* using log directory ‘/Users/ripley/R/packages/tests-devel/metacoder.Rcheck’
* using R Under development (unstable) (2026-06-08 r90118)
* using platform: aarch64-apple-darwin25.5.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.1.1.101)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.5.1
* using session charset: UTF-8
* current time: 2026-06-08 19:07:24 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘metacoder/DESCRIPTION’ ... OK
* this is package ‘metacoder’ version ‘0.3.9’
* 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 ‘metacoder’ can be installed ... [11s/12s] OK
* used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’
* used SDK: ‘MacOSX26.5.sdk’
* 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 ... OK
* checking LazyData ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  Saving _problems/test--calculations-155.R
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 530 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test--parsers_and_writers.R:104:3',
    'test--parsers_and_writers.R:203:3', 'test--simulated_pcr.R:19:3',
    'test--taxmap_parsers.R:139:3', 'test--taxmap_parsers.R:288:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test--calculations.R:153:3'): Comparing groups of samples ───────────
  Error in `if (p < 0.99999) 1 - p else F(z, lower.tail = FALSE)`: missing value where TRUE/FALSE needed
  Backtrace:
       ▆
    1. └─metacoder::compare_groups(...) at test--calculations.R:153:3
    2.   └─base::lapply(...)
    3.     └─metacoder (local) FUN(X[[i]], ...)
    4.       └─metacoder (local) one_comparison(combinations[[i]][1], combinations[[i]][2])
    5.         └─base::lapply(...)
    6.           └─metacoder (local) FUN(X[[i]], ...)
    7.             ├─base::as.list(func(abund_1, abund_2))
    8.             └─metacoder (local) func(abund_1, abund_2)
    9.               ├─stats::wilcox.test(abund_1, abund_2, exact = FALSE)
   10.               └─stats:::wilcox.test.default(abund_1, abund_2, exact = FALSE)
   11.                 └─stats:::.wilcox_test_two_pval_asymp(...)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 530 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/ripley/R/packages/tests-devel/metacoder.Rcheck/00check.log’
for details.

       80.17 real        65.41 user        10.56 sys