Question: Error while getFirehoseData of RTCGAToolbox package
0
gravatar for lawarde.ankita1
18 months ago by
lawarde.ankita120 wrote:

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

 

ADD COMMENTlink modified 18 months ago by Marcel Ramos ♦♦ 410 • written 18 months ago by lawarde.ankita120
Answer: Error while getFirehoseData of RTCGAToolbox package
0
gravatar for Marcel Ramos
18 months ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

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

ADD COMMENTlink written 18 months ago by Marcel Ramos ♦♦ 410
1

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

 

ADD REPLYlink written 18 months ago by lawarde.ankita120
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