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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 57/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.2.0  (landing page)
Martin Morgan
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: RELEASE_3_20
git_last_commit: 2759746
git_last_commit_date: 2024-10-29 11:26:16 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  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: 1.2.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 AlphaMissenseR
StartedAt: 2025-03-31 16:09:33 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 16:31:48 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 1335.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-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
--- finished re-building ‘alphafold.Rmd’

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

Quitting from issues.Rmd:73-75 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_data("gene_hg38")
 2.   └─AlphaMissenseR:::db_table(...)
 3.     └─AlphaMissenseR:::db_table_new(...)
 4.       ├─BiocFileCache::bfcrpath(bfc, rnames = rname, fpath = fpath)
 5.       └─BiocFileCache::bfcrpath(bfc, rnames = rname, fpath = fpath)
 6.         ├─BiocFileCache::bfcrpath(x, rids = rids0)
 7.         └─BiocFileCache::bfcrpath(x, rids = rids0)
 8.           └─base::stopifnot(all(rids %in% bfcrid(x)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'issues.Rmd' failed with diagnostics:
all(rids %in% bfcrid(x)) is not TRUE
--- failed re-building ‘issues.Rmd’

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

Error: Vignette re-building failed.
Execution halted