| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-10 12:51 -0500 (Mon, 10 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1528/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| orthos 1.8.0 (landing page) Panagiotis Papasaikas
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the orthos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/orthos.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: orthos |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data orthos |
| StartedAt: 2025-11-09 17:17:04 -0500 (Sun, 09 Nov 2025) |
| EndedAt: 2025-11-09 17:17:38 -0500 (Sun, 09 Nov 2025) |
| EllapsedTime: 34.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data orthos
###
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* checking for file ‘orthos/DESCRIPTION’ ... OK
* preparing ‘orthos’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘orthosIntro.Rmd’ using rmarkdown
Quitting from orthosIntro.Rmd:280-285 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10003 milliseconds
Consider rerunning with 'localHub=TRUE'
---
Backtrace:
▆
1. └─orthos::decomposeVar(...)
2. └─orthos:::.readGeneInformation(organism, verbose = verbose)
3. └─orthosData::GetorthosContrastDB(...)
4. └─ExperimentHub::ExperimentHub()
5. └─AnnotationHub::.Hub(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'orthosIntro.Rmd' failed with diagnostics:
failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10003 milliseconds
Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘orthosIntro.Rmd’
SUMMARY: processing the following file failed:
‘orthosIntro.Rmd’
Error: Vignette re-building failed.
Execution halted