| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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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 2318/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XeniumIO 1.3.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the XeniumIO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XeniumIO.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: XeniumIO |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data XeniumIO |
| StartedAt: 2025-12-11 20:45:55 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 20:46:31 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 36.0 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 XeniumIO
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* checking for file ‘XeniumIO/DESCRIPTION’ ... OK
* preparing ‘XeniumIO’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘XeniumIO.Rmd’ using rmarkdown
Quitting from XeniumIO.Rmd:181-187 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.sce_to_spe()`:
! all(spatialCoordsNames %in% names(colData(spe))) || all(spatialCoordsNames %in% .... is not TRUE
---
Backtrace:
▆
1. ├─BiocIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression")
2. └─XeniumIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression")
3. └─SpatialExperiment::SpatialExperiment(...)
4. └─SpatialExperiment:::.sce_to_spe(...)
5. └─base::stopifnot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'XeniumIO.Rmd' failed with diagnostics:
all(spatialCoordsNames %in% names(colData(spe))) || all(spatialCoordsNames %in% .... is not TRUE
--- failed re-building ‘XeniumIO.Rmd’
SUMMARY: processing the following file failed:
‘XeniumIO.Rmd’
Error: Vignette re-building failed.
Execution halted