gravatar for leranwangcs

2 hours ago by

Hi,

I'm trying to use SingleR to annotate my Seurat object, but the ImmGenData() keeps throwing me errors:

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')"

Based on some post, I have downgraded dplyr to version 0.8.0, but it doesn't help. My sessionInfo:

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] AnnotationHub_2.18.0        BiocFileCache_1.10.2        dbplyr_2.1.0               
 [4] SingleR_1.0.6               SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
 [7] BiocParallel_1.20.1         matrixStats_0.58.0          Biobase_2.46.0             
[10] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[13] S4Vectors_0.24.4            BiocGenerics_0.32.0         data.table_1.14.0          
[16] randomForest_4.6-14         dendroTools_1.1.1           forcats_0.5.1              
[19] stringr_1.4.0               dplyr_0.8.0                 purrr_0.3.4                
[22] readr_1.4.0                 tidyr_1.1.2                 tibble_3.0.6               
[25] tidyverse_1.3.0             pairwiseAdonis_0.0.1        cluster_2.1.1              
[28] forestmangr_0.9.3           vegan_2.5-7                 lattice_0.20-41            
[31] permute_0.9-5               rstatix_0.7.0               tidylog_1.0.2              
[34] janitor_2.1.0               tximport_1.14.2             ggpubr_0.4.0               
[37] phyloseq_1.30.0             plotly_4.9.3                ggplot2_3.3.3              

loaded via a namespace (and not attached):
  [1] utf8_1.1.4                    tidyselect_1.1.0              RSQLite_2.2.3                
  [4] AnnotationDbi_1.48.0          htmlwidgets_1.5.3             grid_3.6.3                   
  [7] Rtsne_0.15                    devtools_2.3.2                speedyseq_0.5.3.9001         
 [10] munsell_0.5.0                 codetools_0.2-18              units_0.6-7                  
 [13] withr_2.4.1                   colorspace_2.0-0              knitr_1.31                   
 [16] rstudioapi_0.13               ggsignif_0.6.1                GenomeInfoDbData_1.2.2       
 [19] mnormt_2.0.2                  bit64_4.0.5                   rhdf5_2.30.1                 
 [22] rprojroot_2.0.2               brnn_0.8                      vctrs_0.3.6                  
 [25] generics_0.1.0                xfun_0.21                     R6_2.5.0                     
 [28] locfit_1.5-9.4                bitops_1.0-6                  microbiome_1.8.0             
 [31] cachem_1.0.4                  assertthat_0.2.1              promises_1.2.0.1             
 [34] scales_1.1.1                  nnet_7.3-15                   gtable_0.3.0                 
 [37] Cubist_0.2.3                  processx_3.4.5                oce_1.3-0                    
 [40] rlang_0.4.10                  clisymbols_1.2.0              genefilter_1.68.0            
 [43] splines_3.6.3                 lazyeval_0.2.2                broom_0.7.5                  
 [46] checkmate_2.0.0               yaml_2.2.1                    BiocManager_1.30.10          
 [49] reshape2_1.4.4                abind_1.4-5                   modelr_0.1.8                 
 [52] backports_1.2.1               httpuv_1.5.5                  Hmisc_4.4-2                  
 [55] usethis_2.0.1                 tools_3.6.3                   psych_2.0.12                 
 [58] ellipsis_0.3.1                biomformat_1.14.0             RColorBrewer_1.1-2           
 [61] sessioninfo_1.1.1             Rcpp_1.0.6                    plyr_1.8.6                   
 [64] base64enc_0.1-3               progress_1.2.2                zlibbioc_1.32.0              
 [67] classInt_0.4-3                RCurl_1.98-1.2                ps_1.5.0                     
 [70] prettyunits_1.1.1             rpart_4.1-15                  viridis_0.5.1                
 [73] haven_2.3.1                   ggrepel_0.9.1                 fs_1.5.0                     
 [76] magrittr_2.0.1                openxlsx_4.2.3                reprex_1.0.0                 
 [79] truncnorm_1.0-8               tmvnsim_1.0-2                 pkgload_1.2.0                
 [82] mime_0.10                     hms_1.0.0                     xtable_1.8-4                 
 [85] XML_3.99-0.3                  rio_0.5.16                    jpeg_0.1-8.1                 
 [88] readxl_1.3.1                  gridExtra_2.3                 testthat_3.0.2               
 [91] compiler_3.6.3                KernSmooth_2.23-18            crayon_1.4.1                 
 [94] htmltools_0.5.1.1             later_1.1.0.1                 mgcv_1.8-34                  
 [97] gsw_1.0-5                     Formula_1.2-4                 geneplotter_1.64.0           
[100] lubridate_1.7.9.2             DBI_1.1.1                     ExperimentHub_1.12.0         
[103] rappdirs_0.3.3                MASS_7.3-53.1                 sf_0.9-7                     
[106] boot_1.3-27                   Matrix_1.3-2                  ade4_1.7-16                  
[109] car_3.0-10                    cli_2.3.1                     igraph_1.2.6                 
[112] pkgconfig_2.0.3               foreign_0.8-75                xml2_1.3.2                   
[115] foreach_1.5.1                 annotate_1.64.0               multtest_2.42.0              
[118] XVector_0.26.0                rvest_0.3.6                   snakecase_0.11.0             
[121] callr_3.5.1                   digest_0.6.27                 MLmetrics_1.1.1              
[124] Biostrings_2.54.0             cellranger_1.1.0              htmlTable_2.1.0              
[127] DelayedMatrixStats_1.8.0      curl_4.3                      shiny_1.6.0                  
[130] lifecycle_1.0.0               nlme_3.1-152                  jsonlite_1.7.2               
[133] Rhdf5lib_1.8.0                BiocNeighbors_1.4.2           carData_3.0-4                
[136] desc_1.2.0                    viridisLite_0.3.0             fansi_0.4.2                  
[139] pillar_1.5.0                  pkgbuild_1.2.0                fastmap_1.1.0                
[142] httr_1.4.2                    survival_3.2-7                remotes_2.2.0                
[145] interactiveDisplayBase_1.24.0 glue_1.4.2                    zip_2.1.1                    
[148] png_0.1-7                     iterators_1.0.13              BiocVersion_3.10.1           
[151] bit_4.0.4                     class_7.3-18                  stringi_1.5.3                
[154] blob_1.2.1                    DESeq2_1.26.0                 latticeExtra_0.6-29          
[157] memoise_2.0.0                 e1071_1.7-4                   ape_5.4-1

Thank you very much!!

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modified 2 hours ago

written
2 hours ago
by

leranwangcs20



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