An easier way to reproduce is with:
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):
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
Thanks for reporting this. We'll keep you posted here about any progress on this.