############################################################################## ############################################################################## ### ### 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 2024-04-17 00:43:02.352 R[98616:450184926] 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/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