Warning message on startup - undefined subcclass "DataFrameFactor"

Hi everyone!

I'm still new to R, and today I've been trying to figure out why I'm getting this error message on startup, right after loading tidyverse:

> "In .recacheSubclasses(def@className, def, env) :
> undefined subclass "DataFrameFactor" of class "vector_OR_Vector"; definition not updated"

This error message wasn't happening before, and unfortunately I believe it is causing downstream errors on my (what used to be) functioning code. :face_with_diagonal_mouth:

Any help would be greatly appreciated!

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[Workspace loaded from F:/PhD/R/.RData]

Loading required package: phyloseq
> library(phyloseq)
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "DataFrameFactor" of class "vector_OR_Vector"; definition not updated
> library(tidyverse)
── Attaching packages ────────────────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0      ✔ purrr   0.3.5 
✔ tibble  3.1.8      ✔ dplyr   1.0.10
✔ tidyr   1.2.1      ✔ stringr 1.4.1 
✔ readr   2.1.3      ✔ forcats 0.5.2 
── Conflicts ───────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Warning messages:
1: In .recacheSubclasses(def@className, def, env) :
  undefined subclass "DataFrameFactor" of class "vector_OR_Vector"; definition not updated
2: In .recacheSubclasses(def@className, def, env) :
  undefined subclass "DataFrameFactor" of class "vector_OR_Vector"; definition not updated

This is potentially relevant - I updated tidyverse today :S

errors are best approached from top to bottom rather than bottom to top; I would be investigating phyloseq

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Hmm, so no matter what library I try to load first, or even setwd, this error comes up.

my googling suggests this may be Bioconducter related, are you a bioconducter user ?
answering my own question as phyloseq is from Bioconducter.
Therefore I guess I would uninstall - reinstall the bioconducter framework, and see if that solves; and if not seek help from that community; the related github issue trackers etc.
The items mentioned seemed to particularly relate to
Bioconductor - S4Vectors

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Thank you so much nirgrahamuk!
You were right, and it turns out the phyloseq package was the problem - and was being automatically loaded into my environment. A quick package uninstall/resintall solved my issues :slight_smile:

Thank you thank you thank you!!!

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