Modified Initialize_HiTMaP.R to make it silent (not interactive).
Upgrade="always" suppresses the prompt so that the script can run without user intervention.
This allows the script to be included in a Docker build process, so that the resulting image already includes HiTMaP.
I also moved the other packages to the top of the script but including these in DESCRIPTION (imports) will install them automatically.
I also don't think "updating all dependencies" is a good idea.
Better to specify which version (or range of versions) you want in DESCRIPTION imports.
Otherwise there is a risk that a dependency will be updated with changes that break your code.
Modified Initialize_HiTMaP.R to make it silent (not interactive). Upgrade="always" suppresses the prompt so that the script can run without user intervention. This allows the script to be included in a Docker build process, so that the resulting image already includes HiTMaP.
I also moved the other packages to the top of the script but including these in DESCRIPTION (imports) will install them automatically.
I also don't think "updating all dependencies" is a good idea. Better to specify which version (or range of versions) you want in DESCRIPTION imports. Otherwise there is a risk that a dependency will be updated with changes that break your code.