Hello. Recently, when I was running the spacexr package in the R kernel(conda environment, R4.4.1) of Jupyter Notebook on a Linux server(ubantu 18.04), I encountered a situation where the run.RCTD() function got stuck. The following are the specific details of the stuck situation.
#################
3 Extract information to pass to the RCTD Reference function
counts<-ref[["RNA"]]$counts # Extract the expression matrix (with genes as rows and cells as columns) from the RNA assay
cluster<-as.factor(ref$celltype) # Extract the cell type label corresponding to each cell and convert it into a factor.
names(cluster)<-colnames(ref) # Set the cluster names as the cell column names for alignment with the counts matrix.
nUMI<-ref$nCount_RNA # Extract the total number of UMIs for each cell
names(nUMI)<-colnames(ref) # Align the column names in the same way / Ensure the column names are aligned consistently
reference<-Reference(counts,cluster,nUMI)
4 Set up the query using the RCTD function of the SpatialRNA class
counts<-sce.all[["Spatial"]]$counts
coords<-GetTissueCoordinates(sce.all)
colnames(coords)<-c("x","y")
coords[is.na(colnames(coords))]<-NULL
query<-SpatialRNA(coords, counts, colSums(counts))
5 RCTD deconvolution
RCTD<-create.RCTD(query, reference, max_cores=1,test_mode = TRUE)
RCTD<-run.RCTD(RCTD, doublet_mode = "doublet")
###############
And the above codes always stop in step5 which The above steps get stuck at the 5th step, with the prompt showing "fitBulk: decomposing bulk"and another prompt: "chooseSigma: using initial Q_mat with sigma = 1". For this situation, I have already tried reinstalling the spacexr package(remotes::install_local, and I can successfully load the package by "library(spacexr)" after downloading it from GitHub, but above issues still persists.
So , I want to know the reason and thank for your reply!
Hello. Recently, when I was running the spacexr package in the R kernel(conda environment, R4.4.1) of Jupyter Notebook on a Linux server(ubantu 18.04), I encountered a situation where the run.RCTD() function got stuck. The following are the specific details of the stuck situation.
#################
3 Extract information to pass to the RCTD Reference function
counts<-ref[["RNA"]]$counts # Extract the expression matrix (with genes as rows and cells as columns) from the RNA assay
cluster<-as.factor(ref$celltype) # Extract the cell type label corresponding to each cell and convert it into a factor.
names(cluster)<-colnames(ref) # Set the cluster names as the cell column names for alignment with the counts matrix.
nUMI<-ref$nCount_RNA # Extract the total number of UMIs for each cell
names(nUMI)<-colnames(ref) # Align the column names in the same way / Ensure the column names are aligned consistently
reference<-Reference(counts,cluster,nUMI)
4 Set up the query using the RCTD function of the SpatialRNA class
counts<-sce.all[["Spatial"]]$counts
coords<-GetTissueCoordinates(sce.all)
colnames(coords)<-c("x","y")
coords[is.na(colnames(coords))]<-NULL
query<-SpatialRNA(coords, counts, colSums(counts))
5 RCTD deconvolution
RCTD<-create.RCTD(query, reference, max_cores=1,test_mode = TRUE)
RCTD<-run.RCTD(RCTD, doublet_mode = "doublet")
###############
And the above codes always stop in step5 which The above steps get stuck at the 5th step, with the prompt showing "fitBulk: decomposing bulk"and another prompt: "chooseSigma: using initial Q_mat with sigma = 1". For this situation, I have already tried reinstalling the spacexr package(remotes::install_local, and I can successfully load the package by "library(spacexr)" after downloading it from GitHub, but above issues still persists.
So , I want to know the reason and thank for your reply!