| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-01-15 11:35 -0500 (Thu, 15 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4848 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4628 |
| 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 2147/2343 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| svaRetro 1.17.0 (landing page) Ruining Dong
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the svaRetro package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/svaRetro.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: svaRetro |
| Version: 1.17.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data svaRetro |
| StartedAt: 2026-01-14 20:32:10 -0500 (Wed, 14 Jan 2026) |
| EndedAt: 2026-01-14 20:33:16 -0500 (Wed, 14 Jan 2026) |
| EllapsedTime: 66.1 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 svaRetro
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* checking for file ‘svaRetro/DESCRIPTION’ ... OK
* preparing ‘svaRetro’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘svaRetro.Rmd’ using rmarkdown
Quitting from svaRetro.Rmd:86-92 [unnamed-chunk-3]
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<error/rlang_error>
Error in `Seqinfo:::makeNewSeqnames()`:
! The seqlevels in the supplied Seqinfo object are not the same as the seqlevels in 'x'. To map them to the seqlevels of the same name in 'x', the easiest way is to propagate them to 'x' with:
seqlevels(x) <- seqlevels(new_seqinfo)
before calling the 'seqinfo()' setter. Note that you might need to specify a pruning mode (via the 'pruning.mode' argument) if this operation will drop seqlevels that are in use in 'x'.
For any more complicated mapping, please use the 'new2old' argument.
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Backtrace:
▆
1. └─svaRetro::rtDetect(RT_gr, hg19.genes, maxgap = 10, minscore = 0.8)
2. ├─GenomeInfoDb::`seqinfo<-`(`*tmp*`, pruning.mode = "coarse", value = GenomeInfoDb::seqinfo(gr)[common_seqs])
3. └─GenomeInfoDb::`seqinfo<-`(`*tmp*`, pruning.mode = "coarse", value = GenomeInfoDb::seqinfo(gr)[common_seqs])
4. └─Seqinfo:::makeNewSeqnames(x, new2old = new2old, seqlevels(value))
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Error: processing vignette 'svaRetro.Rmd' failed with diagnostics:
The seqlevels in the supplied Seqinfo object are not the same as the seqlevels in 'x'. To map them to the seqlevels of the same name in 'x', the easiest way is to propagate them to 'x' with:
seqlevels(x) <- seqlevels(new_seqinfo)
before calling the 'seqinfo()' setter. Note that you might need to specify a pruning mode (via the 'pruning.mode' argument) if this operation will drop seqlevels that are in use in 'x'.
For any more complicated mapping, please use the 'new2old' argument.
--- failed re-building ‘svaRetro.Rmd’
SUMMARY: processing the following file failed:
‘svaRetro.Rmd’
Error: Vignette re-building failed.
Execution halted