Error while getFirehoseData of RTCGAToolbox package
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@lawardeankita1-14844
Last seen 25 days ago
Estonia

Hi,

I'm using LUAD data from FireBrowse and i was following RTCGAToolbox tutorial (http://genomicsclass.github.io/book/pages/tcga.html) but when try to download the data i'm getting one error,

Here is the R code i used ,

library(RTCGAToolbox)
readData = getFirehoseData (dataset="LUAD", runDate="20160128",forceDownload = TRUE,
                               Mutation=TRUE, Methylation=TRUE, RNASeq2GeneNorm=TRUE)

 

And the error message is,

Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUAD/20160128/"

 

I even tried to remove thr runDate option from the getFirehoseData, but it still gives the same error.

1) Can anyone know why is this error coming ?, and how to get rid og this error?

 

I read some notes from this links https://confluence.broadinstitute.org/display/GDAC/Standardized+Data+Run+Release+Notes

It says: Please use last month's RPPA data if you are analyzing LUAD, so i used rundate as 20170606 but still the error is there.

 

But i'm interested in only clinical data of LUAD. and not in RPPA data.

Any suggestion will really help me remove this query.

here is the session info,

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] devtools_1.13.5    RTCGAToolbox_2.8.0

loaded via a namespace (and not attached):
 [1] XVector_0.18.0             GenomicRanges_1.30.3      
 [3] BiocGenerics_0.24.0        splines_3.4.4             
 [5] zlibbioc_1.24.0            IRanges_2.12.0            
 [7] lattice_0.20-35            R6_2.2.2                  
 [9] httr_1.3.1                 GenomeInfoDb_1.14.0       
[11] tools_3.4.4                SummarizedExperiment_1.8.1
[13] parallel_3.4.4             grid_3.4.4                
[15] Biobase_2.38.0             data.table_1.10.4-3       
[17] git2r_0.21.0               withr_2.1.2               
[19] matrixStats_0.53.1         digest_0.6.15             
[21] survival_2.41-3            RJSONIO_1.3-0             
[23] Matrix_1.2-12              GenomeInfoDbData_1.0.0    
[25] S4Vectors_0.16.0           bitops_1.0-6              
[27] curl_3.2                   RCurl_1.95-4.10           
[29] memoise_1.1.0              DelayedArray_0.4.1        
[31] limma_3.34.9               compiler_3.4.4            
[33] RCircos_1.2.0              stats4_3.4.4              
[35] XML_3.98-1.10              jsonlite_1.5 

 

Thank you in advance.

Ankita

 

firehose R RTCGAToolbox getFirehoseData • 712 views
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Entering edit mode
@marcel-ramos-7325
Last seen 4 weeks ago
United States

Hi Ankita,

I was unable to reproduce the error. I suspect that it may have something to do with your internet connection. 

Please check your connection settings and make sure that a firewall or VPN is not preventing you from
accessing the remote file. 

There are other known issues for users of Windows that prevent a file to be renamed due to long file names.
I hope to be able to resolve these issues for Windows users soon. 
 

Best regards,

Marcel

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1
Entering edit mode

Hi Marcel Ramos,

Yes, I have windows OS on my laptop

and that is the reason i was getting the error.

Thank you so much for the response.

Ankita

 

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