Shuangbin Xu
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/MicrobiotaProcess |
| git_branch: devel |
| git_last_commit: 9b6279e |
| git_last_commit_date: 2025-10-29 10:58:25 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-24 11:35 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 1293/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MicrobiotaProcess 1.23.0 (landing page) Shuangbin Xu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the MicrobiotaProcess package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MicrobiotaProcess.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: MicrobiotaProcess |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MicrobiotaProcess |
| StartedAt: 2026-01-23 17:04:58 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 17:05:46 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 47.6 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 MicrobiotaProcess
###
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* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* preparing ‘MicrobiotaProcess’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MicrobiotaProcess.Rmd’ using rmarkdown
2026-01-23 17:05:42.050 R[69289:824885894] XType: Using static font registry.
Quitting from MicrobiotaProcess.Rmd:208-239 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument '.data' in selecting a method for function 'mp_cal_abundance': attempt access index 19/19 in VECTOR_ELT
---
Backtrace:
▆
1. ├─... %>% ...
2. ├─MicrobiotaProcess::mp_cal_abundance(...)
3. ├─MicrobiotaProcess::mp_cal_abundance(., .abundance = RareAbundance)
4. ├─MicrobiotaProcess::mp_cal_abundance(., .abundance = RareAbundance)
5. │ └─base::lapply(...)
6. │ └─MicrobiotaProcess (local) FUN(X[[i]], ...)
7. │ └─da %<>% as_tibble() %>% ...
8. ├─tidyr::nest(., `:=`(!!bygroup, colnames(.)[colnames(.) != "OTU"]))
9. ├─tibble::as_tibble(.)
10. ├─dtplyr:::as_tibble.dtplyr_step(.)
11. │ ├─tibble::as_tibble(dt_eval(x), .name_repair = .name_repair)
12. │ └─dtplyr:::dt_eval(x)
13. │ └─rlang::eval_tidy(quo)
14. ├─data.table::setcolorder(...)
15. │ └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
16. ├─...[]
17. ├─data.table:::`[.data.table`(...)
18. │ └─base::tryCatch(...)
19. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. │ └─base (local) tryCatchOne(...)
21. │ └─value[[3L]](cond)
22. │ └─data.table:::.checkTypos(e, names_x)
23. │ └─data.table:::stopf("%s", err$message, domain = NA)
24. │ └─data.table:::raise_condition(...)
25. │ └─base (local) signal(obj)
26. └─base (local) `<fn>`(`<smplErrr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MicrobiotaProcess.Rmd' failed with diagnostics:
error in evaluating the argument '.data' in selecting a method for function 'mp_cal_abundance': attempt access index 19/19 in VECTOR_ELT
--- failed re-building ‘MicrobiotaProcess.Rmd’
SUMMARY: processing the following file failed:
‘MicrobiotaProcess.Rmd’
Error: Vignette re-building failed.
Execution halted