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2.2 years ago by
USA/Boston/Dana-Farber Cancer Institute
Sebastien Vigneau10 wrote:

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?

modified 2.2 years ago by Hervé Pagès ♦♦ 13k • written 2.2 years ago by Sebastien Vigneau10
3
2.2 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Sebastien,

An easier way to reproduce is with:

library(rtracklayer)
session <- browserSession()
genome(session) <- "mm10"
# 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 makeTxDbFromUCSC().

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

H.

1

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.

1

Hi Sebastien,

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).

Cheers,

H.

Great!

Thanks,

S.

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!

> library(rtracklayer)
> session <- browserSession()
> genome(session) <- "hg19"
Error in normArgTable(value, x) : unknown table name 'refLink'