Qian Liu
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/VariantExperiment |
| git_branch: devel |
| git_last_commit: 230466e |
| git_last_commit_date: 2025-10-29 10:53:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 2270/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantExperiment 1.25.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: VariantExperiment |
| Version: 1.25.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data VariantExperiment |
| StartedAt: 2025-11-13 18:05:47 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 18:06:04 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 17.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R 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 (it is needed 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