Qian Liu
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/VariantExperiment |
| git_branch: RELEASE_3_20 |
| git_last_commit: dc5092d |
| git_last_commit_date: 2024-10-29 10:39:24 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:31 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 2237/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantExperiment 1.20.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.20.0 |
| 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: 2025-03-31 22:31:51 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 22:32:40 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 48.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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