GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
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hwteng1971 • 0
@hwteng1971-15996
Last seen 3.4 years ago

dear alls

I am suffered from a problem since 2 days ago.

""Error in getURL(url, GET, timeout(600)) : 'getURL()' failed:"

the following code can not work if sample is ""TCGA-COAD""( ps: but TCGA-READ is ok)

query.exp2222 <- GDCquery(project = "TCGA-COAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - FPKM-UQ")

this failue

query.exp2222 <- GDCquery(project = "TCGA-READ",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - FPKM-UQ")

this ok

error message

Error in getURL(url, GET, timeout(600)) : 'getURL()' failed:
URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2493&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:[%22TCGA-COAD%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:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20FPKM-UQ%22]%7D%7D]%7D&format=JSON
error: Failure when receiving data from the peer
In addition: Warning message:
In date_names_lang(date_names) : restarting interrupted promise evaluation

thanks

@dannyteng1971

gdcquery tcgabiolinks • 1.6k views
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hI ALL

IT IS REALLY A PROBLEM, IT SEEM BE THE PROBLEM OF gdc QUERY OF tcga DATA BASE, 

IS ANYONE WITH COMMENT?

PLEASE 

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I met the same problems, GDCquery can work on TCGA-ESCA project, but I met the error hints when I run GDCquery_clinic functions. 

is there a packages can pipeline GDC-client to TCGAbiolinks?

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Hello,

 

I just made an update I believe will solve the problem. Could you update the package from github with

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

and test it, please?

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Hello, 

I have similar problems and I tried to reinstall the package with this command:

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

But R return this:

* installing *source* package 'TCGAbiolinks' ...
** R
Error in parse(outFile) : 
  C:/Users/Adrian/AppData/Local/Temp/RtmpkP0PMF/devtools32c06d807be5/BioinformaticsFMRP-TCGAbiolinks-df8e977/R/analyze.R:994:17: inesperado 'else'
993: 
994:                 else
                     ^
ERROR: unable to collate and parse R files for package 'TCGAbiolinks'
* removing 'C:/Users/Adrian/Documents/R/win-library/3.5/TCGAbiolinks'
* restoring previous 'C:/Users/Adrian/Documents/R/win-library/3.5/TCGAbiolinks'
In R CMD INSTALL
Installation failed: Command failed (1)

What happend? 

Thanks!

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hwteng1971 • 0
@hwteng1971-15996
Last seen 3.4 years ago

now, Tiago Chedraoui Silva

kindly provied the answer to our question.

thanks lots


Hello,

GDC api moved to another path. Some versions of libcurl seems not to be able to redirect. We updated the link to api.

It should be fixed now.

Could you please update the package from GitHub with:

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

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Angus MacGyver Lucas Till Leather Jacket I am suffered from a problem since 2 days ago.

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Jessica • 0
@ca516675
Last seen 9 weeks ago

I also faced this error and did not get resolved.

Visit My Website

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