Bug in ucscTableQuery, UcscTrack

Doyle, Kevin

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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>

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

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Mar 10, 2026, 5:39:01 PMMar 10

to Doyle, Kevin, lawrence...@gene.com, gen...@soe.ucsc.edu

CC'ing the rtracklayer author.

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Maximilian Haeussler

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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

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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

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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:

Doyle, Kevin

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Apr 28, 2026, 3:30:27 PMApr 28

to Sanchit Saini, Maximilian Haeussler, gen...@soe.ucsc.edu

This issue was fixed for a while but now seems to be reappearing. The details are on the same issue on GitHub: https://github.com/lawremi/rtracklayer/issues/148#issuecomment-4338179743

From: Sanchit Saini <sanchit...@gmail.com>
Sent: Sunday, March 15, 2026 6:22 PM
To: Maximilian Haeussler <mhae...@ucsc.edu>
Cc: Doyle, Kevin <kd2...@cumc.columbia.edu>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: [EXTERNAL] Re: [genome] Bug in ucscTableQuery, UcscTrack

You don't often get email from sanchit...@gmail.com. Learn why this is important

Matthew Speir

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May 5, 2026, 4:20:02 PMMay 5

to Doyle, Kevin, Sanchit Saini, Maximilian Haeussler, gen...@soe.ucsc.edu

Hello, Kevin.

Thank you for reporting this issue. Based on the Github ticket you linked, it appears that Sanchit from rtracklayer and Max Haeussler from the UCSC Genome Browser are looking into it. Let us know if there are any software updates needed on our end.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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