• using R version 4.2.1 (2022-06-23)
• using platform: x86_64-pc-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 serialization versions ... OK
• checking whether package ‘treeman’ can be installed ... OK
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [14s/17s] OK
• checking Rd files ... [1s/1s] 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 ... [7s/10s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [22s/33s] ERROR
    Running ‘test-all.R’ [22s/33s]
  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:
    n1, n3, n7
     
    These nodes are invalid:
    n2
     
    Root node `x` not in ndlst
     
    These nodes are invalid:
    n5
     
    These nodes are invalid:
    n5, n7
     
    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 7.72
      ..@ wspn : logi TRUE
      ..@ wtxnyms : logi FALSE
      ..@ ply : logi FALSE
      ..@ updtd : logi TRUE
      ..@ ndmtrx : NULL
      ..@ tinds : int [1:10] 10 11 12 13 14 15 16 17 18 19
      ..@ prinds : num [1:19] 1 1 2 3 4 5 3 5 6 8 ...
      ..@ root : chr "n1"
      ..@ othr_slt_nms: logi(0)
    [1] "TreeMan Object of [10] tips"
    Tree (TreeMan Object):
      + 10 tips
      + 9 internal nodes
      + With node matrix
      + Binary
      + PD 10.2
      + Root node is "n1"
    Node (root node):
      + ID: "n1"
      + ptid: "n2", "n3"
      + nkids: 10
      + predist: 0
      + pd: 9.8
    Tree (TreeMan Object):
      + 10 tips
      + 9 internal nodes
      + Binary
      + PD 10.5
      + Root node is "n1"
      + With additional node slots:
        [binary_val]
    Tree (TreeMan Object):
      + 10 tips
      + 9 internal nodes
      + Binary
      + PD 9.27
      + 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
• DONE

Status: 1 ERROR