TCGAbiolinks error using GDCprepare for methylation data

Question

[Lunky]

Previously when I used the following code it would not give me an error. Has there been some sort of update recently? I have tried searching online but I do not know how to resolve this issue:

Code (I have tried for various projects):

library(TCGAbiolinks)
library(SummarizedExperiment)

queryMethylTumorsKIRC <- GDCquery(project = "TCGA-KIRC",
                                  legacy=F,
                                  data.category = "DNA Methylation",
                                  data.type = "Methylation Beta Value",
                                  platform = c("Illumina Human Methylation 450"),
                                  sample.type = "Primary Tumor")


GDCdownload(queryMethylTumorsKIRC)

tumorsPrepared <- GDCprepare(queryMethylTumorsKIRC, summarizedExperiment=F) 

Error message:

Error in fread(f, header = TRUE, sep = "\t", stringsAsFactors = FALSE, : colClasses= is an unnamed vector of types, length 5, but there are 2 columns in the input. To specify types for a subset of columns, you can use a named vector, list format, or specify types using select= instead of colClasses=. Please see examples in ?fread. Calls: GDCprepare ... llply -> loop_apply -> <Anonymous> -> .fun -> fread Error in if (value == n) { : argument is of length zero

Answer 1

[Timothee]

See the discussion here : https://www.biostars.org/p/9516907/#9517068