ucscGenomes() returns NULL

[endeneon]

> ucscGenomes()
Error in UseMethod("xmlNamespaceDefinitions") : 
  no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

According to the function description it would populate data from http://genome.ucsc.edu/cgi-bin every time when it was called and returns a data.frame. However, starting from this week it seems that either the UCSC genome browser website changed its XML data format or simply put a 403 page there. Does anyone experience the same error (especially when using GViz-related functions such as UcscTrack() that calls this function? Thanks!

[maximilianh]

UCSC here with some comments, as we got a mailing list question: cgi-bin always returned a 404, Rtracklayer doesn't use this URL, it uses the API see https://github.com/lawremi/rtracklayer/blob/master/R/ucsc.R#L1475. AFAIK it uses the endpoint http://api.genome.ucsc.edu/list/ucscGenomes and this endpoint works as it always worked, it lists the genomes. So this seems to be unrelated to anything we did ... ?

[sanchit-saini]

Hi @endeneon,

I wasn't able to replicate it. Can you share your sessionInfo.