| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:00 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 129/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bambu 3.12.0 (landing page) Ying Chen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
To the developers/maintainers of the bambu package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bambu.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: bambu |
| Version: 3.12.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 bambu |
| StartedAt: 2025-12-04 16:34:35 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 16:35:45 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 70.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 bambu
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* checking for file ‘bambu/DESCRIPTION’ ... OK
* preparing ‘bambu’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bambu.Rmd’ using rmarkdown
Quitting from bambu.Rmd:56-69 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
---
Backtrace:
▆
1. └─bambu::bambu(...)
2. └─bambu:::bambu.processReads(...)
3. ├─BiocParallel::bplapply(...)
4. └─BiocParallel::bplapply(...)
5. └─BiocParallel:::.bpinit(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'bambu.Rmd' failed with diagnostics:
BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
--- failed re-building ‘bambu.Rmd’
SUMMARY: processing the following file failed:
‘bambu.Rmd’
Error: Vignette re-building failed.
Execution halted