Hello,

I am having a problem trying to pull GO (or EVIDENCE but not ONTOLOGY) terms from an OrgDB package from AnnotationHub; it's getting confused on the GO and GOALL keytypes:

> BiocManager::version()
[1] ‘3.11’
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2020-04-27
> query(ah, c("OrgDb", "Daphnia"))
AnnotationHub with 1 record
...
# retrieve record with 'object[["AH81226"]]' 
> org.Dm.eg.db <- ah[["AH81226"]]

> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("GO"))
Error in FUN(X[[i]], ...) : 
  Two fields in the source DB have the same name.

> keytypes(org.Dm.eg.db)
 [1] "ACCNUM"      "ALIAS"       "ENTREZID"    "EVIDENCE"   
 [5] "EVIDENCEALL" "GENENAME"    "GID"         "GO"         
 [9] "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "PMID"       
[13] "REFSEQ"      "SYMBOL"

#check the others:
> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("EVIDENCE"))
Error in FUN(X[[i]], ...) : 
  Two fields in the source DB have the same name.
> temp <- select(org.Dm.eg.db, keys = keys(org.Dm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("ONTOLOGY"))
'select()' returned 1:many mapping between keys and columns

Didn't this same error happen in the pre-built OrgDB right when 3.11 was released? That appears to be fixed:

> library(org.Mm.eg.db)

> temp <- select(org.Mm.eg.db, keys = keys(org.Mm.eg.db, keytype = "ENTREZID"),
+                keytype = "ENTREZID", columns = c("GO"))
'select()' returned 1:many mapping between keys and columns

Thanks!

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] org.Mm.eg.db_3.11.4  AnnotationDbi_1.50.1 IRanges_2.22.2      
[4] S4Vectors_0.26.1     Biobase_2.48.0       AnnotationHub_2.20.0
[7] BiocFileCache_1.12.0 dbplyr_1.4.4         BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                    later_1.1.0.1                
 [3] pillar_1.4.6                  compiler_4.0.2               
 [5] BiocManager_1.30.10           tools_4.0.2                  
 [7] digest_0.6.25                 bit_1.1-15.2                 
 [9] RSQLite_2.2.0                 memoise_1.1.0                
[11] lifecycle_0.2.0               tibble_3.0.3                 
[13] pkgconfig_2.0.3               rlang_0.4.7                  
[15] shiny_1.5.0                   DBI_1.1.0                    
[17] rstudioapi_0.11               curl_4.3                     
[19] yaml_2.2.1                    xfun_0.15                    
[21] fastmap_1.0.1                 dplyr_1.0.0                  
[23] httr_1.4.2                    generics_0.0.2               
[25] vctrs_0.3.2                   rappdirs_0.3.1               
[27] bit64_0.9-7.1                 tidyselect_1.1.0             
[29] glue_1.4.1                    R6_2.4.1                     
[31] purrr_0.3.4                   blob_1.2.1                   
[33] magrittr_1.5                  promises_1.1.1               
[35] htmltools_0.5.0               ellipsis_0.3.1               
[37] assertthat_0.2.1              xtable_1.8-4                 
[39] mime_0.9                      interactiveDisplayBase_1.26.3
[41] httpuv_1.5.4                  tinytex_0.24                 
[43] crayon_1.3.4                  BiocVersion_3.11.1 

Hi Jenny,

See here. You should be able to fix that by doing

library(BiocManager)
install("jmacdon/AnnotationDbi")

I sent a PR to Kayla for the same fix yesterday, so I am assuming it will appear via the regular channels in time.