Error in Reductions(obj) : could not find function "Reductions"

[bbimber]

We're calling Vision() from within an R package to load a seurat object. When we call our package's method from R (which in turn calls Vision), the output is this:

Importing counts from obj[["RNA"]]@counts ...
Normalizing to counts per 10,000...
Importing Meta Data from obj@meta.data ...
Error in Reductions(obj) : could not find function "Reductions"

I believe you should either quality the Seurat methods, or @import Seurat here:

VISION/R/methods-Vision.R

Line 591 in b363600

setMethod("Vision", signature(data = "Seurat"),

Is that something you'd consider adding? I'm happy to draft a PR. If I manually run "library(Seurat)" to load seurat, this works, but that's a sub-optimal solution.

[mattjones315]

Hey @bbimber ,

Sorry you're running into this problem! I'll be happy to make this change in a PR soon.

Thanks for suggesting this and I'll circle back when it's solved.

Best,
Matt

[mattjones315]

Hi @bbimber ,

I believe I've made the simple fix that you requested in this PR: #113 . Would you mind taking a look and making sure this addresses your problem so I can merge it in?

Thanks!

-Matt

[bbimber]

@mattjones315 Thanks for checking. I dont think that's best practice on how to do this. I think you should either:

1. In DESCRIPTION, you could put Seurat under Depends. I think this loads it. Not sure if you want to do this since not all applications need seurat

2. Add "Seurat::" to all the Seurat methods in that codepath

3. I think it's a better idea to add "@import Seurat" to the roxygen doc, and then re-run that to update NAMESPACE, rather than put "library(Seurat)" in your code.

[bbimber]

Note: the third point is basically what you're already doing in this file with "@import logging"

[mattjones315]

Hi @bbimber -- I see what you mean, and I see now that this is what we used to handle Seurat 2.X objects.

I've made these changes in the repo, let me know if this works for you.