Addition of vegan::pca() breaks PLSDAbatch

[gavinsimpson]

Because you import the entire vegan namespace at the end of your NAMESPACE, our adding vegan::pca() breaks your package.

For example,

PLSDAbatch/R/alignment_score.R

Line 54 in 779db4d

pca.res <- pca(X = data, ncomp = ncomp, scale = TRUE)

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).

[EvaYiwenWang]

Hello Gavin,
I see the issue, will update my package soon to fix that. Many thanks!

Best regards,
Eva