GDCprepare - Download error for TCGA-PRAD methylation array

[CarlosUziel]

I am getting the following error while running GDCprepare, it seems that some annotation files are no longer available. Any help would be greatly appreciated!

GDCprepare output:

Processing  IDATs with Sesame - http://bioconductor.org/packages/sesame/

Running opensesame - applying quality masking and nondetection masking (threshold P-value 0.05)

Please cite: doi: 10.1093/nar/gky691 and 10.1093/nar/gkt090

This might take a while....

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Creating a SummarizedExperiment from DNA methylation input

Warning message in download.file(url, method = method, ...):
“cannot open URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds': HTTP status was '404 Not Found'”

Error in download.file(url, method = method, ...): cannot open URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds'
Traceback:

1. GDCprepare(query, save = FALSE, directory = data_dir)
2. readIDATDNAmethylation(files, barcode = cases, summarizedExperiment, 
 .     unique(query$platform), query$legacy)
3. makeSEFromDNAMethylationMatrix(betas, genome = ifelse(legacy, 
 .     "hg19", "hg38"), met.platform = met.platform)
4. getInfiniumAnnotation(met.platform, genome)
5. downloader::download(annotation, basename(annotation), mode = mode)
6. download.file(url, method = method, ...)

To reproduce:

data_dir = ...

query <- GDCquery(project = "TCGA-PRAD",
                 data.category = "Raw microarray data",
                 data.type = "Raw intensities",
                 experimental.strategy = "Methylation array",
                 legacy = TRUE,
                 platform = "Illumina Human Methylation 450")

GDCdownload(query, method = "api", files.per.chunk = 20, directory=data_dir)

met <- GDCprepare(query, save = FALSE, directory=data_dir)

[tiagochst]

Please, which Version of TCGAbiolinks are you using? The code below worked on 2.19.0

query <- GDCquery(project = "TCGA-PRAD",
                  data.category = "Raw microarray data",
                  data.type = "Raw intensities",
                  experimental.strategy = "Methylation array",
                  legacy = TRUE,
                  barcode = c("TCGA-VN-A88N","TCGA-ZG-A9MC"),
                  platform = "Illumina Human Methylation 450")
GDCdownload(query, method = "api", files.per.chunk = 20)

met <- GDCprepare(query, save = FALSE)

[CarlosUziel]

Thanks for your response! Unfortunately I don't have the same Anaconda environment with which I got this error anymore. However I can confirm that the above is working now on 2.18.0. Perhaps it was a temporary server error, since the package wasn't able to download a very specific file.