• using R version 4.0.0 alpha (2020-04-01 r78130)
• using platform: x86_64-apple-darwin17.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘theseus/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘theseus’ version ‘0.1.0’
• 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 ‘theseus’ can be installed ... [17s/23s] 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 R 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 dependencies in R code ... NOTE
  Namespaces in Imports field not imported from:
    ‘gridExtra’ ‘splancs’ ‘tidyverse’
    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 ... [11s/15s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... NOTE
  Package unavailable to check Rd xrefs: ‘dada2’
• 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 data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [5s/7s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/12s] ERROR
    Running ‘testthat.R’ [8s/12s]
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    >
    > test_check("theseus")
    ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
    attempting to coerce non-factor
    Backtrace:
     1. base::table(...)
     2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
     3. base::as.character.factor(df[[tax_level]])
    
    ══ testthat results ═══════════════════════════════════════════════════════════
    [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18)
    
    Error: testthat unit tests failed
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] NONE
    ‘general_usage.Rmd’ using ‘UTF-8’... [0s/0s] OK
• checking re-building of vignette outputs ... [1s/1s] WARNING
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘general_usage.Rmd’ using rmarkdown
  dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
    Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
    Expected in: /usr/lib/libSystem.B.dylib
  
  dyld: Symbol not found: ____chkstk_darwin
    Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
    Expected in: /usr/lib/libSystem.B.dylib
  
  Error: processing vignette 'general_usage.Rmd' failed with diagnostics:
  pandoc document conversion failed with error 6
  --- failed re-building ‘general_usage.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘general_usage.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE
  Status: 1 ERROR, 1 WARNING, 2 NOTEs