Mattia Furlan
| Snapshot Date: 2025-03-20 13:40 -0400 (Thu, 20 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/methylPipe |
| git_branch: devel |
| git_last_commit: 9ff081a |
| git_last_commit_date: 2024-10-29 09:54:17 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-21 11:44 -0400 (Fri, 21 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 1246/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylPipe 1.41.0 (landing page) Mattia Furlan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the methylPipe package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylPipe.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: methylPipe |
| Version: 1.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data methylPipe |
| StartedAt: 2025-03-20 17:32:15 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 17:34:04 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 108.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data methylPipe
###
##############################################################################
##############################################################################
* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* preparing ‘methylPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘methylPipe.rnw’ using knitr
Warning in in_dir(input_dir(), expr) :
You changed the working directory to /private/tmp/RtmpngvKHE (probably via setwd()). It will be restored to /private/tmp/Rtmp5k0pFg/Rbuilde4ec2d7d967/methylPipe/vignettes. See the Note section in ?knitr::knit
Quitting from methylPipe.rnw:239-245 [pmeth]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `errorHandler()`:
! Internal Server Error
---
Backtrace:
x
1. \-methylPipe::plotMeth(...)
2. \-Gviz::IdeogramTrack(genome = gen, chromosome = chr)
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 'methylPipe.rnw' failed with diagnostics:
Internal Server Error
--- failed re-building ‘methylPipe.rnw’
SUMMARY: processing the following file failed:
‘methylPipe.rnw’
Error: Vignette re-building failed.
Execution halted