| Back to Workflows build report for BioC 3.22 |
This page was generated on 2025-08-15 16:30 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| 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 27/29 | Hostname | OS / Arch | INSTALL | BUILD | ||||||||
| spicyWorkflow 1.9.0 (landing page) SOMS Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | |||||||||
|
To the developers/maintainers of the spicyWorkflow package: - 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: spicyWorkflow |
| Version: 1.9.0 |
| Command: chmod a+r spicyWorkflow -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data spicyWorkflow |
| StartedAt: 2025-08-15 13:18:20 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 13:45:14 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 1614.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r spicyWorkflow -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data spicyWorkflow
###
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* checking for file 'spicyWorkflow/DESCRIPTION' ... OK
* preparing 'spicyWorkflow':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'spicyWorkflow.Rmd' using rmarkdown
Quitting from spicyWorkflow.Rmd:275-284 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `serialize()`:
! error writing to connection
---
Backtrace:
▆
1. └─cytomapper::measureObjects(...)
2. ├─BiocParallel::bpmapply(...)
3. └─BiocParallel::bpmapply(...)
4. ├─BiocParallel::bplapply(...)
5. └─BiocParallel::bplapply(...)
6. └─BiocParallel:::.bpinit(...)
7. ├─BiocParallel::bpstop(BPPARAM)
8. └─BiocParallel::bpstop(BPPARAM)
9. └─BiocParallel::.bpstop_impl(x)
10. └─BiocParallel:::.bpstop_nodes(x)
11. ├─BiocParallel::.manager_send_all(manager, .DONE())
12. └─BiocParallel::.manager_send_all(manager, .DONE())
13. ├─BiocParallel::.send_all(manager$backend, value)
14. └─BiocParallel::.send_all(manager$backend, value)
15. ├─BiocParallel::.send_to(backend, node, value)
16. └─BiocParallel::.send_to(backend, node, value)
17. ├─parallel:::sendData(backend[[node]], value)
18. └─parallel:::sendData.SOCKnode(backend[[node]], value)
19. └─base::serialize(data, node$con)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spicyWorkflow.Rmd' failed with diagnostics:
error writing to connection
--- failed re-building 'spicyWorkflow.Rmd'
SUMMARY: processing the following file failed:
'spicyWorkflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize