* using log directory 'd:/Rcompile/CRANpkg/local/4.6/OpenSpecy.Rcheck'
* using R Under development (unstable) (2025-12-23 r89222 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'OpenSpecy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OpenSpecy' version '1.5.3'
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'OpenSpecy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s] OK
* checking loading without being on the library search path ... [4s] OK
* checking whether startup messages can be suppressed ... [4s] 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 ... [13s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 ... [0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [6s] ERROR
Running examples in 'OpenSpecy-Ex.R' failed
The error most likely occurred in:

> ### Name: collapse_spec
> ### Title: Define features
> ### Aliases: collapse_spec collapse_spec.default collapse_spec.OpenSpecy
> ###   def_features def_features.default def_features.OpenSpecy
> 
> ### ** Examples
> 
> ## Don't show: 
> data.table::setDTthreads(2)
> ## End(Don't show)
> tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
> identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0)
Error in `[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id") : 
  attempt access index 26/26 in VECTOR_ELT
Calls: def_features -> def_features.OpenSpecy -> [ -> [.data.table
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [29s] ERROR
  Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenSpecy)
  > 
  > library(data.table)
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  > setDTthreads(2)
  > 
  > test_check("OpenSpecy")
  Saving _problems/test-def_features-15.R
  Saving _problems/test-def_features-30.R
  Saving _problems/test-def_features-93.R
  Saving _problems/test-def_features-208.R
  [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-def_features.R:118:3', 'test-def_features.R:139:3',
    'test-manage_lib.R:7:3', 'test-manage_lib.R:28:3', 'test-match_spec.R:63:3',
    'test-match_spec.R:201:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-def_features.R:15:3'): features are identified when given logical ──
  Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 27/27 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:15:3
   2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles)
   3.   ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"]
   4.   └─data.table:::`[.data.table`(...)
  ── Error ('test-def_features.R:30:5'): features are identified with sig_noise and smoothing with closing ──
  Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─OpenSpecy::def_features(map, map$metadata$snr > 0.1) at test-def_features.R:30:5
   2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$snr > 0.1)
   3.   ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"]
   4.   └─data.table:::`[.data.table`(...)
  ── Error ('test-def_features.R:93:3'): particles are identified when given character ──
  Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:93:3
   2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles)
   3.   ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"]
   4.   └─data.table:::`[.data.table`(...)
  ── Error ('test-def_features.R:208:5'): RGB values are correctly extracted and stored in metadata ──
  Error in ``[.data.table`(md, , `:=`(mean_r = as.integer(sqrt(mean(r^2))), mean_g = as.integer(sqrt(mean(g^2))), mean_b = as.integer(sqrt(mean(b^2)))), by = "feature_id")`: attempt access index 25/25 in VECTOR_ELT
  Backtrace:
      ▆
   1. ├─OpenSpecy::def_features(...) at test-def_features.R:208:5
   2. └─OpenSpecy:::def_features.OpenSpecy(...)
   3.   ├─...[]
   4.   └─data.table:::`[.data.table`(...)
  
  [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s] OK
* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... [10s] OK
* DONE
Status: 2 ERRORs