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This page was generated on 2024-06-17 12:23 -0400 (Mon, 17 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
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 2190/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.51.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/VariantAnnotation
git_branch: devel
git_last_commit: 6d549f2
git_last_commit_date: 2024-04-30 10:25:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD results for VariantAnnotation on nebbiolo2

To the developers/maintainers of the VariantAnnotation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.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: VariantAnnotation
Version: 1.51.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VariantAnnotation
StartedAt: 2024-06-16 20:10:10 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 20:12:27 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 137.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VariantAnnotation
###
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘VariantAnnotation.Rmd’ using rmarkdown
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
--- finished re-building ‘VariantAnnotation.Rmd’

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

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

Quitting from lines 210-214 [mcf7regulatoryRegions] (filterVcf.Rmd)
Error: processing vignette 'filterVcf.Rmd' failed with diagnostics:
failed to load resource
  name: AH27589
  title: wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak.gz
  reason: scan() expected 'a real', got 'SQLiteformat3'
--- failed re-building ‘filterVcf.Rmd’

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

Error: Vignette re-building failed.
Execution halted