##############################################################################
##############################################################################
###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
###
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* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘recount-quickstart.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

2024-04-17 00:43:02.352 R[98616:450184926] XType: Using static font registry.
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'SRP009615-results.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Content type 'binary/octet-stream' length 15267923 bytes (14.6 MB)
==================================================
downloaded 14.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_jx.Rdata'
Content type 'binary/octet-stream' length 8515523 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 10
--- failed re-building ‘recount-quickstart.Rmd’

"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "library(rmarkdown); render('recount-quickstart.Rmd')"

Attaching package: ‘BiocStyle’

The following objects are masked from ‘package:rmarkdown’:

    html_document, md_document, pdf_document



processing file: recount-quickstart.Rmd
1/100                   
2/100 [vignetteSetup]   
3/100                   
4/100 [installDer]      
5/100                   
6/100 [citation]        
7/100                   
8/100 [ultraQuick]      
9/100                   
10/100 [er_analysis]     
11/100                   
12/100 [install]         
13/100                   
14/100 [start]           
15/100                   
16/100 [search_abstract] 
17/100                   
18/100 [download]        
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

19/100                   
20/100 [explore_rse]     
21/100                   
22/100 [browse]          
23/100                   
24/100 [sample_info]     
25/100                   
26/100 [scale_counts]    
27/100                   
28/100 [add_sample_info] 
29/100                   
30/100 [de_analysis]     
31/100                   
32/100 [maplot]          
2024-04-17 00:47:52.037 R[445:450190777] XType: Using static font registry.
33/100                   
34/100 [make_report]     
35/100                   
36/100 [make_report_real]
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'SRP009615-results.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
37/100                   
38/100 [geneSymbols]     
39/100                   
40/100 [define_ers]      
41/100                   
42/100 [compute_covMat]  
43/100                   
44/100 [to_integer]      
45/100                   
46/100 [phenoData]       
47/100                   
48/100 [ers_dds]         
49/100                   
50/100 [de_analysis_ers] 
51/100                   
52/100 [maploters]       
53/100                   
54/100 [report2]         
55/100                   
56/100 [gene_annotation] 
57/100                   
58/100 [exon_annotation] 
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Content type 'binary/octet-stream' length 15267923 bytes (14.6 MB)
==================================================
downloaded 14.6 MB

59/100                   
60/100 [unnamed-chunk-1] 
61/100                   
62/100 [gene_fusions]    
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_jx.Rdata'
Content type 'binary/octet-stream' length 8515523 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

63/100                   
64/100 [snaptron]        
65/100                   
66/100 [rse-fc example]  
67/100                   
68/100 [recount-brain]   
69/100                   
70/100 [downloadAll]     
71/100                   
72/100 [actuallyDownload]
73/100                   
74/100 [Figure1]         
75/100                   
76/100 [Figure2]         
77/100                   
78/100 [Figure3]         
79/100                   
80/100 [Figure4]         
81/100                   
82/100 [Figure5]         
83/100                   
84/100 [Figure6]         
85/100                   
86/100 [ER-sciserver]    
87/100                   
88/100 [createVignette]  
89/100                   
90/100 [reproduce1]      
91/100                   
92/100 [reproduce2]      
93/100                   
94/100 [reproduce3]      
95/100                   
96/100 [datasetup]       
97/100                   
98/100 [cleanup]         
99/100                   
100/100 [vignetteBiblio]  
output file: recount-quickstart.knit.md

/opt/homebrew/bin/pandoc +RTS -K512m -RTS recount-quickstart.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output recount-quickstart.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --wrap preserve --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tmp/Rtmp1w2vBS/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocStyle/resources/html/bioconductor.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp1w2vBS/rmarkdown-str1bd6352ff7f.html --variable code_folding=show --variable code_menu=1 

Output created: recount-quickstart.html
cp fakeVignettes/*.Rmd .
SUMMARY: processing the following file failed:
  ‘recount-quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted