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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methrix_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methrix.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘methrix/DESCRIPTION’ ... OK
* this is package ‘methrix’ version ‘1.14.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methrix’ 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 loading without being on the library search path ... 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 ... NOTE
convert_HDF5_methrix: no visible global function definition for
  ‘metadata’
convert_methrix: no visible global function definition for ‘metadata’
extract_CPGs: no visible global function definition for
  ‘standardChromosomes’
get_region_summary: no visible binding for global variable ‘..keep’
get_stats: no visible global function definition for ‘metadata’
is_h5: no visible global function definition for ‘metadata’
methrix_pca: no visible global function definition for ‘barplot’
methrix_pca: no visible global function definition for ‘points’
methrix_report: no visible global function definition for ‘metadata’
remove_snps: no visible global function definition for ‘metadata’
remove_snps: no visible global function definition for
  ‘seqlevelsStyle<-’
write_bigwigs: no visible global function definition for ‘metadata’
write_bigwigs: no visible global function definition for ‘seqlengths<-’
write_bigwigs: no visible global function definition for ‘seqlengths’
show,methrix: no visible global function definition for ‘metadata’
Undefined global functions or variables:
  ..keep barplot metadata points seqlengths seqlengths<-
  seqlevelsStyle<- standardChromosomes
Consider adding
  importFrom("graphics", "barplot", "points")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
remove_snps 5.314  0.251   6.131
* 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 ...
  ‘methrix.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘methrix.Rmd’ using rmarkdown

Quitting from lines 108-110 [unnamed-chunk-5] (methrix.Rmd)
Error: processing vignette 'methrix.Rmd' failed with diagnostics:

--- failed re-building ‘methrix.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/methrix.Rcheck/00check.log’
for details.