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mksamur / RTCGAToolbox

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New Issue with getFirehoseData #44

Closed biostars-nyc closed 1 year ago

biostars-nyc commented 1 year ago

I've been using this exact command for months with no issue, but suddenly produces the error below.

Error in UseMethod("xmlNamespaceDefinitions") : no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

Code:

library(RTCGAToolbox)
ov <- getFirehoseData(
     dataset = 'OV',
     runDate = "20120306",
     clinical = TRUE,
     forceDownload = TRUE,
     destdir = getwd(),
     fileSizeLimit = 500)
LiNk-NY commented 1 year ago

I can't reach http://gdac.broadinstitute.org/runs/stddata__2012_03_06/data/OV/20120306/ and it looks like gdac.broadinstitute.org is down. Best, Marcel

LiNk-NY commented 1 year ago

It looks like the gdac page has changed. I've updated the code to make use of this new layout. 9118e046ffe371398ae10205346d4cc83189dcbe -MR