Multiple platform build/check report for BioC 3.22 - BUILD results for DMRcate on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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*

BUILD results for DMRcate on nebbiolo2

To the developers/maintainers of the DMRcate package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.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: DMRcate

Version: 3.5.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DMRcate

StartedAt: 2025-08-08 17:00:46 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 17:13:21 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 754.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DMRcate
###
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* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr
--- finished re-building ‘EPICv1_and_450K.Rnw’

--- re-building ‘EPICv2.Rnw’ using knitr
--- finished re-building ‘EPICv2.Rnw’

--- re-building ‘sequencing.Rnw’ using knitr

Quitting from sequencing.Rnw:114-119 [seqdmrcate]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': unable to find an inherited method for function 'findOverlaps' for signature 'query = "GRanges", subject = "data.frame"'
---
Backtrace:
    x
 1. +-DMRcate::extractRanges(dmrcate.res, genome = "mm10")
 2. | +-BiocGenerics::as.data.frame(findOverlaps(ranges, grt))
 3. | \-IRanges::findOverlaps(ranges, grt)
 4. |   \-methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
 5. |     \-base::stop(...)
 6. \-base::.handleSimpleError(...)
 7.   \-base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sequencing.Rnw' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': unable to find an inherited method for function 'findOverlaps' for signature 'query = "GRanges", subject = "data.frame"'
--- failed re-building ‘sequencing.Rnw’

SUMMARY: processing the following file failed:
  ‘sequencing.Rnw’

Error: Vignette re-building failed.
Execution halted