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Error in GDCprepare in TCGAbiolinks

Hi, I have used the code below to download and prepare data from TCGA using the TCGAbiolinks package for R. library("TCGAbiolinks") query <- GDCquery(project = "TCGA-PRAD", data.category = "DNA Methylation", experimental.strategy = "Methylation Array")

GDCdownload(query, chunks.per.download = 5)

data <- GDCprepare(query) return(data)

After the download is completed, I get the error.

data <- GDCprepare(query)

Read 485577 rows and 11 (of 11) columns from 0.132 GB file in 00:00:03=============================================| 100%

Read 485577 rows and 11 (of 11) columns from 0.132 GB file in 00:00:04

Starting to add information to samples

=> Add clinical information to samples

Error: lexical error: invalid char in json text. <respons (right="" here)="" ------^<="" p="">

return(data)

Error: no function to return from, jumping to top level

Can anyone help me sort this error? Thanks in advance Sandhanakrishnan

r tcgabiolinks

1 answer

tiagochst answered here:

https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/65

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