| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-11 11:35 -0500 (Thu, 11 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" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| 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 874/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggspavis 1.17.0 (landing page) Lukas M. Weber
| 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 ggspavis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggspavis.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: ggspavis |
| Version: 1.17.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ggspavis |
| StartedAt: 2025-12-10 18:46:03 -0500 (Wed, 10 Dec 2025) |
| EndedAt: 2025-12-10 18:55:31 -0500 (Wed, 10 Dec 2025) |
| EllapsedTime: 567.5 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 ggspavis
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* checking for file ‘ggspavis/DESCRIPTION’ ... OK
* preparing ‘ggspavis’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ggspavis_overview.Rmd’ using rmarkdown
adding: LICENSE.txt (deflated 37%)
adding: barcode_mappings.parquet (deflated 56%)
adding: binned_outputs/ (stored 0%)
adding: binned_outputs/square_016um/ (stored 0%)
adding: binned_outputs/square_016um/spatial/ (stored 0%)
adding: binned_outputs/square_016um/spatial/tissue_lowres_image.png (deflated 0%)
adding: binned_outputs/square_016um/spatial/scalefactors_json.json (deflated 42%)
adding: binned_outputs/square_016um/spatial/tissue_positions.parquet (deflated 2%)
adding: binned_outputs/square_016um/clustering.csv.gz (deflated 0%)
adding: binned_outputs/square_016um/filtered_feature_bc_matrix.h5 (deflated 1%)
adding: binned_outputs/square_008um/ (stored 0%)
adding: binned_outputs/square_008um/spatial/ (stored 0%)
adding: binned_outputs/square_008um/spatial/tissue_lowres_image.png (deflated 0%)
adding: binned_outputs/square_008um/spatial/scalefactors_json.json (deflated 42%)
adding: binned_outputs/square_008um/spatial/tissue_positions.parquet (deflated 2%)
adding: binned_outputs/square_008um/deconvolution.csv.gz (deflated 15%)
adding: binned_outputs/square_008um/clustering.csv.gz (deflated 0%)
adding: binned_outputs/square_008um/filtered_feature_bc_matrix.h5 (deflated 1%)
adding: segmented_outputs/ (stored 0%)
adding: segmented_outputs/filtered_feature_cell_matrix.h5 (deflated 2%)
adding: segmented_outputs/spatial/ (stored 0%)
adding: segmented_outputs/spatial/tissue_lowres_image.png (deflated 0%)
adding: segmented_outputs/spatial/scalefactors_json.json (deflated 38%)
adding: segmented_outputs/spatial/tissue_hires_image.png (deflated 0%)
adding: segmented_outputs/nucleus_segmentations.geojson (deflated 81%)
adding: segmented_outputs/cell_segmentations.geojson (deflated 78%)
Quitting from ggspavis_overview.Rmd:223-240 [loadvhd8sub]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'j' in selecting a method for function '[': subscript out of bounds
---
Backtrace:
▆
1. ├─...[]
2. └─base (local) `<fn>`(`<sbscOOBE>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ggspavis_overview.Rmd' failed with diagnostics:
error in evaluating the argument 'j' in selecting a method for function '[': subscript out of bounds
--- failed re-building ‘ggspavis_overview.Rmd’
SUMMARY: processing the following file failed:
‘ggspavis_overview.Rmd’
Error: Vignette re-building failed.
Execution halted