| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-04-07 11:36 -0400 (Tue, 07 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4630 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences" | 4541 |
| 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 2258/2381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| topdownr 1.33.0 (landing page) Sebastian Gibb
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for topdownr in R Universe. | ||||||||||||||
|
To the developers/maintainers of the topdownr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/topdownr.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: topdownr |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data topdownr |
| StartedAt: 2026-04-06 21:17:21 -0400 (Mon, 06 Apr 2026) |
| EndedAt: 2026-04-06 21:18:22 -0400 (Mon, 06 Apr 2026) |
| EllapsedTime: 61.1 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 topdownr
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* checking for file ‘topdownr/DESCRIPTION’ ... OK
* preparing ‘topdownr’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘analysis.Rmd’ using rmarkdown
Quitting from analysis.Rmd:104-132 [importFiles]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'i' in selecting a method for function '[': object of type 'closure' is not subsettable
---
Backtrace:
▆
1. ├─topdownr::readTopDownFiles(...)
2. │ └─topdownr:::.calculateFragments(...)
3. │ ├─ProtGenerics::calculateFragments(...)
4. │ └─PSMatch::calculateFragments(...)
5. │ └─PSMatch (local) .local(sequence, ...)
6. │ └─PTMods::convertAnnotation(sequence, "name")
7. │ └─...[]
8. └─base (local) `<fn>`(`<ntSbsttE>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
error in evaluating the argument 'i' in selecting a method for function '[': object of type 'closure' is not subsettable
--- failed re-building ‘analysis.Rmd’
--- re-building ‘data-generation.Rmd’ using rmarkdown
--- finished re-building ‘data-generation.Rmd’
SUMMARY: processing the following file failed:
‘analysis.Rmd’
Error: Vignette re-building failed.
Execution halted