| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-23 11:35 -0500 (Tue, 23 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" | 4878 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 692/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| escape 2.7.0 (landing page) Nick Borcherding
| 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 escape package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/escape.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: escape |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data escape |
| StartedAt: 2025-12-22 17:31:40 -0500 (Mon, 22 Dec 2025) |
| EndedAt: 2025-12-22 17:32:20 -0500 (Mon, 22 Dec 2025) |
| EllapsedTime: 40.0 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 escape
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* checking for file ‘escape/DESCRIPTION’ ... OK
* preparing ‘escape’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘escape.Rmd’ using rmarkdown
Quitting from escape.Rmd:188-200 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─escape::escape.matrix(...)
2. └─escape:::.cntEval(input.data, assay = "RNA", type = "counts")
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. ├─SeuratObject::GetAssayData(obj, assay = assay, slot = type)
6. └─SeuratObject:::GetAssayData.Seurat(obj, assay = assay, slot = type)
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'escape.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 ‘escape.Rmd’
SUMMARY: processing the following file failed:
‘escape.Rmd’
Error: Vignette re-building failed.
Execution halted