• using R Under development (unstable) (2026-06-09 r90126)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-10 15:45:26 UTC
• checking for file ‘metacoder/DESCRIPTION’ ... OK
• this is package ‘metacoder’ version ‘0.3.9’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/3s] OK
• 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 ‘metacoder’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] 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 ... [15s/22s] 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 ... [1s/2s] 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 ... [22s/27s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [23s/34s] ERROR   Running ‘testthat.R’ [23s/34s] 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 ... [1s/1s] OK
• checking PDF version of manual ... [11s/15s] OK
• checking HTML version of manual ... [15s/25s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR