GDCprepare truncated when downloading TCGA methylation data

Question

[melissachua90]

I want to download the methylation data of the TCGA-KIRC project using GDCquery and GDCprepare. My code raised a warning message that implies that the GDCprepare step is truncated, with the "Warning message: In open.connection(con, "rb") : ... [... truncated]" message. What is the solution?

query.met.kirc <- GDCquery(
  project = "TCGA-KIRC", 
  legacy = TRUE,
  data.category = "DNA methylation",
  platform = "Illumina Human Methylation 450", 
)
GDCdownload(query.met.kirc)

met.kirc.450 <- GDCprepare(
  query = query.met.kirc,
  save = TRUE, 
  save.filename = "kircDNAmet450k.rda",
  summarizedExperiment = TRUE
)

Warning message:

--------------------
oo Merging 485 files
--------------------
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
kirc subtype information from:doi:10.1038/nature12222
=> Saving file: kircDNAmet450k.rda
=> File saved
Warning message:
In open.connection(con, "rb") :
  URL 'https://api.gdc.cancer.gov/cases/?pretty=true&expand=samples,project,diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures&size=10&filters=%7B%22op%22:%22or%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.submitter_id%22,%22value%22:["TCGA-BP-4993-01A","TCGA-CZ-5982-01A","TCGA-B0-4703-01A","TCGA-CJ-4908-01A","TCGA-CZ-5470-11A","TCGA-B0-4811-01A","TCGA-BP-5183-11A","TCGA-DV-5574-01A","TCGA-CZ-5451-01A","TCGA-B0-5099-11A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_sample_ids%22,%22value%22:["TCGA-BP-4993-01A","TCGA-CZ-5982-01A","TCGA-B0-4703-01A","TCGA-CJ-4908-01A","TCGA-CZ-5470-11A","TCGA-B0-4811-01A","TCGA-BP-5183-11A","TCGA-DV-5574-01A","TCGA-CZ-5451-01A","TCGA-B0-5099-11A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_aliquot_ids%22,%22value%22:["TCGA-BP-4993-01A","TCGA-CZ-5982-01A","TCGA-B0-4703-01A","TCGA-CJ-4908-01A","TCGA-CZ-5470-11A","TCGA-B0-4811-01A","TCGA-BP-51 [... truncated]