Attaching package: ‘plotly’ The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Loading required package: S4Vectors Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:BiocGenerics’: colMeans, colSums, rowMeans, rowSums The following object is masked from ‘package:plotly’: rename The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:plotly’: slice Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. There were 50 or more warnings (use warnings() to see the first 50) [1] TRUE processing file: rmarkdown_report.Rmd | | | 0% | |... | 5% ordinary text without R code | |...... | 9% label: setup (with options) List of 3 $ include: logi FALSE $ warning: logi FALSE $ message: logi FALSE | |......... | 14% ordinary text without R code | |............ | 18% label: unnamed-chunk-1 (with options) List of 2 $ echo : logi FALSE $ engine: chr "css" | |............... | 23% ordinary text without R code | |.................. | 27% label: unnamed-chunk-2 (with options) List of 1 $ echo: logi FALSE | |..................... | 32% ordinary text without R code | |........................ | 36% label: unnamed-chunk-3 (with options) List of 2 $ eval: logi FALSE $ echo: logi FALSE | |........................... | 41% ordinary text without R code | |.............................. | 45% label: unnamed-chunk-4 (with options) List of 1 $ echo: logi FALSE | |................................ | 50% ordinary text without R code | |................................... | 55% label: unnamed-chunk-5 | |...................................... | 59% ordinary text without R code | |......................................... | 64% label: unnamed-chunk-6 | |............................................ | 68% ordinary text without R code | |............................................... | 73% label: unnamed-chunk-7 (with options) List of 1 $ warning: logi FALSE | |.................................................. | 77% ordinary text without R code | |..................................................... | 82% label: unnamed-chunk-8 | |........................................................ | 86% ordinary text without R code | |........................................................... | 91% label: unnamed-chunk-9 | |.............................................................. | 95% ordinary text without R code | |.................................................................| 100% label: unnamed-chunk-10 (with options) List of 1 $ echo: logi FALSE output file: rmarkdown_report.knit.md /isg/treegenes/treegenes_store/_conda/envs/mulled-v1-426bf8835728df51c5e5560a038d8ecee064c9da3c67e3cfebbd222b92eb0901/bin/pandoc +RTS -K512m -RTS rmarkdown_report.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output rmarkdown_report.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /isg/treegenes/treegenes_store/_conda/envs/mulled-v1-426bf8835728df51c5e5560a038d8ecee064c9da3c67e3cfebbd222b92eb0901/lib/R/library/rmarkdown/rmd/h/default.html --highlight-style pygments --variable 'theme:bootstrap' --include-in-header /isg/treegenes/treegenes_store/Galaxy/Galaxy/database/tmp/Rtmpdqv7oh/rmarkdown-str35842aa6d2a1.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' Output created: rmarkdown_report.html