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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings missMethyl_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/missMethyl.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.41.0’
* 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 ‘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 code 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 ... WARNING
'::' or ':::' import not declared from: ‘dplyr’
Package in Depends field not imported from: ‘IlluminaHumanMethylationEPICv2anno.20a1.hg38’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RUVadj.Rd: variance_adjust, ruv, ruv_summary, MArrayLM-class, RUV2,
    RUV4, RUVinv, RUVrinv, get_empirical_variances, sigmashrink
  RUVfit.Rd: lmFit, limma, RUV2, RUV4, RUVinv, RUVrinv, ruv,
    design.matrix
  SWAN.Rd: RGChannelSet-class, MethylSet-class, MethyLumiSet-class,
    IlluminaMethylationManifest-class
  densityByProbeType.Rd: densityPlot, densityBeanPlot
  getAdj.Rd: MArrayLM-class
  getINCs.Rd: RGChannelSet-class
  getMappedEntrezIDs.Rd: minfi, getAnnotation
  gometh.Rd: minfi, getAnnotation
  goregion.Rd: minfi, getAnnotation
  gsameth.Rd: minfi, getAnnotation
  gsaregion.Rd: minfi, getAnnotation
  gsaseq.Rd: goana, kegga, camera, roast
  varFit.Rd: MArrayLM-class, lmFit, eBayes, topTable, decideTests, voom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 11.844  0.355  12.209
topRUV 10.013  0.467  10.494
RUVfit  9.535  0.366   9.921
SWAN    8.442  0.704   9.171
getAdj  7.229  0.381   7.620
topGSA  7.132  0.266   7.418
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/missMethyl.Rcheck/00check.log’
for details.