The following command fails with the message below, using R version 3.3.1 and Bioconductor version 3.3 on Ubuntu 16.04:

> txdb <- makeTxDbFromUCSC(genome = 'mm10', tablename = "refGene")
Download the refGene table ... OK
Download the refLink table ... Error in normArgTable(value, x) : unknown table name 'refLink'

Do you know what the problem might be and how to solve it?

Thank you for your help!

Hi Sebastien,

An easier way to reproduce is with:

library(rtracklayer)
session <- browserSession()
genome(session) <- "mm10"
query <- ucscTableQuery(session, table="refLink")
# Error in normArgTable(value, x) : unknown table name 'refLink'

This worked until very recently. So something must have changed at UCSC that breaks it. And indeed (after browsing around a bit):

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download35

In short, the refLink table has changed location and is now in a separate (shared across organisms) db. However, for whatever reason, I don't seem to be able to access the table at its new location (using its fully qualified name) with rtracklayer:

> query <- ucscTableQuery(session, table="hgFixed.refLink")
Error in normArgTable(value, x) : unknown table name 'hgFixed.refLink'

So we will need assistance from Michael, our rtracklayer expert, before we can come up with a fix for makeTxDbFromUCSC().

Thanks for reporting this. We'll keep you posted here about any progress on this.

H.