Hello,

I was following the TCGAbiolinks tutorial (https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/download_prepare.html)

but whenever i run the GDCprepare command, it throws following error,

query <- GDCquery(project = "TCGA-GBM",

                  data.category = "Transcriptome Profiling",

                  data.type = "Gene Expression Quantification", 

                  workflow.type = "HTSeq - FPKM-UQ",

                  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"))

GDCdownload(query)

data <- GDCprepare(query)
  |======================================================================================| 100%
Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at: 
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
Error in gene.location$ensembl_gene_id : 
  $ operator is invalid for atomic vectors

And I checked the URL  to see if the website is available, then it shows as follows,

<MartRegistry>
  <MartURLLocation database="ensembl_mart_91" default="1" displayName="Ensembl Genes 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_91" default="" displayName="Mouse strains 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_91" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_91" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_91" default="" displayName="Genomic features 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_91" default="" displayName="Ensembl Variation 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_91" default="" displayName="Ensembl Regulation 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

1. But if i state the summerizedEXperiment to FALSe then the GDCprepare runs without error, but i want to keep that summerizedExperiment option to set to TRUE.

2. So can anyone please help me solve this issue? any suggestions will be valuable.

Thank you.