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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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gdcRNADownload error with GDC-client #11

Open IL2liu opened 5 years ago

IL2liu commented 5 years ago

When using the follwing code:

####### Download mature miRNA data #######
gdcRNADownload(project.id     = 'TCGA-BRCA', 
               data.type      = 'miRNAs', 
               write.manifest = FALSE,
               method         = 'gdc-client',
               directory      = mirdir)

ERROR: An unexpected error has occurred during normal operation of the client. Please report the following exception to GDC support support@nci-gdc.datacommons.io. ERROR: 'NoneType' object has no attribute 'status_code' Traceback (most recent call last): File "gdc-client", line 99, in File "build\bdist.win-amd64\egg\gdc_client\download\parser.py", line 111, in download File "build\bdist.win-amd64\egg\gdc_client\download\client.py", line 234, in download_small_groups File "build\bdist.win-amd64\egg\gdc_client\download\client.py", line 171, in _download_tarfile AttributeError: 'NoneType' object has no attribute 'status_code' ERROR: Exiting Traceback (most recent call last): File "logging__init.py", line 861, in emit File "logging__init__.py", line 734, in format File "build\bdist.win-amd64\egg\gdc_client\log\log.py", line 36, in format File "logging\init.py", line 465, in format File "logging\init.py", line 325, in getMessage TypeError: str__ returned non-string (type SysCallError) Logged from file client.py, line 150

IL2liu commented 5 years ago

Following the suggestion of Dr. Li, This problem was solved by using update R to 3.6.1 .

Thank you for your help.

MahsaMonshizade commented 4 years ago

Hi. I have this problem too. I updated my r to the latest version(4.0.0) but I still get this error. I would appreciate it if someone could help me.

BioLiu commented 4 years ago

Hi. I have this problem too. I updated my r to the latest version(4.0.0) but I still get this error. I would appreciate it if someone could help me.

Hi. I got the same problem. I found gdc-client has different packages for different Python version, you can check it in their web site. I checked code of gdcRNADownload.R and didn't found related test the version of Python; it downloads the gdc-client for Python 2.7. I solved the problem by downloading the gdc-client according to the version of Python of my platform, since my version is Python 3, I downloaded gdc-client_v1.5.0 and solved the problem. Best wishes!

romylland commented 4 years ago

Hi. I have this problem too. I updated my r to the latest version(4.0.0) but I still get this error. I would appreciate it if someone could help me.

Hi @mahsa-moony were you able to fix your problem? I was in the same situation as you but following @BioLiu's suggestion it solved it.