Bug in ucscTableQuery, UcscTrack

46 views
Skip to first unread message

Doyle, Kevin

unread,
Mar 10, 2026, 4:30:29 PMMar 10
to gen...@soe.ucsc.edu
Hello,

As of two weeks ago, I was able to use functions from the R package rtracklayer, such as ucscTableQuery and UcscTrack, to query track data from UCSC. When currently running them, however, I am met with the following errors:

```
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'table' in selecting a method for function '%in%': Invalid genome :'hg38'
In addition: Warning messages:
1: In grepl("\\\\u[0-9A-Fa-f]", str) :
  unable to translate '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<HTML>
<HEAD>

<meta http-equiv='Content-Security-Policy' content="default-src *; script-src 'self' blob: 'unsafe-inline' 'nonce-DNTi70zOLWc965lidICs...' to a wide string
2: In grepl("\\\\u[0-9A-Fa-f]", str) : input string 1 is invalid
```
and
```
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
  !anyNA(m32) is not TRUE
```

Does anyone know why this might be occurring?

Maximilian Haeussler

unread,
Mar 10, 2026, 5:39:01 PMMar 10
to Doyle, Kevin, lawrence...@gene.com, gen...@soe.ucsc.edu
CC'ing the rtracklayer author.

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/DS0PR02MB9572004DC34C8743B02A53168C46A%40DS0PR02MB9572.namprd02.prod.outlook.com.

Maximilian Haeussler

unread,
Mar 10, 2026, 7:10:25 PMMar 10
to Doyle, Kevin, sanchit...@gmail.com, gen...@soe.ucsc.edu
Looks like Michael is not at Genentech anymore, so CCing Sanchit 

Sanchit Saini

unread,
Mar 15, 2026, 6:30:26 PMMar 15
to Maximilian Haeussler, Doyle, Kevin, gen...@soe.ucsc.edu
No need, I just found an open issue on GitHub. I'll investigate  and share findings on github issue

Sanchit


On Mon, Mar 16, 2026 at 3:46 AM Sanchit Saini <sanchit...@gmail.com> wrote:
Can you please share the reproducible code? I will look into it.


Sanchit

Sanchit Saini

unread,
Mar 15, 2026, 6:30:27 PMMar 15
to Maximilian Haeussler, Doyle, Kevin, gen...@soe.ucsc.edu
Can you please share the reproducible code? I will look into it.


Sanchit

On Wed, Mar 11, 2026 at 4:40 AM Maximilian Haeussler <mhae...@ucsc.edu> wrote:
Reply all
Reply to author
Forward
0 new messages