| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 794/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gemma.R 3.3.0 (landing page) Ogan Mancarci
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the gemma.R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.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: gemma.R |
| Version: 3.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
| StartedAt: 2025-03-18 16:54:08 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 16:58:53 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 285.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R
###
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* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown
2025-03-18 16:55:19.013 R[3348:435152182] XType: com.apple.fonts is not accessible.
2025-03-18 16:55:19.013 R[3348:435152182] XType: XTFontStaticRegistry is enabled.
Quitting from gemma.R.Rmd:378-424 [diffExpr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'head': ℹ In argument: `..1 = contrast_bipolar disorder has_modifier manic
phase_pvalue`.
Caused by error:
! object 'contrast_bipolar disorder has_modifier manic phase_pvalue' not found
---
Backtrace:
▆
1. ├─... %>% gemma_kable()
2. ├─gemma.R::gemma_kable(.)
3. │ └─base::ncol(table)
4. ├─utils::head(., 10)
5. ├─dplyr::select(...)
6. ├─dplyr::arrange(., `contrast_bipolar disorder has_modifier manic phase_pvalue`)
7. ├─dplyr:::arrange.data.frame(., `contrast_bipolar disorder has_modifier manic phase_pvalue`)
8. │ └─dplyr:::arrange_rows(.data, dots = dots, locale = .locale)
9. │ ├─dplyr::mutate(data, `:=`("{name}", !!dot), .keep = "none")
10. │ └─dplyr:::mutate.data.frame(data, `:=`("{name}", !!dot), .keep = "none")
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ └─mask$eval_all_mutate(quo)
15. │ └─dplyr (local) eval()
16. ├─base::.handleSimpleError(...)
17. │ └─dplyr (local) h(simpleError(msg, call))
18. │ └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. └─base (local) `<fn>`(`<dply:::_>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'head': ℹ In argument: `..1 = contrast_bipolar disorder has_modifier manic
phase_pvalue`.
Caused by error:
! object 'contrast_bipolar disorder has_modifier manic phase_pvalue' not found
--- failed re-building ‘gemma.R.Rmd’
--- re-building ‘metadata.Rmd’ using rmarkdown
--- finished re-building ‘metadata.Rmd’
--- re-building ‘metanalysis.Rmd’ using rmarkdown
--- finished re-building ‘metanalysis.Rmd’
SUMMARY: processing the following file failed:
‘gemma.R.Rmd’
Error: Vignette re-building failed.
Execution halted