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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2188/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantExperiment 1.19.2  (landing page)
Qian Liu
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/VariantExperiment
git_branch: devel
git_last_commit: 0dcd4c3
git_last_commit_date: 2024-05-22 15:56:32 -0400 (Wed, 22 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for VariantExperiment on palomino4

To the developers/maintainers of the VariantExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantExperiment.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: VariantExperiment
Version: 1.19.2
Command: chmod a+r VariantExperiment -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantExperiment
StartedAt: 2024-06-09 23:03:37 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:04:56 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 79.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r VariantExperiment -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantExperiment
###
##############################################################################
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* checking for file 'VariantExperiment/DESCRIPTION' ... OK
* preparing 'VariantExperiment':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'VariantExperiment-class.Rmd' using rmarkdown

Quitting from lines 245-248 [makeVariantExperimentFromVCF] (VariantExperiment-class.Rmd)
Error: processing vignette 'VariantExperiment-class.Rmd' failed with diagnostics:
The GDS node "$ref" does not exist.
--- failed re-building 'VariantExperiment-class.Rmd'

SUMMARY: processing the following file failed:
  'VariantExperiment-class.Rmd'

Error: Vignette re-building failed.
Execution halted