Error in validObject(.Object) : invalid class “sample_data” object: superclass "vector_OR_Vector" not defined in the environment of the object's class

[A_Rosenfeld]

I keep getting this error message:
"
Error in validObject(.Object) :
invalid class “sample_data” object: superclass "vector_OR_Vector" not defined in the environment of the object's class
"
Please help!!

[nirgrahamuk]

Does the example from the documentation work?

mapfile <- system.file("extdata", "master_map.txt", package = "phyloseq")
 import_qiime_sample_data(mapfile)

[A_Rosenfeld]

@nirgrahamuk

mapfile <- system.file("extdata", "master_map.txt", package = "phyloseq") import_qiime_sample_data(mapfile)

I get the same error message :\

[nirgrahamuk]

what is your packageVersion("phyloseq") ?
it works for me with version 1.30.0
Edit, as I had another thought, the error message references S4Vectors class, so checking packageVersion("S4Vectors") might be useful also

[A_Rosenfeld]

Phyloseq is '1.30.0' and S4Vectors is '0.22.1'

[nirgrahamuk]

oh right, lets try installing S4Vectors higher version ?
for that to be possible you'd need to restart your session so that its not loaded (Ctrl+Shft+F10)
then
BiocManager::install("S4Vectors")