I am trying to install TCGAbiolinks package in both google colab with r runtime and new version of r in r studio but it is showing an error message.

Question

[Salsabil]

Code in google colab:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")

Error message:

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)

Installing package(s) 'BiocVersion', 'TCGAbiolinks'

Warning message:
“package ‘TCGAbiolinks’ is not available for Bioconductor version '3.17'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages”
Old packages: 'bit', 'bslib', 'devtools', 'digest', 'dplyr', 'fontawesome',
  'fs', 'gargle', 'gert', 'highr', 'isoband', 'jsonlite', 'pkgload',
  'processx', 'ps', 'roxygen2', 'stringr', 'tidyverse', 'tinytex', 'vctrs',
  'whisker', 'xfun', 'xml2', 'zip', 'boot', 'foreign', 'MASS'

Code in r studio:

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("TCGAbiolinksGUI.data")
install.packages("TCGAbiolinksGUI.data")
install.packages("tidyverse")
library(TCGAbiolinks)

Error message:

The downloaded source packages are in
    ‘/tmp/Rtmp4m1HBJ/downloaded_packages’
> library(TCGAbiolinksGUI.data)
> library(TCGAbiolinks)
Error in library(TCGAbiolinks) : 
  there is no package called ‘TCGAbiolinks’
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
> library(maftools)
Error in library(maftools) : there is no package called ‘maftools’

Answer 1

[Akanksha]

Hi Salsabil,\ I tried installing and this works,

BiocManager::install("remotes")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
library(TCGAbiolinks)

Answer 2

[wyt1995]

How about install it from Github instad from bioconductor? (https://github.com/BioinformaticsFMRP/TCGAbiolinks.)