| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-29 11:58 -0500 (Mon, 29 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 2182/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TAPseq 1.22.0 (landing page) Andreas R. Gschwind
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the TAPseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TAPseq.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: TAPseq |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 TAPseq |
| StartedAt: 2025-12-25 20:35:20 -0500 (Thu, 25 Dec 2025) |
| EndedAt: 2025-12-25 20:37:59 -0500 (Thu, 25 Dec 2025) |
| EllapsedTime: 159.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 TAPseq
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* checking for file ‘TAPseq/DESCRIPTION’ ... OK
* preparing ‘TAPseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘tapseq_primer_design.Rmd’ using rmarkdown
--- finished re-building ‘tapseq_primer_design.Rmd’
--- re-building ‘tapseq_target_genes.Rmd’ using rmarkdown
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
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Quitting from tapseq_target_genes.Rmd:54-59 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─TAPseq::selectTargetGenes(bone_marrow_genex)
2. ├─Seurat::GetAssayData(object, slot = "counts", assay = "RNA")
3. └─SeuratObject:::GetAssayData.Seurat(object, slot = "counts", assay = "RNA")
4. └─SeuratObject::.Deprecate(...)
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tapseq_target_genes.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 ‘tapseq_target_genes.Rmd’
SUMMARY: processing the following file failed:
‘tapseq_target_genes.Rmd’
Error: Vignette re-building failed.
Execution halted