Multiple platform build/check report for BioC 3.20 - BUILD results for DMRcate on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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 palomino8

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: 3.2.1

Command: chmod a+r DMRcate -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data DMRcate

StartedAt: 2025-03-17 18:29:19 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 18:48:59 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 1179.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r DMRcate -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data DMRcate
###
##############################################################################
##############################################################################


* 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

Quitting from EPICv2.Rnw:110-115 [cpg.annotate]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! cannot subset by character when names are NULL
---
Backtrace:
     x
  1. \-DMRcate::cpg.annotate(...)
  2.   +-BiocGenerics::cbind(anno, EPICv2manifest[rownames(anno), 73:80])
  3.   | \-BiocGenerics (local) standardGeneric("cbind")
  4.   |   +-BiocGenerics::eval(quote(list(...)), env)
  5.   |   \-base::eval(quote(list(...)), env)
  6.   |     \-base::eval(quote(list(...)), env)
  7.   +-EPICv2manifest[rownames(anno), 73:80]
  8.   \-EPICv2manifest[rownames(anno), 73:80]
  9.     \-S4Vectors:::subset_along_ROWS(x, i, drop = drop)
 10.       +-S4Vectors::extractROWS(x, i)
 11.       \-S4Vectors::extractROWS(x, i)
 12.         \-S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
 13.           +-S4Vectors::NSBS(...)
 14.           \-S4Vectors::NSBS(...)
 15.             \-S4Vectors:::.subscript_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EPICv2.Rnw' failed with diagnostics:
cannot subset by character when names are NULL
--- failed re-building 'EPICv2.Rnw'

--- re-building 'sequencing.Rnw' using knitr
--- finished re-building 'sequencing.Rnw'

SUMMARY: processing the following file failed:
  'EPICv2.Rnw'

Error: Vignette re-building failed.
Execution halted