| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-12 11:35 -0500 (Fri, 12 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 2119/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| struct 1.23.0 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the struct package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/struct.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: struct |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data struct |
| StartedAt: 2025-12-11 20:22:16 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 20:22:51 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 35.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data struct
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* checking for file ‘struct/DESCRIPTION’ ... OK
* preparing ‘struct’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘struct_templates_and_helper_functions.Rmd’ using rmarkdown
Quitting from struct_templates_and_helper_functions.Rmd:670-682 [unnamed-chunk-27]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'Ontology' is not an exported object from 'namespace:rols'
---
Backtrace:
▆
1. ├─struct::ontology(P)
2. └─struct::ontology(P)
3. └─struct::ontology_list(ont)
4. ├─BiocGenerics::lapply(...)
5. └─base::lapply(...)
6. └─struct (local) FUN(X[[i]], ...)
7. └─struct::ontology_term(id = x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'struct_templates_and_helper_functions.Rmd' failed with diagnostics:
'Ontology' is not an exported object from 'namespace:rols'
--- failed re-building ‘struct_templates_and_helper_functions.Rmd’
SUMMARY: processing the following file failed:
‘struct_templates_and_helper_functions.Rmd’
Error: Vignette re-building failed.
Execution halted