GDCPrepare error (No such process)

Question

[aUser]

Hi,

I am trying to do mutation analysis from TCGA data, and I am doing it using a simple process like this:

query.met <- GDCquery(
    project = project, 
    data.category = "Simple Nucleotide Variation", 
    access = "open", 
    data.type = "Masked Somatic Mutation", 
    workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking")

GDCdownload(query.met)

mut <- GDCprepare(query.met)

But, it is giving me an error as:

Error: No such process.

I tried TCGA-LUAD, TCGA-LUSC, and TCGA-COAD as projects, but the error is the same in all cases.

R4.2.1, TCGAbiolinks v2.25.3

I tried googling but did not get any clue. If anybody could point out any error or hint, that would be great.

Answer 1

[aUser]

Just restarting the R session fixed the problems. It may be due to pending updates (the already loaded libraries do not update) or any other unknown error that was not visible/discernable from this error. I don't want to restart the session that was the reason I was looking for some help.