| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-03 12:04 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1781/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RgnTX 1.12.0 (landing page) Yue Wang
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the RgnTX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RgnTX.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: RgnTX |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX |
| StartedAt: 2025-11-02 18:29:37 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 18:33:08 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 211.2 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 RgnTX
###
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* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RgnTX.Rmd’ using rmarkdown
2025-11-02 18:31:58.955 R[89367:708633038] XType: com.apple.fonts is not accessible.
2025-11-02 18:31:58.955 R[89367:708633038] XType: XTFontStaticRegistry is enabled.
Quitting from RgnTX.Rmd:738-757 [unnamed-chunk-30]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! subscript contains invalid names
---
Backtrace:
▆
1. ├─cds.tx0[trans.ids]
2. └─cds.tx0[trans.ids]
3. ├─methods::callNextMethod(x = x, i = i)
4. │ └─base::eval(call, callEnv)
5. │ └─base::eval(call, callEnv)
6. └─S4Vectors (local) .nextMethod(x = x, i = i)
7. └─S4Vectors:::subset_along_ROWS(x, i, drop = drop)
8. ├─S4Vectors::extractROWS(x, i)
9. └─GenomicRanges (local) extractROWS(x, i)
10. └─IRanges (local) METHOD(x, i)
11. └─S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
12. ├─S4Vectors::NSBS(...)
13. └─S4Vectors::NSBS(...)
14. └─S4Vectors:::.subscript_error("subscript contains invalid ", what)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RgnTX.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘RgnTX.Rmd’
SUMMARY: processing the following file failed:
‘RgnTX.Rmd’
Error: Vignette re-building failed.
Execution halted