Error parsing XML files

[shaniAmare]

Hi to the developers,

I don't understand why only for the clinical data processing, I get the following error:

read_xml.character(xmlfile) : 
  Start tag expected, '<' not found [4]

I have done the following;

query_clin <- GDCquery(project = "TCGA-BRCA",
                       data.type = "Clinical Supplement", 
                       data.category = "Clinical",
                       data.format = "XML")
GDCdownload(query_clin, files.per.chunk = 20)
clinical_data <- GDCprepare_clinic(query_clin, clinical.info = "patient")

and it hits with that error above about 31% in.

I manually checked if there is a XML ill-formatting in the dowloaded files, but cannot seem to find any.

To check I tried

cd ~/BC_CosMx/GDCdata/TCGA-BRCA/Clinical/Clinical_Supplement
find . -type f -name "*.xml" | while read -r file; do   first_char=$(head -c 1 "$file");   if [ "$first_char" != "<" ]; then
    echo "<$(cat "$file")" > "$file";   fi; done

None of them returned as modified. SO the XML files are fine that means.

I have been doing all this on the latest R Studio and R studio terminal (checking XML format) supplied to me through a HPC cluster.

Please help me figure out what am I doing wrong. If it is soon, that would be great! I have a conference in a few days which I like to present some results of this in.

Many thanks,
Shani.