[R] problem with package development and older defs earlier in search order

[Duncan Murdoch]

On 12-11-07 7:11 PM, Martin J Reed wrote:
> Hi,
>
> I have a problem with a package I have developed in that functions do not get loaded due to older versions of the functions being in the .GlobalEnv’ fetched from .Rdata files stored from previous saved workspaces. I need to be able to fix this somehow when I load the package. I do not want to mess up the search order to fix the problem.
>
> How I got myself into this mess is that I started developing using a bunch of R files and a dynamic library and then loaded these from an R function rather than a package. This is great when developing as it allows quick reloading. After doing this for about a year now I have (unknowingly) populated all my favourite working directories with .Rdata files that contain various versions of my functions. And I shared this collection of code, with its flakey loading mechanism, with PhD students and colleagues who have used it and nicely populated their working directories with it as well….
>
> So now I have learnt how to turn it into a package as it is in a more stable state. But when I load it of course the .GlobalEnv with the definition from old saved .Rdata files is first in the search order. I say "of course" but tt has taken me a while to find this out. At first I thought I was going mad as the old functions seemed to magically turn up even though I had updated the package and checked that the new versions of the functions were the only ones in the system (or so I thought)…
>
> My question is: how can I force a package to overwrite the "old" definitions in the .GlobalEnv. If it cannot be done automatically it could be a user triggered function. While developing I still want newer versions of functions to take precedence in the .GlobalEnv over the package versions. i.e. I do not want the package to be earlier in the search order than .GlobalEnv (if this is even possible), I just want to be able to delete the old definitions. I do not want to delete the .Rdata files as there is useful state in them...
>
> Any help getting me out of this mess would be appreciated!

Rolf's advice is good:  delete the copies from your global env, and the 
ones in your package won't be hidden.

Here's some more long term advice:  keep your global environment empty 
at the start of each session, and thereby avoid this problem.  If you 
want to temporarily edit a function from your package, you can still 
make a copy in the global environment, and it will take precedence (when 
called from the top level; the package functions that call each other 
won't see it).  At the end of your session, when offered the chance to 
save your workspace, just say no.

Regarding your specific question:  a package could overwrite user 
objects in the global environment, but that's very bad practice.  The 
user owns those, and packages should avoid messing with them.  Let the 
user say

foo <- foo

to make a copy of the foo function in the global environment, don't 
force your own copy there.  (The user will still be able to get back to 
the original one using the pkg::foo notation, and as I mentioned, 
packages will generally look internally first, so they'll see the 
original one.)

Duncan Murdoch