Multiple platform build/check report for BioC 3.20 - BUILD results for AlphaMissenseR on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4420
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 AlphaMissenseR on merida1

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

Version: 1.2.0

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

StartedAt: 2025-03-24 16:52:11 -0400 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 16:58:48 -0400 (Mon, 24 Mar 2025)

EllapsedTime: 397.3 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 AlphaMissenseR
###
##############################################################################
##############################################################################


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

--- re-building ‘benchmarking.Rmd’ using rmarkdown
--- finished re-building ‘benchmarking.Rmd’

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

Quitting from clinvar.Rmd:60-62 [plot_P37023]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! vector memory limit of 64.0 Gb reached, see mem.maxVSize()
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::clinvar_plot(uniprotId = "P37023")
 2.   └─AlphaMissenseR:::clinvar_filter_cv_table(...)
 3.     ├─dplyr::mutate(...)
 4.     ├─tidyr::separate(...)
 5.     └─tidyr:::separate.data.frame(...)
 6.       └─tidyr:::str_separate(...)
 7.         └─tidyr:::str_split_fixed(...)
 8.           └─tidyr:::simplifyPieces(pieces, n, fill == "left")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clinvar.Rmd' failed with diagnostics:
vector memory limit of 64.0 Gb reached, see mem.maxVSize()
--- failed re-building ‘clinvar.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘issues.Rmd’ using rmarkdown
--- finished re-building ‘issues.Rmd’

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

Error: Vignette re-building failed.
Execution halted