##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.workflows
###
##############################################################################
##############################################################################


* checking for file ‘OSCA.workflows/DESCRIPTION’ ... OK
* preparing ‘OSCA.workflows’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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'
Could not fetch http://bioconductor.org/books/3.23/OSCA.workflows
HttpExceptionRequest Request {
  host                 = "bioconductor.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/books/3.23/OSCA.workflows"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'stub.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.23-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.workflows'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> work.dir <- rebook::bookCache('OSCA.workflows'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)


processing file: index.Rmd
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output file: index.knit.md



processing file: lun-416b.Rmd
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output file: lun-416b.knit.md



processing file: zeisel-brain.Rmd
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44/48 [unref-zeisel-heat-cell]  
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48/48 [sessionInfo]             
output file: zeisel-brain.knit.md



processing file: tenx-unfiltered-pbmc4k.Rmd
1/50                             
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4/50 [loading]                   
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16/50 [unref-unfiltered-pbmc-qc]  
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18/50 [unref-unfiltered-pbmc-mito]
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28/50 [unref-unfiltered-pbmc-var] 
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30/50 [dimensionality-reduction]  
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32/50 [unnamed-chunk-4]           
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34/50 [clustering]                
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36/50 [unnamed-chunk-5]           
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38/50 [unref-unfiltered-pbmc-tsne]
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40/50 [unnamed-chunk-6]           
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46/50 [unnamed-chunk-9]           
47/50                             
48/50 [unref-mono-pbmc-markers]   
49/50                             
50/50 [sessionInfo]               
output file: tenx-unfiltered-pbmc4k.knit.md



processing file: tenx-repertoire-pbmc8k.Rmd
1/36                           
2/36 [unref-setup]             
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4/36 [loading]                 
5/36                           
6/36 [unnamed-chunk-1]         
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9/36                           
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11/36                           
12/36 [unref-pbmc-adt-qc]       
13/36                           
14/36 [unref-pbmc-adt-qc-mito]  
15/36                           
16/36 [normalization]           
17/36                           
18/36 [unnamed-chunk-3]         
19/36                           
20/36 [unref-norm-pbmc-adt]     
21/36                           
22/36 [dimensionality-reduction]
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24/36 [clustering]              
25/36                           
26/36 [unnamed-chunk-4]         
27/36                           
28/36 [unref-clustmod-pbmc-adt] 
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30/36 [unref-tsne-pbmc-adt]     
31/36                           
32/36 [subclustering]           
33/36                           
34/36 [unnamed-chunk-5]         
35/36                           
36/36 [sessionInfo]             
output file: tenx-repertoire-pbmc8k.knit.md



processing file: grun-pancreas.Rmd
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output file: grun-pancreas.knit.md



processing file: muraro-pancreas.Rmd
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40/40 [sessionInfo]             
output file: muraro-pancreas.knit.md



processing file: lawlor-pancreas.Rmd
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37/38                           
38/38 [sessionInfo]             
output file: lawlor-pancreas.knit.md



processing file: segerstolpe-pancreas.Rmd
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40/56 [unref-seger-tsne-correct]
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46/56 [multi-sample-comparison] 
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55/56                           
56/56 [sessionInfo]             
output file: segerstolpe-pancreas.knit.md



processing file: grun-hsc.Rmd
1/46                           
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16/46 [unref-hgrun-qc-dist]     
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output file: grun-hsc.knit.md



processing file: nestorowa-hsc.Rmd
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18/56 [normalization]           
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23/56                           
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26/56 [unref-nest-var]          
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30/56 [unnamed-chunk-5]         
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36/56 [unref-nest-tsne]         
37/56                           
38/56 [marker-detection]        
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40/56 [unnamed-chunk-7]         
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42/56 [unref-heat-nest-markers] 
43/56                           
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47/56                           
48/56 [unref-assignments-nest]  
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51/56                           
52/56 [unref-nest-facs]         
53/56                           
54/56 [unnamed-chunk-10]        
55/56                           
56/56 [sessionInfo]             
output file: nestorowa-hsc.knit.md



processing file: paul-hsc.Rmd
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36/40 [unref-paul-tsne]         
37/40                           
38/40 [unref-paul-tsne2]        
39/40                           
40/40 [sessionInfo]             
output file: paul-hsc.knit.md



processing file: bach-mammary.Rmd
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18/38 [normalization]           
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28/38 [dimensionality-reduction]
29/38                           
30/38 [unnamed-chunk-4]         
31/38                           
32/38 [clustering]              
33/38                           
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35/38                           
36/38 [unref-bach-tsne]         
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38/38 [sessionInfo]             
output file: bach-mammary.knit.md



processing file: messmer-hesc.Rmd
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6/46 [gene-annotations]            
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12/46 [unref-messmer-hesc-qc]       
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14/46 [normalization]               
15/46                               
16/46 [unref-messmer-hesc-norm]     
17/46                               
18/46 [cell-cycle]                  
19/46                               
20/46 [unnamed-chunk-3]             
21/46                               
22/46 [unref-messmer-hesc-cyclone]  
23/46                               
24/46 [feature-selection]           
25/46                               
26/46 [unref-messmer-hesc-var]      
27/46                               
28/46 [batch-correction]            
29/46                               
30/46 [dimensionality-reduction]    
31/46                               
32/46 [unref-messmer-hesc-tsne]     
33/46                               
34/46 [contrastive-pca]             
35/46                               
36/46 [sparse-contrastive-pca]      
37/46                               
38/46 [tsne]                        
39/46                               
40/46 [unref-messmer-hesc-cpca-tsne]
41/46                               
42/46 [unnamed-chunk-4]             
43/46                               
44/46 [unnamed-chunk-5]             
45/46                               
46/46 [unnamed-chunk-6]             
output file: messmer-hesc.knit.md



processing file: hca-bone-marrow.Rmd
1/62                             
2/62 [unref-setup]               
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4/62 [loading]                   
5/62                             
6/62 [gene-annotation]           
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9/62                             
10/62 [unref-hca-bone-qc]         
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14/62 [normalization]             
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20/62 [unref-hca-bone-var]        
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26/62 [dimensionality-reduction]  
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40/62 [unref-hca-bone-heatmap]    
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42/62 [unnamed-chunk-5]           
43/62                             
44/62 [cell-type-classification]  
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46/62 [unnamed-chunk-6]           
47/62                             
48/62 [annotation-mapping]        
49/62                             
50/62 [annotation-pathways]       
51/62                             
52/62 [annotation-fgsea]          
53/62                             
54/62 [annotation-viz-fgsea-table]
55/62                             
56/62 [annotation-viz-fgsea-es]   
57/62                             
58/62 [trajectory]                
59/62                             
60/62 [viz-trajectory]            
61/62                             
62/62 [sessionInfo]               
output file: hca-bone-marrow.knit.md

/usr/bin/pandoc +RTS -K512m -RTS OSCA.workflows.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output OSCA.workflows.html --lua-filter /home/biocbuild/bbs-3.23-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.23-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.23-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.23-bioc/R/site-library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmprl6LYr/file2077272d669f43 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.23-bioc/R/site-library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --mathjax --include-in-header /tmp/Rtmprl6LYr/rmarkdown-str20772735e694fb.html --filter /usr/bin/pandoc-citeproc 

Output created: docs/index.html
[1] "/home/biocbuild/.cache/rebook/OSCA.workflows/1.19.0/docs/index.html"
> 
"/home/biocbuild/bbs-3.23-bioc/R/bin/R" -e "rebook::createRedirects(file='redirect.txt')"

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> rebook::createRedirects(file='redirect.txt')
> 
SUMMARY: processing the following file failed:
  ‘stub.Rmd’

Error: Vignette re-building failed.
Execution halted