    knitr_1.49                        TFBSTools_1.42.0                 
 [65] UCSC.utils_1.0.0                  TFMPvalue_0.0.9                   timechange_0.3.0                  foreach_1.5.2                    
 [69] fansi_1.0.6                       dittoSeq_1.16.0                   caTools_1.18.3                    grid_4.4.1                       
 [73] data.table_1.16.2                 rhdf5_2.48.0                      pwalign_1.0.0                     R.oo_1.27.0                      
 [77] poweRlaw_0.80.0                   RSpectra_0.16-2                   irlba_2.3.5.1                     fastDummies_1.7.4                
 [81] lazyeval_0.2.2                    yaml_2.3.10                       survival_3.6-4                    scattermore_1.2                  
 [85] crayon_1.5.3                      RcppAnnoy_0.0.22                  RColorBrewer_1.1-3                progressr_0.15.0                 
 [89] later_1.3.2                       ggridges_0.5.6                    codetools_0.2-20                  KEGGREST_1.42.0                  
 [93] Rtsne_0.17                        limma_3.60.6                      Rsamtools_2.18.0                  filelock_1.0.3                   
 [97] pkgconfig_2.0.3                   xml2_1.3.6                        spatstat.univar_3.1-1             ggpubr_0.6.0                     
[101] GenomicAlignments_1.38.2          spatstat.sparse_3.1-0             BSgenome_1.70.2                   viridisLite_0.4.2                
[105] xtable_1.8-4                      car_3.1-3                         plyr_1.8.9                        httr_1.4.7                       
[109] tools_4.4.1                       globals_0.16.3                    pkgbuild_1.4.5                    beeswarm_0.4.0                   
[113] broom_1.0.7                       nlme_3.1-164                      loo_2.8.0                         dbplyr_2.5.0                     
[117] hdf5r_1.3.11                      shinyjs_2.1.0                     digest_0.6.37                     farver_2.1.2                     
[121] tzdb_0.4.0                        AnnotationFilter_1.26.0           reshape2_1.4.4                    WriteXLS_6.7.0                   
[125] viridis_0.6.5                     DirichletMultinomial_1.44.0       glue_1.8.0                        cachem_1.1.0                     
[129] BiocFileCache_2.10.2              polyclip_1.10-7                   generics_0.1.3                    Biostrings_2.72.1                
[133] googledrive_2.1.1                 presto_1.0.0                      parallelly_1.39.0                 statmod_1.5.0                    
[137] RcppHNSW_0.6.0                    ragg_1.3.3                        ScaledMatrix_1.12.0               carData_3.0-5                    
[141] pbapply_1.7-2                     spam_2.11-0                       dqrng_0.4.1                       utf8_1.2.4                       
[145] StanHeaders_2.32.10               gtools_3.9.5                      ggsignif_0.6.4                    RcppEigen_0.3.4.0.2              
[149] gridExtra_2.3                     shiny_1.9.1                       GenomeInfoDbData_1.2.12           R.utils_2.12.3                   
[153] rhdf5filters_1.16.0               RCurl_1.98-1.16                   memoise_2.0.1                     rmarkdown_2.29                   
[157] pheatmap_1.0.12                   scales_1.3.0                      R.methodsS3_1.8.2                 googlesheets4_1.1.1              
[161] future_1.34.0                     RANN_2.6.2                        spatstat.data_3.1-4               rstudioapi_0.17.1                
[165] cluster_2.1.6                     QuickJSR_1.4.0                    rstantools_2.4.0                  spatstat.utils_3.1-1             
[169] hms_1.1.3                         fitdistrplus_1.2-1                munsell_0.5.1                     colorspace_2.1-1                 
[173] rlang_1.1.4                       DelayedMatrixStats_1.24.0         sparseMatrixStats_1.14.0          dotCall64_1.2                    
[177] shinydashboard_0.7.2              xfun_0.49                         CNEr_1.38.0                       remotes_2.5.0                    
[181] iterators_1.0.14                  abind_1.4-8                       MCMCprecision_0.4.0               EnsDb.Hsapiens.v86_2.99.0        
[185] rstan_2.32.6                      Rhdf5lib_1.26.0                   bitops_1.0-9                      promises_1.3.0                   
[189] inline_0.3.20                     RSQLite_2.3.8                     fgsea_1.30.0                      DelayedArray_0.30.1              
[193] GO.db_3.18.0                      compiler_4.4.1                    prettyunits_1.2.0                 beachmat_2.20.0                  
[197] listenv_0.9.1                     BSgenome.Hsapiens.UCSC.hg38_1.4.5 Rcpp_1.0.13-1                     enrichR_3.2                      
[201] edgeR_4.2.2                       BiocSingular_1.20.0               tensor_1.5                        MASS_7.3-60.2                    
[205] progress_1.2.3                    BiocParallel_1.38.0               UCell_2.8.0                       spatstat.random_3.3-2            
[209] R6_2.5.1                          fastmap_1.2.0                     fastmatch_1.1-4                   rstatix_0.7.2                    
[213] vipor_0.4.7                       ensembldb_2.26.0                  ROCR_1.0-11                       SeuratDisk_0.0.0.9021            
[217] rsvd_1.0.5                        gtable_0.3.6                      KernSmooth_2.23-24                miniUI_0.1.1.1                   
[221] deldir_2.0-4                      htmltools_0.5.8.1                 RcppParallel_5.1.9                bit64_4.5.2                      
[225] spatstat.explore_3.3-3            lifecycle_1.0.4                   restfulr_0.0.15                   vctrs_0.6.5                      
[229] spatstat.geom_3.3-4               scran_1.32.0                      future.apply_1.11.3               pracma_2.4.4                     
[233] pillar_1.9.0                      GenomicFeatures_1.54.4            metapod_1.12.0                    locfit_1.5-9.10                  
[237] combinat_0.0-8                    jsonlite_1.8.9
yls2g13 commented 2 hours ago

Closing as it seems the error has resolved itself!