Build/check report for BioC 3.24 - BIOCCHECK results for BEclear on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
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*
BIOCCHECK results for BEclear on nebbiolo2

To the developers/maintainers of the BEclear package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BEclear.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: BEclear
Version: 2.29.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BEclear_2.29.0.tar.gz','quit-with-status'=TRUE)"
StartedAt: 2026-05-09 06:21:20 -0400 (Sat, 09 May 2026)
EndedAt: 2026-05-09 06:21:49 -0400 (Sat, 09 May 2026)
EllapsedTime: 29.0 seconds
RetCode: 0
Status: OK
CheckDir: None
Warnings: 0
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BEclear_2.29.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing BEclear ──────────────────────────────────────────────────────────
✔ Package installed successfully
── BEclear session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear
→ BiocVersion: 3.24
→ Package: BEclear
→ PackageVersion: 2.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BEclear.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear
→ installDir: /tmp/RtmpuHdYrQ/file5a3e94578cde7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BEclear ────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (8%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • BEclear.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-methylation-data.Rd:26: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-sample-data.Rd:20: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-package.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:89: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:91: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:93: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:149: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:151: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:153: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/ex.corrected.data.Rd:23: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:165: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:167: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:169: unknown macro '\insertRef'
* Checking for library/require of BEclear...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/calcBatchEffectsForBatch.R (line 39, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • makeBoxplot() (R/makeBoxplot.R): 194 lines
    • ...
    • calcBlockFrame() (R/calcBlockFrame.R): 69 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-methylation-data.Rd:26: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-sample-data.Rd:20: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-package.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:89: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:91: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:93: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:149: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:151: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:153: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/ex.corrected.data.Rd:23: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:165: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:167: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:169: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-methylation-data.Rd:26: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-sample-data.Rd:20: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-package.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:89: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:91: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:93: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:149: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:151: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:153: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/ex.corrected.data.Rd:23: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:165: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:167: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:169: unknown macro '\insertRef'
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • localLoss.Rd
  • loss.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-methylation-data.Rd:26: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-example-sample-data.Rd:20: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/BEclear-package.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:89: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:91: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/calcScore.Rd:93: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:149: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:151: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/correctBatchEffect.Rd:153: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/ex.corrected.data.Rd:23: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:165: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:167: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHdYrQ/file5a3e91a34539b/BEclear/man/imputeMissingData.Rd:169: unknown macro '\insertRef'
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • BEclear-package.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • BEclear-package.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 79 lines (3%) are > 80 characters long.
  First few lines:
    • R/BEclear.R#L12 #' in DNA methylation data. The core fun ...
    • ...
    • vignettes/BEclear.Rmd#L318 ```{r boxplot2, fig.wide = TRUE, fig.cap ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 480 lines (20%) are
not.
  First few lines:
    • R/BEclear.R#L108 "batch_id", "beta.value", "feature", " ...
    • ...
    • vignettes/BEclear.Rmd#L322 xlab = "Batch", ylab = "Beta value", s ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 10 NOTES
ℹ See the BEclear.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.