My lab is currently working towards generating a new tool that uses R and several R packages but sort of depends on having R and the ability to install bioconductor packages. I have a code that automatically does it some linux distributions but not all. Should the install process include installation of R and the required packages or inform the user that R environment could not be found or that the bioconductor packages needed could not be installed?
On a similar note the way it is set up now when installed 3rd party software is extracted and compiled automatically. Should these be the case or should I just inform them that this third party software is needed?