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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_1.47.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/missMethyl.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 02:35:05 UTC
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.47.0’
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'topRUV.Rd':
  ‘[limma:marraylm]{MArrayLM}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

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 12.820  0.188  13.040
RUVfit  9.917  0.083  10.013
topRUV  9.707  0.140   9.851
getAdj  9.650  0.116   9.816
SWAN    8.697  0.183   9.023
topGSA  6.915  0.180   7.111
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL missMethyl
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘missMethyl’ ...
** this is package ‘missMethyl’ version ‘1.47.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (missMethyl)