SingleR::mouseRNAseqData Error in UseMethod(filter_)
0
Entering edit mode
Collins • 0
@collins-24835
Last seen 5 days ago

I have SingleR package intalled on R version 3.6.2 and have been using it until now. All of a sudden i get this error when i want to load either MouseRNAseqData or ImmgenData. I would be grateful if someone could help me out

Code should be placed in three backticks as shown below

mouseRNA.se <- MouseRNAseqData()
immgen.se <- ImmGenData()

#I get this error
Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"


sessionInfo( )
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

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

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

other attached packages:
 [1] harmony_1.0                 Rcpp_1.0.6                  viridis_0.5.1              
 [4] viridisLite_0.3.0           DoubletFinder_2.0.3         SeuratWrappers_0.3.0       
 [7] gplots_3.1.1                caret_6.0-86                lattice_0.20-38            
[10] patchwork_1.1.1             stringr_1.4.0               qlcMatrix_0.9.7            
[13] sparsesvd_0.2               slam_0.1-47                 future.apply_1.7.0         
[16] future_1.21.0               doParallel_1.0.15           iterators_1.0.12           
[19] foreach_1.5.0               monocle3_0.2.3.0            SingleCellExperiment_1.8.0 
[22] monocle_2.14.0              DDRTree_0.1.5               irlba_2.3.3                
[25] VGAM_1.1-5                  devtools_2.3.2              usethis_2.0.0              
[28] biomaRt_2.42.1              BiocManager_1.30.10         ggrastr_0.2.1              
[31] ggridges_0.5.2              RColorBrewer_1.1-2          org.Mm.eg.db_3.10.0        
[34] AnnotationDbi_1.48.0        clusterProfiler_3.14.3      SingleR_1.0.6              
[37] SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1        
[40] matrixStats_0.58.0          Biobase_2.46.0              GenomicRanges_1.38.0       
[43] GenomeInfoDb_1.22.1         IRanges_2.20.2              S4Vectors_0.24.4           
[46] BiocGenerics_0.32.0         ggthemes_4.2.4              pheatmap_1.0.12            
[49] Seurat_3.2.3                tidyr_1.1.2                 dplyr_1.0.4                
[52] scales_1.1.1                ggbeeswarm_0.6.0            ggplot2_3.3.3              
[55] Matrix_1.2-18               data.table_1.13.6          

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1                scattermore_0.7               ModelMetrics_1.2.2.2         
  [4] bit64_4.0.5                   knitr_1.28                    rpart_4.1-15                 
  [7] RCurl_1.98-1.2                generics_0.1.0                callr_3.5.1                  
 [10] cowplot_1.1.1                 RSQLite_2.2.3                 RANN_2.6.1                   
 [13] europepmc_0.4                 combinat_0.0-8                bit_4.0.4                    
 [16] enrichplot_1.6.1              lubridate_1.7.9.2             spatstat.data_1.7-0          
 [19] xml2_1.3.2                    httpuv_1.5.5                  assertthat_0.2.1             
 [22] gower_0.2.2                   xfun_0.12                     hms_1.0.0                    
 [25] promises_1.1.1                progress_1.2.2                caTools_1.18.1               
 [28] dbplyr_2.1.0                  igraph_1.2.6                  DBI_1.1.1                    
 [31] htmlwidgets_1.5.1             purrr_0.3.4                   ellipsis_0.3.1               
 [34] deldir_0.2-9                  vctrs_0.3.6                   remotes_2.2.0                
 [37] ROCR_1.0-11                   abind_1.4-5                   withr_2.4.1                  
 [40] ggforce_0.3.2                 triebeard_0.3.0               sctransform_0.3.2            
 [43] prettyunits_1.1.1             goftest_1.2-2                 cluster_2.1.0                
 [46] DOSE_3.12.0                   ExperimentHub_1.12.0          lazyeval_0.2.2               
 [49] crayon_1.4.0                  labeling_0.4.2                recipes_0.1.15               
 [52] pkgconfig_2.0.3               tweenr_1.0.1                  nlme_3.1-142                 
 [55] vipor_0.4.5                   pkgload_1.1.0                 nnet_7.3-12                  
 [58] rlang_0.4.10                  globals_0.14.0                lifecycle_0.2.0              
 [61] miniUI_0.1.1.1                BiocFileCache_1.10.2          rsvd_1.0.3                   
 [64] AnnotationHub_2.18.0          rprojroot_2.0.2               polyclip_1.10-0              
 [67] lmtest_0.9-37                 urltools_1.7.3                zoo_1.8-8                    
 [70] beeswarm_0.2.3                processx_3.4.5                png_0.1-7                    
 [73] bitops_1.0-6                  pROC_1.17.0.1                 KernSmooth_2.23-16           
 [76] blob_1.2.1                    DelayedMatrixStats_1.8.0      qvalue_2.18.0                
 [79] parallelly_1.23.0             gridGraphics_0.5-1            memoise_1.1.0                
 [82] magrittr_2.0.1                plyr_1.8.6                    ica_1.0-2                    
 [85] zlibbioc_1.32.0               compiler_3.6.2                HSMMSingleCell_1.6.0         
 [88] fitdistrplus_1.1-3            cli_2.3.0                     XVector_0.26.0               
 [91] listenv_0.8.0                 pbapply_1.4-3                 ps_1.5.0                     
 [94] MASS_7.3-51.4                 mgcv_1.8-31                   tidyselect_1.1.0             
 [97] stringi_1.5.3                 densityClust_0.3              yaml_2.2.1                   
[100] GOSemSim_2.12.1               askpass_1.1                   ggrepel_0.9.1                
[103] grid_3.6.2                    fastmatch_1.1-0               tools_3.6.2                  
[106] rstudioapi_0.13               gridExtra_2.3                 prodlim_2019.11.13           
[109] farver_2.0.3                  Rtsne_0.15                    ggraph_2.0.4                 
[112] digest_0.6.27                 rvcheck_0.1.8                 lava_1.6.8.1                 
[115] FNN_1.1.3                     shiny_1.6.0                   BiocVersion_3.10.1           
[118] later_1.1.0.1                 RcppAnnoy_0.0.18              httr_1.4.2                   
[121] colorspace_2.0-0              XML_3.99-0.3                  fs_1.5.0                     
[124] tensor_1.5                    reticulate_1.18               uwot_0.1.10                  
[127] spatstat.utils_2.0-0          graphlayouts_0.7.1            ggplotify_0.0.5              
[130] plotly_4.9.2.1                sessioninfo_1.1.1             xtable_1.8-4                 
[133] jsonlite_1.7.2                spatstat_1.64-1               tidygraph_1.2.0              
[136] timeDate_3043.102             ipred_0.9-9                   testthat_3.0.1               
[139] R6_2.5.0                      pillar_1.4.7                  htmltools_0.5.1.1            
[142] mime_0.9                      glue_1.4.2                    fastmap_1.0.1                
[145] BiocNeighbors_1.4.2           class_7.3-15                  interactiveDisplayBase_1.24.0
[148] codetools_0.2-16              fgsea_1.12.0                  pkgbuild_1.2.0               
[151] tibble_3.0.6                  curl_4.3                      leiden_0.3.7                 
[154] gtools_3.8.2                  GO.db_3.10.0                  openssl_1.4.3                
[157] survival_3.1-8                limma_3.42.2                  docopt_0.7.1                 
[160] desc_1.2.0                    fastICA_1.2-2                 munsell_0.5.0                
[163] DO.db_2.9                     GenomeInfoDbData_1.2.2        reshape2_1.4.4               
[166] gtable_0.3.0
SingleR ImmgenData() mouseRNAseqData() • 76 views
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Entering edit mode
Mike Smith ♦ 4.8k
@mike-smith
Last seen 19 hours ago
EMBL Heidelberg / de.NBI

This is actually the result of a change in the dplyr package. You're using fairly old versions of R and Bioconductor, and so the copies of the packages that you have installed are not compatible with this new dplyr. There's quite a few posts on here about the issue e.g. Answer: BiomaRt::getBM Error in UseMethod(filter_)

The two possible solutions are to either upgrade R and Bioconductor to the latest release versions, or downgrade dplyr (and make sure R doesn't automatically update it every time you install something else).

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