ANCOMBC.check failure

[martin-g]

biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data ANCOMBC
* checking for file ‘ANCOMBC/DESCRIPTION’ ... OK
* preparing ‘ANCOMBC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: ANCOMBC
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ANCOMBC_2.1.3.tar.gz’

biocbuild@kunpeng1 ~/git> R CMD check ANCOMBC_2.1.3.tar.gz 
* using log directory ‘/home/biocbuild/git/ANCOMBC.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ANCOMBC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ANCOMBC’ version ‘2.1.3’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ANCOMBC’ can be installed ... 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 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 ... 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 data for ASCII and uncompressed saves ... 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ANCOM.Rmd’ using ‘UTF-8’... OK
  ‘ANCOMBC.Rmd’ using ‘UTF-8’... OK
  ‘ANCOMBC2.Rmd’ using ‘UTF-8’... OK
  ‘SECOM.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ANCOM.Rmd’ using rmarkdown
--- finished re-building ‘ANCOM.Rmd’

--- re-building ‘ANCOMBC.Rmd’ using rmarkdown
--- finished re-building ‘ANCOMBC.Rmd’

--- re-building ‘ANCOMBC2.Rmd’ using rmarkdown
Quitting from lines 1093-1103 (ANCOMBC2.Rmd) 
Error: processing vignette 'ANCOMBC2.Rmd' failed with diagnostics:
object 'out' not found
--- failed re-building ‘ANCOMBC2.Rmd’

--- re-building ‘SECOM.Rmd’ using rmarkdown
--- finished re-building ‘SECOM.Rmd’

SUMMARY: processing the following file failed:
  ‘ANCOMBC2.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/git/ANCOMBC.Rcheck/00check.log’
for details.

[martin-g]

Reported upstream - FrederickHuangLin/ANCOMBC#163

[martin-g]

https://bioconductor.org/checkResults/3.18/bioc-LATEST/ANCOMBC/kunpeng2-checksrc.html is fully green!