Is the current R version (4.1.2) are not suitable for the packages related with TCGA

Question

[nonaddldy]

I cannot install series of packages related with TCGA, no matter through BiocManager::install or install.packages

[Hamid Ghaedi]

It is very unlikely. Restart the R session and then try again. Also however I couldn't see in the posted images, sometimes a missing/outdated Linux library can be the cause. Inspect the error you may find that.

[nonaddldy]

I tried to install the related library from the warning report: "ERROR: dependencies: ..." (Picture 2). But the outputs are still like the above.

[ATpoint]

There must be some initial error at the very beginning that causes this whole chain of errors. Probably some lib is missing. Is this the full error message?

[nonaddldy]

Actually, I cannot install almost all of the library mentioned in the warning messages.

Answer 1

[rpolicastro]

TCGAretriever requires r-base >=3.6,<3.7.0. I recommend using a software environment manager like conda supplemented with mamba to create an environment specifically for TCGAretriever to avoid having to downgrade your system R.

Once conda and mamba are installed and configured you can run the following command to install TCGAretriever.

mamba create -n tcgaretriever -c conda-forge -c bioconda r-tcgaretriever

It will automatically install the proper R version.

You can then activate and use the environment via conda activate tcgaretriever.

[nonaddldy]

Thanks a lot. I will try it.