| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-03-20 12:11 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 589/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DMRcate 3.2.1 (landing page) Tim Peters
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 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 DMRcate package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DMRcate |
| Version: 3.2.1 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate |
| StartedAt: 2025-03-18 00:36:27 -0000 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 00:52:55 -0000 (Tue, 18 Mar 2025) |
| EllapsedTime: 988.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate
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* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr
--- finished re-building ‘EPICv1_and_450K.Rnw’
--- re-building ‘EPICv2.Rnw’ using knitr
--- finished re-building ‘EPICv2.Rnw’
--- re-building ‘sequencing.Rnw’ using knitr
Quitting from sequencing.Rnw:122-132 [seqDMRplot1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
x
1. \-DMRcate::DMR.plot(...)
2. \-Gviz::IdeogramTrack(genome = genome, chromosome = as.character(seqnames(ranges.inplot)))
3. \-methods::new(...)
4. +-methods::initialize(value, ...)
5. \-Gviz::initialize(value, ...)
6. \-Gviz (local) .local(.Object, ...)
7. \-Gviz:::.cacheGenomes(genome = genome)
8. +-Gviz::.doCache(...)
9. | +-BiocGenerics::eval(expression, envir = callEnv)
10. | \-base::eval(expression, envir = callEnv)
11. | \-base::eval(expression, envir = callEnv)
12. +-rtracklayer::getTable(query)
13. \-rtracklayer::getTable(query)
14. \-rtracklayer (local) .local(object, ...)
15. +-restfulr::read(url$getData$track, query)
16. \-restfulr::read(url$getData$track, query)
17. +-base::tryCatch(...)
18. | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
19. | \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. | \-base (local) doTryCatch(return(expr), name, parentenv, handler)
21. \-x@protocol$read(x, cacheInfo)
22. \-restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
23. \-restfulr (local) errorHandler(responseError)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sequencing.Rnw' failed with diagnostics:
Internal Server Error
--- failed re-building ‘sequencing.Rnw’
SUMMARY: processing the following file failed:
‘sequencing.Rnw’
Error: Vignette re-building failed.
Execution halted