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April 24, 2020 02:43
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For replying to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html
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| ## Generate the HTML report | |
| report <- derfinderReport( | |
| prefix = "report", browse = FALSE, | |
| nBestRegions = 15, makeBestClusters = TRUE, outdir = "html", | |
| fullCov = list("21" = genomeDataRaw$coverage), optionsStats = optionsStats | |
| ) | |
| ## Registered S3 method overwritten by 'GGally': | |
| ## method from | |
| ## +.gg ggplot2 | |
| ## Writing 9 Bibtex entries ... OK | |
| ## Results written to file 'report/html/basicExploration.bib' | |
| ## extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens | |
| ## processing file: basicExploration.Rmd | |
| ## The magick package is required to crop "basicExploration_files/figure-html/pvals-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/regLen-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/regArea-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/nullLengthArea-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/meanCov-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/MAstyle-1.png" but not available. | |
| ## Scale for 'x' is already present. Adding another scale for 'x', which will | |
| ## replace the existing scale. | |
| ## Scale for 'x' is already present. Adding another scale for 'x', which will | |
| ## replace the existing scale. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/genomeOverview1-1.png" but not available. | |
| ## Scale for 'x' is already present. Adding another scale for 'x', which will | |
| ## replace the existing scale. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/genomeOverview2-1.png" but not available. | |
| ## Scale for 'x' is already present. Adding another scale for 'x', which will | |
| ## replace the existing scale. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/genomeOverview3-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-2.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-3.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-4.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-5.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-6.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-7.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-8.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-9.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-10.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-11.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-12.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-13.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-14.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-15.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-16.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/plotRegions-17.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/vennDiagram-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/vennDiagramSignificant-1.png" but not available. | |
| ## Parsing transcripts... | |
| ## Parsing exons... | |
| ## Parsing cds... | |
| ## Parsing utrs... | |
| ## ------exons... | |
| ## ------cdss... | |
| ## ------introns... | |
| ## ------utr... | |
| ## aggregating... | |
| ## Done | |
| ## Constructing graphics... | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Parsing transcripts... | |
| ## Parsing exons... | |
| ## Parsing cds... | |
| ## Parsing utrs... | |
| ## ------exons... | |
| ## ------cdss... | |
| ## ------introns... | |
| ## ------utr... | |
| ## aggregating... | |
| ## Done | |
| ## Constructing graphics... | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/bestClusters-1.png" but not available. | |
| ## The magick package is required to crop "basicExploration_files/figure-html/bestClusters-2.png" but not available. | |
| ## output file: basicExploration.knit.md | |
| ## /usr/local/bin/pandoc +RTS -K512m -RTS basicExploration.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output basicExploration.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tmp/RtmpKRmget/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --css /usr/local/lib/R/host-site-library/BiocStyle/resources/html/bioconductor.css --variable 'theme:bootstrap' --include-in-header /tmp/RtmpKRmget/rmarkdown-str76b62d9d4ba.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/local/lib/R/host-site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/local/lib/R/host-site-library/rmarkdown/rmd/lua/latex-div.lua --variable code_folding=hide --variable code_menu=1 | |
| ## | |
| ## Output created: basicExploration.html |
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