Clinical Data Download Fails on Windows

DarioS commented 4 years ago

On Windows computer (in office, Windows 7 32-bit)

> GDCdownload(clinical)
Downloading data for project TCGA-HNSC
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-client_v1.4.0_Windows_x64.zip'
Content type 'application/zip' length 16374028 bytes (15.6 MB)
downloaded 15.6 MB

GDCdownload will download: 167.697538 MB
Executing GDC client with the following command:
H:\Windows\Documents\gdc-client.exe download -m gdc_manifest.txt
Error in move(i, file.path(path, i)) : 
  I could not find the file: 52398f96-f15d-4468-bfc3-9692a1fb006f

On Debian computer

> GDCdownload(clinical)
Downloading data for project TCGA-HNSC
GDCdownload will download 8 files. A total of 942.121 KB
Downloading as: Tue_Dec__3_16_11_23_2019.tar.gz
Downloading: 150 kB

I seem to get the right data on Debian. Why does it install software and try to download 167 MB instead of 942 KB?

tiagochst commented 4 years ago

@DarioS I don't have a windows machine to test it right now. But could you provide the full query, please?

DarioS commented 4 years ago

Please use

GDCquery(project = "TCGA-HNSC",  data.category = "Clinical", data.type = "Clinical Supplement", data.format = "BCR Biotab")

BioinformaticsFMRP / TCGAbiolinks

Clinical Data Download Fails on Windows #371