Vignettes are outdated?

[tetomonti]

This would be a great tool. Alas, most of the commands do not work as advertised in the vignettes.

E.g., here's an example from the vignette "TCGAbiolinks: Downloading and preparing files for analysis" (I had to set workflow.type = "STAR - Counts", because the original didn't work).

query <- GDCquery(
  project = "TCGA-GBM",
  data.category = "Transcriptome Profiling",
  data.type = "Gene Expression Quantification", 
  workflow.type = "STAR - Counts",
  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01")
)
GDCdownload(query)
dat <- GDCprepare(query)

Which gives the following error

|====================================================================|100%                      Completed after 1 s 
Error in `y[, 2:4]`:
! Can't subset columns past the end.
ℹ Locations 2, 3, and 4 don't exist.
ℹ There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
Warning messages:
1: One or more parsing issues, see `problems()` for details 
2: One or more parsing issues, see `problems()` for details 

Another example, adapted from the vignettes

query_meth.hg38 <- GDCquery(
  project = c("TCGA-LUAD"),
  data.category = "DNA Methylation",
  legacy = FALSE,
  platform = c("Illumina Human Methylation 450"),
  data.type = "Methylation Beta Value", # this argument is not specified in the vignette and is needed or you'll get an error
  sample.type = "Primary Tumor",
  barcode =  c("TCGA-55-8615-01A-11D-2398-05",
               "TCGA-97-8177-01A-11D-2285-05",
               "TCGA-91-6848-01A-11D-1947-05")
)
GDCdownload(query_meth.hg38)
data.hg38 <- GDCprepare(query_meth.hg38)

which gives the following error

|                                                                    |  0%                      Error in fread(f, header = TRUE, sep = "\t", stringsAsFactors = FALSE,  : 
  colClasses= is an unnamed vector of types, length 5, but there are 2 columns in the input. To specify types for a subset of columns, you can use a named vector, list format, or specify types using select= instead of colClasses=. Please see examples in ?fread.
Error in if (value == n) { : argument is of length zero

[tiagochst]

Hi,

It looks like your package is outdated. Please, update it with the following command: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

[tetomonti]

Thank you, it worked!

Perhaps worth updating the Bioconductor page: searching for TCGAbiolinks sends you here: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html

Thanks

On Sep 19, 2022, at 11:09 PM, Tiago Chedraoui Silva @.***> wrote:

Hi,

It looks like your package is outdated. Please, update it with the following command: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

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