Build/check report for BioC 3.24 - BUILD results for sketchR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4796
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*

BUILD results for sketchR on nebbiolo2

To the developers/maintainers of the sketchR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sketchR.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.

raw results

Summary

Package: sketchR

Version: 1.7.1

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 sketchR

StartedAt: 2026-04-21 20:56:22 -0400 (Tue, 21 Apr 2026)

EndedAt: 2026-04-21 20:57:39 -0400 (Tue, 21 Apr 2026)

EllapsedTime: 77.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 sketchR
###
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* checking for file ‘sketchR/DESCRIPTION’ ... OK
* preparing ‘sketchR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘sketchR.Rmd’ using rmarkdown

Quitting from sketchR.Rmd:133-138 [geosketch]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lock()`:
! Cannot open lock file: No such file or directory
---
Backtrace:
    ▆
 1. └─sketchR::geosketch(reducedDim(pbmc3k, "PCA"), N = 800, seed = 123)
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::lockExternalDir(exdir, exclusive = FALSE)
 6.           └─dir.expiry::lockDirectory(path, ...)
 7.             └─filelock::lock(plock, exclusive = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketchR.Rmd' failed with diagnostics:
Cannot open lock file: No such file or directory
--- failed re-building ‘sketchR.Rmd’

--- re-building ‘sketching_workflows.Rmd’ using rmarkdown

Quitting from sketching_workflows.Rmd:60-97 [process-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lock()`:
! Cannot open lock file: No such file or directory
---
Backtrace:
    ▆
 1. └─snifter::fitsne(...)
 2.   └─snifter:::.create_tsne(...)
 3.     └─basilisk::basiliskStart(python_env)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::lockExternalDir(exdir, exclusive = FALSE)
 6.           └─dir.expiry::lockDirectory(path, ...)
 7.             └─filelock::lock(plock, exclusive = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketching_workflows.Rmd' failed with diagnostics:
Cannot open lock file: No such file or directory
--- failed re-building ‘sketching_workflows.Rmd’

SUMMARY: processing the following files failed:
  ‘sketchR.Rmd’ ‘sketching_workflows.Rmd’

Error: Vignette re-building failed.
Execution halted