I was trying to download clinical data from the TCGA-KIRC project and it is failing.
I found out it was downloading a TXT file and trying to read it as an XML (id:
64a1b6e7-d037-4502-bbad-0d07849fc32e and file:
> gdc$clinical <- GDCprepare_clinic(query$clinical, clinical.info = 'patient') |== | 2%Error in doc_parse_file(con, encoding = encoding, as_html = as_html, options = options) : Start tag expected, '<' not found 
The code to replicate is below, using bioconductor 3.7 and TCGAbiolinks 2.8.1
project <- 'TCGA-KIRC' query <- list() query$clinical <- GDCquery(project = project, data.category = "Clinical") download.out <- GDCdownload(query$clinical, method = 'api') gdc <- list() gdc$clinical <- GDCprepare_clinic(query$clinical, clinical.info = 'patient')