problem downloading data: incomplete final line found error with gdcRNADownload()

[IyadSultan]

######## Download mature miRNA data ####### gdcRNADownload(project.id = 'TARGET-NBL',

• data.type = 'miRNAs',
• write.manifest = FALSE,
• method = 'gdc-client',
• directory = mirdir) incomplete final line found by readTableHeader on 'https://api.gdc.cancer.gov/files?filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-NBL%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%22Transcriptome%20Profiling%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:%22Isoform%20Expression%20Quantification%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:%22BCGSC%20miRNA%20Profiling%22%7D%7D]%7D&pretty=true&format=JSON&size=10000&expand=analysis,analysis.input_files,associated_entities,cases,cases.diagnoses,cases.diagnoses.treatments,cases.demographic,cases.project,cases.samples,cases.samples.portions,cases.samples.portions.analytes,cases.samples.portions.analytes.aliquots,cases.samples.portions.slides&return_type=manifest'Successfully downloaded: 0

[Josuerinho]

Hi all! I'm having the same problem. In my case is just with data.type = "RNAseq". "miRNAs" works just fine. I'm working on Apple's M1 chip though so I don't know if this could be causing the problem. I've installed all packages and dependencies as suggested to avoid issues but still, the same error. Has anyone provided a fix for this? Thanks for your help!

PS: I've been trying to understand the error and accessed the code behind gdcRNADownload() function step by step to pinpoint the problem. However, when I try to independently run each line of code inside this function, it already fails at:

url <- gdcGetURL(project.id=project.id, data.type=data.type)

Here it says the function doesn't exist. How is that possible that inside the installed function gdcRNADownload(), gdcGetURL() does its job but when tried independently isn't working?? I can't wrap my head around it.