AnnotationHub() Error

[JojoZhangxinye]

Hi,

When I try hub <- AnnotationHub() I got 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')" Could you help me?

Details

> packageVersion("AnnotationHub")
[1] ‘2.18.0’
> BiocManager::version()
[1] ‘3.10’
>BiocManager::valid(pkgs = "AnnotationHub")
[1] TRUE
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] RUnit_0.4.32         AnnotationHub_2.18.0 BiocFileCache_1.10.2
[4] dbplyr_2.0.0         BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                  matrixStats_0.57.0           
 [3] bit64_4.0.5                   RColorBrewer_1.1-2           
 [5] httr_1.4.2                    GenomeInfoDb_1.22.1          
 [7] tools_3.6.1                   backports_1.2.0              
 [9] R6_2.5.0                      rpart_4.1-15                 
[11] Hmisc_4.4-1                   DBI_1.1.0                    
[13] colorspace_2.0-0              nnet_7.3-14                  
[15] tidyselect_1.1.0              gridExtra_2.3                
[17] DESeq2_1.26.0                 bit_4.0.4                    
[19] curl_4.3                      compiler_3.6.1               
[21] cli_2.1.0                     Biobase_2.46.0               
[23] htmlTable_2.1.0               DelayedArray_0.12.3          
[25] scales_1.1.1                  checkmate_2.0.0              
[27] genefilter_1.68.0             rappdirs_0.3.1               
[29] stringr_1.4.0                 digest_0.6.27                
[31] foreign_0.8-71                XVector_0.26.0               
[33] base64enc_0.1-3               jpeg_0.1-8.1                 
[35] pkgconfig_2.0.3               htmltools_0.5.0              
[37] fastmap_1.0.1                 htmlwidgets_1.5.2            
[39] rlang_0.4.8                   rstudioapi_0.13              
[41] RSQLite_2.2.1                 shiny_1.5.0                  
[43] generics_0.1.0                BiocParallel_1.20.1          
[45] dplyr_1.0.2                   RCurl_1.98-1.2               
[47] magrittr_1.5                  GenomeInfoDbData_1.2.2       
[49] Formula_1.2-4                 Matrix_1.2-18                
[51] Rcpp_1.0.5                    munsell_0.5.0                
[53] S4Vectors_0.24.4              fansi_0.4.1                  
[55] lifecycle_0.2.0               stringi_1.4.6                
[57] yaml_2.2.1                    SummarizedExperiment_1.16.1  
[59] zlibbioc_1.32.0               grid_3.6.1                   
[61] blob_1.2.1                    promises_1.1.1               
[63] crayon_1.3.4                  lattice_0.20-41              
[65] splines_3.6.1                 annotate_1.64.0              
[67] locfit_1.5-9.4                knitr_1.30                   
[69] pillar_1.4.7                  GenomicRanges_1.38.0         
[71] geneplotter_1.64.0            stats4_3.6.1                 
[73] XML_3.99-0.3                  glue_1.4.2                   
[75] BiocVersion_3.10.1            latticeExtra_0.6-29          
[77] data.table_1.13.2             BiocManager_1.30.10          
[79] png_0.1-7                     vctrs_0.3.4                  
[81] httpuv_1.5.4                  gtable_0.3.0                 
[83] purrr_0.3.4                   assertthat_0.2.1             
[85] ggplot2_3.3.2                 xfun_0.19                    
[87] mime_0.9                      xtable_1.8-4                 
[89] later_1.1.0.1                 survival_3.2-7               
[91] tibble_3.0.4                  AnnotationDbi_1.48.0         
[93] memoise_1.1.0                 IRanges_2.20.2               
[95] cluster_2.1.0                 ellipsis_0.3.1               
[97] interactiveDisplayBase_1.24.0

[lshep]

This has been corrected in more recent versions of AnnotationHub and has to do with changes in the underlying dplyr method. Is it possible to update your version of R to use the most recent version of the package?

[JojoZhangxinye]

This has been corrected in more recent versions of AnnotationHub and has to do with changes in the underlying dplyr method. Is it possible to update your version of R to use the most recent version of the package?

It works!Thanks! Now the details:

> packageVersion("AnnotationHub")
[1] ‘2.22.0’
> BiocManager::version()
[1] ‘3.12’
> BiocManager::valid(pkgs = "AnnotationHub")
[1] TRUE
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

[lshep]

Good to hear. Thank you for your report.