| 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 2261/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TreeSummarizedExperiment 2.18.0 (landing page) Ruizhu Huang
| 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 TreeSummarizedExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TreeSummarizedExperiment.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: TreeSummarizedExperiment |
| Version: 2.18.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TreeSummarizedExperiment |
| StartedAt: 2025-12-19 06:00:45 -0000 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 06:01:48 -0000 (Fri, 19 Dec 2025) |
| EllapsedTime: 63.0 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 TreeSummarizedExperiment
###
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* checking for file ‘TreeSummarizedExperiment/DESCRIPTION’ ... OK
* preparing ‘TreeSummarizedExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_to_treeSummarizedExperiment.Rmd’ using rmarkdown
Quitting from Introduction_to_treeSummarizedExperiment.Rmd:144-154 [plot-rtree]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get()`:
! object 'ggtree' not found
---
Backtrace:
▆
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 'Introduction_to_treeSummarizedExperiment.Rmd' failed with diagnostics:
object 'ggtree' not found
--- failed re-building ‘Introduction_to_treeSummarizedExperiment.Rmd’
--- re-building ‘The_combination_of_multiple_TSEs.Rmd’ using rmarkdown
--- finished re-building ‘The_combination_of_multiple_TSEs.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_treeSummarizedExperiment.Rmd’
Error: Vignette re-building failed.
Execution halted