| Back to Build/check report for BioC 3.22 experimental data |
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This page was generated on 2025-12-11 15:41 -0500 (Thu, 11 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 |
| 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 274/435 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| NanoporeRNASeq 1.20.0 (landing page) Ying Chen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
|
To the developers/maintainers of the NanoporeRNASeq package: - 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: NanoporeRNASeq |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoporeRNASeq |
| StartedAt: 2025-12-11 11:34:21 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 11:35:20 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 59.3 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 NanoporeRNASeq
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* checking for file ‘NanoporeRNASeq/DESCRIPTION’ ... OK
* preparing ‘NanoporeRNASeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NanoporeRNASeq.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/1a6d341889c931_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/1a6d341889c931_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/1a6d341889c931_3845'
Quitting from NanoporeRNASeq.Rmd:83-87 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
1 remote errors, element index: 1
5 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 'NanoporeRNASeq.Rmd' failed with diagnostics:
BiocParallel errors
1 remote errors, element index: 1
5 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 ‘NanoporeRNASeq.Rmd’
SUMMARY: processing the following file failed:
‘NanoporeRNASeq.Rmd’
Error: Vignette re-building failed.
Execution halted