Running ‘testthat.R’ [6s/9s]
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 /home/hornik/tmp/scratch/RtmpGFYxsd/RData/node0.RData
  Node 0: done for clustering
  Time difference of 0.003137589 secs
  Node 0: Start clustering
  Node 0: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/RData/node0.RData
  Node 0: done for clustering
  Time difference of 0.002726793 secs
  Node 0: Start clustering
  Node 0: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/RData/node0.RData
  Running ... IPCAPS 
  	output: /home/hornik/tmp/scratch/RtmpGFYxsd 
  	label file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IPCAPS/extdata/ipcaps_example_individuals.txt.gz
  	label column: 2
  	threshold: 0.18
  	minimum Fst: 8e-04
  	maximum thread: 1
  	method: mix
  	bed: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IPCAPS/extdata/ipcaps_example.bed
  	minimum in group: 20
  	data type: snp
  	missing: NA
  In preprocessing step
  Note: the directory '/home/hornik/tmp/scratch/RtmpGFYxsd' is existed. 
  The result files will be saved to this directory: /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output 
  Input data: 103 individuals, 2000 markers
  Start calculating
  Node 1: Start the process
  Node 1: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 1: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/condition.RData
  Node 1: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/rawdata.RData
  Node 1: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/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 /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/node1.RData
  Node 1: done for clustering
  Time difference of 0.3791475 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 0.834322690963745 secs
  Node 1: 103 individuals were splitted into: 2 groups
  Node 1: Return status 0
  Node 1: Split to sub-nodes
  Node 1: Saving /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/node2.RData
  Node 1: Saving /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/node3.RData
  Node 1: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 1: Updating /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 1: Done!
  Time difference of 1.29443 secs
  Node 2: Start the process
  Node 2: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 2: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/condition.RData
  Node 2: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/rawdata.RData
  Node 2: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/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 /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/leafnode.RData
  Node 2: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 2: Updating /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 2: Done!
  Time difference of 0.08192396 secs
  Node 3: Start the process
  Node 3: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/tree.RData
  Node 3: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/condition.RData
  Node 3: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/rawdata.RData
  Node 3: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/node3.RData
  Node 3: Check for splitting
  Node 3: Reducing matrix
  Node 3: EigenFit = 0.343228072167861, Threshold = 0.18, no. significant PCs = 3
  Node 3: Start clustering
  Node 3: Loading /home/hornik/tmp/scratch/RtmpGFYxsd/cluster_output/RData/node3.RData
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_clusteringmode.R:27:3): test clustering.mode ────────────────────
  Error in `xtfrm.data.frame(x)`: cannot xtfrm data frames
  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.               └─Rmixmod::is.dataType(data)
   13.                 ├─base::nlevels(as.factor(x))
   14.                 │ └─base::levels(x)
   15.                 └─base::as.factor(x)
   16.                   └─base::factor(x)
   17.                     └─base::order(y)
   18.                       └─base::lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x)
   19.                         └─base:::FUN(X[[i]], ...)
   20.                           ├─base::as.vector(xtfrm(x))
   21.                           ├─base::xtfrm(x)
   22.                           └─base::xtfrm.data.frame(x)
  ── Error (test_ipcaps.R:8:3): test clustering.mode ─────────────────────────────
  Error in `xtfrm.data.frame(x)`: cannot xtfrm data frames
  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.                     └─Rmixmod::is.dataType(data)
   16.                       ├─base::nlevels(as.factor(x))
   17.                       │ └─base::levels(x)
   18.                       └─base::as.factor(x)
   19.                         └─base::factor(x)
   20.                           └─base::order(y)
   21.                             └─base::lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x)
   22.                               └─base:::FUN(X[[i]], ...)
   23.                                 ├─base::as.vector(xtfrm(x))
   24.                                 ├─base::xtfrm(x)
   25.                                 └─base::xtfrm.data.frame(x)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted