- 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