GDC server down???

Question

[Gabriel Wajnberg]

I am trying to use TCGAbiolinks package to analyze illumina methylation array data, but it is saying to me that the server is down, this is happening since last Friday night. Anyone have some information about it??

[GenoMax]

Not sure what URL TCGAbiolinks uses but the GDC portal is very much up and available here.

[Jade]

I also have such problem....

[Kevin Blighe]

What exact commands have you both tried? It's possible that the data has just shifted to a new location. The TCGA data is constantly being refined.

Also, which R and package versions?

[giselesimasrs]

I'm having the same problem (I was using it last week without any problems) My r-base package version is 3.4.4-1xenial0 and TCGAbiolinks version is 2.9.1

#Code:
library(TCGAbiolinks)
query <- GDCquery(project = 'TCGA-LAML',
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type="HTSeq - Counts")

#Error:
Error in value[[3L]](cond) : 
  GDC server down, try to use this package later

[Kevin Blighe]

I report the same:

Error in value[[3L]](cond) : 
  GDC server down, try to use this package later

I will explore further / contact people who may know better.

[Gabriel Wajnberg]

thanks a lot! Let's see what is going on!

Answer 1

[Jade]

I solved this problem by using devtools::install_github('BioinformaticsFMRP/TCGAbiolinks') to install this package instead of biocLite("TCGAbiolinks"). You can try this way.

[Kevin Blighe]

Yes, installing the development version from GitHub also works for me. That's now the second time that a package that interacts with the GDC serves could only function properly after an installation from GitHub. The other was GenomicDataCommons:

[Gabriel Wajnberg]

Thanks!!!!It worked Fine

[Agata]

That worked for me as well. Thanks!