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This page was generated on 2025-10-16 12:04 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1317/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.43.1  (landing page)
Belinda Phipson
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/missMethyl
git_branch: devel
git_last_commit: 182f5d3
git_last_commit_date: 2025-09-09 00:31:52 -0400 (Tue, 09 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for missMethyl on nebbiolo2

To the developers/maintainers of the missMethyl package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/missMethyl.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: missMethyl
Version: 1.43.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings missMethyl_1.43.1.tar.gz
StartedAt: 2025-10-16 02:23:55 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 02:58:52 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 2096.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: missMethyl.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings missMethyl_1.43.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/missMethyl.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.43.1’
* 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 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 loading without being on the library search path ... 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             37.840  2.224  40.585
RUVfit             33.288  0.758  34.746
SWAN               22.812  1.081  24.054
getAdj             21.125  0.745  21.873
topRUV             18.834  0.343  19.177
topGSA             15.622  0.326  15.950
densityByProbeType 10.447  0.093  10.540
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/missMethyl.Rcheck/00check.log’
for details.


Installation output

missMethyl.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL missMethyl
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘missMethyl’ ...
** this is package ‘missMethyl’ version ‘1.43.1’
** 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)

Tests output


Example timings

missMethyl.Rcheck/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj37.840 2.22440.585
RUVfit33.288 0.75834.746
SWAN22.812 1.08124.054
contrasts.varFit0.0370.0010.039
densityByProbeType10.447 0.09310.540
getAdj21.125 0.74521.873
getINCs0.1910.0090.199
getLeveneResiduals0.0070.0010.008
getMappedEntrezIDs000
gometh000
goregion000
gsameth000
gsaregion0.0000.0000.001
gsaseq0.0010.0000.000
topGSA15.622 0.32615.950
topRUV18.834 0.34319.177
topVar0.0090.0000.010
varFit0.0080.0010.009