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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Error/Bug: "All samples have been already downloaded" #531

Open biostars-nyc opened 2 years ago

biostars-nyc commented 2 years ago

I had previously downloaded data from a legacy query using GDCdownload without issue. However, the data was deleted and I'd like to download it again. Each time I try and do so, I'm met with this message. However, the files are clearly not downloaded because GDCprepare comes up NULL and I've confirmed the files aren't there. How can I fix this bug?

GDCdownload(query = query, method = 'api', files.per.chunk = 100) Downloading data for project TCGA-OV All samples have been already downloaded

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.5.1

tiagochst commented 2 years ago

@biostars-nyc Could you send the query code? It is the first time that issue happens, so I need to see the query. I need to check if the query returned any results, if so, I need to check why it says it already downloaded the data and is not able to prepare it.