* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/treeman.Rcheck’
* using R Under development (unstable) (2022-07-24 r82619)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘treeman/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treeman’ version ‘1.1.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘treeman’ can be installed ... [11s/14s] OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/20s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [9s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [26s/35s]
 [26s/36s] ERROR
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("treeman")
  Loading required package: treeman
  [4] in treelst is not a TreeMan object
  These nodes are invalid:
  n8
   
  These nodes are invalid:
  n5
   
  Root node `x` not in ndlst
   
  These nodes are invalid:
  n2
   
  These nodes are invalid:
  n2
   
  Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ ndlst       :List of 19
    ..@ nds         : chr [1:9] "n1" "n2" "n3" "n4" ...
    ..@ nnds        : int 9
    ..@ tips        : chr [1:10] "t1" "t10" "t2" "t3" ...
    ..@ ntips       : int 10
    ..@ all         : chr [1:19] "n1" "n2" "n3" "n4" ...
    ..@ nall        : int 19
    ..@ pd          : num 8.87
    ..@ wspn        : logi TRUE
    ..@ wtxnyms     : logi FALSE
    ..@ ply         : logi FALSE
    ..@ updtd       : logi TRUE
    ..@ ndmtrx      :Formal class 'big.matrix' [package "bigmemory"] with 1 slot
    ..@ tinds       : int [1:10] 10 11 12 13 14 15 16 17 18 19
    ..@ prinds      : num [1:19] 1 1 1 2 2 5 3 7 4 3 ...
    ..@ root        : chr "n1"
    ..@ othr_slt_nms: logi(0) 
  [1] "TreeMan Object of [10] tips"
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 8.88
    + Root node is "n1"
  Node (root node):
    + ID: "n1"
    + ptid: "n2", "n4"
    + nkids: 10
    + predist: 0
    + pd: 7.9
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + With node matrix
    + Binary
    + PD 9.01
    + Root node is "n1"
    + With additional node slots:
      [binary_val]
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 10.2
    + Root node is "n1"
  [1] "TreeMen Object of [3] trees"
  TreeMen Object of [3] trees[ FAIL 1 | WARN 1 | SKIP 9 | PASS 246 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (9)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-manip-methods.R:153:3): rmClade() works ─────────────────────────
  Error in `splitter_a(.data, .margins, .expand, .id)`: Invalid margin
  Backtrace:
      ▆
   1. └─treeman::getAge(t2) at test-manip-methods.R:153:2
   2.   └─treeman:::.getTreeAgeFrmMtrx(...)
   3.     └─treeman:::.getNdsPrdstsFrmMtrx(...)
   4.       └─plyr::adply(...)
   5.         └─plyr:::splitter_a(.data, .margins, .expand, .id)
  
  [ FAIL 1 | WARN 1 | SKIP 9 | PASS 246 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/treeman.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:46.69, 114.39 + 9.83