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In the case of any difficulties, it is highly recommended to instead use a docker deployment  (cluster installations may require singularity instead, which is somewhat still a work-in-progress)

When running R diagnostic commands outside flow, the environment should include a reference to the ~/.R folder:

export R_LIBS_USER=$HOME/.R

CNVkit

Requires Python 2.7 or later.

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These packages include the dependencies for both CNVkit and DESeq2

When running R diagnostic commands outside flow, it can simplify things if the environment includes a reference to the ~/.R folder:

export R_LIBS_USER=$HOME/.R

list loaded packages: 

(.packages())

get the version:

packageVersion("packageName")

see also:  Minimum System Requirements

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