Since upgrading to Bioconductor 3.5 I get this error when running AnnotationDbi::keys() on EnsDb.Hsapiens.v75 or other ensembldb objects:

> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationFilter
Warning messages:
1: multiple methods tables found for ‘rowSums’
2: multiple methods tables found for ‘colSums’
3: multiple methods tables found for ‘rowMeans’
4: multiple methods tables found for ‘colMeans’
> keys(EnsDb.Hsapiens.v75)
Error in validObject(.Object) :
  invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

Matrix products: default
BLAS: /GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/lib/libRblas.so
LAPACK: /GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] EnsDb.Hsapiens.v75_2.1.0 ensembldb_2.0.1          AnnotationFilter_1.0.0
 [4] GenomicFeatures_1.28.0   AnnotationDbi_1.38.0     Biobase_2.36.2
 [7] GenomicRanges_1.28.1     GenomeInfoDb_1.12.0      IRanges_2.10.1
[10] S4Vectors_0.14.1         BiocGenerics_0.22.0      nvimcom_0.9-25

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10                  BiocInstaller_1.26.0
 [3] compiler_3.4.0                XVector_0.16.0
 [5] AnnotationHub_2.8.1           ProtGenerics_1.8.0
 [7] bitops_1.0-6                  tools_3.4.0
 [9] zlibbioc_1.22.0               biomaRt_2.32.0
[11] digest_0.6.12                 RSQLite_1.1-2
[13] memoise_1.1.0                 lattice_0.20-35
[15] Matrix_1.2-10                 shiny_1.0.3
[17] DelayedArray_0.2.2            DBI_0.6-1
[19] yaml_2.1.14                   GenomeInfoDbData_0.99.0
[21] rtracklayer_1.36.0            httr_1.2.1
[23] Biostrings_2.44.0             grid_3.4.0
[25] R6_2.2.1                      XML_3.98-1.7
[27] BiocParallel_1.10.1           htmltools_0.3.6
[29] Rsamtools_1.28.0              matrixStats_0.52.2
[31] GenomicAlignments_1.12.1      SummarizedExperiment_1.6.1
[33] xtable_1.8-2                  mime_0.5
[35] interactiveDisplayBase_1.14.0 httpuv_1.3.3
[37] RCurl_1.95-4.8                lazyeval_0.2.0

keys() works fine on other OrgDb objects such as org.Hs.eg.db.

Any fix or workaround for getting the keys out of this object?

Thanks!

P.S.: are ensembldb OrgDb objects ever going to be supported by the Bioconductor Core Team?

Hi,

can you please provide the output of sessionInfo()? I have no problem with the keys call. To get the Ensembl gene IDs out of an EnsDb object you can also:

library(EnsDb.Hsapiens.v75)
gene_ids <- genes(EnsDb.Hsapiens.v75, columns = "gene_id")$gene_id

head(gene_ids)
[1] "ENSG00000223972" "ENSG00000227232" "ENSG00000243485" "ENSG00000237613"
[5] "ENSG00000268020" "ENSG00000240361"

Regarding the support of EnsDb by Bioconductor: I'll build for each Ensembl release EnsDb databases for all species in Ensembl. They will then be made available through AnnotationHub:

library(AnnotationHub)
ah <- AnnotationHub()

query(ah, c("EnsDb"))
AnnotationHub with 136 records
# snapshotDate(): 2017-04-25
# $dataprovider: Ensembl
# $species: Ailuropoda Melanoleuca, Anas Platyrhynchos, Anolis Carolinensis,...
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53185"]]'

            title                                      
  AH53185 | Ensembl 87 EnsDb for Anolis Carolinensis   
  AH53186 | Ensembl 87 EnsDb for Ailuropoda Melanoleuca
  AH53187 | Ensembl 87 EnsDb for Astyanax Mexicanus    
  ...       ...                                        
  AH53754 | Ensembl 88 EnsDb for Vicugna Pacos         
  AH53755 | Ensembl 88 EnsDb for Xiphophorus Maculatus
  AH53756 | Ensembl 88 EnsDb for Xenopus Tropicalis   

Looks like that error was reported elsewhere too:

https://github.com/joey711/phyloseq/issues/717

Eventually re-install S4Vectors, ensembldb, AnnotationFilter might help.

BiocInstaller::biocLite(c("S4Vectors", "ensembldb", "AnnotationFilter") type="source")