| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-01-21 11:34 -0500 (Wed, 21 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4805 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4539 |
| 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 1615/2343 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| poem 1.3.0 (landing page) Siyuan Luo
| 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 poem package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/poem.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: poem |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data poem |
| StartedAt: 2026-01-20 19:23:12 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 19:24:40 -0500 (Tue, 20 Jan 2026) |
| EllapsedTime: 88.1 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 poem
###
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* checking for file ‘poem/DESCRIPTION’ ... OK
* preparing ‘poem’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MetricsInPoem.rmd’ using rmarkdown
--- finished re-building ‘MetricsInPoem.rmd’
--- re-building ‘PoemOnSpatialExperiment.Rmd’ using rmarkdown
Quitting from PoemOnSpatialExperiment.Rmd:217-220 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unknown type for 'data'
---
Backtrace:
▆
1. ├─poem::getSpatialExternalMetrics(...)
2. └─poem::getSpatialExternalMetrics(...)
3. ├─poem::getSpatialExternalMetrics(...)
4. └─poem::getSpatialExternalMetrics(...)
5. ├─base::do.call(level_functions[[level]], args)
6. └─poem (local) `<fn>`(...)
7. ├─base::do.call(...)
8. └─poem (local) `<fn>`(labels = `<fct>`, location = `<df[,2]>`, k = 6, alpha = 0.5)
9. └─poem::knnComposition(...)
10. └─poem::findSpatialKNN(location, k, ...)
11. └─BiocNeighbors::findKNN(...)
12. ├─BiocNeighbors::buildIndex(X, ..., BNPARAM = BNPARAM)
13. └─BiocNeighbors::buildIndex(X, ..., BNPARAM = BNPARAM)
14. ├─methods::callGeneric(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
15. │ └─base::eval(call, parent.frame())
16. │ └─base::eval(call, parent.frame())
17. ├─BiocNeighbors::buildIndex(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
18. └─BiocNeighbors::buildIndex(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
19. ├─BNPARAM$class(ptr = generic_build(BNPARAM$builder, X), names = cn)
20. │ └─methods::new("AnnoyIndex", ptr = ptr, names = names)
21. │ ├─methods::initialize(value, ...)
22. │ └─methods::initialize(value, ...)
23. └─BiocNeighbors:::generic_build(BNPARAM$builder, X)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PoemOnSpatialExperiment.Rmd' failed with diagnostics:
unknown type for 'data'
--- failed re-building ‘PoemOnSpatialExperiment.Rmd’
--- re-building ‘poem.Rmd’ using rmarkdown
--- finished re-building ‘poem.Rmd’
SUMMARY: processing the following file failed:
‘PoemOnSpatialExperiment.Rmd’
Error: Vignette re-building failed.
Execution halted