Between the lack of a reproducible example and the question being about a Bioconductor package, you probably won't see much response here. Try the Bioconductor mailing list?
Sent from my phone. Please excuse my brevity.
>I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data.
>following error occurs after this command line below:
>>pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(
>gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native
>same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up"))
>Start tag expected, '<' not found
>Warning: Parsing test/hsa04510.xml file failed, please check the file!
>That .xml file is empty, while .png file exists. The issue is there is
>pathway with my data mapped (red and blue nodes). Can you please help
> [[alternative HTML version deleted]]
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.