| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-12-22 12:07 -0500 (Mon, 22 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 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| 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 2296/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.28.0 (landing page) Benjamin Jean-Marie Tremblay
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the universalmotif package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/universalmotif.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: universalmotif |
| Version: 1.28.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data universalmotif |
| StartedAt: 2025-12-19 06:07:30 -0000 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 06:13:20 -0000 (Fri, 19 Dec 2025) |
| EllapsedTime: 349.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data universalmotif
###
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* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* preparing ‘universalmotif’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction.Rmd’ using rmarkdown
--- finished re-building ‘Introduction.Rmd’
--- re-building ‘IntroductionToSequenceMotifs.Rmd’ using rmarkdown
--- finished re-building ‘IntroductionToSequenceMotifs.Rmd’
--- re-building ‘MotifComparisonAndPvalues.Rmd’ using rmarkdown
Quitting from MotifComparisonAndPvalues.Rmd:299-312 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get()`:
! object 'ggtree' not found
---
Backtrace:
x
1. \-tools::buildVignettes(dir = ".", tangle = TRUE)
2. +-base::tryCatch(...)
3. | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
4. | \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. | \-base (local) doTryCatch(return(expr), name, parentenv, handler)
6. \-engine$weave(file, quiet = quiet, encoding = enc)
7. \-knitr:::vweave_rmarkdown(...)
8. \-rmarkdown::render(...)
9. \-knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. \-knitr:::process_file(text, output)
11. +-xfun:::handle_error(...)
12. +-base::withCallingHandlers(...)
13. \-knitr:::process_group(group)
14. \-knitr:::call_block(x)
15. \-knitr:::block_exec(params)
16. \-knitr:::eng_r(options)
17. +-knitr:::in_input_dir(...)
18. | \-knitr:::in_dir(input_dir(), expr)
19. \-knitr (local) evaluate(...)
20. \-evaluate::evaluate(...)
21. +-base::withRestarts(...)
22. | \-base (local) withRestartList(expr, restarts)
23. | +-base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24. | | \-base (local) doWithOneRestart(return(expr), restart)
25. | \-base (local) withRestartList(expr, restarts[-nr])
26. | \-base (local) withOneRestart(expr, restarts[[1L]])
27. | \-base (local) doWithOneRestart(return(expr), restart)
28. +-evaluate:::with_handlers(...)
29. | +-base::eval(call)
30. | | \-base::eval(call)
31. | \-base::withCallingHandlers(...)
32. \-watcher$print_value(ev$value, ev$visible, envir)
33. +-base::withVisible(handle_value(handler, value, visible, envir))
34. \-evaluate:::handle_value(handler, value, visible, envir)
35. \-handler$value(value, visible)
36. \-knitr (local) fun(x, options = options)
37. +-base::withVisible(knit_print(x, ...))
38. +-knitr::knit_print(x, ...)
39. \-knitr:::knit_print.default(x, ...)
40. \-knitr::normal_print(x)
41. +-base::print(x)
42. \-ggtree:::print.ggtree(x)
43. \-ggtree:::is_ggtree_interactive()
44. \-yulab.utils::get_cache_item("ggtree")
45. \-base::get(item, envir = env, inherits = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MotifComparisonAndPvalues.Rmd' failed with diagnostics:
object 'ggtree' not found
--- failed re-building ‘MotifComparisonAndPvalues.Rmd’
--- re-building ‘MotifManipulation.Rmd’ using rmarkdown
--- finished re-building ‘MotifManipulation.Rmd’
--- re-building ‘SequenceSearches.Rmd’ using rmarkdown
--- finished re-building ‘SequenceSearches.Rmd’
SUMMARY: processing the following file failed:
‘MotifComparisonAndPvalues.Rmd’
Error: Vignette re-building failed.
Execution halted