[ensembl-dev] biomaRt: listDatasets(ensmart) only contains hsapiens sometimes !

[Vivek Iyer]

Hi,

I’m getting a weird sporadic error when I follow the bioconductor vignette for biomaRt - see the dialogue in R below - the hsapiens_gene_ensembl dataset simply vanishes sometimes. Rerunning the line "human = useDataset("hsapiens_gene_ensembl",mart=ensembl)” works sometimes and fails others. I thought I was going mad for a bit because the dataset would "come back” sporadically and I couldn’t work out what I had changed. 

The biomaRt vignette records (about) 92 datasets returned in the main mart, and during the ‘failures' I only see 72, so there seem to be a bunch dropping out, for no apparent reason? Any insight appreciated. Note: I have tried this against archive hosts as well (e.g. apr2018.archive.ensembl.org <http://apr2018.archive.ensembl.org/>) and the same thing happens. Is anyone else able to reproduce this?

Cheers,

Vivek

library(“biomaRt")
listMarts()

ensembl=useMart("ensembl")
View(listDatasets(ensembl))

dim(listDatasets(ensembl))
[1] 72  3

library(dplyr)

 listDatasets(ensembl) %>% filter(dataset=="hsapiens_gene_ensembl")
[1] dataset     description version    
<0 rows> (or 0-length row.names)

> human = useDataset("hsapiens_gene_ensembl",mart=ensembl)
Error in useDataset("hsapiens_gene_ensembl", mart = ensembl) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid. …



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