Question

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

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3.0 years ago

nonaddldy ▴ 10

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

enter image description here

TCGA R • 2.3k views

ADD COMMENT • link updated 2.9 years ago by rpolicastro 13k • written 3.0 years ago by nonaddldy ▴ 10

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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 Also however I couldn't see in the posted images, sometimes a missing/outdated Linux library can be the cause.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.

ADD REPLY • link 3.0 years ago by Hamid Ghaedi 3.3k

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

ADD REPLY • link 3.0 years ago by nonaddldy ▴ 10

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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?

ADD REPLY • link 3.0 years ago by ATpoint 85k

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

ADD REPLY • link 2.9 years ago by nonaddldy ▴ 10

score 1 · Answer 1 · 2021-12-15

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2.9 years ago

rpolicastro 13k

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.