Change rgl.* calls to *3d

[dmurdoch]

Some upcoming changes to the rgl package will require changes to nat.
I will be deprecating a number of rgl.* function calls. You can read
about the issues here:

https://dmurdoch.github.io/rgl/articles/deprecation.html

I have made the required changes in the attached patches.

Duncan Murdoch

[jefferis]

Dear @dmurdoch, many thanks for this. Do we need to change e.g.

https://github.com/natverse/nat/blob/master/R/neuronlist_interactive_3d.R#L197-L198

        sapply(pl, rgl.pop, type='shape')
        sapply(more_rgl_ids, rgl.pop, type='shape')

as well?

[dmurdoch]

rgl.pop is not being deprecated because it is identical to pop3d. I've generally been suggesting that change because rgl.pop won't show up in the help index for rgl, but you won't get warnings or errors for it. Not sure why I didn't do it in this PR. Been sending out a lot of them...

[jefferis]

Thanks for clarifying! If you looked for someting rgl.pop( you wouldn't find this as I used sapply here.

[jefferis]

remaining errors seem to be due to old versions of alphashape3d

[jefferis]

Thanks for the PR @dmurdoch. I will be submitting an update to CRAN shortly.