| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-25 11:59 -0500 (Thu, 25 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" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 2079/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialDecon 1.20.0 (landing page) Maddy Griswold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the SpatialDecon package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialDecon.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: SpatialDecon |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SpatialDecon |
| StartedAt: 2025-12-22 20:18:25 -0500 (Mon, 22 Dec 2025) |
| EndedAt: 2025-12-22 20:20:35 -0500 (Mon, 22 Dec 2025) |
| EllapsedTime: 129.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SpatialDecon
###
##############################################################################
##############################################################################
* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* preparing ‘SpatialDecon’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SpatialDecon_vignette.Rmd’ using rmarkdown
Quitting from SpatialDecon_vignette.Rmd:207-239 [createSeuratmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
▆
1. ├─SpatialDecon::create_profile_matrix(...)
2. ├─Seurat::GetAssayData(object = seuratObject, assay = "RNA", slot = "counts")
3. └─SeuratObject:::GetAssayData.Seurat(...)
4. └─SeuratObject::.Deprecate(...)
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SpatialDecon_vignette.Rmd' failed with diagnostics:
The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘SpatialDecon_vignette.Rmd’
--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown
--- finished re-building ‘SpatialDecon_vignette_NSCLC.Rmd’
SUMMARY: processing the following file failed:
‘SpatialDecon_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted