What is wrong with my scripts?

Question

[nuorain]

Hi, I have checked with ChatGPT but got no clue. Can anyone help me with this? Thank you very much.

# Prepare the clinical data
> clinical_data <- GDCprepare_clinic(query_clinical, clinical.info = "patient")
  |============                                                            |  17%Error in read_xml.character(xmlfile) : 
  Start tag expected, '<' not found [4]
> 

Answer 1

[Ming Tommy Tang]

add data.format="bcr xml" in the GDCquery()

[nuorain]

Thank you so much. It works now.

Answer 2

[Pierre Lindenbaum]

an input file is not a valid XML file.

[nuorain]

Thank you for your comments.