Vladimir Kiselev
| Snapshot Date: 2025-04-10 13:40 -0400 (Thu, 10 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/SC3 |
| git_branch: devel |
| git_last_commit: 9b5ac20 |
| git_last_commit_date: 2024-10-29 10:06:24 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-11 11:45 -0400 (Fri, 11 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4568 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4382 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4481 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4541 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4559 |
| 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 1875/2335 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SC3 1.35.0 (landing page) Vladimir Kiselev
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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 | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the SC3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SC3.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: SC3 |
| Version: 1.35.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SC3 |
| StartedAt: 2025-04-10 18:20:12 -0400 (Thu, 10 Apr 2025) |
| EndedAt: 2025-04-10 18:27:15 -0400 (Thu, 10 Apr 2025) |
| EllapsedTime: 422.4 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 SC3
###
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* checking for file ‘SC3/DESCRIPTION’ ... OK
* preparing ‘SC3’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SC3.Rmd’ using rmarkdown
2025-04-10 18:21:09.104 R[97479:635665234] XType: com.apple.fonts is not accessible.
2025-04-10 18:21:09.105 R[97479:635665234] XType: XTFontStaticRegistry is enabled.
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No outliers detected in cluster 3. Small number of cells in the cluster.
Quitting from SC3.Rmd:390-395 [unnamed-chunk-37]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `serverSocket()`:
! creation of server socket failed: port 11973 cannot be opened
---
Backtrace:
▆
1. ├─SC3::sc3_calc_biology(sce, ks = 2:4)
2. └─SC3::sc3_calc_biology(sce, ks = 2:4)
3. └─parallel::makeCluster(n_cores, outfile = "")
4. └─parallel::makePSOCKcluster(names = spec, ...)
5. └─base::serverSocket(port = port)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SC3.Rmd' failed with diagnostics:
creation of server socket failed: port 11973 cannot be opened
--- failed re-building ‘SC3.Rmd’
SUMMARY: processing the following file failed:
‘SC3.Rmd’
Error: Vignette re-building failed.
Execution halted