Back to Books build report for BioC 3.22

This page was generated on 2025-10-15 14:30 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
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 10/11HostnameOS / ArchINSTALLBUILDCHECK
OSTA 0.99.28  (landing page)
Lukas M. Weber
Snapshot Date: 2025-10-15 06:00 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/OSTA
git_branch: devel
git_last_commit: a4bf4b9
git_last_commit_date: 2025-10-05 16:20:23 -0400 (Sun, 05 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skipped

BUILD results for OSTA on nebbiolo2

To the developers/maintainers of the OSTA 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.

raw results


Summary

Package: OSTA
Version: 0.99.28
Command: /home/biocbuild/bbs-3.22-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
StartedAt: 2025-10-15 06:18:14 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 06:21:37 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 203.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
##############################################################################
##############################################################################


* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/38] index.qmd


processing file: index.qmd
1/4 [unnamed-chunk-1]
2/4                  
3/4 [carousel]       
4/4                  
output file: index.knit.md


[ 2/38] pages/bkg-introduction.qmd

[ 3/38] pages/bkg-spatial-omics.qmd

[ 4/38] pages/bkg-infrastructure.qmd


processing file: bkg-infrastructure.qmd
1/5                        
2/5 [fig-spatialexperiment]
3/5                        
4/5 [fig-spatialdata]      
5/5                        
output file: bkg-infrastructure.knit.md


[ 5/38] pages/bkg-ecosystem.qmd


processing file: bkg-ecosystem.qmd
1/19                  
2/19 [unnamed-chunk-1]
3/19                  
4/19 [unnamed-chunk-2]
5/19                  
6/19 [unnamed-chunk-3]
7/19                  
8/19 [unnamed-chunk-4]
9/19                  
10/19 [unnamed-chunk-5]
11/19                  
12/19 [unnamed-chunk-6]
13/19                  
14/19 [unnamed-chunk-7]
15/19                  
16/19 [unnamed-chunk-8]
17/19                  
18/19 [unnamed-chunk-9]
19/19                  
output file: bkg-ecosystem.knit.md


[ 6/38] pages/bkg-importing-data.qmd


processing file: bkg-importing-data.qmd
1/9                  
2/9 [unnamed-chunk-1]
3/9                  
4/9 [unnamed-chunk-2]
5/9                  
6/9 [unnamed-chunk-3]
7/9                  
8/9 [unnamed-chunk-4]
9/9                  
output file: bkg-importing-data.knit.md


[ 7/38] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
1/5                     
2/5 [list-data]         
3/5                     
4/5 [list-stexampledata]
5/5                     
output file: bkg-example-datasets.knit.md


[ 8/38] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
1/31                  
2/31 [libraries]      
3/31                  
4/31 [env]            
Error in lock(plock, exclusive = FALSE) : 
  Cannot open lock file: Permission denied
Calls: .main ... %||% -> obtainEnvironmentPath -> lockDirectory -> lock

Quitting from bkg-python-interoperability.qmd:34-44 [env]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lock()`:
! Cannot open lock file: Permission denied
---
Backtrace:
    ▆
 1. ├─reticulate::use_virtualenv(obtainEnvironmentPath(env))
 2. │ └─reticulate:::virtualenv_path(virtualenv)
 3. │   └─reticulate:::python_environment_resolve(...)
 4. │     └─envname %||% Sys.getenv("RETICULATE_PYTHON_ENV", unset = "r-reticulate")
 5. └─basilisk::obtainEnvironmentPath(env)
 6.   └─dir.expiry::lockDirectory(envdir, exclusive = !file.exists(envpath))
 7.     └─filelock::lock(plock, exclusive = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted