Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/OSTA
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.1 LTS)/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo2 Summary

[top]

Package: OSTA
Version: 0.99.0
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
BuildTime: 0 minutes 18.14 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: OSTA_20250707142150
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: OSTA. Starting Build package.
PostProcessing: Finished Git clone. Package type: Book. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 1.

nebbiolo2 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* 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
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.knit'
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/36] index.qmd


processing file: index.qmd
1/2 [welcome]
2/2          
output file: index.knit.md


[ 2/36] pages/bkg-introduction.qmd

[ 3/36] pages/bkg-spatial-omics.qmd

[ 4/36] pages/bkg-interoperability.qmd


processing file: bkg-interoperability.qmd
1/31                  
2/31 [libraries]      
3/31                  
4/31 [env]            
Error in lock(plock, exclusive = FALSE) : 
  Directory of lock file does not exist: '/var/cache/basilisk'
Calls: .main ... obtainEnvironmentPath -> lockExternalDir -> lockDirectory -> lock
In addition: Warning message:
Duplicated chunk option(s) 'label' in both chunk header and pipe comments of the chunk 'spatial_scatter'. 

Quitting from bkg-interoperability.qmd:57-69 [env]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lock()`:
! Directory of lock file does not exist: '/var/cache/basilisk'
---
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.   └─basilisk::lockExternalDir(exdir, exclusive = FALSE)
 7.     └─dir.expiry::lockDirectory(path, ...)
 8.       └─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

nebbiolo2 CHECK output

[top]


                				
 

                            
 
                                
                				
nebbiolo2 BUILD BIN output
 
                    			
[top]