* using log directory ‘/srv/hornik/tmp/CRAN_pretest/radEmu.Rcheck’
* using R Under development (unstable) (2026-03-09 r89580)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-03-09 21:17:27 UTC
* checking for file ‘radEmu/DESCRIPTION’ ... OK
* this is package ‘radEmu’ version ‘2.3.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Amy D Willis <adwillis@uw.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  microbiome (8:66)
  pseudocounts (8:226)
  radEmu (8:83)
* 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 ‘radEmu’ can be installed ... [5s/5s] OK
* 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 ... [10s/10s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [159s/159s] OK
  Running ‘testthat.R’ [159s/159s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [294s/294s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_radEmu.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘intro_radEmu.Rmd’

--- re-building ‘intro_radEmu_with_phyloseq.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘intro_radEmu_with_phyloseq.Rmd’

--- re-building ‘intro_radEmu_with_tse.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘intro_radEmu_with_tse.Rmd’

--- re-building ‘parallel_radEmu.Rmd’ using rmarkdown

Quitting from parallel_radEmu.Rmd:150-160 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.check_ncores()`:
! 31 simultaneous processes spawned
---
Backtrace:
    ▆
 1. └─parallel::mclapply(1:5, emuTest, mc.cores = ncores)
 2.   └─parallel:::.check_ncores(cores)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'parallel_radEmu.Rmd' failed with diagnostics:
31 simultaneous processes spawned
--- failed re-building ‘parallel_radEmu.Rmd’

--- re-building ‘quick_start.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘quick_start.Rmd’

--- re-building ‘radEmu_clustered_data.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘radEmu_clustered_data.Rmd’

--- re-building ‘radEmu_with_reference_taxon.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘radEmu_with_reference_taxon.Rmd’

SUMMARY: processing the following file failed:
  ‘parallel_radEmu.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE