Question: TCGAbiolinks 403 Forbidden Error
0
gravatar for Marcel Ramos
3.3 years ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hello everyone, 

I am posting this issue for the `TCGAbiolinks` package because I'm trying to download data but it seems like the link it uses is now broken. 

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

The code that I ran encountering this '403 Forbidden Error' is as follows: 

library(TCGAbiolinks)

coad <- TCGAquery_maf("coad")

## Select option 1

Downloading maf file

downloaded 0 bytes

Error in download.file(url, method = method, ...) : 
  cannot download all files
In addition: Warning message:
In download.file(url, method = method, ...) :
  URL 'https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/broad.mit.edu_COAD.IlluminaGA_DNASeq_automated.Level_2.1.0.0/gsc_COAD_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf': status was '403 Forbidden'

 

This seems to be due to changes originating from the TCGA data portal. 

I am currently unable to download any data. 

 

Thanks, 

Marcel 

 

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] TCGAbiolinks_1.3.6

[truncated...]

bug tcgabiolinks issue • 611 views
ADD COMMENTlink modified 3.3 years ago by tiagochst150 • written 3.3 years ago by Marcel Ramos ♦♦ 410

Core team member Valerie pointed out that this error was missed because of numerous \dontrun flags that were used in the documentation. Particularly in the TCGAquery_maf.Rd file (pertinent to this issue, but there are more). 

It is good to have tests so that when something goes wrong, it is easily caught. 

Thanks for looking into this. 

ADD REPLYlink written 3.3 years ago by Marcel Ramos ♦♦ 410
Answer: TCGAbiolinks 403 Forbidden Error
1
gravatar for tiagochst
3.3 years ago by
tiagochst150
Brazil
tiagochst150 wrote:

Hi,

The problem is related to the maintenance of TCGA data portal. 

As we are not sure it will comeback, we are rewriting the code to make TCGAbiolinks use GDC database instead the old TCGA data portal.

There should be an update in the coming weeks in Bioconductor repository.

Best regards,

Tiago

ADD COMMENTlink written 3.3 years ago by tiagochst150
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