Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
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@mithil-gaikwad-16865
Last seen 2.3 years ago
Tezpur University, India

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

tcgabiolinks dplyr DT • 845 views
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Hi, this is an internal function, but it should be visible.

Please, could you sent the listSamples and the package version (packageVersion("TCGAbiolinks"))?



 

 

 

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> 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"

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