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This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4878
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4663
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 59/2366HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.9.0  (landing page)
Martin Morgan
Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: devel
git_last_commit: 4f9db03
git_last_commit_date: 2026-04-28 09:02:04 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped
See other builds for AlphaMissenseR in R Universe.

BUILD results for AlphaMissenseR on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: AlphaMissenseR
Version: 1.9.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR
StartedAt: 2026-05-05 01:41:26 -0000 (Tue, 05 May 2026)
EndedAt: 2026-05-05 01:42:30 -0000 (Tue, 05 May 2026)
EllapsedTime: 64.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘alphafold.Rmd’ using rmarkdown

Quitting from alphafold.Rmd:57-60 [am_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'alphafold.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: CSV Error on Line: 55536625
Original Line: P43251	Q193Y	0.7
Expected Number of Columns: 4 Found: 3
Possible fixes:
* Disable the parser's strict mode (strict_mode=false) to allow reading rows that do not comply with the CSV standard.
* Enable null padding (null_padding=true) to replace missing values with NULL
* Enable ignore errors (ignore_errors=true) to skip this row

  file = /home/biocbuild/.cache/R/BiocFileCache/14c67b36faf81b_content
  delimiter = 	 (Set By User)
  quote = (empty) (Auto-Detected)
  escape = (empty) (Auto-Detected)
  new_line = \n (Auto-Detected)
  header = true (Auto-Detected)
  skip_rows = 3 (Auto-Detected)
  comment = (empty) (Auto-Detected)
  strict_mode = true (Auto-Detected)
  date_format =  (Auto-Detected)
  timestamp_format =  (Auto-Detected)
  null_padding = 0
  sample_size = 20480
  ignore_errors = false
  all_varchar = 0


ℹ Context: rapi_execute
ℹ Error type: INVALID
ℹ Raw message: Invalid Input Error: CSV Error on Line: 55536625
Original Line: P43251	Q193Y	0.7
Expected Number of Columns: 4 Found: 3
Possible fixes:
* Disable the parser's strict mode (strict_mode=false) to allow reading rows that do not comply with the CSV standard.
* Enable null padding (null_padding=true) to replace missing values with NULL
* Enable ignore errors (ignore_errors=true) to skip this row

  file = /home/biocbuild/.cache/R/BiocFileCache/14c67b36faf81b_content
  delimiter = 	 (Set By User)
  quote = (empty) (Auto-Detected)
  escape = (empty) (Auto-Detected)
  new_line = \n (Auto-Detected)
  header = true (Auto-Detected)
  skip_rows = 3 (Auto-Detected)
  comment = (empty) (Auto-Detected)
  strict_mode = true (Auto-Detected)
  date_format =  (Auto-Detected)
  timestamp_format =  (Auto-Detected)
  null_padding = 0
  sample_size = 20480
  ignore_errors = false
  all_varchar = 0


--- failed re-building ‘alphafold.Rmd’

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

Quitting from benchmarking.Rmd:19-26 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'ExperimentHub'
---
Backtrace:
    ▆
 1. └─base::library(ExperimentHub)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘benchmarking.Rmd’

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

Quitting from clinvar.Rmd:60-62 [plot_P37023]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clinvar.Rmd' failed with diagnostics:
Invalid Error: Invalid Input Error: CSV Error on Line: 55536625
Original Line: P43251	Q193Y	0.7
Expected Number of Columns: 4 Found: 3
Possible fixes:
* Disable the parser's strict mode (strict_mode=false) to allow reading rows that do not comply with the CSV standard.
* Enable null padding (null_padding=true) to replace missing values with NULL
* Enable ignore errors (ignore_errors=true) to skip this row

  file = /home/biocbuild/.cache/R/BiocFileCache/14c67b36faf81b_content
  delimiter = 	 (Set By User)
  quote = (empty) (Auto-Detected)
  escape = (empty) (Auto-Detected)
  new_line = \n (Auto-Detected)
  header = true (Auto-Detected)
  skip_rows = 3 (Auto-Detected)
  comment = (empty) (Auto-Detected)
  strict_mode = true (Auto-Detected)
  date_format =  (Auto-Detected)
  timestamp_format =  (Auto-Detected)
  null_padding = 0
  sample_size = 20480
  ignore_errors = false
  all_varchar = 0


ℹ Context: rapi_execute
ℹ Error type: INVALID
ℹ Raw message: Invalid Input Error: CSV Error on Line: 55536625
Original Line: P43251	Q193Y	0.7
Expected Number of Columns: 4 Found: 3
Possible fixes:
* Disable the parser's strict mode (strict_mode=false) to allow reading rows that do not comply with the CSV standard.
* Enable null padding (null_padding=true) to replace missing values with NULL
* Enable ignore errors (ignore_errors=true) to skip this row

  file = /home/biocbuild/.cache/R/BiocFileCache/14c67b36faf81b_content
  delimiter = 	 (Set By User)
  quote = (empty) (Auto-Detected)
  escape = (empty) (Auto-Detected)
  new_line = \n (Auto-Detected)
  header = true (Auto-Detected)
  skip_rows = 3 (Auto-Detected)
  comment = (empty) (Auto-Detected)
  strict_mode = true (Auto-Detected)
  date_format =  (Auto-Detected)
  timestamp_format =  (Auto-Detected)
  null_padding = 0
  sample_size = 20480
  ignore_errors = false
  all_varchar = 0


--- failed re-building ‘clinvar.Rmd’

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

Quitting from introduction.Rmd:220-225 [ahub-homo-sap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'AnnotationHub'
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 3.     └─base (local) withOneRestart(expr, restarts[[1L]])
 4.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'AnnotationHub'
--- failed 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’ ‘clinvar.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted