| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-22 11:46 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 2256/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.53.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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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: 1.53.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data VariantAnnotation |
| StartedAt: 2025-03-21 17:59:26 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 18:05:35 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 368.6 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 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
2025-03-21 18:00:01.980 R[7795:777420222] XType: Using static font registry.
[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 `curl::curl_fetch_memory()`:
! Server returned nothing (no headers, no data) [rest.ensembl.org]: Empty reply from server
---
Backtrace:
▆
1. ├─VariantAnnotation::vep_by_region(...)
2. │ └─VariantAnnotation::post_Hs_region(...)
3. │ └─httr::POST(...)
4. │ └─httr:::request_perform(req, hu$handle$handle)
5. │ ├─httr:::request_fetch(req$output, req$url, handle)
6. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. │ └─curl::curl_fetch_memory(url, handle = handle)
8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ensemblVEP.Rmd' failed with diagnostics:
Server returned nothing (no headers, no data) [rest.ensembl.org]: Empty reply from server
--- 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