Bug in ucscTableQuery, UcscTrack

Doyle, Kevin

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Mar 10, 2026, 4:30:29 PM (16 hours ago) Mar 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 PM (15 hours ago) Mar 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 PM (14 hours ago) Mar 10

to Doyle, Kevin, sanchit...@gmail.com, gen...@soe.ucsc.edu

Looks like Michael is not at Genentech anymore, so CCing Sanchit

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