joey711/phyloseq — Issue #80: Address targeted vegan-package import
Author: joey711
Created: 2012-03-01 07:03:28+00:00
State: open
Labels: Build

The latest build throws a warning regarding the double import of two `vegan::function`s. Here is the warning:

```R
Warning messages:
1: replacing previous import ‘diversity’ when loading ‘vegan’
2: replacing previous import ‘estimateR’ when loading ‘vegan’
```

The reason is because the `NAMESPACE` currently includes both a full `import(vegan)` directive, as well as a `importFrom(vegan, diversity)` directive.

Solution:

Either (1 - quick) remove the `@importFrom vegan diversity` tag (and `estimateR`) ...
or (2 - long, best practice) remove all naked `@import vegan` tags, and replace them with the specific `vegan` objects used in each function. This is time-consuming, and should have been done from the beginning. Not possible when vegan did not include a namespace file at the beginning of this project. The quick solution is probably the most prudent until there is an additional vegan-associated conflict that this might also resolve.