Multiple platform build/check report for BioC 3.23 - BUILD results for AlphaMissenseR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4875
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4589
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 nebbiolo1

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: 1.7.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR

StartedAt: 2025-12-16 16:12:09 -0500 (Tue, 16 Dec 2025)

EndedAt: 2025-12-16 16:14:45 -0500 (Tue, 16 Dec 2025)

EllapsedTime: 156.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘alphafold.Rmd’ using rmarkdown

Quitting from alphafold.Rmd:50-52 [am_available]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168'
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_available()
 2.   └─AlphaMissenseR:::am_available_from_internet(record, bfc)
 3.     ├─AlphaMissenseR:::am_record_json(record)
 4.     │ ├─base::withVisible(eval(mc, parent.frame()))
 5.     │ └─base::eval(mc, parent.frame())
 6.     │   └─base::eval(mc, parent.frame())
 7.     └─AlphaMissenseR (local) `<fn>`(record = record)
 8.       └─base::readLines(url, warn = FALSE)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'alphafold.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168'
--- failed 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
--- finished re-building ‘issues.Rmd’

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

Error: Vignette re-building failed.
Execution halted