genomeToTranscript function not found

[pamelarussell]

I just installed ensembldb and EnsDB.Hsapiens.V86 from Bioconductor today. I want to use genomeToTranscript but the function does not appear to be exported in the package.

I'm running the example from the vignette:

library(ensembldb)
library(EnsDb.Hsapiens.v86)
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X") 
gnm <- GRanges("X:107716399-107716401") 
gnm_tx <- genomeToTranscript(gnm, edbx)

This is the output:

Error in genomeToTranscript(gnm, edbx) : 
  could not find function "genomeToTranscript"

I also did:

> ensembldb::genomeToTranscript
Error: 'genomeToTranscript' is not an exported object from 'namespace:ensembldb'

Here is my session info:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.2.2           AnnotationFilter_1.2.0    GenomicFeatures_1.30.3    AnnotationDbi_1.40.0      Biobase_2.38.0           
 [7] GenomicRanges_1.30.3      GenomeInfoDb_1.14.0       IRanges_2.12.0            S4Vectors_0.16.0          BiocGenerics_0.24.0      

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.8.1    progress_1.2.0                lattice_0.20-35               htmltools_0.3.6               rtracklayer_1.38.3           
 [6] yaml_2.2.0                    interactiveDisplayBase_1.16.0 blob_1.1.1                    XML_3.98-1.13                 rlang_0.2.1                  
[11] later_0.7.3                   DBI_1.0.0                     BiocParallel_1.12.0           bit64_0.9-7                   matrixStats_0.54.0           
[16] GenomeInfoDbData_1.0.0        ProtGenerics_1.10.0           stringr_1.3.1                 zlibbioc_1.24.0               Biostrings_2.46.0            
[21] memoise_1.1.0                 biomaRt_2.34.2                BiocInstaller_1.28.0          httpuv_1.4.5                  curl_3.2                     
[26] Rcpp_0.12.18                  xtable_1.8-2                  promises_1.0.1                DelayedArray_0.4.1            XVector_0.18.0               
[31] mime_0.5                      bit_1.1-14                    Rsamtools_1.30.0              AnnotationHub_2.10.1          RMySQL_0.10.15               
[36] hms_0.4.2                     digest_0.6.15                 stringi_1.2.4                 shiny_1.1.0                   grid_3.4.3                   
[41] tools_3.4.3                   bitops_1.0-6                  magrittr_1.5                  RCurl_1.95-4.11               lazyeval_0.2.1               
[46] RSQLite_2.1.1                 crayon_1.3.4                  pkgconfig_2.0.1               Matrix_1.2-14                 prettyunits_1.0.2            
[51] assertthat_0.2.0              httr_1.3.1                    rstudioapi_0.7                R6_2.2.2                      GenomicAlignments_1.14.2     
[56] compiler_3.4.3               

[jorainer]

Dear Pamela,

the coordinate mapping functionality has been added to ensembldb starting with version 2.4.0. You need to install a recent R (version 3.5.1) and the current Bioconductor version 3.7 to get ensembldb with this functionality.

[jorainer]

Closing this issue - feel free to re-open if needed.