I have been trying to create an EnsDb object using AnnotationHub. This code had worked just fine for me till today. Now when I run the following code I get the error

library(ensembldb)
library(dplyr)
library(AnnotationHub)

## Load the annotation resource.
ah <-  AnnotationHub()

## Query for all available EnsDb databases
query(ah, "EnsDb")

ahDb <- query(ah, pattern = c("Homo sapiens", "EnsDb", 97))

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')"
Traceback:

1. AnnotationHub()
2. .Hub("AnnotationHub", hub, cache, proxy, localHub, ...)
3. .create_cache(.class, url, cache, proxy, localHub)
4. .updateHubDB(hub_bfc, .class, url, proxy, localHub)
5. bfcquery(bfc, paste0(tolower(.class), ".sqlite3"), field = "rname", 
 .     exact = TRUE)
6. bfcquery(bfc, paste0(tolower(.class), ".sqlite3"), field = "rname", 
 .     exact = TRUE)
7. bfcinfo(x, rids)
8. bfcinfo(x, rids)
9. .sql_get_resource_table(x, rids)
10. tryCatch({
  .     con <- .sql_connect_RO(.sql_dbfile(bfc))
  .     src <- src_dbi(con)
  .     tbl <- tbl(src, "resource")
  .     if (missing(rids)) {
  .     }
  .     else if (length(rids) == 0) {
  .         tbl <- tbl %>% filter_(~rid == NA_character_)
  .     }
  .     else if (length(rids) == 1) {
  .         tbl <- tbl %>% filter_(~rid == rids)
  .     }
  .     else {
  .         tbl <- tbl %>% filter_(~rid %in% rids)
  .     }
  .     meta <- setdiff(dbListTables(con), .RESERVED$TABLES)
  .     for (m in meta) tbl <- left_join(tbl, tbl(src, m), by = "rid")
  .     tbl <- tbl %>% collect
  . }, finally = {
  .     dbDisconnect(con)
  . })
11. tryCatchList(expr, classes, parentenv, handlers)
12. tbl %>% filter_(~rid == NA_character_)
13. withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
14. eval(quote(`_fseq`(`_lhs`)), env, env)
15. eval(quote(`_fseq`(`_lhs`)), env, env)
16. `_fseq`(`_lhs`)
17. freduce(value, `_function_list`)
18. withVisible(function_list[[k]](value))
19. function_list[[k]](value)
20. filter_(., ~rid == NA_character_)

Thank you in advance

Best,

Georgia

Here is my sessionInfo()

sessionInfo( )

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

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

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

other attached packages:
 [1] httr_1.4.2             forcats_0.5.0          stringr_1.4.0         
 [4] purrr_0.3.4            readr_1.3.1            tidyverse_1.3.0       
 [7] AnnotationHub_2.16.1   BiocFileCache_1.10.2   dbplyr_2.0.0          
[10] ensembldb_2.8.1        AnnotationFilter_1.8.0 GenomicFeatures_1.38.2
[13] AnnotationDbi_1.48.0   Biobase_2.46.0         ggbio_1.32.0          
[16] ggpubr_0.4.0           Gviz_1.28.3            GenomicRanges_1.38.0  
[19] GenomeInfoDb_1.22.1    IRanges_2.20.2         S4Vectors_0.24.4      
[22] BiocGenerics_0.32.0    scales_1.1.1           gridExtra_2.3         
[25] edgeR_3.26.8           limma_3.42.2           pheatmap_1.0.12       
[28] RColorBrewer_1.1-2     ggrepel_0.8.2          ggplot2_3.3.2         
[31] tibble_3.0.4           tidyr_1.1.2            dplyr_1.0.2.9000      

loaded via a namespace (and not attached):
  [1] tidyselect_1.1.0              RSQLite_2.2.1                
  [3] htmlwidgets_1.5.2             BiocParallel_1.20.1          
  [5] devtools_2.3.2                munsell_0.5.0                
  [7] pbdZMQ_0.3-3                  withr_2.3.0                  
  [9] colorspace_1.4-1              OrganismDbi_1.26.0           
 [11] knitr_1.30                    uuid_0.1-4                   
 [13] rstudioapi_0.11               ggsignif_0.6.0               
 [15] repr_1.1.0                    GenomeInfoDbData_1.2.2       
 [17] bit64_4.0.5                   rprojroot_1.3-2              
 [19] vctrs_0.3.4                   generics_0.1.0               
 [21] xfun_0.17                     biovizBase_1.32.0            
 [23] R6_2.5.0                      locfit_1.5-9.4               
 [25] bitops_1.0-6                  reshape_0.8.8                
 [27] DelayedArray_0.12.3           assertthat_0.2.1             
 [29] promises_1.1.1                nnet_7.3-14                  
 [31] gtable_0.3.0                  processx_3.4.4               
 [33] rlang_0.4.8                   splines_3.6.1                
 [35] rtracklayer_1.46.0            rstatix_0.6.0                
 [37] lazyeval_0.2.2                dichromat_2.0-0              
 [39] broom_0.7.0                   checkmate_2.0.0              
 [41] BiocManager_1.30.10           yaml_2.2.1                   
 [43] reshape2_1.4.4                abind_1.4-5                  
 [45] modelr_0.1.8                  backports_1.2.0              
 [47] httpuv_1.5.4                  Hmisc_4.4-1                  
 [49] RBGL_1.60.0                   usethis_1.6.3                
 [51] tools_3.6.1                   ellipsis_0.3.1               
 [53] sessioninfo_1.1.1             Rcpp_1.0.5                   
 [55] plyr_1.8.6                    base64enc_0.1-3              
 [57] progress_1.2.2                zlibbioc_1.32.0              
 [59] RCurl_1.98-1.2                ps_1.4.0                     
 [61] prettyunits_1.1.1             rpart_4.1-15                 
 [63] openssl_1.4.3                 SummarizedExperiment_1.16.1  
 [65] haven_2.3.1                   cluster_2.1.0                
 [67] fs_1.5.0                      magrittr_1.5                 
 [69] data.table_1.13.2             openxlsx_4.2.2               
 [71] reprex_0.3.0                  ProtGenerics_1.16.0          
 [73] matrixStats_0.57.0            pkgload_1.1.0                
 [75] hms_0.5.3                     mime_0.9                     
 [77] evaluate_0.14                 xtable_1.8-4                 
 [79] XML_3.99-0.3                  rio_0.5.16                   
 [81] jpeg_0.1-8.1                  readxl_1.3.1                 
 [83] testthat_3.0.0                compiler_3.6.1               
 [85] biomaRt_2.42.1                crayon_1.3.4                 
 [87] htmltools_0.5.0               later_1.1.0.1                
 [89] Formula_1.2-3                 lubridate_1.7.9              
 [91] DBI_1.1.0                     rappdirs_0.3.1               
 [93] Matrix_1.2-18                 car_3.0-9                    
 [95] cli_2.1.0                     pkgconfig_2.0.3              
 [97] GenomicAlignments_1.22.1      foreign_0.8-74               
 [99] IRdisplay_0.7.0               xml2_1.3.2                   
[101] XVector_0.26.0                rvest_0.3.6                  
[103] VariantAnnotation_1.30.1      callr_3.5.1                  
[105] digest_0.6.27                 graph_1.62.0                 
[107] Biostrings_2.54.0             cellranger_1.1.0             
[109] htmlTable_2.1.0               curl_4.3                     
[111] shiny_1.5.0                   Rsamtools_2.2.3              
[113] lifecycle_0.2.0               jsonlite_1.7.1               
[115] carData_3.0-4                 desc_1.2.0                   
[117] askpass_1.1                   BSgenome_1.52.0              
[119] fansi_0.4.1                   pillar_1.4.6                 
[121] lattice_0.20-41               GGally_2.0.0                 
[123] fastmap_1.0.1                 pkgbuild_1.1.0               
[125] survival_3.2-3                remotes_2.2.0                
[127] interactiveDisplayBase_1.22.0 glue_1.4.2                   
[129] zip_2.1.1                     png_0.1-7                    
[131] bit_4.0.4                     stringi_1.5.3                
[133] blob_1.2.1                    latticeExtra_0.6-29          
[135] memoise_1.1.0.9000            IRkernel_1.1.1

This does not happen in a current version of Bioconductor,

> BiocManager::version()
[1] '3.12'
> BiocManager::valid()
[1] TRUE

so i suggest you update your installation (this includes updating R to version 4.0.3)

I think the problem can be avoided in your version of R / Bioconductor by loading dplyr after the query

library(ensembldb)
library(AnnotationHub)

## Load the annotation resource.
ah <-  AnnotationHub()

## Query for all available EnsDb databases
query(ah, "EnsDb")

ahDb <- query(ah, pattern = c("Homo sapiens", "EnsDb", 97))

library(dplyr)

Updated my R and Bioconductor worked.