| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-03-24 12:06 -0400 (Mon, 24 Mar 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" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4521 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4448 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4414 |
| 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 2236/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.52.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK |  | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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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. |
| Package: VariantAnnotation |
| Version: 1.52.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VariantAnnotation |
| StartedAt: 2025-03-20 19:30:45 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 19:33:08 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 143.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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
Quitting from ensemblVEP.Rmd:53-58 [lksnv]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `post_Hs_region()`:
! Internal Server Error (HTTP 500).
---
Backtrace:
▆
1. └─VariantAnnotation::vep_by_region(...)
2. └─VariantAnnotation::post_Hs_region(...)
3. └─httr::stop_for_status(ans)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ensemblVEP.Rmd' failed with diagnostics:
Internal Server Error (HTTP 500).
--- failed re-building ‘ensemblVEP.Rmd’
--- re-building ‘filterVcf.Rmd’ using rmarkdown
--- finished re-building ‘filterVcf.Rmd’
SUMMARY: processing the following file failed:
‘ensemblVEP.Rmd’
Error: Vignette re-building failed.
Execution halted