| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-12-27 11:34 -0500 (Sat, 27 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4806 |
| 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 636/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EasyCellType 1.13.0 (landing page) Ruoxing Li
| 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 EasyCellType package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EasyCellType.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: EasyCellType |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EasyCellType |
| StartedAt: 2025-12-26 17:23:00 -0500 (Fri, 26 Dec 2025) |
| EndedAt: 2025-12-26 17:24:51 -0500 (Fri, 26 Dec 2025) |
| EllapsedTime: 110.1 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 EasyCellType
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* checking for file ‘EasyCellType/DESCRIPTION’ ... OK
* preparing ‘EasyCellType’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘my-vignette.Rmd’ using rmarkdown
* installing *source* package ‘EasyCellType’ ...
** this is package ‘EasyCellType’ version ‘1.5.4’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EasyCellType)
Performing log-normalization
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Quitting from my-vignette.Rmd:129-134 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.frame`:
! undefined columns selected
---
Backtrace:
▆
1. └─EasyCellType::easyct(...)
2. └─base::lapply(...)
3. └─EasyCellType (local) FUN(X[[i]], ...)
4. └─clusterProfiler::GSEA(...)
5. └─enrichit::gsea_gson(...)
6. ├─gsea_res[, c(expected_cols, other_cols)]
7. └─base::`[.data.frame`(gsea_res, , c(expected_cols, other_cols))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted