Another error with addIterativeLSI - "Error in clusterDF$clusters : $ operator is invalid for atomic vectors"

[solvi808]

This seems to be a new bug because I did not get this before, I am suspecting it might have something to do with the new Seurat version as Seurat has been the source of several errors before in ArchR.

Seurat version is 4.3.0.1 SeuratObject 4.1.3 ArchR version 1.0.2 (latest)

Attach your log file ArchR-addIterativeLSI-f21764d38aa-Date-2023-09-20_Time-11-00-28.log

Describe the bug Error when running addIterativeLSI() as part of the standard pipeline.

Exact code

proj <- addIterativeLSI(ArchRProj = proj ,
                        useMatrix = "TileMatrix" ,
                        iterations = 5 ,  
                        force = TRUE , 
                        name = "IterativeLSI")

Error output

Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-f21764d38aa-Date-2023-09-20_Time-11-00-28.log
If there is an issue, please report to github with logFile!
2023-09-20 11:00:28 : Computing Total Across All Features, 0 mins elapsed.
2023-09-20 11:00:28 : Computing Top Features, 0.009 mins elapsed.
###########
2023-09-20 11:00:30 : Running LSI (1 of 5) on Top Features, 0.046 mins elapsed.
###########
2023-09-20 11:00:30 : Creating Partial Matrix, 0.046 mins elapsed.
2023-09-20 11:00:34 : Computing LSI, 0.101 mins elapsed.
2023-09-20 11:00:47 : Identifying Clusters, 0.318 mins elapsed.

************************************************************
2023-09-20 11:00:47 : ERROR Found in FindClusters for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-f21764d38aa-Date-2023-09-20_Time-11-00-28.log

<simpleError in check_valid_matrix(x): no slot of name "i" for this object of class "Graph">

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2023-09-20 11:00:47 : ERROR Found in runClusters for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-f21764d38aa-Date-2023-09-20_Time-11-00-28.log

<simpleError in .logError(e, fn = "FindClusters", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************


************************************************************
2023-09-20 11:00:47 : ERROR Found in .LSICluster for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-f21764d38aa-Date-2023-09-20_Time-11-00-28.log

<simpleError in .logError(e, fn = "runClusters", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

************************************************************

Error in clusterDF$clusters : $ operator is invalid for atomic vectors