| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-23 11:35 -0400 (Mon, 23 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4868 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4548 |
| 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 609/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DMRcate 3.7.0 (landing page) Tim Peters
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for DMRcate in R Universe. | ||||||||||||||
|
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. |
| Package: DMRcate |
| Version: 3.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate |
| StartedAt: 2026-03-22 16:23:35 -0400 (Sun, 22 Mar 2026) |
| EndedAt: 2026-03-22 16:30:37 -0400 (Sun, 22 Mar 2026) |
| EllapsedTime: 421.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate
###
##############################################################################
##############################################################################
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr
Quitting from EPICv1_and_450K.Rnw:125-132 [plotting]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_http_504>
Error in `req_perform()`:
! HTTP 504 Gateway Timeout.
---
Backtrace:
x
1. \-DMRcate::DMR.plot(...)
2. +-base::suppressWarnings(...)
3. | \-base::withCallingHandlers(...)
4. \-biomaRt::useEnsembl(...)
5. \-biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
6. \-biomaRt:::.getAttributes(mart, verbose = verbose)
7. \-biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
8. \-biomaRt:::bmRequest(...)
9. \-httr2::req_perform(request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'EPICv1_and_450K.Rnw' failed with diagnostics:
HTTP 504 Gateway Timeout.
--- failed re-building ‘EPICv1_and_450K.Rnw’
--- re-building ‘EPICv2.Rnw’ using knitr
--- finished re-building ‘EPICv2.Rnw’
--- re-building ‘sequencing.Rnw’ using knitr
--- finished re-building ‘sequencing.Rnw’
SUMMARY: processing the following file failed:
‘EPICv1_and_450K.Rnw’
Error: Vignette re-building failed.
Execution halted