* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/BIGr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘BIGr/DESCRIPTION’ ... OK
* this is package ‘BIGr’ version ‘0.5.5’
* 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 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 ‘BIGr’ can be installed ... [17s/22s] OK
See 'https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/BIGr-00install.html' for details.
* checking installed package size ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/7s] OK
* checking whether the package can be unloaded cleanly ... [5s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/8s] OK
* checking loading without being on the library search path ... [5s/10s] 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/17s] OK
* checking Rd files ... [0s/0s] 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 examples ... [11s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [13s/22s] ERROR
  Running ‘testthat.R’ [13s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGr)
  > 
  > test_check("BIGr")
  The Ref_0001 sequence had to be added for: 0 tags
  The Alt_0002 sequence had to be added for: 1 tags
  Tags discarded due to lack of Ref_0001 sequence: 0 tags
  Tags discarded due to lack of Alt_0002 sequence: 0 tags
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant count: 499
    column count: 159
  
  Meta line 14 read in.
  All meta lines processed.
  gt matrix initialized.
  Character matrix gt created.
    Character matrix gt rows: 499
    Character matrix gt cols: 159
    skip: 0
    nrows: 499
    row_num: 0
  
  Processed variant: 499
  All variants processed
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant count: 499
    column count: 159
  
  Meta line 14 read in.
  All meta lines processed.
  gt matrix initialized.
  Character matrix gt created.
    Character matrix gt rows: 499
    Character matrix gt cols: 159
    skip: 0
    nrows: 499
    row_num: 0
  
  Processed variant: 499
  All variants processed
  Scanning file to determine attributes.
  File attributes:
    meta lines: 14
    header_line: 15
    variant count: 499
    column count: 159
  
  Meta line 14 read in.
  All meta lines processed.
  gt matrix initialized.
  Character matrix gt created.
    Character matrix gt rows: 499
    Character matrix gt cols: 159
    skip: 0
    nrows: 499
    row_num: 0
  
  Processed variant: 499
  All variants processed
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-madc2vcf_all.R:16:3'): test madc offtargets ────────────────────
  Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: 'recursive' must be a length-1 vector
  Backtrace:
      ▆
   1. └─BIGr::madc2vcf_all(...) at test-madc2vcf_all.R:16:3
   2.   └─BIGr:::loop_though_dartag_report(...)
   3.     └─parallel::parLapply(...)
   4.       ├─base::do.call(...)
   5.       └─parallel::clusterApply(...)
   6.         └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
   7.           └─parallel:::checkForRemoteErrors(val)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  In addition: Warning messages:
  1: In if (is.character(fun)) fun <- get(fun, mode = "function", envir = envir) :
    closing unused connection 6 (<-localhost:11365)
  2: In if (is.character(fun)) fun <- get(fun, mode = "function", envir = envir) :
    closing unused connection 5 (<-localhost:11365)
  Execution halted
* checking PDF version of manual ... [5s/5s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 3:37