I am facing the problem while running GDCquery in Rstudio using 'TCGAbiolinks' package stating that
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
while other function of GDC are running successfully like GDCDownload and GDCprepare, What could be the problem? I am using the https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html pipeline.
Thanking you in advance.
This is the command:
query <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Gene expression",
+ data.type = "Gene expression quantification",
+ experimental.strategy = "RNA-Seq",
+ platform = "Illumina HiSeq",
+ file.type = "results",
+ barcode = listSamples,
+ legacy = TRUE)
Error in print.header("GDCquery: Searching in GDC database", "section") :
could not find function "print.header"
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
Hi, this is an internal function, but it should be visible.
Please, could you sent the listSamples and the package version (
packageVersion("TCGAbiolinks"))?
> packageVersion("TCGAbiolinks")
[1] ‘2.8.4’
> listSamples <- c("TCGA-E9-A1NG-11A-52R-A14M-07","TCGA-BH-A1FC-11A-32R-A13Q-07",
+ "TCGA-A7-A13G-11A-51R-A13Q-07","TCGA-BH-A0DK-11A-13R-A089-07",
+ "TCGA-E9-A1RH-11A-34R-A169-07","TCGA-BH-A0AU-01A-11R-A12P-07",
+ "TCGA-C8-A1HJ-01A-11R-A13Q-07","TCGA-A7-A13D-01A-13R-A12P-07",
+ "TCGA-A2-A0CV-01A-31R-A115-07","TCGA-AQ-A0Y5-01A-11R-A14M-07")
> query <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Gene expression",
+ data.type = "Gene expression quantification",
+ experimental.strategy = "RNA-Seq",
+ platform = "Illumina HiSeq",
+ file.type = "results",
+ barcode = listSamples,
+ legacy = TRUE)
Error in print.header("GDCquery: Searching in GDC database", "section") :
could not find function "print.header"