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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings missMethyl_1.33.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.33.1’
* 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 ‘missMethyl’ 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
goregion: no visible global function definition for ‘seqlevelsStyle<-’
Undefined global functions or variables:
  seqlevelsStyle<-
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
RUVadj             37.487  1.960  39.448
SWAN               27.220  0.720  27.941
RUVfit             26.448  0.764  27.213
getAdj             23.393  0.386  23.781
topRUV             23.492  0.264  23.758
topGSA             19.124  0.256  19.381
densityByProbeType 11.623  0.132  11.756
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘missMethyl.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘missMethyl.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/betasByType-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplotadj-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplotadj1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4DV-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4DVhapmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/gometh4-1.png" but not available.
Killed

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

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