Use Remotes to install Maaslin2

[bobular]

This works in DESCRIPTION:

Remotes:
  bioc::3.22/Maaslin2

It would be nice to have this added to v5.1.6 - we'd need to make a branch off of that tag and then tag it v5.1.6.1 or something?

I'm not sure how VEuPathDB/Rserve would like to install v5.1.7 which installs mbioUtils. The Rserve image would then have veupathUtils and mbioUtils and I expect a lot of namespace clashes, unless function call is fully-qualified?

@asizemore @d-callan

PS. I'm cleaning up R dependencies. Here is how veupathUtils now installs DESeq2 instead of expecting consumer packages to install it.

https://github.com/VEuPathDB/veupathUtils/blob/b113fd80e1bc93793c1ef9e2aeccb09f3c95fd79/DESCRIPTION#L33-L34

[bobular]

I'm happy to do this, by the way. If you could add me to the access list.

Or alternatively, if we could port v5.1.6 back to VEuPathDB/microbiomeComputations - I can work on it there.

We should probably meet and figure out a sustainable strategy!

[bobular]

I think I have access actually! I think there was a network glitch that made me think otherwise.

[d-callan]

nice find on maasliin. i noticed it wasnt installing but didnt get a min to investigate. i guess its tied to a specific bioc version.. and yes you should have access already.

i had other reasons to not keep on w veupathutils dep here other than it breaking isntall. its overkill for what we were actually using from it, for ex. the handful of things that are duplicated in mbioUtils, were calling using the explicit namespace in all instances ( i always do that)

[d-callan]

just sat back down and read that back to myself, feel its worth saying one thing more. if mbio wants to continue on a path to getting these in cran or bioc, publishing etc the r package suite, then veupathutils as a dep stands in the way of that. i never see that repo getting to cran or bioc for a number of reasons, so having it as a dep in a package that might isnt very workable. wasnt a big deal since unclear when the r package suite would find time to keep moving that direction, but it seemed the reasons to cut the dep were piling up.

[bobular]

Thanks @d-callan for the background/context. That makes sense to make a clean break. I'll discuss it more with Ann.

There's a reasonable summary of the dependency clean-up here: VEuPathDB/Rserve#35