Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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/

[ 1/36] 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-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
1/31                  
2/31 [libraries]      
3/31                  
4/31 [env]            
5/31                  
6/31 [load-sce]       
7/31                  
8/31 [uniq-celltype]  
9/31                  
10/31 [anndata2sce]    
11/31                  
12/31 [sce2anndata]    
13/31                  
14/31 [load-spe]       
15/31                  
16/31 [scalefactors]   
17/31                  
18/31 [spe2anndata]    
19/31                  
20/31 [coords]         
21/31                  
22/31 [uns]            
23/31                  
24/31 [writeh5ad]      
25/31                  
26/31 [modules]        
27/31                  
28/31 [spatial-scatter]
29/31                  
30/31 [unnamed-chunk-1]
31/31                  
output file: bkg-python-interoperability.knit.md

Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate

[ 5/36] pages/bkg-data-infrastructure.qmd


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


[ 6/36] 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


[ 7/36] 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


[ 8/36] pages/seq-introduction.qmd


processing file: seq-introduction.qmd
1/3                  
2/3 [unnamed-chunk-1]
3/3                  
output file: seq-introduction.knit.md


[ 9/36] pages/seq-reads-to-counts.qmd

[10/36] pages/seq-quality-control.qmd


processing file: seq-quality-control.qmd
1/57                   
2/57 [load-libs]       
Error: package 'BiocGenerics' required by 'GenomicRanges' could not be found

Quitting from seq-quality-control.qmd:49-56 [load-libs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package 'BiocGenerics' required by 'GenomicRanges' could not be found
---
Backtrace:
    ▆
 1. └─base::library(STexampleData)
 2.   └─base::.getRequiredPackages2(...)
 3.     └─base::library(...)
 4.       └─base::.getRequiredPackages2(...)
 5.         └─base::library(...)
 6.           └─base::.getRequiredPackages2(...)
 7.             └─base::library(...)
 8.               └─base::.getRequiredPackages2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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