############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount ### ############################################################################## ############################################################################## * 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 2025-02-04 06:26:24.537 R[98810:186071318] XType: Using static font registry. [WARNING] This document format requires a nonempty 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/SRP009615/bw/mean_SRP009615.bw' Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB) ================================================== downloaded 1327.5 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw' Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB) ================================================== downloaded 90.3 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw' Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB) ================================================== downloaded 102.8 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw' Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB) ================================================== downloaded 93.1 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw' Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB) ================================================== downloaded 91.3 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw' Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB) ================================================== downloaded 63.2 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw' Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB) ================================================== downloaded 74.6 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw' Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB) ================================================== downloaded 121.9 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw' Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB) ================================================== downloaded 83.8 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw' Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB) ================================================== downloaded 75.7 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw' Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB) ================================================== downloaded 60.2 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw' Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB) ================================================== downloaded 66.5 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw' Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB) ================================================== downloaded 63.9 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/SRP009615.tsv' Content type 'text/tab-separated-values' length 5016 bytes ================================================== downloaded 5016 bytes 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 1/102 2/102 [vignetteSetup] 3/102 4/102 [installDer] 5/102 6/102 [citation] 7/102 8/102 [ultraQuick] 9/102 10/102 [er_analysis] 11/102 12/102 [install] 13/102 14/102 [start] 15/102 16/102 [search_abstract] 17/102 18/102 [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 19/102 20/102 [explore_rse] 21/102 22/102 [browse] 23/102 24/102 [sample_info] 25/102 26/102 [scale_counts] 27/102 28/102 [add_sample_info] 29/102 30/102 [de_analysis] 31/102 32/102 [maplot] 2025-02-04 06:30:44.274 R[4551:186084499] XType: Using static font registry. 33/102 34/102 [make_report] 35/102 36/102 [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="...". 37/102 38/102 [geneSymbols] 39/102 40/102 [download_bigwigs] trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw' Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB) ================================================== downloaded 1327.5 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw' Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB) ================================================== downloaded 90.3 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw' Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB) ================================================== downloaded 102.8 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw' Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB) ================================================== downloaded 93.1 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw' Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB) ================================================== downloaded 91.3 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw' Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB) ================================================== downloaded 63.2 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw' Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB) ================================================== downloaded 74.6 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw' Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB) ================================================== downloaded 121.9 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw' Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB) ================================================== downloaded 83.8 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw' Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB) ================================================== downloaded 75.7 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw' Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB) ================================================== downloaded 60.2 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw' Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB) ================================================== downloaded 66.5 MB trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw' Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB) ================================================== downloaded 63.9 MB 41/102 42/102 [define_ers] 43/102 44/102 [compute_covMat] trying URL 'http://duffel.rail.bio/recount/SRP009615/SRP009615.tsv' Content type 'text/tab-separated-values' length 5016 bytes ================================================== downloaded 5016 bytes 45/102 46/102 [to_integer] 47/102 48/102 [phenoData] 49/102 50/102 [ers_dds] 51/102 52/102 [de_analysis_ers] 53/102 54/102 [maploters] 55/102 56/102 [report2] 57/102 58/102 [gene_annotation] 59/102 60/102 [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 61/102 62/102 [newer annotation] 63/102 64/102 [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 65/102 66/102 [snaptron] 67/102 68/102 [rse-fc example] 69/102 70/102 [recount-brain] 71/102 72/102 [downloadAll] 73/102 74/102 [actuallyDownload] 75/102 76/102 [Figure1] 77/102 78/102 [Figure2] 79/102 80/102 [Figure3] 81/102 82/102 [Figure4] 83/102 84/102 [Figure5] 85/102 86/102 [Figure6] 87/102 88/102 [ER-sciserver] 89/102 90/102 [createVignette] 91/102 92/102 [reproduce1] 93/102 94/102 [reproduce2] 95/102 96/102 [reproduce3] 97/102 98/102 [datasetup] 99/102 100/102 [cleanup] 101/102 102/102 [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/4.4-arm64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-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/RtmpTfKd4u/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /Library/Frameworks/R.framework/Versions/4.4-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/RtmpTfKd4u/rmarkdown-str11c755046dbe.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