Multiple platform build/check report for BioC 3.21 - BUILD results for EWCE on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4667
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 EWCE on kunpeng2

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

Version: 1.16.0

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

StartedAt: 2025-04-16 22:42:12 -0000 (Wed, 16 Apr 2025)

EndedAt: 2025-04-16 22:43:51 -0000 (Wed, 16 Apr 2025)

EllapsedTime: 99.0 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 EWCE
###
##############################################################################
##############################################################################


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

Quitting from EWCE.Rmd:115-122 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `getListElement()`:
! GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment
---
Backtrace:
    ▆
 1. └─EWCE::bootstrap_enrichment_test(...)
 2.   └─EWCE:::check_bootstrap_args(...)
 3.     └─EWCE:::is_celltypedataset(ctd = sct_data)
 4.       ├─c("annot", "mean_exp", "specificity") %in% names(ctd[[1]])
 5.       ├─ctd[[1]]
 6.       └─ctd[[1]]
 7.         ├─S4Vectors::getListElement(x, i, ...)
 8.         └─GenomicRanges (local) getListElement(x, i, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EWCE.Rmd' failed with diagnostics:
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment
--- failed re-building ‘EWCE.Rmd’

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

Quitting from extended.Rmd:99-116 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `getListElement()`:
! GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment
---
Backtrace:
    ▆
 1. ├─ctd[[1]]
 2. └─ctd[[1]]
 3.   ├─S4Vectors::getListElement(x, i, ...)
 4.   └─GenomicRanges (local) getListElement(x, i, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'extended.Rmd' failed with diagnostics:
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment
--- failed re-building ‘extended.Rmd’

SUMMARY: processing the following files failed:
  ‘EWCE.Rmd’ ‘extended.Rmd’

Error: Vignette re-building failed.
Execution halted