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This page was generated on 2025-12-22 12:05 -0500 (Mon, 22 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 58/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.6.1  (landing page)
Martin Morgan
Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: RELEASE_3_22
git_last_commit: 6684a18
git_last_commit_date: 2025-11-26 14:34:30 -0500 (Wed, 26 Nov 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for AlphaMissenseR on kjohnson1

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: 1.6.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR
StartedAt: 2025-12-18 19:00:32 -0500 (Thu, 18 Dec 2025)
EndedAt: 2025-12-18 19:02:28 -0500 (Thu, 18 Dec 2025)
EllapsedTime: 115.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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

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
2025-12-18 19:01:35.737 R[97160:323075054] XType: Using static font registry.
--- finished re-building ‘benchmarking.Rmd’

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

Quitting from clinvar.Rmd:60-62 [plot_P37023]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
     ▆
  1. └─AlphaMissenseR::clinvar_plot(uniprotId = "P37023")
  2.   └─AlphaMissenseR:::clinvar_filter_am_table(...)
  3.     └─AlphaMissenseR::am_data("aa_substitutions")
  4.       └─AlphaMissenseR::am_available(record = record)
  5.         └─AlphaMissenseR:::am_available_from_internet(record, bfc)
  6.           ├─AlphaMissenseR:::am_record_is_latest(record)
  7.           │ ├─base::withVisible(eval(mc, parent.frame()))
  8.           │ └─base::eval(mc, parent.frame())
  9.           │   └─base::eval(mc, parent.frame())
 10.           └─AlphaMissenseR (local) `<fn>`(record = record)
 11.             └─base::readLines(latest_version_url, warn = FALSE)
 12.               └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from introduction.Rmd:82-84 [am_available]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_available()
 2.   └─AlphaMissenseR:::am_available_from_internet(record, bfc)
 3.     ├─AlphaMissenseR:::am_record_is_latest(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(latest_version_url, warn = FALSE)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from issues.Rmd:73-75 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
     ▆
  1. └─AlphaMissenseR::am_data("gene_hg38")
  2.   └─AlphaMissenseR::am_available(record = record)
  3.     └─AlphaMissenseR:::am_available_from_internet(record, bfc)
  4.       ├─AlphaMissenseR:::am_record_is_latest(record)
  5.       │ ├─base::withVisible(eval(mc, parent.frame()))
  6.       │ └─base::eval(mc, parent.frame())
  7.       │   └─base::eval(mc, parent.frame())
  8.       └─AlphaMissenseR (local) `<fn>`(record = record)
  9.         └─base::readLines(latest_version_url, warn = FALSE)
 10.           └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following files failed:
  ‘alphafold.Rmd’ ‘clinvar.Rmd’ ‘introduction.Rmd’ ‘issues.Rmd’

Error: Vignette re-building failed.
Execution halted