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EvaYiwenWang / PLSDAbatch

Development repository for R package 'PLSDAbatch ' hosted on Bioconductor.
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Addition of `vegan::pca()` breaks PLSDAbatch #4

Open gavinsimpson opened 2 months ago

gavinsimpson commented 2 months ago

Because you import the entire vegan namespace at the end of your NAMESPACE, our adding vegan::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 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 commented 2 months ago

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

Best regards, Eva