bioconductor / biocstyle Goto Github PK

View Code? Open in Web Editor NEW

12.0 18.0 19.0 610 KB

Issues and pull requests for BiocStyle should go here.

R 47.19% CSS 5.65% JavaScript 2.22% HTML 0.52% TeX 44.41%

core-package bioconductor-package

biocstyle's People

Contributors

Stargazers

Watchers

Forkers

c5sire michalsharabi alenzhao fpcmotif j-lawson mtmorgan leandroroser ltla kjohnsen drgrimshaw sunyoungshin kevinrue grimbough atusy smartgamer villafup neurogenomics

biocstyle's Issues

Documentation for, export status of html_fragment

What's the official status of html_fragment in the test workflow? Should I switch simpleSingleCell to use it, or is there a reason why it is not exported?

Missing package version in Rmd PDF vignettes

PDF vignettes produced with R Markdown format function BiocStyle::pdf_document are missing the package version field on the title page.

---
title: Title
author: Author
output:
  BiocStyle::pdf_document:
    toc: false
package: BiocStyle
---

Document with missing package version field.

LaTeX errors (Dimension too large) in Bioconductor package cosmiq possibly caused by recent changes to BiocStyle::latex()

Hi Andrzej,

R CMD build cosmiq started to fail on Linux and Mac at some point between Jun 27 (date of last commit to the package) and today:

https://bioconductor.org/checkResults/3.6/bioc-LATEST/cosmiq/malbec1-buildsrc.html
https://bioconductor.org/checkResults/3.6/bioc-LATEST/cosmiq/veracruz1-buildsrc.html

This seems to be caused by the recent changes to BiocStyle::latex(). If I install the release version of BiocStyle then R CMD build cosmiq completes successfully (tested on Linux only).

It is not clear to me if the problem could somehow be addressed by making some adjustments to BiocStyle::latex() or if the cosmiq maintainers need to do something on their side to make the poster.Rnw vignette compatible with the current BiocStyle::latex().

Any advice would be appreciated.

Thanks,
H.

CSS for code chunks not applied

Hi Andrzej, @aoles
It seems like the CSS in bioconductor2.css isn't being applied across classes. Particularly, function calls are not highlighted in the resulting document.

See the following link for an example Rmd file: https://gist.github.com/LiNk-NY/85f655731ae141b792079a6cf3b147b5

> sessionInfo()
R version 3.4.0 Patched (2017-05-04 r72654)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.0  backports_1.0.5 BiocStyle_2.5.0 magrittr_1.5    rsconnect_0.7   rprojroot_1.2   htmltools_0.3.6 tools_3.4.0    
 [9] yaml_2.1.14     Rcpp_0.12.10    stringi_1.1.5   rmarkdown_1.5   knitr_1.15.1    stringr_1.2.0   digest_0.6.12   evaluate_0.10 

> BiocInstaller::biocVersion()
[1] ‘3.6’

enc2utf8(text) error when using BiocStyle::html_document2

Hi,

The latest build reports for regionReport and recount in Bioconductor show errors like this:

Quitting from lines 88-109 (bumphunterExample.Rmd) 
Error: processing vignette 'bumphunterExample.Rmd' failed with diagnostics:
argumemt is not a character vector
Execution halted

Quitting from lines 354-375 (recount-quickstart.Rmd) 
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
argumemt is not a character vector
Execution halted

My initial google search lead me to rmarkdown rstudio/rmarkdown#717 but I've verified that this seems to be a BiocStyle issue (although the latest build report for 2.3.16 is ok at Bioconductor). In the other thread you'll see a report using BiocStyle 2.3.16 and in the logs here I'm using the latest (2.3.19, installed from Github). I have verified that this is not a problem when using the output format rmarkdown::html_document() or BiocStyle::html_document(). Beyond that, I don't have much of a clue of what exactly is the step that's going wrong. Hopefully you'll be able to trace it.

The code is from the example of regionReport::DESeq2Report() where I just change the ouptut_format argument. The default uses BiocStyle::html_document2().

Best,
Leo

rmarkdown::html_document case

Clean code

## Load example data from the pasilla package
library('regionReport')
library('pasilla')
library('DESeq')
library('DESeq2')

## Create DESeqDataSet object from the pasilla package
data('pasillaGenes')
countData <- counts(pasillaGenes)
colData <- pData(pasillaGenes)[, c('condition', 'type')]
dds <- DESeqDataSetFromMatrix(countData = countData,
   colData = colData,
   design = ~ condition)
dds <- DESeq(dds)

## The output will be saved in the 'DESeq2Report-example' directory
dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)

## Generate the HTML report
report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
    outdir = 'DESeq2Report-example', output_format = 'html_document')

## Info
options(width = 120)
devtools::session_info()

Evaluated code

> ## Load example data from the pasilla package
> library('regionReport')

This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.

> library('pasilla')
> library('DESeq')
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

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")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating
    to 'DESeq2'.
> library('DESeq2')
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment

Attaching package: ‘DESeq2’

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

    estimateSizeFactorsForMatrix, getVarianceStabilizedData, varianceStabilizingTransformation

> 
> ## Create DESeqDataSet object from the pasilla package
> data('pasillaGenes')
> countData <- counts(pasillaGenes)
> colData <- pData(pasillaGenes)[, c('condition', 'type')]
> dds <- DESeqDataSetFromMatrix(countData = countData,
+    colData = colData,
+    design = ~ condition)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> ## The output will be saved in the 'DESeq2Report-example' directory
> dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)
> 
> ## Generate the HTML report
> report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
+     outdir = 'DESeq2Report-example', output_format = 'html_document')
Writing 9 Bibtex entries ... OK
Results written to file 'DESeq2Report-example/DESeq2Exploration.bib'


processing file: DESeq2Exploration.Rmd
  |.                                                                |   2%
  |...                                                              |   4%
  |....                                                             |   6%
  |......                                                           |   9%
label: setup (with options) 
List of 1
 $ bootstrap.show.message: logi FALSE

  |.......                                                          |  11%
  |........                                                         |  13%
label: PCA
  |..........                                                       |  15%
  |...........                                                      |  17%
label: sampleDist
  |............                                                     |  19%
  |..............                                                   |  21%
  |...............                                                  |  23%
  |.................                                                |  26%
label: MAplotalphaHalf
  |..................                                               |  28%
  |...................                                              |  30%
label: MAplotalpha-nBest
  |.....................                                            |  32%
  |......................                                           |  34%
label: pvalueHistogram
  |........................                                         |  36%
  |.........................                                        |  38%
  |..........................                                       |  40%
  |............................                                     |  43%
  |.............................                                    |  45%
  |..............................                                   |  47%
label: padjHistogram
  |................................                                 |  49%
  |.................................                                |  51%
  |...................................                              |  53%
  |....................................                             |  55%
  |.....................................                            |  57%
  |.......................................                          |  60%
label: topFeatures (with options) 
List of 1
 $ results: chr "asis"

  |........................................                         |  62%
  |.........................................                        |  64%
label: plotCounts
  |...........................................                      |  66%
  |............................................                     |  68%
  |..............................................                   |  70%
  |...............................................                  |  72%
  |................................................                 |  74%
  |..................................................               |  77%
  |...................................................              |  79%
  |.....................................................            |  81%
  |......................................................           |  83%
  |.......................................................          |  85%
  |.........................................................        |  87%
  |..........................................................       |  89%
  |...........................................................      |  91%
  |.............................................................    |  94%
  |..............................................................   |  96%
   inline R code fragments

  |................................................................ |  98%
  |.................................................................| 100%
  ordinary text without R code


output file: DESeq2Exploration.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS DESeq2Exploration.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output DESeq2Exploration.html --smart --email-obfuscation none --self-contained --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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:spacelab' --include-in-header /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//RtmpTPN0zr/rmarkdown-stre36a3486e390.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --variable code_folding=hide --variable code_menu=1 

Output created: DESeq2Exploration.html
Warning message:
In c.bibentry(knitcitations = citation("knitcitations"), regionReport = citation("regionReport")[1],  :
  method is only applicable to ‘bibentry’ objects
> 
> ## Info
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
 setting  value                                             
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0                              
 ui       AQUA                                              
 language (EN)                                              
 collate  en_US.UTF-8                                       
 tz       America/New_York                                  
 date     2016-12-02                                        

Packages ---------------------------------------------------------------------------------------------------------------
 package              * version  date       source                                   
 acepack                1.4.1    2016-10-29 CRAN (R 3.4.0)                           
 annotate               1.53.0   2016-10-23 Bioconductor                             
 AnnotationDbi          1.37.0   2016-10-26 Bioconductor                             
 assertthat             0.1      2013-12-06 CRAN (R 3.4.0)                           
 backports              1.0.4    2016-10-24 CRAN (R 3.4.0)                           
 bibtex                 0.4.0    2014-12-31 CRAN (R 3.4.0)                           
 Biobase              * 2.35.0   2016-10-23 Bioconductor                             
 BiocGenerics         * 0.21.1   2016-12-01 Bioconductor                             
 BiocParallel           1.9.2    2016-11-18 Bioconductor                             
 BiocStyle              2.3.19   2016-12-02 Github (Bioconductor/BiocStyle@8688158)  
 biomaRt                2.31.3   2016-12-01 Bioconductor                             
 Biostrings             2.43.1   2016-11-17 Bioconductor                             
 bitops                 1.0-6    2013-08-17 CRAN (R 3.4.0)                           
 BSgenome               1.43.1   2016-11-11 Bioconductor                             
 bumphunter             1.15.0   2016-10-23 Bioconductor                             
 checkmate              1.8.2    2016-11-02 CRAN (R 3.4.0)                           
 cluster                2.0.5    2016-10-08 CRAN (R 3.4.0)                           
 codetools              0.2-15   2016-10-05 CRAN (R 3.4.0)                           
 colorspace             1.3-1    2016-11-18 CRAN (R 3.4.0)                           
 data.table             1.9.8    2016-11-25 CRAN (R 3.4.0)                           
 DBI                    0.5-1    2016-09-10 CRAN (R 3.4.0)                           
 DEFormats              1.3.0    2016-10-23 Bioconductor                             
 derfinder              1.9.5    2016-11-30 Bioconductor                             
 derfinderHelper        1.9.3    2016-11-29 Bioconductor                             
 DESeq                * 1.27.0   2016-10-23 Bioconductor                             
 DESeq2               * 1.15.17  2016-11-29 Bioconductor                             
 devtools             * 1.12.0   2016-06-24 CRAN (R 3.4.0)                           
 digest                 0.6.10   2016-08-02 CRAN (R 3.4.0)                           
 doRNG                  1.6      2014-03-07 CRAN (R 3.4.0)                           
 DT                   * 0.2      2016-08-09 CRAN (R 3.4.0)                           
 edgeR                  3.17.4   2016-11-29 Bioconductor                             
 evaluate               0.10     2016-10-11 CRAN (R 3.4.0)                           
 foreach                1.4.3    2015-10-13 CRAN (R 3.4.0)                           
 foreign                0.8-67   2016-09-13 CRAN (R 3.4.0)                           
 Formula                1.2-1    2015-04-07 CRAN (R 3.4.0)                           
 genefilter             1.57.0   2016-10-23 Bioconductor                             
 geneplotter            1.53.0   2016-10-23 Bioconductor                             
 GenomeInfoDb         * 1.11.6   2016-11-17 Bioconductor                             
 GenomicAlignments      1.11.4   2016-12-01 Bioconductor                             
 GenomicFeatures        1.27.4   2016-12-01 Bioconductor                             
 GenomicFiles           1.11.3   2016-11-29 Bioconductor                             
 GenomicRanges        * 1.27.13  2016-12-01 Bioconductor                             
 ggplot2              * 2.2.0    2016-11-11 CRAN (R 3.4.0)                           
 gridExtra              2.2.1    2016-02-29 CRAN (R 3.4.0)                           
 gtable                 0.2.0    2016-02-26 CRAN (R 3.4.0)                           
 highr                  0.6      2016-05-09 CRAN (R 3.4.0)                           
 Hmisc                  4.0-0    2016-11-01 CRAN (R 3.4.0)                           
 htmlTable              1.7      2016-10-19 CRAN (R 3.4.0)                           
 htmltools              0.3.5    2016-03-21 CRAN (R 3.4.0)                           
 htmlwidgets            0.8      2016-11-09 CRAN (R 3.4.0)                           
 httr                   1.2.1    2016-07-03 CRAN (R 3.4.0)                           
 IRanges              * 2.9.13   2016-12-01 Bioconductor                             
 iterators              1.0.8    2015-10-13 CRAN (R 3.4.0)                           
 jsonlite               1.1      2016-09-14 CRAN (R 3.4.0)                           
 knitcitations          1.0.7    2015-10-28 CRAN (R 3.4.0)                           
 knitr                * 1.15.1   2016-11-22 CRAN (R 3.4.0)                           
 knitrBootstrap         1.0.0    2016-11-15 Github (jimhester/knitrBootstrap@cdaa4a9)
 labeling               0.3      2014-08-23 CRAN (R 3.4.0)                           
 lattice              * 0.20-34  2016-09-06 CRAN (R 3.4.0)                           
 latticeExtra           0.6-28   2016-02-09 CRAN (R 3.4.0)                           
 lazyeval               0.2.0    2016-06-12 CRAN (R 3.4.0)                           
 limma                  3.31.6   2016-11-29 Bioconductor                             
 locfit               * 1.5-9.1  2013-04-20 CRAN (R 3.4.0)                           
 lubridate              1.6.0    2016-09-13 CRAN (R 3.4.0)                           
 magrittr               1.5      2014-11-22 CRAN (R 3.4.0)                           
 markdown               0.7.7    2015-04-22 CRAN (R 3.4.0)                           
 Matrix                 1.2-7.1  2016-09-01 CRAN (R 3.4.0)                           
 matrixStats            0.51.0   2016-10-09 CRAN (R 3.4.0)                           
 memoise                1.0.0    2016-01-29 CRAN (R 3.4.0)                           
 munsell                0.4.3    2016-02-13 CRAN (R 3.4.0)                           
 nnet                   7.3-12   2016-02-02 CRAN (R 3.4.0)                           
 pasilla              * 1.3.0    2016-11-15 Bioconductor                             
 pheatmap             * 1.0.8    2015-12-11 CRAN (R 3.4.0)                           
 pkgmaker               0.22     2014-05-14 CRAN (R 3.4.0)                           
 plyr                   1.8.4    2016-06-08 CRAN (R 3.4.0)                           
 qvalue                 2.7.0    2016-10-23 Bioconductor                             
 R6                     2.2.0    2016-10-05 CRAN (R 3.4.0)                           
 RColorBrewer         * 1.1-2    2014-12-07 CRAN (R 3.4.0)                           
 Rcpp                   0.12.8   2016-11-17 CRAN (R 3.4.0)                           
 RCurl                  1.95-4.8 2016-03-01 CRAN (R 3.4.0)                           
 RefManageR             0.13.1   2016-11-13 CRAN (R 3.4.0)                           
 regionReport         * 1.9.3    2016-11-29 Bioconductor                             
 registry               0.3      2015-07-08 CRAN (R 3.4.0)                           
 reshape2               1.4.2    2016-10-22 CRAN (R 3.4.0)                           
 RJSONIO                1.3-0    2014-07-28 CRAN (R 3.4.0)                           
 rmarkdown              1.2      2016-11-21 CRAN (R 3.4.0)                           
 rngtools               1.2.4    2014-03-06 CRAN (R 3.4.0)                           
 rpart                  4.1-10   2015-06-29 CRAN (R 3.4.0)                           
 rprojroot              1.1      2016-10-29 CRAN (R 3.4.0)                           
 Rsamtools              1.27.5   2016-12-01 Bioconductor                             
 RSQLite                1.1      2016-11-27 CRAN (R 3.4.0)                           
 rstudioapi             0.6      2016-06-27 CRAN (R 3.4.0)                           
 rtracklayer            1.35.1   2016-10-29 Bioconductor                             
 S4Vectors            * 0.13.5   2016-12-01 Bioconductor                             
 scales                 0.4.1    2016-11-09 CRAN (R 3.4.0)                           
 stringi                1.1.2    2016-10-01 CRAN (R 3.4.0)                           
 stringr                1.1.0    2016-08-19 CRAN (R 3.4.0)                           
 SummarizedExperiment * 1.5.3    2016-11-11 Bioconductor                             
 survival               2.40-1   2016-10-30 CRAN (R 3.4.0)                           
 tibble                 1.2      2016-08-26 CRAN (R 3.4.0)                           
 VariantAnnotation      1.21.10  2016-12-01 Bioconductor                             
 withr                  1.0.2    2016-06-20 CRAN (R 3.4.0)                           
 XML                    3.98-1.5 2016-11-10 CRAN (R 3.4.0)                           
 xtable                 1.8-2    2016-02-05 CRAN (R 3.4.0)                           
 XVector                0.15.0   2016-10-23 Bioconductor                             
 yaml                   2.1.14   2016-11-12 CRAN (R 3.4.0)                           
 zlibbioc               1.21.0   2016-10-23 Bioconductor                             
>

BiocStyle::html_document2 case

Clean code

## Load example data from the pasilla package
library('regionReport')
library('pasilla')
library('DESeq')
library('DESeq2')

## Create DESeqDataSet object from the pasilla package
data('pasillaGenes')
countData <- counts(pasillaGenes)
colData <- pData(pasillaGenes)[, c('condition', 'type')]
dds <- DESeqDataSetFromMatrix(countData = countData,
   colData = colData,
   design = ~ condition)
dds <- DESeq(dds)

## The output will be saved in the 'DESeq2Report-example' directory
dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)

## Generate the HTML report
report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
    outdir = 'DESeq2Report-example')

## Error info
traceback()
options(width = 120)
devtools::session_info()

Evaluated code

> ## Load example data from the pasilla package
> library('regionReport')

This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.

> library('pasilla')
> library('DESeq')
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

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")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating
    to 'DESeq2'.
> library('DESeq2')
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment

Attaching package: ‘DESeq2’

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

    estimateSizeFactorsForMatrix, getVarianceStabilizedData, varianceStabilizingTransformation

> 
> ## Create DESeqDataSet object from the pasilla package
> data('pasillaGenes')
> countData <- counts(pasillaGenes)
> colData <- pData(pasillaGenes)[, c('condition', 'type')]
> dds <- DESeqDataSetFromMatrix(countData = countData,
+    colData = colData,
+    design = ~ condition)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> ## The output will be saved in the 'DESeq2Report-example' directory
> dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)
> 
> ## Generate the HTML report
> report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
+     outdir = 'DESeq2Report-example')
Writing 9 Bibtex entries ... OK
Results written to file 'DESeq2Report-example/DESeq2Exploration.bib'


processing file: DESeq2Exploration.Rmd
  |.                                                                  |   2%
  |...                                                                |   4%
  |....                                                               |   6%
  |......                                                             |   9%
label: setup (with options) 
List of 1
 $ bootstrap.show.message: logi FALSE

  |.......                                                            |  11%
  |.........                                                          |  13%
label: PCA
  |..........                                                         |  15%
  |...........                                                        |  17%
label: sampleDist
  |.............                                                      |  19%
  |..............                                                     |  21%
label: MAplotalpha
  |................                                                   |  23%
  |.................                                                  |  26%
label: MAplotalphaHalf
  |...................                                                |  28%
  |....................                                               |  30%
label: MAplotalpha-nBest
  |.....................                                              |  32%
  |.......................                                            |  34%
label: pvalueHistogram
  |........................                                           |  36%
  |..........................                                         |  38%
  |...........................                                        |  40%
  |.............................                                      |  43%
  |..............................                                     |  45%
  |...............................                                    |  47%
label: padjHistogram
  |.................................                                  |  49%
  |..................................                                 |  51%
  |....................................                               |  53%
  |.....................................                              |  55%
  |......................................                             |  57%
  |........................................                           |  60%
label: topFeatures (with options) 
List of 1
 $ results: chr "asis"

  |.........................................                          |  62%
  |...........................................                        |  64%
label: plotCounts
  |............................................                       |  66%
  |..............................................                     |  68%
  |...............................................                    |  70%
  |................................................                   |  72%
  |..................................................                 |  74%
  |...................................................                |  77%
  |.....................................................              |  79%
  |......................................................             |  81%
  |........................................................           |  83%
  |.........................................................          |  85%
  |..........................................................         |  87%
  |............................................................       |  89%
  |.............................................................      |  91%
  |...............................................................    |  94%
label: reproducibility3 (with options) 
List of 1
 $ echo: logi FALSE

  |................................................................   |  96%
  |.................................................................. |  98%
label: bibliography (with options) 
List of 3
 $ results: chr "asis"
 $ echo   : logi FALSE
 $ warning: logi FALSE

  |...................................................................| 100%
  ordinary text without R code


output file: DESeq2Exploration.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS DESeq2Exploration.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output DESeq2Exploration.html --smart --email-obfuscation none --self-contained --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 /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//RtmpZN24wQ/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --css /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocStyle/resources/html/bioconductor2.css --variable 'theme:bootstrap' --include-in-header /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//RtmpZN24wQ/rmarkdown-stre3a35e596df1.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --variable code_folding=hide --variable code_menu=1 
Error in enc2utf8(text) : argumemt is not a character vector
In addition: Warning message:
In c.bibentry(knitcitations = citation("knitcitations"), regionReport = citation("regionReport")[1],  :
  method is only applicable to ‘bibentry’ objects
> 
> ## Error info
> traceback()
9: writeLines(enc2utf8(text), ..., useBytes = TRUE)
8: writeUTF8(x, output)
7: overlay(metadata, input_file, output_file, ...)
6: post(metadata, input, output, clean, verbose)
5: output_format$post_processor(yaml_front_matter, utf8_input, output_file, 
       clean, !quiet)
4: render(paste0(output, ".Rmd"), output_format, clean = .advanced_argument("clean", 
       TRUE, ...))
3: eval(expr, envir = parent.frame())
2: with_wd(outdir, {
       file.copy(template, to = paste0(output, ".Rmd"))
       output_format <- .advanced_argument("output_format", "BiocStyle::html_document2", 
           ...)
       outputIsHTML <- output_format %in% c("html_document", "knitrBootstrap::bootstrap_document", 
           "BiocStyle::html_document2")
       if (!outputIsHTML) {
           if (device == "png") 
               warning("You might want to switch the 'device' argument from 'png' to 'pdf' for better quality plots.")
       }
       knitrBootstrapFlag <- packageVersion("knitrBootstrap") < 
           "1.0.0"
       if (knitrBootstrapFlag & output_format == "knitrBootstrap::bootstrap_document") {
           tmp <- knit_bootstrap(paste0(output, ".Rmd"), chooser = c("boot", 
               "code"), show_code = TRUE)
           res <- file.path(tmpdir, outdir, paste0(output, ".html"))
           unlink(paste0(output, ".md"))
       }
       else {
           res <- render(paste0(output, ".Rmd"), output_format, 
               clean = .advanced_argument("clean", TRUE, ...))
       }
       if (templateNull) 
           file.remove(paste0(output, ".Rmd"))
       if (browse) 
           browseURL(res)
   })
1: DESeq2Report(dds, "DESeq2-example", c("condition", "type"), outdir = "DESeq2Report-example")
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
 setting  value                                             
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0                              
 ui       AQUA                                              
 language (EN)                                              
 collate  en_US.UTF-8                                       
 tz       America/New_York                                  
 date     2016-12-02                                        

Packages ---------------------------------------------------------------------------------------------------------------
 package              * version  date       source                                   
 acepack                1.4.1    2016-10-29 CRAN (R 3.4.0)                           
 annotate               1.53.0   2016-10-23 Bioconductor                             
 AnnotationDbi          1.37.0   2016-10-26 Bioconductor                             
 assertthat             0.1      2013-12-06 CRAN (R 3.4.0)                           
 backports              1.0.4    2016-10-24 CRAN (R 3.4.0)                           
 bibtex                 0.4.0    2014-12-31 CRAN (R 3.4.0)                           
 Biobase              * 2.35.0   2016-10-23 Bioconductor                             
 BiocGenerics         * 0.21.1   2016-12-01 Bioconductor                             
 BiocParallel           1.9.2    2016-11-18 Bioconductor                             
 BiocStyle            * 2.3.19   2016-12-02 Github (Bioconductor/BiocStyle@8688158)  
 biomaRt                2.31.3   2016-12-01 Bioconductor                             
 Biostrings             2.43.1   2016-11-17 Bioconductor                             
 bitops                 1.0-6    2013-08-17 CRAN (R 3.4.0)                           
 bookdown               0.3      2016-11-28 CRAN (R 3.4.0)                           
 BSgenome               1.43.1   2016-11-11 Bioconductor                             
 bumphunter             1.15.0   2016-10-23 Bioconductor                             
 checkmate              1.8.2    2016-11-02 CRAN (R 3.4.0)                           
 cluster                2.0.5    2016-10-08 CRAN (R 3.4.0)                           
 codetools              0.2-15   2016-10-05 CRAN (R 3.4.0)                           
 colorspace             1.3-1    2016-11-18 CRAN (R 3.4.0)                           
 data.table             1.9.8    2016-11-25 CRAN (R 3.4.0)                           
 DBI                    0.5-1    2016-09-10 CRAN (R 3.4.0)                           
 DEFormats              1.3.0    2016-10-23 Bioconductor                             
 derfinder              1.9.5    2016-11-30 Bioconductor                             
 derfinderHelper        1.9.3    2016-11-29 Bioconductor                             
 DESeq                * 1.27.0   2016-10-23 Bioconductor                             
 DESeq2               * 1.15.17  2016-11-29 Bioconductor                             
 devtools             * 1.12.0   2016-06-24 CRAN (R 3.4.0)                           
 digest                 0.6.10   2016-08-02 CRAN (R 3.4.0)                           
 doRNG                  1.6      2014-03-07 CRAN (R 3.4.0)                           
 DT                   * 0.2      2016-08-09 CRAN (R 3.4.0)                           
 edgeR                  3.17.4   2016-11-29 Bioconductor                             
 evaluate               0.10     2016-10-11 CRAN (R 3.4.0)                           
 foreach                1.4.3    2015-10-13 CRAN (R 3.4.0)                           
 foreign                0.8-67   2016-09-13 CRAN (R 3.4.0)                           
 Formula                1.2-1    2015-04-07 CRAN (R 3.4.0)                           
 genefilter             1.57.0   2016-10-23 Bioconductor                             
 geneplotter            1.53.0   2016-10-23 Bioconductor                             
 GenomeInfoDb         * 1.11.6   2016-11-17 Bioconductor                             
 GenomicAlignments      1.11.4   2016-12-01 Bioconductor                             
 GenomicFeatures        1.27.4   2016-12-01 Bioconductor                             
 GenomicFiles           1.11.3   2016-11-29 Bioconductor                             
 GenomicRanges        * 1.27.13  2016-12-01 Bioconductor                             
 ggplot2              * 2.2.0    2016-11-11 CRAN (R 3.4.0)                           
 gridExtra              2.2.1    2016-02-29 CRAN (R 3.4.0)                           
 gtable                 0.2.0    2016-02-26 CRAN (R 3.4.0)                           
 highr                  0.6      2016-05-09 CRAN (R 3.4.0)                           
 Hmisc                  4.0-0    2016-11-01 CRAN (R 3.4.0)                           
 htmlTable              1.7      2016-10-19 CRAN (R 3.4.0)                           
 htmltools              0.3.5    2016-03-21 CRAN (R 3.4.0)                           
 htmlwidgets            0.8      2016-11-09 CRAN (R 3.4.0)                           
 httr                   1.2.1    2016-07-03 CRAN (R 3.4.0)                           
 IRanges              * 2.9.13   2016-12-01 Bioconductor                             
 iterators              1.0.8    2015-10-13 CRAN (R 3.4.0)                           
 jsonlite               1.1      2016-09-14 CRAN (R 3.4.0)                           
 knitcitations          1.0.7    2015-10-28 CRAN (R 3.4.0)                           
 knitr                * 1.15.1   2016-11-22 CRAN (R 3.4.0)                           
 knitrBootstrap         1.0.0    2016-11-15 Github (jimhester/knitrBootstrap@cdaa4a9)
 labeling               0.3      2014-08-23 CRAN (R 3.4.0)                           
 lattice              * 0.20-34  2016-09-06 CRAN (R 3.4.0)                           
 latticeExtra           0.6-28   2016-02-09 CRAN (R 3.4.0)                           
 lazyeval               0.2.0    2016-06-12 CRAN (R 3.4.0)                           
 limma                  3.31.6   2016-11-29 Bioconductor                             
 locfit               * 1.5-9.1  2013-04-20 CRAN (R 3.4.0)                           
 lubridate              1.6.0    2016-09-13 CRAN (R 3.4.0)                           
 magrittr               1.5      2014-11-22 CRAN (R 3.4.0)                           
 markdown               0.7.7    2015-04-22 CRAN (R 3.4.0)                           
 Matrix                 1.2-7.1  2016-09-01 CRAN (R 3.4.0)                           
 matrixStats            0.51.0   2016-10-09 CRAN (R 3.4.0)                           
 memoise                1.0.0    2016-01-29 CRAN (R 3.4.0)                           
 munsell                0.4.3    2016-02-13 CRAN (R 3.4.0)                           
 nnet                   7.3-12   2016-02-02 CRAN (R 3.4.0)                           
 pasilla              * 1.3.0    2016-11-15 Bioconductor                             
 pheatmap             * 1.0.8    2015-12-11 CRAN (R 3.4.0)                           
 pkgmaker               0.22     2014-05-14 CRAN (R 3.4.0)                           
 plyr                   1.8.4    2016-06-08 CRAN (R 3.4.0)                           
 qvalue                 2.7.0    2016-10-23 Bioconductor                             
 R6                     2.2.0    2016-10-05 CRAN (R 3.4.0)                           
 RColorBrewer         * 1.1-2    2014-12-07 CRAN (R 3.4.0)                           
 Rcpp                   0.12.8   2016-11-17 CRAN (R 3.4.0)                           
 RCurl                  1.95-4.8 2016-03-01 CRAN (R 3.4.0)                           
 RefManageR             0.13.1   2016-11-13 CRAN (R 3.4.0)                           
 regionReport         * 1.9.3    2016-11-29 Bioconductor                             
 registry               0.3      2015-07-08 CRAN (R 3.4.0)                           
 reshape2               1.4.2    2016-10-22 CRAN (R 3.4.0)                           
 RJSONIO                1.3-0    2014-07-28 CRAN (R 3.4.0)                           
 rmarkdown              1.2      2016-11-21 CRAN (R 3.4.0)                           
 rngtools               1.2.4    2014-03-06 CRAN (R 3.4.0)                           
 rpart                  4.1-10   2015-06-29 CRAN (R 3.4.0)                           
 rprojroot              1.1      2016-10-29 CRAN (R 3.4.0)                           
 Rsamtools              1.27.5   2016-12-01 Bioconductor                             
 RSQLite                1.1      2016-11-27 CRAN (R 3.4.0)                           
 rstudioapi             0.6      2016-06-27 CRAN (R 3.4.0)                           
 rtracklayer            1.35.1   2016-10-29 Bioconductor                             
 S4Vectors            * 0.13.5   2016-12-01 Bioconductor                             
 scales                 0.4.1    2016-11-09 CRAN (R 3.4.0)                           
 stringi                1.1.2    2016-10-01 CRAN (R 3.4.0)                           
 stringr                1.1.0    2016-08-19 CRAN (R 3.4.0)                           
 SummarizedExperiment * 1.5.3    2016-11-11 Bioconductor                             
 survival               2.40-1   2016-10-30 CRAN (R 3.4.0)                           
 tibble                 1.2      2016-08-26 CRAN (R 3.4.0)                           
 VariantAnnotation      1.21.10  2016-12-01 Bioconductor                             
 withr                  1.0.2    2016-06-20 CRAN (R 3.4.0)                           
 XML                    3.98-1.5 2016-11-10 CRAN (R 3.4.0)                           
 xtable                 1.8-2    2016-02-05 CRAN (R 3.4.0)                           
 XVector                0.15.0   2016-10-23 Bioconductor                             
 yaml                   2.1.14   2016-11-12 CRAN (R 3.4.0)                           
 zlibbioc               1.21.0   2016-10-23 Bioconductor                             
>

BiocStyle::html_document case

Clean code

## Load example data from the pasilla package
library('regionReport')
library('pasilla')
library('DESeq')
library('DESeq2')

## Create DESeqDataSet object from the pasilla package
data('pasillaGenes')
countData <- counts(pasillaGenes)
colData <- pData(pasillaGenes)[, c('condition', 'type')]
dds <- DESeqDataSetFromMatrix(countData = countData,
   colData = colData,
   design = ~ condition)
dds <- DESeq(dds)

## The output will be saved in the 'DESeq2Report-example' directory
dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)

## Generate the HTML report
report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
    outdir = 'DESeq2Report-example', output_format = 'BiocStyle::html_document')

## Info
options(width = 120)
devtools::session_info()

Evaluated code

> ## Load example data from the pasilla package
> library('regionReport')

This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.

> library('pasilla')
> library('DESeq')
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

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")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating
    to 'DESeq2'.
> library('DESeq2')
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment

Attaching package: ‘DESeq2’

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

    estimateSizeFactorsForMatrix, getVarianceStabilizedData, varianceStabilizingTransformation

> 
> ## Create DESeqDataSet object from the pasilla package
> data('pasillaGenes')
> countData <- counts(pasillaGenes)
> colData <- pData(pasillaGenes)[, c('condition', 'type')]
> dds <- DESeqDataSetFromMatrix(countData = countData,
+    colData = colData,
+    design = ~ condition)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> ## The output will be saved in the 'DESeq2Report-example' directory
> dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)
> 
> ## Generate the HTML report
> report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
+     outdir = 'DESeq2Report-example', output_format = 'BiocStyle::html_document')
Writing 9 Bibtex entries ... OK
Results written to file 'DESeq2Report-example/DESeq2Exploration.bib'


processing file: DESeq2Exploration.Rmd
  |.                                                                |   2%
  |...                                                              |   4%
label: docSetup (with options) 
List of 3
 $ bootstrap.show.code   : logi FALSE
 $ dev                   : symbol device
 $ bootstrap.show.message: logi FALSE

  |....                                                             |   6%
  |......                                                           |   9%
label: setup (with options) 
List of 1
 $ bootstrap.show.message: logi FALSE

  |.......                                                          |  11%
  |........                                                         |  13%
label: PCA
  |..........                                                       |  15%
  |...........                                                      |  17%
label: sampleDist
  |............                                                     |  19%
  |..............                                                   |  21%
label: MAplotalpha
  |...............                                                  |  23%
  |.................                                                |  26%
label: MAplotalphaHalf
  |..................                                               |  28%
  |...................                                              |  30%
  |.....................                                            |  32%
  |......................                                           |  34%
label: pvalueHistogram
  |........................                                         |  36%
  |.........................                                        |  38%
  |..........................                                       |  40%
  |............................                                     |  43%
  |.............................                                    |  45%
  |..............................                                   |  47%
label: padjHistogram
  |................................                                 |  49%
  |.................................                                |  51%
  |...................................                              |  53%
  |....................................                             |  55%
  |.....................................                            |  57%
  |.......................................                          |  60%
  |........................................                         |  62%
  |.........................................                        |  64%
label: plotCounts
  |...........................................                      |  66%
  |............................................                     |  68%
  |..............................................                   |  70%
  |...............................................                  |  72%
  |................................................                 |  74%
  |..................................................               |  77%
  |...................................................              |  79%
  |.....................................................            |  81%
  |......................................................           |  83%
  |.......................................................          |  85%
  |.........................................................        |  87%
  |..........................................................       |  89%
  |...........................................................      |  91%
  |.............................................................    |  94%
label: reproducibility3 (with options) 
List of 1
 $ echo: logi FALSE

  |..............................................................   |  96%
  |................................................................ |  98%
label: bibliography (with options) 
List of 3
 $ results: chr "asis"
 $ echo   : logi FALSE
 $ warning: logi FALSE

  |.................................................................| 100%
  ordinary text without R code


output file: DESeq2Exploration.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS DESeq2Exploration.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output DESeq2Exploration.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocStyle/resources/html/template.html --no-highlight --variable highlightjs=1 --number-sections --css /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BiocStyle/resources/html/bioconductor.css --include-in-header /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//RtmpfFQL9q/rmarkdown-stre47671b13d3c.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

Output created: DESeq2Exploration.html
Warning messages:
1: In c.bibentry(knitcitations = citation("knitcitations"), regionReport = citation("regionReport")[1],  :
  method is only applicable to ‘bibentry’ objects
2: In eval(expr, envir = parent.frame()) :
  You might want to switch the 'device' argument from 'png' to 'pdf' for better quality plots.
> ## Info
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
 setting  value                                             
 version  R Under development (unstable) (2016-10-26 r71594)
 system   x86_64, darwin13.4.0                              
 ui       AQUA                                              
 language (EN)                                              
 collate  en_US.UTF-8                                       
 tz       America/New_York                                  
 date     2016-12-02                                        

Packages ---------------------------------------------------------------------------------------------------------------
 package              * version  date       source                                   
 acepack                1.4.1    2016-10-29 CRAN (R 3.4.0)                           
 annotate               1.53.0   2016-10-23 Bioconductor                             
 AnnotationDbi          1.37.0   2016-10-26 Bioconductor                             
 assertthat             0.1      2013-12-06 CRAN (R 3.4.0)                           
 backports              1.0.4    2016-10-24 CRAN (R 3.4.0)                           
 bibtex                 0.4.0    2014-12-31 CRAN (R 3.4.0)                           
 Biobase              * 2.35.0   2016-10-23 Bioconductor                             
 BiocGenerics         * 0.21.1   2016-12-01 Bioconductor                             
 BiocParallel           1.9.2    2016-11-18 Bioconductor                             
 BiocStyle            * 2.3.19   2016-12-02 Github (Bioconductor/BiocStyle@8688158)  
 biomaRt                2.31.3   2016-12-01 Bioconductor                             
 Biostrings             2.43.1   2016-11-17 Bioconductor                             
 bitops                 1.0-6    2013-08-17 CRAN (R 3.4.0)                           
 BSgenome               1.43.1   2016-11-11 Bioconductor                             
 bumphunter             1.15.0   2016-10-23 Bioconductor                             
 checkmate              1.8.2    2016-11-02 CRAN (R 3.4.0)                           
 cluster                2.0.5    2016-10-08 CRAN (R 3.4.0)                           
 codetools              0.2-15   2016-10-05 CRAN (R 3.4.0)                           
 colorspace             1.3-1    2016-11-18 CRAN (R 3.4.0)                           
 data.table             1.9.8    2016-11-25 CRAN (R 3.4.0)                           
 DBI                    0.5-1    2016-09-10 CRAN (R 3.4.0)                           
 DEFormats              1.3.0    2016-10-23 Bioconductor                             
 derfinder              1.9.5    2016-11-30 Bioconductor                             
 derfinderHelper        1.9.3    2016-11-29 Bioconductor                             
 DESeq                * 1.27.0   2016-10-23 Bioconductor                             
 DESeq2               * 1.15.17  2016-11-29 Bioconductor                             
 devtools             * 1.12.0   2016-06-24 CRAN (R 3.4.0)                           
 digest                 0.6.10   2016-08-02 CRAN (R 3.4.0)                           
 doRNG                  1.6      2014-03-07 CRAN (R 3.4.0)                           
 DT                   * 0.2      2016-08-09 CRAN (R 3.4.0)                           
 edgeR                  3.17.4   2016-11-29 Bioconductor                             
 evaluate               0.10     2016-10-11 CRAN (R 3.4.0)                           
 foreach                1.4.3    2015-10-13 CRAN (R 3.4.0)                           
 foreign                0.8-67   2016-09-13 CRAN (R 3.4.0)                           
 Formula                1.2-1    2015-04-07 CRAN (R 3.4.0)                           
 genefilter             1.57.0   2016-10-23 Bioconductor                             
 geneplotter            1.53.0   2016-10-23 Bioconductor                             
 GenomeInfoDb         * 1.11.6   2016-11-17 Bioconductor                             
 GenomicAlignments      1.11.4   2016-12-01 Bioconductor                             
 GenomicFeatures        1.27.4   2016-12-01 Bioconductor                             
 GenomicFiles           1.11.3   2016-11-29 Bioconductor                             
 GenomicRanges        * 1.27.13  2016-12-01 Bioconductor                             
 ggplot2              * 2.2.0    2016-11-11 CRAN (R 3.4.0)                           
 gridExtra              2.2.1    2016-02-29 CRAN (R 3.4.0)                           
 gtable                 0.2.0    2016-02-26 CRAN (R 3.4.0)                           
 highr                  0.6      2016-05-09 CRAN (R 3.4.0)                           
 Hmisc                  4.0-0    2016-11-01 CRAN (R 3.4.0)                           
 htmlTable              1.7      2016-10-19 CRAN (R 3.4.0)                           
 htmltools              0.3.5    2016-03-21 CRAN (R 3.4.0)                           
 htmlwidgets            0.8      2016-11-09 CRAN (R 3.4.0)                           
 httr                   1.2.1    2016-07-03 CRAN (R 3.4.0)                           
 IRanges              * 2.9.13   2016-12-01 Bioconductor                             
 iterators              1.0.8    2015-10-13 CRAN (R 3.4.0)                           
 knitcitations          1.0.7    2015-10-28 CRAN (R 3.4.0)                           
 knitr                * 1.15.1   2016-11-22 CRAN (R 3.4.0)                           
 knitrBootstrap         1.0.0    2016-11-15 Github (jimhester/knitrBootstrap@cdaa4a9)
 labeling               0.3      2014-08-23 CRAN (R 3.4.0)                           
 lattice              * 0.20-34  2016-09-06 CRAN (R 3.4.0)                           
 latticeExtra           0.6-28   2016-02-09 CRAN (R 3.4.0)                           
 lazyeval               0.2.0    2016-06-12 CRAN (R 3.4.0)                           
 limma                  3.31.6   2016-11-29 Bioconductor                             
 locfit               * 1.5-9.1  2013-04-20 CRAN (R 3.4.0)                           
 lubridate              1.6.0    2016-09-13 CRAN (R 3.4.0)                           
 magrittr               1.5      2014-11-22 CRAN (R 3.4.0)                           
 markdown               0.7.7    2015-04-22 CRAN (R 3.4.0)                           
 Matrix                 1.2-7.1  2016-09-01 CRAN (R 3.4.0)                           
 matrixStats            0.51.0   2016-10-09 CRAN (R 3.4.0)                           
 memoise                1.0.0    2016-01-29 CRAN (R 3.4.0)                           
 munsell                0.4.3    2016-02-13 CRAN (R 3.4.0)                           
 nnet                   7.3-12   2016-02-02 CRAN (R 3.4.0)                           
 pasilla              * 1.3.0    2016-11-15 Bioconductor                             
 pheatmap             * 1.0.8    2015-12-11 CRAN (R 3.4.0)                           
 pkgmaker               0.22     2014-05-14 CRAN (R 3.4.0)                           
 plyr                   1.8.4    2016-06-08 CRAN (R 3.4.0)                           
 qvalue                 2.7.0    2016-10-23 Bioconductor                             
 R6                     2.2.0    2016-10-05 CRAN (R 3.4.0)                           
 RColorBrewer         * 1.1-2    2014-12-07 CRAN (R 3.4.0)                           
 Rcpp                   0.12.8   2016-11-17 CRAN (R 3.4.0)                           
 RCurl                  1.95-4.8 2016-03-01 CRAN (R 3.4.0)                           
 RefManageR             0.13.1   2016-11-13 CRAN (R 3.4.0)                           
 regionReport         * 1.9.3    2016-11-29 Bioconductor                             
 registry               0.3      2015-07-08 CRAN (R 3.4.0)                           
 reshape2               1.4.2    2016-10-22 CRAN (R 3.4.0)                           
 RJSONIO                1.3-0    2014-07-28 CRAN (R 3.4.0)                           
 rmarkdown              1.2      2016-11-21 CRAN (R 3.4.0)                           
 rngtools               1.2.4    2014-03-06 CRAN (R 3.4.0)                           
 rpart                  4.1-10   2015-06-29 CRAN (R 3.4.0)                           
 rprojroot              1.1      2016-10-29 CRAN (R 3.4.0)                           
 Rsamtools              1.27.5   2016-12-01 Bioconductor                             
 RSQLite                1.1      2016-11-27 CRAN (R 3.4.0)                           
 rstudioapi             0.6      2016-06-27 CRAN (R 3.4.0)                           
 rtracklayer            1.35.1   2016-10-29 Bioconductor                             
 S4Vectors            * 0.13.5   2016-12-01 Bioconductor                             
 scales                 0.4.1    2016-11-09 CRAN (R 3.4.0)                           
 stringi                1.1.2    2016-10-01 CRAN (R 3.4.0)                           
 stringr                1.1.0    2016-08-19 CRAN (R 3.4.0)                           
 SummarizedExperiment * 1.5.3    2016-11-11 Bioconductor                             
 survival               2.40-1   2016-10-30 CRAN (R 3.4.0)                           
 tibble                 1.2      2016-08-26 CRAN (R 3.4.0)                           
 VariantAnnotation      1.21.10  2016-12-01 Bioconductor                             
 withr                  1.0.2    2016-06-20 CRAN (R 3.4.0)                           
 XML                    3.98-1.5 2016-11-10 CRAN (R 3.4.0)                           
 xtable                 1.8-2    2016-02-05 CRAN (R 3.4.0)                           
 XVector                0.15.0   2016-10-23 Bioconductor                             
 yaml                   2.1.14   2016-11-12 CRAN (R 3.4.0)                           
 zlibbioc               1.21.0   2016-10-23 Bioconductor                             
>

How does \@ref() work?

Could anyone explain me how the cross-references described here works/is implemented.

The reason I am asking is that it works in vignettes compiled with rmarkdown::render given a properly formatted header, but it doesn't when creating vignettes as part of a pkgdown site that compiles and includes vignettes:

LaTeX undefined control sequence

When knitting an RMarkdown with BiocStyle (with the help of MikTex on Windows), I get an undefined control sequenc error if there is an image. For example:

---
title: "Test"
output: 
  BiocStyle::pdf_document
---

This chunk causes errors

```{r cars}
summary(cars)
plot(pressure)
```

I get this error:

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS test2.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandocec44b153a57.tex --table-of-contents --toc-depth 2 --template "C:\Users\erikor\AppData\Local\Temp\RtmpgvaLn4/BiocStyle/template.tex" --number-sections --highlight-style tango --latex-engine pdflatex --include-in-header "C:\Users\erikor\AppData\Local\Temp\RtmpgvaLn4\ec4710a6e74.tex" --variable graphics=yes --variable tables=yes --standalone 
output file: test2.knit.md

! Undefined control sequence.
\grffile@filename ->C:\Users 
                             \erikor \AppData \Local \Temp \RtmpGI 6qxP\prev...
l.164 ...1942.dir\test2_files/figure-latex/cars-1}
                                                   \end{adjustwidth}

I am working on a Bioconductor package, and thus I am using the development version of Bioconductor and the development version of R:

R Under development (unstable) (2018-03-06 r74362)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Here is my MikTex version:

MiKTeX-pdfTeX 2.9.6607 (1.40.19) (MiKTeX 2.9.6630 64-bit)

Is this a problem with the BiocStyle, or am I Doing It Wrong™?

Code formatting overflows in magin note

As shown below, the \Rcode{times = 10} inline code formatting somehow overflows in the side margin.

If I remove the formatting (remove \Rcode), the margin note displays as expected

BiocStyle and png image not usable in the same document

---
title: "test"
author: "xyz"
date: "9 Februar 2018"
output: BiocStyle::pdf_document
vignette: >
  %\VignetteIndexEntry{test}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
![](image.png)

does not work. On Windows 10 64 bit 16299.214 / RStudio 1.1.423 / R 3.4.3 knitting the document reports ! Package pdftex.def Error: File image.png not found: using draft setting. Changing output: pdf_document solves the issue and a pdf is successfully created.

The original file with BiocStyle:: works under Ubuntu 17.10 / RStudio 1.1.423 / R-devel. Was this solved with the #32 issue or is it caused by something else?

I am sorry, but I don't have the expertise to install R-devel under Windows, so I cannot test that. Can you give me hint, whether this problem is fixed in R-devel?

LaTeX undefined control sequence due to pipe operator

It appears that when BiocStyle::pdf_document2 is called by knitr::rmarkdown to render a package vignette, LaTeX fails to compile when a %>% pipe operator from the magrittr package is present in the RMarkdown source code. I've checked other PDF rendering options, such as bookdown and the issue seems to be specific to BiocStyle.

Here's the error from the RMarkdown console:

! Undefined control sequence.
<argument> ...ption"}\NormalTok {)) }\OperatorTok 
                                                  {%>%}\StringTok { }\Normal...
l.329 ...peratorTok{%>%}\StringTok{ }\NormalTok{t}

parnotes rev. 2 / custom definition of \parnotemarkfmt

Dear Maintainer,

I believe a recent release of parnotes (rev. 2, https://www.ctan.org/pkg/parnotes) is causing problem with Bioconductor LATEX Style 2.0.

While a day ago Travis CI was perfectly happy compiling my package currently hosted on GitHub, the same Travis configuration now returns the following error:

! Package parnotes Error: Cannot use custom definition of \parnotemarkfmt
(parnotes)                in parnotes rev. 2 or later. Use \theparnotemark
(parnotes)                and \parnotecusmarkfmt instead.

I can see in your vignette that parnotes is one of the LaTeX packages that is loaded and used by this style.
I'll appreciate if you could look into the issue, and update your code accordingly.

Thank you very much for the great work
Kevin

First sentence of figure caption ending with a full stop, no line break?

Is it possible to provide this as an option? The current scheme (line break with no full stop) makes sense for short first sentences, but it looks odd when the first sentence is longer. This is the case for many of my figures where the description for a figure takes up one sentence that isn't easily broken up.

To be clear, I wouldn't require this as an option for each individual figure; a global setting would be sufficient, as I write my figure captions in the same way across any single document.

"Borrow" template from BiocStyle

Hi All,

Thanks for the nice work! Recently I wrote a package called prettydoc that provides some lightweight themes and templates for R Markdown. Dirk reminded me that BiocStyle also contains a nice template, so I wonder if I could include this theme in future versions of my package.

My consideration is that for non-BioC users, they tend to only install packages from CRAN, so it may be more convenient for them to obtain this template from a CRAN package. But before doing that I think it would be better to get a permission from you authors, although technically the Artistic license that BiocStyle uses should be compatible with Apache 2 under which prettydoc is licensed. Of course I will list all of you in the authors field and your work will be appropriately acknowledged.

How do you think of this? Thanks!

Improve formatting of TOC in `html_document2`

See the discussion at https://stat.ethz.ch/pipermail/bioc-devel/2016-July/009524.html and the following screen for an illustration of the issue.

`R CMD build` timeouts on some Bioconductor packages with recent devel version of BiocStyle

Hi Andrzej,

We recently started to observe R CMD build timeouts on some Bioconductor packages (e.g. TRONCO):

https://bioconductor.org/checkResults/3.6/bioc-LATEST/

They seem to be caused by some recent changes to BiocStyle::latex(). If I install the release version of BiocStyle then R CMD build TRONCO finishes in less than 1 minute.

Thanks,
H.

Remove defunct functions

Follow Step 3 of Function Deprecation Guidelines to clean up the package from defunct functions.

Add `relative_path` option to `pdf_document `

Use similar mechanism as latex(..., relative.path=TRUE) to copy the bioconductor .sty file to the vignette build dir in order to circumvent issues on Windows machines when pathname contains spaces.

file does not exist with pdf_document2

With the latest version (2.1.23) I am getting an error about non-existing file:

render("p1.Rmd", output_format = BiocStyle::pdf_document2())

shows

rocessing file: p1.Rmd
  |...................                                      |  33%
   inline R code fragments

  |......................................                   |  67%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |.........................................................| 100%
   inline R code fragments


output file: p1.knit.md

/usr/bin/pandoc +RTS -K512m -RTS p1.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output p1.tex --table-of-contents --toc-depth 2 --template /tmp/RtmpjXaq2i/BiocStyle/template.tex --number-sections --highlight-style tango --latex-engine pdflatex --include-in-header /tmp/RtmpjXaq2i/779391352c4.tex --bibliography OncoSimulR.bib --filter /usr/bin/pandoc-citeproc 
Latexmk: This is Latexmk, John Collins, 22 April 2016, version: 4.45.

Output created: p1.pdf
Error in tools::file_path_as_absolute(output_file) : 
  file 'p1.pdf' does not exist

and

traceback()
3: stop(gettextf("file '%s' does not exist", x), domain = NA)
2: tools::file_path_as_absolute(output_file)
1: render("p1.Rmd", output_format = BiocStyle::pdf_document2())

Note that this does not happen with BiocStyle::pdf_document() (or bookdown::pdf_document2()).

Display pandoc version in BiocStyle vignette

Besides of sessionInfo, include in the vignette the pandoc version used to convert it

html_document2: tables are full column width without stripped rows

I think tables from BiocStyle::html_document2 are not as nice as those from BiocStyle::html_document (though this is of course highly subjective). Those from BiocStyle::html_document, as explained in https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html#additional-formatting-features, have stripped rows table rows and, in addition, do not span the full column width. But with BiocStyle::html_document2 they are not stripped and even small tables (below) span the full column width. For instance:


---
output: 
  BiocStyle::html_document2

---


Fruit   | Price
------- | -----
bananas | 1.2
apples  | 1.0
oranges | 2.5

The stripping I can get by using the bioconductor.css as a custom css but I haven't been able to tweak the CSS so as to obtain centered tables that do not span the full column width.

Vignette Ambiguous Wording for Code Width

In the vignette, it states

The line length of output code chunks is set to the optimal width of typically 80 characters, so it is not neccessary to adjust it manually through options("width").

This implies that it is possible to use a commands such as options(width = 120);BiocStyle::markdown(); but it has no effect.

Affiliation for single author

Could you clarify how to define an affiliation for a single author html_document2. I tried

author: my name
affiliation: my affiliation

but the latter is ignored.

I also tried

author:
  - name: my name
  - affiliation: my affiliation

but then it print my name and NULL.

author:
  - name: my name
    affiliation: my affiliation

fails when building the package.

CRANpkg links to a mirror instead of the CRAN

When using CRANpkg("data.table") it links to the mirror of CRAN at http://cran.fhcrc.org. The mirror itself says:

Please use the canonical form https://CRAN.R-project.org/package=data.table to link to this page.

While the link CRANpkg produces is http://cran.fhcrc.org/web/packages/data.table/index.html. I tried using http://cran.fhcrc.org/packages=data.table but it couldn't be resolved.

The FAQ question What is CRAN? explicitly says:

Please always use the URL of the master site when referring to CRAN.

I know you are aware of this, but I couldn't find the reason behind this decision. Why does the BiocStyle link to FHCRC CRAN mirror instead of the recommended master site?

TOC Chapter headings are small font

In my updated version of the csaw user's guide, using BiocStyle yields a TOC where the chapter headings seem to be of a smaller font than the section headings. They are bold, which is nice, but should the chapter headings be larger than - or at least, of equal size to - the section headings?

Footnotes not being resolved in BiocStyle::html_document output format

Footnotes, at least those defined using the inline_notes pandoc extension, don't appear to be properly resolved when using BiocStyle::html_document output format. They do appear to work when using html_document output format, so this suggests to me it's something going wonky with BiocStyle rather than rmarkdown.

An example is given in https://github.com/Bioconductor/BiocStyle/blob/master/vignettes/AuthoringRmdVignettes.Rmd#margin-notes, which doesn't appear to be rendered in https://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html#10_margin_notes.

no page break in bibliography

I am using BiocStyle::pdf_document: to create a pdf from rmarkdown. My bibliography is more than one page in length but the pdf doesn't have a page break with the consequence that the bibliography simply continues into the bottom margin, with whatever references are left simply not printed. I recreated with a simple .rmd that only contains references (more than one page worth) and attached below. I updated RStudio, rmarkdown, bookdown, BiocStyle (to 2.7.8), the macTex distribution but no luck. Running OS Sierra 10.12.6
throw_away.pdf

pdf_document: cannot add includes

I believe there is a bug in pdf_document and pdf_document2, where includes are concatenated:

includes$in_header = c(includes$in_header, inc)

should be

includes$in_header = c(includes$in_header, inc$in_header)

Duplicated References entry in toc

I use the bibliography: refs.bib entry in my header and then cite paper with [@ref] in my vignette. Using it like this add the reference at the end of the document (Session information in the example below) without any space of section header. I then decided to add one myself, manually, at the very end of the document

This however results in two entries in the table of content

(The links are http://127.0.0.1:22796/library/MSnbase/doc/MSnbase-development.html#references and http://127.0.0.1:22796/library/MSnbase/doc/MSnbase-development.html#references7 respectively).

Any idea?

no \@ref in html_document

It seems BiocStyle::html_document does not allow using custom labels as {#somelabel} and referencing it with \@ref(somelabel) (see, e.g., https://bookdown.org/yihui/bookdown/cross-references.html ).

Playing with the code, I think that the only things that would need to be added to html_document are copying the post_processor function from html_document2 and adding post_processor = post_porcessor in the final call to rmarkdown::output_format.

I tried it, and it seems to work. I can submit a pull request, but am I missing something here?

Compatibility with the combination of code chunk options `fig.align='center'` and `fig.show='hold'`

Using both fig.align='center' and fig.show='hold' options to a code chunk producing multiple figures without a caption results in an invalid .tex output.

.Rnw

\documentclass{article}

<<style-knitr, eval=TRUE, echo=FALSE, results="asis">>=
BiocStyle::latex()
@ 

\begin{document}

<<setup, include=FALSE>>=
library(knitr)
opts_chunk$set(fig.show="hold", fig.align="center")
@

<<fig>>=
plot(cars)
plot(faithful)
@

\end{document}

relevant .tex fragment

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.941, 0.941, 0.941}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{plot}\hlstd{(cars)}
\hlkwd{plot}\hlstd{(faithful)}
\end{alltt}
\end{kframe}\begin{adjustwidth}{\fltoffset}{0mm}

{\centering \includegraphics[width=\maxwidth]{figure/fig-1} \end{adjustwidth}\begin{adjustwidth}{\fltoffset}{0mm}\includegraphics[width=\maxwidth]{figure/fig-2} 

}

\end{adjustwidth}
\end{knitrout}

Figures aspect ratio

The different figure environments are really nice. There are however cases where I would like to display a large (as in not smallfigure) square figure. I tried using fig.asp = 1, but without effect. Is this a desired behaviour?

I am running BiocStyle 2.1.7.

BiocStyle & kableExtra

Hi,

Thanks a lot for creating the package. I'm wondering if it is possible to make it more compatible with kableExtra, e.g. I would like to reduce the table font when using knitr::kable. At the moment it only changes the font of the column names. You'll find a MWE below. Thanks.

MWE:

    ---
    title: "MWE; BiocStyle & KableExtra"
    author: Nikolai 
    date: "`r Sys.Date()`"
    package: BiocStyle
    output: BiocStyle::html_document
    vignette: >
      %\VignetteIndexEntry{MWE; BiocStyle & KableExtra}
      %\VignetteEngine{knitr::rmarkdown}
      %\VignetteEncoding{UTF-8}
    ---

    ```{r, echo = FALSE, message=FALSE}
    library(knitr, quietly = T, verbose = F)
    library(kableExtra, quietly = T, verbose = F)
    options(knitr.table.format = "html")
    ```

    ```{r, echo = FALSE}
    X <- matrix(10*15, 10, 15)
    DF <- as.data.frame(X)
    colnames(DF) <- paste0("x", 1:15)
    ```

    ```{r, echo = FALSE}
    kable(DF) %>% kable_styling(bootstrap_options = "striped")
    ```

    ```{r, echo = FALSE}
    kable(DF) %>% kable_styling(bootstrap_options = "striped", font_size = 10)
    ```

Triple colons

It seems Bioconductor, unlike CRAN, is more friendly to :::. In general, it is a bad idea, but I confess I use it, too. However, I only use it when I feel I can grab my phone and bother the package maintainer immediately whenever there is a problem, e.g. the maintainer is myself, my colleague, or a close friend.

I found by chance that this package made heavy use of :::. Unfortunately, these internal functions in other people's package are not guaranteed to be stable. They are not exported for reasons. Basically no public API means no responsibility. For example, you will find BiocStyle::html_document will be broken with the next version of rmarkdown due to changes in rmarkdown:::pandoc_html_highlight_args (you can test the current dev version on Github).

If the only things you want to tweak are the CSS and the template, you may well use the css and template arguments, e.g.

output:
  html_document:
    css: !expr BiocStyle::biocCSS()
    template: !expr BiocStyle::biocTemplate()

That way, there is no need to provide an html_document format in BiocStyle.

I don't understand the need to copy code from rmarkdown. If you do copy source code, rmarkdown authors may need to be attributed somehow. Personally I don't care too much about this (CRAN requires it but you are not on CRAN), but since the license is changed to Artistic-2.0 in this package, I'm a little concerned. For example, GPL-3 states

For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.

But the documentation ?BiocStyle::html_document mentioned nothing about the differences between BiocStyle::html_document and rmarkdown::html_document. On the contrary, the help pages look so similar, and I'm worried that confusion can be even stronger.

I'm not an expert of different open-source licenses. Just some thoughts on both technical and legal aspects here. I'm by no means saying anything is necessarily wrong or bad. I'm all for open source, and always hope open source projects can succeed.

knitr should be moved from Suggests to Imports.

In using bioc-devel without knitr installed, and trying to install BiocStyle, I get the following error:

* installing *source* package ‘BiocStyle’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(name) : there is no package called ‘knitr’
Error : unable to load R code in package ‘BiocStyle’
ERROR: lazy loading failed for package ‘BiocStyle’
* removing ‘/usr/local/google/home/sidb/lib/R/library/BiocStyle’

The downloaded source packages are in
        ‘/tmp/RtmpQlYKcL/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocStyle’ had non-zero exit status

Width of code boxes is smaller in html_document2, figures not the same size as html_document by default

Hi,

I just started using the new html_document2 style and noticed a couple of things. The figures are smaller than in BiocStyle::html_document and rmarkdown::html_document. I see at #9 how to address this, but it'd be nice if the default size was the same (or about the same) as BiocStyle::html_document.

Similarly, the width of the code boxes are smaller, so code that is less than 80 characters long that used to fit in one line now gets split into two.

It's also missing some of the nice things from BiocStyle::html_document such as the colors (I loved the green/blue colors!). I don't really use tables like reported in #13 but the issue might be related.

In any case, I do like how html_document2 was written so it's very similar to rmardown::html_document and can work with the new stuff the rmarkdown folks keep adding.

Edit: messed up something here, will post it below.

Best,
Leo

BiocStyle::latex[2] on Travis-CI

I am building MSnbase on Travis-CI and had to do some testing with the .travis.yml to get the LaTeX dependencies right. I seems that adding this at the beginning of the config file works (here's the full .travis.yml for details):

before_install:
  - tlmgr install bera nowidow parnotes marginfix etoolbox titlesec sectsty framed enumitem parskip soul placeins footmisc changepage xstring caption mathtools

(Note that some of the packages might not be needed explicitly)

Posting here for reference or to see if there's a better way.

Width in code chunk is causing a wrapper to appear in a vignette

Hi,

have a look at Bioconductor/Contributions#607 (comment).

Inside the vignette a longer character is displayed, which cannot be shortened, causing a wrapper with a horizontal scrollbar to appear. This might be due to the fact, that the character does not contain any space and only the letters ".><"

@hpages suggest opening an issue and or asking for help on this. I don't, what I can do on my end to resolve the issue. Please advice.

How to reference multiple plots from the same code chunk

Hi,

In previous versions I was able to use \@ref(fig:chunkname1) and \@ref(fig:chunkname2) if a single Rmd chunk (here called chunkname) generated two plots. In the current devel version (2.7.8) this doesn't work.

You can see an example at http://research.libd.org/recount-brain/example_SRP027383/example_SRP027383.html that matches this commit LieberInstitute/recount-brain@614316a. I include a screenshot here for simplicity.

I also tried using \@ref(fig:chunkname-1) and it failed. Note that \@ref(fig:chunkname) did work, but it doesn't make sense to me to reference several figures with the same number (even if they come from the same code chunk) as in:

I guess that I could use \@ref(fig:chunkname)-1 and \@ref(fig:chunkname)-2 although the links won't point to the correct location.

Is is still possible to reference multiple plots from the same chunk? Maybe there's a new syntax that I'm missing. There are cases where I can't break the code and separate the code so that each code chunk makes a single figure. For example, when a function makes more than 1 plot.

Thanks!
Leo

Resolve references to commits

Need to fix broken references to commits replaced after the switcheroo.

#2: version 2.1.12
#3: version 2.1.15
#12: version 2.1.5
#16: version 2.1.25
#17: version 2.3.6
#19: version 2.3.12
#20: version 2.3.16
#25: version 2.3.27

pdf_document2 breaks with `A = 12`


---
output: 
  BiocStyle::pdf_document2:
    keep_tex: true 

---

# Something

If I write `A = 1` , the 1 is missing (from pdf_decoment2 in BiocStyle).

If I write `A = 12` this breaks "BiocStyle::pdf_document2" (but
not "BiocStyle::pdf_document", nor "bookdown::pdf_document2")

Trying to tex the file, it seems to be related to the soul package:

./file1.tex:121: Package soul Error: Reconstruction failed.

See the soul package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.121 If I write \texttt{A\ =\ 12}
                                   this breaks ``BiocStyle::pdf\_document2''
?

Suggestion: spell Warnings with a capital

The \warning macro is nice to keep warning or important messages consistent throughout different vignette. I was wondering what you thought about capitalising the first Warning word in the paragraph. IMHO, it does look a bit weird that a paragraph suddenly starts with a lower case.

Figures in html_document2

Are there, or will there by different types of figures (regular, small, wide) in the html style, like there is in latex2?

fig.asp interpretation seems to be flipped

Reading the user guide suggests that the figure aspect ratio is WIDTH/HEIGHT, e.g., a wide figure has a ratio of 2. However, setting something like:

<<smallfig, fig.asp=2>>=
plot(1, 1)
@

... gives me a tall figure rather than a fat figure. Similarly, setting fig.asp=0.5 gives me a fat figure rather than a tall figure. Presumably this is not intended?

BiocStyle repo should not be a Bioc-mirror fork

There should be no forks coming out of Bioconductor-mirror.
The mirror is deprecated.

Please update the BiocStyle repository in the git server if there are any differences
and use the git server repository version to create a new repository under
the Bioconductor account.

Thanks!

Regards,
Marcel

Deprecation message for latex2 breaks LaTeX

Hi Andrzej,

See https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011750.html for the details.

Thanks,
H.

BiocStyle::html_document not working with rmarkdown 1.2

Hi!

I currently have no idea what is wrong, but it seems its either rmarkdown or BiocStyle problem with the latest versions. When I used older versions it worked, also changing to BiocStyle::html_document2 works. I haven't found anything in the internet on this problem, checked on my windows with the same problem.

My test.Rmd file contents:

---
title: "why me no good"
output: BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{test}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

When trying to knit file I get:

|.................................................................| 100%
  inline R code fragments

processing file: test.Rmd
output file: test.knit.md

Error in rmarkdown:::pandoc_html_highlight_args(highlight, template = "default",  : 
 unused arguments (self_contained, lib_dir, output_dir)
Calls: <Anonymous> -> <Anonymous> -> overlay -> <Anonymous>
Execution halted


> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] backports_1.0.4 BiocStyle_2.2.0 magrittr_1.5    rprojroot_1.1   htmltools_0.3.5 tools_3.3.1     yaml_2.1.14    
[8] Rcpp_0.12.8     stringi_1.1.2   rmarkdown_1.2   knitr_1.15.1    stringr_1.1.0   digest_0.6.10   evaluate_0.10

Vertical spacing after htmlwidgets

Fix it in our templates unless rstudio/rmarkdown#1343 is resolved.

Add code folding

Hi,

Jim Hester just commented at the knitrBootstrap package jimhester/knitrBootstrap#68 (comment) that the new rmarkdown release supports code folding as described at http://blog.rstudio.org/2016/03/21/rmarkdown-v0-9-5/.

I don't know how much work it would be, but it'd be great if BiocStyle also supported code folding. For example, the current test does not work:


---
title: "test"
author: "L Collado-Torres"
date: "`r doc_date()`"
output: 
  BiocStyle::html_document:
    code_folding: hide

---

```{r}
plot(1:10, 1:10)
```

Best,
Leo

> packageVersion('rmarkdown')
[1] ‘0.9.5’
> packageVersion('BiocStyle')
[1] ‘1.8.0’

latex 2.0 style footnotes

The margin notes are very nice in most cases, but I stumbled on the following issues

When the footnote is actually an URL, it displays really badly in the margin. Is there a way to force it to be a footnote?

~~Is there a dedicated way to specify the authors' affiliations and/or email address. I think the email in the margin below looks a bit weird~~

Found this in the LatexStyle2 vignette.

I have the case where the footnote appears at the bottom of the page and overflows on the page number

Convenience function to link between workflows

It would be nice if we had way to easily add references to other Bioconductor workflows, other than copying-and-pasting the URL. The idea would be to have something similar to the Biocpkg() function, but for workflows. For example, I would like to be able to write something like

Biocworkflow("simpleSingleCell/part1")

... and this would return a link to https://bioconductor.org/help/workflows/simpleSingleCell/part1/. One could extend this to reference specific sections or even figures (though I'm not sure how feasible the latter is).

The motivation is to centralize the linking decisions into BiocStyle, which will provide some robustness to changes to how the Bioconductor website is organized. Indeed, now that we're getting release and devel versions of the workflows, one could imagine that a Biocworkflow() function would automatically link to the correct version, depending on the environment in which the workflow was being built.

BTW, this originates from a half-forgotten discussion at Euro-BioC-2017.

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.