Back to Multiple platform build/check report for BioC 3.22:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4878
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4624
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4669
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: 2025-12-01 13:45 -0500 (Mon, 01 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    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

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: 1.6.1
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR
StartedAt: 2025-12-01 23:22:38 -0000 (Mon, 01 Dec 2025)
EndedAt: 2025-12-01 23:56:13 -0000 (Mon, 01 Dec 2025)
EllapsedTime: 2014.6 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
--- finished 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
--- finished re-building ‘introduction.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted