will now be run with vegan::pca() not the intended mixOmics::pca(). Ideally, you would change to selectively importing from the vegan namespace only those functions that you actually use. If you don't want to do that, you'll need to use the fully-qualified function name, in this case mixOmics::pca( ... ), but that will still raise a warning from R CMD check.
We are planning to release a version of vegan with these changes in August (although that may slip).
Because you import the entire vegan namespace at the end of your
NAMESPACE
, our addingvegan::pca()
breaks your package.For example, https://github.com/EvaYiwenWang/PLSDAbatch/blob/779db4d05ab8cbdd894b9e0753f81aeeff4330c6/R/alignment_score.R#L54
will now be run with
vegan::pca()
not the intendedmixOmics::pca()
. Ideally, you would change to selectively importing from the vegan namespace only those functions that you actually use. If you don't want to do that, you'll need to use the fully-qualified function name, in this casemixOmics::pca( ... )
, but that will still raise a warning fromR CMD check
.We are planning to release a version of vegan with these changes in August (although that may slip).