Running ‘testthat.R’ [11s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("IPCAPS")
  Loading required package: IPCAPS
  Node 0: Start clustering
  Node 0: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/RData/node0.RData
  Node 0: done for clustering
  Time difference of 0.004952431 secs
  Node 0: Start clustering
  Node 0: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/RData/node0.RData
  Node 0: done for clustering
  Time difference of 0.02104712 secs
  Node 0: Start clustering
  Node 0: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/RData/node0.RData
  Running ... IPCAPS 
  	output: /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh 
  	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/Rtmp2OmhOh' is existed. 
  The result files will be saved to this directory: /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output 
  Input data: 103 individuals, 2000 markers
  Start calculating
  Node 1: Start the process
  Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/condition.RData
  Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/rawdata.RData
  Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/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/Rtmp2OmhOh/cluster_output/RData/node1.RData
  Node 1: done for clustering
  Time difference of 0.9224954 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 2.685387134552 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/Rtmp2OmhOh/cluster_output/RData/node2.RData
  Node 1: Saving /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/node3.RData
  Node 1: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 1: Updating /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 1: Done!
  Time difference of 3.973827 secs
  Node 2: Start the process
  Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/condition.RData
  Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/rawdata.RData
  Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/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/Rtmp2OmhOh/cluster_output/RData/leafnode.RData
  Node 2: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 2: Updating /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 2: Done!
  Time difference of 0.1870298 secs
  Node 3: Start the process
  Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/tree.RData
  Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/condition.RData
  Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/cluster_output/RData/rawdata.RData
  Node 3: Loading /tmp/Rtmp2X4KLr/working_dir/Rtmp2OmhOh/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/Rtmp2OmhOh/cluster_output/RData/node3.RData
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_clusteringmode.R:27:3): test clustering.mode ────────────────────
  Error in `validityMethod(as(object, superClass))`: number of factors too small!
  Backtrace:
       █
    1. └─IPCAPS:::clustering.mode(node, workdir, "mixmod") test_clusteringmode.R:27:2
    2.   └─Rmixmod::mixmodCluster(...)
    3.     └─methods::new("MixmodCluster", ...)
    4.       ├─methods::initialize(value, ...)
    5.       └─Rmixmod:::initialize(value, ...)
    6.         └─Rmixmod:::.local(.Object, ...)
    7.           ├─methods::callNextMethod(...)
    8.           │ └─base::eval(call, callEnv)
    9.           │   └─base::eval(call, callEnv)
   10.           └─Rmixmod:::.nextMethod(...)
   11.             └─Rmixmod:::.local(.Object, ...)
   12.               └─methods::validObject(.Object)
   13.                 ├─methods:::anyStrings(validityMethod(as(object, superClass)))
   14.                 │ └─base::isTRUE(x)
   15.                 └─Rmixmod:::validityMethod(as(object, superClass))
  ── Error (test_ipcaps.R:8:3): test clustering.mode ─────────────────────────────
  Error in `validityMethod(as(object, superClass))`: number of factors too small!
  Backtrace:
       █
    1. └─IPCAPS::ipcaps(...) test_ipcaps.R:8:2
    2.   └─IPCAPS:::process.each.node(node = idx, work.dir = result.dir)
    3.     └─IPCAPS:::clustering(...)
    4.       └─IPCAPS:::clustering.mode(...)
    5.         └─Rmixmod::mixmodCluster(...)
    6.           └─methods::new("MixmodCluster", ...)
    7.             ├─methods::initialize(value, ...)
    8.             └─Rmixmod:::initialize(value, ...)
    9.               └─Rmixmod:::.local(.Object, ...)
   10.                 ├─methods::callNextMethod(...)
   11.                 │ └─base::eval(call, callEnv)
   12.                 │   └─base::eval(call, callEnv)
   13.                 └─Rmixmod:::.nextMethod(...)
   14.                   └─Rmixmod:::.local(.Object, ...)
   15.                     └─methods::validObject(.Object)
   16.                       ├─methods:::anyStrings(validityMethod(as(object, superClass)))
   17.                       │ └─base::isTRUE(x)
   18.                       └─Rmixmod:::validityMethod(as(object, superClass))
  
  [ FAIL 2 | WARN 10 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted