Question: GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
0
gravatar for hwteng1971
18 months ago by
hwteng19710
hwteng19710 wrote:

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

tcgabiolinks gdcquery • 568 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by hwteng19710

hI ALL

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

IS ANYONE WITH COMMENT?

PLEASE 

ADD REPLYlink written 18 months ago by hwteng19710

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?

ADD REPLYlink written 18 months ago by 03101yly0

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?

ADD REPLYlink written 18 months ago by Tiago Chedraoui Silva240

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!

ADD REPLYlink written 18 months ago by adrian_garcia030
Answer: GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-REA
0
gravatar for hwteng1971
18 months ago by
hwteng19710
hwteng19710 wrote:

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")

ADD COMMENTlink written 18 months ago by hwteng19710

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

ADD REPLYlink written 18 months ago by stephanyortega4830
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