I am trying to download and prepare expression data with TCGAbiolinks. And I've got several errors.

Code:

query <- TCGAquery(tumor = BRCA, platform = "IlluminaHiSeq_RNASeqV2", level=3)
barcodes <- unlist(strsplit(query$barcode,","))
querySamples <- TCGAquery_MatchedCoupledSampleTypes(barcodes, c("NT","TP"))
TCGAdownload(query, path = "BRCAdata", type = "rsem.genes.results", samples=querySamples)

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)

I already have downloaded data (3 weeks ago) and TCGAprepare also does not work.

Code:

query <- TCGAquery(tumor = BRCA, platform = "IlluminaHiSeq_RNASeqV2", level=3)
barcodes <- unlist(strsplit(query$barcode,","))
querySamples <- TCGAquery_MatchedCoupledSampleTypes(barcodes, c("NT","TP"))
data <- TCGAprepare(query, dir = "BRCAdata", type = "rsem.genes.results")

Error:

  |===================================================================================| 100%
Adding batch info to summarizedExperiment object
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)

R session Info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Russian_Russia.1251  LC_CTYPE=Russian_Russia.1251   
[3] LC_MONETARY=Russian_Russia.1251 LC_NUMERIC=C                   
[5] LC_TIME=Russian_Russia.1251    

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

other attached packages:
[1] cgdsr_1.2.5                SummarizedExperiment_1.2.3 Biobase_2.32.0            
[4] GenomicRanges_1.24.2       GenomeInfoDb_1.8.2         IRanges_2.6.1             
[7] S4Vectors_0.10.1           BiocGenerics_0.18.0        TCGAbiolinks_1.2.5  

I've read about TCGA portal was down for maintenance. I just want to know if TCGAbiolinks package is to update accordingly TCGA portal.

Thank you!

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