Error in gene.location$ensembl_gene_id : $ operator is invalid for atomic vectors

[igordot]

I am trying to download RNA-seq data. The actual download works:

gdc_query = GDCquery(project = "TCGA-LUAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - FPKM-UQ")
GDCdownload(gdc_query, chunks.per.download = 50)

Then I run:

gdc = GDCprepare(gdc_query)

And I get an error:

Starting to add information to samples
 => Add clinical information to samples
 => Adding subtype information to samples
Subtype information from:doi:10.1038/nature13385
Entity 'copy' not defined
Error in gene.location$ensembl_gene_id : 
  $ operator is invalid for atomic vectors

I saw an earlier issue about it (https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/77) but I don't think the solution listed actually fixes the problem.

The error is probably due to biomaRt issues, but I am not sure how to get around that.

> listMarts()
Entity 'copy' not defined
Error: 1: Entity 'copy' not defined
> listMarts(host="www.ensembl.org")
Entity 'copy' not defined
Error: 1: Entity 'copy' not defined
> listMarts(host="useast.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 88
2   ENSEMBL_MART_MOUSE      Mouse strains 88
3     ENSEMBL_MART_SNP  Ensembl Variation 88
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 88
5    ENSEMBL_MART_VEGA               Vega 68

[tiagochst]

I just updated the package with the new biomaRt function. Please, could you try to update both packages and see if it works ?

devtools::install_github("Bioconductor-mirror/biomaRt")
devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

[igordot]

Yes. That worked. Thank you!

[jonaszierer]

I updated both packages using the most reason versions from github and get the same error when GDCprepare