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

[Martin J Reed]

Rolf and Duncan

Many thanks. Your answers pointed me to a refinement that is closer to what I want:

  rm(list=intersect(ls(".GlobalEnv"),ls("package:reedgraph")),
     pos=".GlobalEnv")

This only removes items that are "masked" by GlobalEnv from my package.

As this is a bit long for some of the people that need to update their workspaces I have created a function to fix it:

<packagename>.update2package  <- function() {
  rm(list=intersect(ls(".GlobalEnv"),ls("package:<packagename>")),
     pos=".GlobalEnv")
}

Just for completeness (if anyone else reads this). It is possible to make this happen automatically at package load using

.onAttach <- function(libname, pkgname) { <packagename>.update2package() }

However, as Duncan says this is REALLY bad practice, but is useful to me while debugging….

Duncan: you say avoid saving the workspace. While I can understand why you are saying this, one of the really powerful features of R is the ability to start R in a working directory and have the state saved so you can come back to it. While this may be bad for the GUI versions of R as the workspace would just keep growing, if you start it from a particular directory this is not a problem and allows coming back to where you left off…

Regards,

Martin

On 8 Nov 2012, at 02:38, Rolf Turner <rolf.turner at xtra.co.nz> wrote:

> 
> Suggestions:
> 
> (1) Work in a different directory (so that you will have a different --- initially
> empty) .RData file.
> 
> (2) Or:  Clean up the .Rdata file in the directory that you are currently using;
> rm(list=ls()) does this for you.  Every so slightly dangerous! :-)
> 
> (3) Possibly:  Before doing (2), save stuff that you actually *want*, e.g. via
> 
>    save(mung,gorp,clyde,irving,melvin,file="savedStuff.rda")
> 
> Then you can recover mung, gorp, etc. via
> 
>    load("savedStuff.rda")
> 
>    cheers,
> 
>        Rolf Turner
> 
> On 08/11/12 13:11, 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!