Multiple platform build/check report for BioC 3.22 - BUILD results for OmicsMLRepoR on lconway

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"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4535
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4517
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 OmicsMLRepoR on lconway

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

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmicsMLRepoR

StartedAt: 2025-08-01 17:53:19 -0400 (Fri, 01 Aug 2025)

EndedAt: 2025-08-01 17:54:04 -0400 (Fri, 01 Aug 2025)

EllapsedTime: 44.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmicsMLRepoR
###
##############################################################################
##############################################################################


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

Quitting from Quickstart.Rmd:109-112 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'nrow': non-character argument
---
Backtrace:
    ▆
 1. ├─base::nrow(tree_filter(cmd, disease, "Colorectal Carcinoma"))
 2. ├─OmicsMLRepoR::tree_filter(cmd, disease, "Colorectal Carcinoma")
 3. │ └─OmicsMLRepoR:::.getOntos(.data, feat_name)
 4. │   ├─base::unlist(strsplit(ontos, "\\|"))
 5. │   └─base::strsplit(ontos, "\\|")
 6. └─base::.handleSimpleError(...)
 7.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Quickstart.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'nrow': non-character argument
--- failed re-building ‘Quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘Quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted