readRDS(object) requires UpdateSeuratObject(object) - results in Error in [[<-: ! Cannot add new cells with [[<-

[MGjorgoska]

After updating my R Studio to version 4.3.2, and the package "Matrix" to version 1.6-1.1, I have problems reading rds files with readRDS().
I am using the developer Seurat version 5.0.0.
I am accessing the rds file via synapser, with synGet(object), reading the file with readRDS(object$path).
After this I get a message to run UpdateSeuratObject(), after which I receive this error:
object<-UpdateSeuratObject(object)
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Updating matrix keys for DimReduc ‘pca’
Updating matrix keys for DimReduc ‘umap’
Updating matrix keys for DimReduc ‘harmony’
Updating matrix keys for DimReduc ‘umapharmony’
Warning: Assay RNA changing from Assay to Assay
Error in [[<-:
! Cannot add new cells with [[<-
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in [[<-:
! Cannot add new cells with [[<-

Backtrace:
▆

└─SeuratObject::UpdateSeuratObject(object)
├─base::suppressWarnings(...)
│ └─base::withCallingHandlers(...)
├─methods (local) [[<-(tmp, obj, value = <Assay[,24025]>)
└─SeuratObject (local) [[<-(tmp, obj, value = <Assay[,24025]>)
Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.

[eddelbuettel]

Likely duplicate of #166 -- you most likely need to reinstall SeuratObject following the upgrade to Matrix 1.6-2.

[mojaveazure]

Hi @MGjorgoska,

This is likely because your object has cells present in one part of the object, but not another. This behavior isn't allowed in SeuratObject v5. If you can provide the original Rds, I'd be happy to take a look

[MGjorgoska]

Hi @mojaveazure,
Thanks, that would be great.
The rds file (ID: syn25569736) is a 37 GB file, stored on synapse.org (https://www.synapse.org/#!Synapse:syn51091882).
I am accessing it via synapser package, with synGet().
Looking forward to your feedback.
Best, MGjorgoska

[MGjorgoska]

@mojaveazure anything new on this? I am still getting the same error.