| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-22 11:34 -0400 (Wed, 22 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4738 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4701 |
| 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 167/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bedbaser 1.3.6 (landing page) Andres Wokaty
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for bedbaser in R Universe. | ||||||||||||||
|
To the developers/maintainers of the bedbaser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bedbaser.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: bedbaser |
| Version: 1.3.6 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data bedbaser |
| StartedAt: 2026-04-21 16:32:49 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 16:33:25 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 36.0 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 bedbaser
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* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* preparing ‘bedbaser’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘bedbaser.Rmd’ using rmarkdown
Quitting from bedbaser.Rmd:123-127 [bb_to_granges]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `scan()`:
! scan() expected 'a real', got 'JUN::JUNB'
---
Backtrace:
▆
1. └─bedbaser::bb_to_granges(bedbase, ex_bed$id, quietly = FALSE)
2. └─bedbaser:::.bed_file_to_granges(...)
3. └─bedbaser:::.import_with_genome(args)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
8. ├─base::do.call(rtracklayer::import, within(args, rm("genome")))
9. ├─BiocIO (local) `<stndrdGn>`(con = `<chr>`, format = "bed")
10. └─BiocIO (local) `<stndrdGn>`(con = `<chr>`, format = "bed")
11. ├─BiocIO::import(FileForFormat(con, format), ...)
12. └─rtracklayer::import(FileForFormat(con, format), ...)
13. └─rtracklayer (local) .local(con, format, text, ...)
14. ├─S4Vectors::DataFrame(...)
15. └─utils::read.table(...)
16. └─base::scan(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'bedbaser.Rmd' failed with diagnostics:
scan() expected 'a real', got 'JUN::JUNB'
--- failed re-building ‘bedbaser.Rmd’
SUMMARY: processing the following file failed:
‘bedbaser.Rmd’
Error: Vignette re-building failed.
Execution halted