Running examples in ‘QuantumClone-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: One_step_clustering
> ### Title: Cellularity clustering
> ### Aliases: One_step_clustering
> ### Keywords: Clonal inference
> 
> ### ** Examples
> 
> Mutations<-QuantumClone::Input_Example
>  for(i in 1:2){
+  Mutations[[i]]<-cbind(rep(paste("Example_",i,sep=""),times=10),Mutations[[i]])
+  colnames(Mutations[[i]])[1]<-"Sample"
+ }
> print("The data should look like this:")
[1] "The data should look like this:"
> print(head(Mutations[[1]]))
     Sample  SampleName Chr Start Depth Alt Genotype
1 Example_1 Timepoint_1   1     1   149  67       AB
2 Example_1 Timepoint_1   4     2   162   2       AB
3 Example_1 Timepoint_1   4     3   132   5       AB
4 Example_1 Timepoint_1   4     4    57   1       AB
5 Example_1 Timepoint_1   4     5    93   0       AB
6 Example_1 Timepoint_1   4     6    95   0       AB
> 
> cat("Cluster data: will try to cluster between 3 and 4 clones, with 1 maximum search each time,
+       and will use priors from preclustering (e.g. k-medoids on A and AB sites)")
Cluster data: will try to cluster between 3 and 4 clones, with 1 maximum search each time,
      and will use priors from preclustering (e.g. k-medoids on A and AB sites)> print("The genotype is provided in the list frame, and
+           there is no associated data from FREEC to get genotype from.")
[1] "The genotype is provided in the list frame, and\n          there is no associated data from FREEC to get genotype from."
> print("The computation will run on a single CPU.")
[1] "The computation will run on a single CPU."
> Clustering_output<-One_step_clustering(SNV_list = Mutations,
+ FREEC_list = NULL,contamination = c(0,0),nclone_range = 3:4,
+ clone_priors = NULL,prior_weight = NULL ,
+ Initializations = 1,preclustering = "FLASH", simulated = TRUE,
+ save_plot = TRUE,ncores=1,output_directory="Example")
FREEC_list is empty. Checking that there is a genotype column in all samples...
Genotype is provided.
epsilon set to: 0.00678978815860945
Checking all possibilities for Example_1
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: One_step_clustering ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted