[Bioc-devel] TCGAbiolinks fails

[Vincent Carey]

The problem is that it is in an error state

--- re-building ‘subtypes.Rmd’ using rmarkdown
Quitting from lines 114-121 (subtypes.Rmd)
Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
object 'lgg.gbm.subtype' not found
--- failed re-building ‘subtypes.Rmd’

so the standard installation approach isn't working now.


https://github.com/BioinformaticsFMRP/TCGAbiolinks -- file an issue


In an emergency you might succeed with

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")




On Fri, Apr 28, 2023 at 9:07 AM Elizabeth Cattaneo <
elizabethcattaneo using gmail.com> wrote:

> Hello!
> I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got
> this error:
>
> Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
> Installing package(s) 'TCGAbiolinks' Warning message: *“package
> ‘TCGAbiolinks’ is not available for *
> *Bioconductor version '3.17'*
>
> What should I do to fix it?
>
> Thanks!
>
> Elizabeth
>
> --
> Bioq. Elizabeth Cattaneo
> Dra Fac. Cs. Exactas, UNLP
> INIBIOLP, Fac. Cs.Médicas, UNLP
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> Argentina
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