| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-10 12:03 -0400 (Fri, 10 Oct 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" | 4854 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 78/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotatr 1.35.1 (landing page) Raymond G. Cavalcante
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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To the developers/maintainers of the annotatr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotatr.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: annotatr |
| Version: 1.35.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 annotatr |
| StartedAt: 2025-10-09 16:15:47 -0400 (Thu, 09 Oct 2025) |
| EndedAt: 2025-10-09 16:18:01 -0400 (Thu, 09 Oct 2025) |
| EllapsedTime: 134.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 annotatr
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* checking for file ‘annotatr/DESCRIPTION’ ... OK
* preparing ‘annotatr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘annotatr-vignette.Rmd’ using rmarkdown
Quitting from annotatr-vignette.Rmd:153-171 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mergeNamedAtomicVectors()`:
! sequence chrMT has incompatible circularity flags:
- in 'x': TRUE
- in 'y': FALSE
---
Backtrace:
▆
1. └─annotatr::build_annotations(genome = "hg19", annotations = annots)
2. ├─methods (local) c(...)
3. └─S4Vectors (local) c(...)
4. └─S4Vectors (local) .local(x, ...)
5. ├─S4Vectors::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
6. └─IRanges::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
7. ├─S4Vectors::bindROWS(...)
8. └─GenomicRanges::bindROWS(...)
9. └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
10. ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
11. ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
12. ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`)
13. └─Seqinfo (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`)
14. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
15. └─Seqinfo:::.merge_two_Seqinfo_objects(x, y)
16. └─Seqinfo:::mergeNamedAtomicVectors(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics:
sequence chrMT has incompatible circularity flags:
- in 'x': TRUE
- in 'y': FALSE
--- failed re-building ‘annotatr-vignette.Rmd’
SUMMARY: processing the following file failed:
‘annotatr-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted