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This page was generated on 2025-10-08 12:50 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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

Package 58/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.5.3  (landing page)
Martin Morgan
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: devel
git_last_commit: edb4db6
git_last_commit_date: 2025-07-31 17:43:22 -0400 (Thu, 31 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for AlphaMissenseR on nebbiolo2

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: 1.5.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 AlphaMissenseR
StartedAt: 2025-10-07 16:10:11 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 16:11:47 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 96.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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

Quitting from alphafold.Rmd:82-84 [median-pathogenicity]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `vapply()`:
! values must be length 1,
 but FUN(X[[1]]) result is length 3
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::af_prediction_view(P35557_aa)
 2.   ├─BiocFileCache::bfcrpath(bfc, rnames = basename(pdb_url), fpath = pdb_url)
 3.   └─BiocFileCache::bfcrpath(bfc, rnames = basename(pdb_url), fpath = pdb_url)
 4.     └─base::vapply(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'alphafold.Rmd' failed with diagnostics:
values must be length 1,
 but FUN(X[[1]]) result is length 3
--- failed re-building ‘alphafold.Rmd’

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

Quitting from benchmarking.Rmd:297-330 [raincloud]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
--- failed re-building ‘benchmarking.Rmd’

--- re-building ‘clinvar.Rmd’ using rmarkdown
--- finished 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 files failed:
  ‘alphafold.Rmd’ ‘benchmarking.Rmd’

Error: Vignette re-building failed.
Execution halted