Add note or better handling for dealing with installing packages from source vs. binary in packrat.init

When using packrat.init(), I think in most cases there is an expectation that this works automatically, with no user input required once the command has been issued.

For example, I have a project that requires the "sp" package, which in my environment has a newer source version than binary. When installing "sp" with install.packages(), it brings up the prompt:

  There is a binary version available but the source version is later:
   binary source needs_compilation
sp  1.1-1  1.2-0              TRUE

Do you want to install from sources the package which needs compilation?
y/n: 

However, with packrat.init(), most of that prompt is cut off and all I get is y/n: and I have to make a choice for the initialization to proceed. This is bad first of all because the average user won't y/n is referring to, but also because I don't want packrat.init() to be interactive.

After looking here, I realized I could just set

options(install.packages.compile.from.source = TRUE)

which takes care of the problem. This might be worth noting in the docs.

Start with the packrat.init() behavior described in the issue and review the R installation prompt and the install.packages.compile.from.source option. Update the relevant documentation to explain the source-versus-binary prompt, why packrat.init() may show only y/n, and how the option avoids interactive input.