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Question: Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
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gravatar for Mithil Gaikwad
12 weeks ago by
Tezpur University, India
Mithil Gaikwad0 wrote:

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

ADD COMMENTlink written 12 weeks ago by Mithil Gaikwad0

Hi, this is an internal function, but it should be visible.

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



 

 

 

ADD REPLYlink written 12 weeks ago by Tiago Chedraoui Silva150

> 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"

ADD REPLYlink written 12 weeks ago by Mithil Gaikwad0
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