Multiple platform build/check report for BioC 3.22 - BUILD results for methodical on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 methodical on taishan

To the developers/maintainers of the methodical package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methodical.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: methodical

Version: 1.5.1

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data methodical

StartedAt: 2025-10-21 01:05:44 -0000 (Tue, 21 Oct 2025)

EndedAt: 2025-10-21 01:08:46 -0000 (Tue, 21 Oct 2025)

EllapsedTime: 182.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data methodical
###
##############################################################################
##############################################################################


* checking for file ‘methodical/DESCRIPTION’ ... OK
* preparing ‘methodical’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘calculating_methylation_transcription_correlations.Rmd’ using rmarkdown

Quitting from calculating_methylation_transcription_correlations.Rmd:144-158 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.Call2()`:
! 'filepath' must be a single string
---
Backtrace:
     ▆
  1. ├─base::system.time(...)
  2. └─methodical::calculateMethSiteTranscriptCors(...)
  3.   ├─SummarizedExperiment::assays(meth_rse)
  4.   └─SummarizedExperiment::assays(meth_rse)
  5.     └─S4Vectors::endoapply(...)
  6.       ├─BiocGenerics::lapply(X, FUN, ...)
  7.       └─S4Vectors::lapply(X, FUN, ...)
  8.         ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
  9.         └─base::lapply(as.list(X), match.fun(FUN), ...)
 10.           └─SummarizedExperiment (local) FUN(X[[i]], ...)
 11.             ├─methods (local) dimnames(a)
 12.             └─DelayedArray (local) dimnames(a)
 13.               ├─methods::callNextMethod()
 14.               └─DelayedArray (local) .nextMethod(x = x)
 15.                 ├─methods (local) dimnames(x@seed)
 16.                 └─HDF5Array (local) dimnames(x@seed)
 17.                   └─h5mread::h5readDimnames(x@filepath, x@name, as.character = TRUE)
 18.                     └─h5mread::get_h5dimnames(filepath, name)
 19.                       └─h5mread:::h5getdimscales(filepath, name, scalename = "dimnames")
 20.                         └─S4Vectors::.Call2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'calculating_methylation_transcription_correlations.Rmd' failed with diagnostics:
'filepath' must be a single string
--- failed re-building ‘calculating_methylation_transcription_correlations.Rmd’

--- re-building ‘working_with_meth_rses.Rmd’ using rmarkdown

Quitting from working_with_meth_rses.Rmd:56-70 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.Call2()`:
! 'filepath' must be a single string
---
Backtrace:
     ▆
  1. └─methodical::extractGRangesMethSiteValues(...)
  2.   ├─IRanges::subsetByOverlaps(meth_rse, genomic_regions)
  3.   └─IRanges::subsetByOverlaps(meth_rse, genomic_regions)
  4.     ├─x[ov_any]
  5.     └─x[ov_any]
  6.       ├─x@assays[ii, ]
  7.       └─x@assays[ii, ]
  8.         └─SummarizedExperiment:::.extract_Assays_subset(x, i, j)
  9.           ├─methods::as(endoapply(assays, extract_assay_subset), class(x))
 10.           │ └─methods:::.class1(object)
 11.           └─S4Vectors::endoapply(assays, extract_assay_subset)
 12.             ├─BiocGenerics::lapply(X, FUN, ...)
 13.             └─S4Vectors::lapply(X, FUN, ...)
 14.               ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
 15.               └─base::lapply(as.list(X), match.fun(FUN), ...)
 16.                 └─SummarizedExperiment (local) FUN(X[[i]], ...)
 17.                   ├─BiocGenerics::do.call(`[`, args)
 18.                   ├─base::do.call(`[`, args)
 19.                   ├─methods (local) `<fn>`(`<HDF5Mtrx[,100]>`, `<lgl>`, , drop = FALSE)
 20.                   └─DelayedArray (local) `<fn>`(`<HDF5Mtrx[,100]>`, `<lgl>`, , drop = FALSE)
 21.                     └─DelayedArray:::stash_DelayedSubset(x, Nindex)
 22.                       └─DelayedArray:::new_DelayedSubset(x@seed, Nindex)
 23.                         └─S4Arrays:::normalize_Nindex(Nindex, seed)
 24.                           ├─methods (local) dimnames(x)
 25.                           └─HDF5Array (local) dimnames(x)
 26.                             └─h5mread::h5readDimnames(x@filepath, x@name, as.character = TRUE)
 27.                               └─h5mread::get_h5dimnames(filepath, name)
 28.                                 └─h5mread:::h5getdimscales(filepath, name, scalename = "dimnames")
 29.                                   └─S4Vectors::.Call2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'working_with_meth_rses.Rmd' failed with diagnostics:
'filepath' must be a single string
--- failed re-building ‘working_with_meth_rses.Rmd’

SUMMARY: processing the following files failed:
  ‘calculating_methylation_transcription_correlations.Rmd’
  ‘working_with_meth_rses.Rmd’

Error: Vignette re-building failed.
Execution halted