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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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GDCprepare can't find the files #438

Closed MercedesBentata closed 3 years ago

MercedesBentata commented 3 years ago

Hello,

I successfully ran the GDCquery function.

Then, I ran the GDCdownload. Everything was downloaded and ran smoothly besides these warnings: (here is one example) <simpleWarning in file.copy(from = from, to = todir, recursive = TRUE): problem copying ... No such file or directory> So I just copied manually the downloaded files to this directory: GDCdata\TCGA-LGG\harmonized\DNA_Methylation\Methylation_Beta_Value

Next, I ran GDCprepare and the next problem appeared: Error in GDCprepare(query = query) : I couldn't find all the files from the query. Please check if the directory parameter is right or GDCdownload downloaded the samples.

I am sure I am in the correct directory and my files are there. What could be the problem? Has someone faced this problem before?

Thanks a lot in advance!

MercedesBentata commented 3 years ago

I solved the problem. The length of the path name was too long.

tjhwangxiong commented 10 months ago

I solved the problem. The length of the path name was too long.

How did you solve the length of the path name ? I have this problem too.