I am following the tutorial to use TCGAbiolinks to download expression and survival data but have not been able to download anything:

Code:

query <- TCGAquery(tumor = "brca", platform = "IlluminaHiSeq_RNASeqV2", level = "3") 

TCGAdownload(query, path = "../dataBrca", type = "rsem.genes.results",samples = listSamples) 

Error:

Error in fread(paste0(root, url, "/", files[grep("MANIFEST", files)]),  : 
  Expected sep (',') but new line or EOF ends field 1 on line 33 when reading data: -->
In addition: Warning messages:
1: In fread(paste0(root, url, "/", files[grep("MANIFEST", files)]),  :
  Unable to find 5 lines with expected number of columns (+ middle)
2: In fread(paste0(root, url, "/", files[grep("MANIFEST", files)]),  :
  Unable to find 5 lines with expected number of columns (+   last)

what am I missing?

Edit: I checked the TCGA portal and it seems down for maintenance. SO that might be the cause. I am not sure though because this is my first time trying it.

Here are my session info:

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.2       SummarizedExperiment_1.2.3 Biobase_2.32.0            
[4] GenomicRanges_1.24.2       GenomeInfoDb_1.8.1         IRanges_2.6.1             
[7] S4Vectors_0.10.1           BiocGenerics_0.18.0        TCGAbiolinks_1.2.5        

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 might be an update next weeks in the bioconductor repository.

Best regards,

Tiago