As a new user of TCGAbiolinks, I have troubling running the TCGAdownload().

Errors are as following:

#1

 TCGAdownload(query.met, path = "methylation")
-=-=-=-=-=-=-=-=-=
| Downloading:23 folders
| Path:methylation
-=-=-=-=-=-=-=-=-=

  |                                                                         
  |                                                                   |   0%
Downloading:jhu-usc.edu_COAD.HumanMethylation27.Level_3.8.3.0.tar.gz
The data downloaded might be corrupted. We will download it again
The data downloaded might be corrupted. We will download it again
The data downloaded might be corrupted. We will download it again

#2

samples <- c("TCGA-26-1442-01A-01R-1850-01")
> query <- TCGAquery(tumor = "gbm",
+ platform = "IlluminaHiSeq_RNASeqV2",
+ level = "3",
+ samples = samples)
> TCGAdownload(query,path = "RNA",
+ samples = samples,
+ type ="rsem.genes.results")
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)
3: In fread(paste0(root, url, "/", files[grep("MANIFEST", files)]),  :
  Stopped reading at empty line 26 but text exists afterwards (discarded): var checkForIe6 = function() {

#3

 sessionInfo() 
R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

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

other attached packages:
[1] SummarizedExperiment_1.0.2 Biobase_2.30.0            
[3] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[5] IRanges_2.4.8              S4Vectors_0.8.11          
[7] BiocGenerics_0.16.1        TCGAbiolinks_1.0.10       

Thanks very much!

Sincerely,

Zin Wong

Sun Yat-Sen University Cancer Center, Guangzhou, China

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, but if you would like we have some code working in the github repository.

https://github.com/BioinformaticsFMRP/TCGAbiolinks

For DNA methylation the following code will solve your problem:

query <- GDCquery(project = "TCGA-GBM",data.category = "DNA methylation", platform = "Illumina Human Methylation 27",legacy = TRUE,barcode = c("TCGA-02-0047-01A-01D-0186-05","TCGA-06-2559-01A-01D-0788-05"))
GDCDownload(query)
data <- GDCPrepare(query)

Best regards,

Tiago