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This page was generated on 2025-03-21 11:44 -0400 (Fri, 21 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 2257/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantExperiment 1.21.0  (landing page)
Qian Liu
Snapshot Date: 2025-03-20 13:40 -0400 (Thu, 20 Mar 2025)
git_url: https://git.bioconductor.org/packages/VariantExperiment
git_branch: devel
git_last_commit: f3af19f
git_last_commit_date: 2024-10-29 10:39:24 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for VariantExperiment on lconway

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: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data VariantExperiment
StartedAt: 2025-03-20 19:01:15 -0400 (Thu, 20 Mar 2025)
EndedAt: 2025-03-20 19:01:57 -0400 (Thu, 20 Mar 2025)
EllapsedTime: 42.2 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 VariantExperiment
###
##############################################################################
##############################################################################


* 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 VariantExperiment-class.Rmd:244-248 [makeVariantExperimentFromVCF]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `seqGetData()`:
! The GDS node "$ref" does not exist.
---
Backtrace:
    ▆
 1. └─VariantExperiment::makeVariantExperimentFromVCF(vcf, out.dir = tempfile())
 2.   └─VariantExperiment::makeVariantExperimentFromGDS(...)
 3.     └─VariantExperiment::makeVariantExperimentFromSEQGDS(...)
 4.       └─VariantExperiment:::.rowRanges_seqgds(...)
 5.         └─VariantExperiment:::.granges_seqgds(seqgdsfile)
 6.           ├─SeqArray::granges(f)
 7.           └─SeqArray::granges(f)
 8.             └─SeqArray::seqGetData(x, "$ref")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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