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

> ### Name: export.groups
> ### Title: Export the IPCAPS result to a text file
> ### Aliases: export.groups
> 
> ### ** Examples
> 
> 
> # Importantly, bed file, bim file, and fam file are required
> # Use the example files embedded in the package
> 
> BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS")
> LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS")
> 
> my.cluster <- ipcaps(bed=BED.file,label.file=LABEL.file,lab.col=2,out=tempdir())
Running ... IPCAPS 
	output: /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3 
	label file: /data/gannet/ripley/R/packages/tests-clang/IPCAPS.Rcheck/IPCAPS/extdata/ipcaps_example_individuals.txt.gz
	label column: 2
	threshold: 0.18
	minimum Fst: 8e-04
	maximum thread: 1
	method: mix
	bed: /data/gannet/ripley/R/packages/tests-clang/IPCAPS.Rcheck/IPCAPS/extdata/ipcaps_example.bed
	minimum in group: 20
	data type: snp
	missing: NA
In preprocessing step
Note: the directory '/tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3' is existed. 
The result files will be saved to this directory: /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output 
Input data: 103 individuals, 2000 markers
Start calculating
Node 1: Start the process
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/condition.RData
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/rawdata.RData
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node1.RData
Node 1: Check for splitting
Node 1: Reducing matrix
Node 1: EigenFit = 0.652486925995028, Threshold = 0.18, no. significant PCs = 3
Node 1: Start clustering
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node1.RData
Node 1: done for clustering
Time difference of 1.382245 secs
Node 1: Checking Fst of group 1 and group 2
Node 1: Checking Fst of group 1 and group 3
Node 1: Checking Fst of group 1 and group 4
Node 1: Checking Fst of group 2 and group 3
Node 1: Checking Fst of group 2 and group 4
Node 1: Checking Fst of group 3 and group 4
Node 1 times took 3.39258694648743 secs
Node 1: 103 individuals were splitted into: 2 groups
Node 1: Return status 0
Node 1: Split to sub-nodes
Node 1: Saving /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node2.RData
Node 1: Saving /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node3.RData
Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 1: Updating /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 1: Done!
Time difference of 5.391157 secs
Node 2: Start the process
Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/condition.RData
Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/rawdata.RData
Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node2.RData
Node 2: Check for splitting
Node 2: A number of node is lower than the minimum number (20), therefore split was not performed
Node 2: Return status 1
Node 2: No split was performed, Status=1
Node 2: Updating /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/leafnode.RData
Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 2: Updating /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 2: Done!
Time difference of 0.2351949 secs
Node 3: Start the process
Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/tree.RData
Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/condition.RData
Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/rawdata.RData
Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node3.RData
Node 3: Check for splitting
Node 3: Reducing matrix
Node 3: EigenFit = 0.343228072167863, Threshold = 0.18, no. significant PCs = 3
Node 3: Start clustering
Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp1rYJR3/cluster_output/RData/node3.RData
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in is.dataType(data) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in isQualitative(x) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in validityMethod(as(object, superClass)) : 
  number of factors too small!
Calls: ipcaps ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted