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.
For some reason the table browser does not report hgFixed.refLink when selecting "All Tables" for the group. Seems like a bug in the table browser to me. I guess we should bring it up with UCSC.
Thank you for looking into this. I am looking forward to Michael's feedback.
This is fixed in GenomicFeatures 1.24.5 (release) and 1.25.16 (devel). Both versions should become available via
biocLite()in the next 48 hours or so (maybe a little bit more for the devel version).
I still have this problem in R 3.3.2. bioconductor 3.4. and rstacklayer 1.34.1
Is there any solution for me? Thank you!
As stated in the post above, the table is now called "hgFixed.refLink".