Panagiotis Papasaikas
| Snapshot Date: 2025-11-20 10:00 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/orthos |
| git_branch: devel |
| git_last_commit: dc6b128 |
| git_last_commit_date: 2025-10-29 11:24:17 -0500 (Wed, 29 Oct 2025) |
| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.23 Report updated every 6 hours |
This page was generated on 2025-11-20 13:45 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | R Under development (unstable) (2025-11-17 r89032) -- "Unsuffered Consequences" | 276 |
| kakapo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-31 r88977) -- "Unsuffered Consequences" | 263 |
| 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 1/3 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| orthos 1.9.0 (landing page) Panagiotis Papasaikas
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | |||||||
| kakapo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the orthos 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: orthos |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data orthos |
| StartedAt: 2025-11-20 15:48:49 -0000 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 15:49:58 -0000 (Thu, 20 Nov 2025) |
| EllapsedTime: 69.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/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 (it is needed 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 `lock()`:
! Directory of lock file does not exist: '/var/cache/basilisk'
---
Backtrace:
▆
1. └─orthos::decomposeVar(...)
2. └─basilisk::basiliskStart(orthosenv, testload = "tensorflow")
3. └─basilisk::obtainEnvironmentPath(env)
4. └─basilisk::lockExternalDir(exdir, exclusive = FALSE)
5. └─dir.expiry::lockDirectory(path, ...)
6. └─filelock::lock(plock, exclusive = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'orthosIntro.Rmd' failed with diagnostics:
Directory of lock file does not exist: '/var/cache/basilisk'
--- failed re-building ‘orthosIntro.Rmd’
SUMMARY: processing the following file failed:
‘orthosIntro.Rmd’
Error: Vignette re-building failed.
Execution halted