CHANGES IN VERSION 2.4.0 ------------------------ NEW FEATURES o Vignette "Authoring R Markdown vignettes" o R Markdown templates for 'pdf_document2' and 'html_document2' o Standard way of specifying author affiliations o Support for short title in R Markdown PDF output o Argument 'relative.path' to 'latex2()' (https://support.bioconductor.org/p/90352/) SIGNIFICANT USER-VISIBLE CHANGES o Increase column width in order to accommodate 80 characters wide code chunks o Separate caption title from description with newline o Use canonical URL to link to CRAN packages (https://github.com/Bioconductor/BiocStyle/issues/24) o Consistently number equations on right hand side across different output formats o Numerous CSS tweaks BUG FIXES AND IMPROVEMENTS o Support for PDFs typeset with 9pt and 8pt font size o Proper formatting of 'longtable' captions o Fix to retain spaces in '\texttt' o Replace carets "\^{}" by "\textasciicircum" to fix incompatibility with LaTeX 'soul' package used for inline code highlighting o Patch to avoid overfull pages containing a float followed by a longtable CHANGES IN VERSION 2.2.0 ------------------------ NEW FEATURES o New Bioconductor HTML Style. See package vignettes for details. BUG FIXES AND IMPROVEMENTS to Bioconductor LaTeX Style 2 o Use `\path` for file names to allow long line breaks o Load 'nowidow' LaTeX package to prevent widows and orphans o Patch bug in 'titlesec' 2.10.1 (http://tex.stackexchange.com/q/299969/102422) o Pass option `multiple` to 'footmisc' for better handling of consecutive footnotes o Load 'marginfix' LaTeX package to prevent margin notes from overflowing the bottom margin o Fix the issue with color spilling out on margin notes (https://github.com/Bioconductor/BiocStyle/issues/5) o Use `fig.asp` to override figure height (https://github.com/Bioconductor/BiocStyle/issues/4) o Fix compatibility with the 'float' package, in particular the `[H]` placement specifier o Load 'marginfix' LaTeX package to prevent margin notes from overflowing the bottom margin o Enclose wide floats in `\blockmargin` and `\unblockmargin` to prevent footnotes from entering them o Move the footnote mark inside margin notes o Add vertical skip after margin phantoms of wide floats for better alignment of margin notes with paragraph text o Fix concatenation of `includes` reported in https://github.com/Bioconductor/BiocStyle/issues/8 o Stratify parnote mark definition depending on package version (https://github.com/Bioconductor/BiocStyle/issues/7) o Capitalize default opening words in `\comment`, `\warning` and `\fixme`, and mention the optional argument in the vignette CHANGES IN VERSION 2.0.0 ------------------------ o New Bioconductor LaTeX Style. See package vignettes for details. CHANGES IN VERSION 1.8.0 ------------------------ o R Markdown templates for Bioconductor HTML and PDF documents o Suggest 'rmarkdown' as the default engine for .Rmd documents o Simplified use with 'rmarkdown' - no need to include a separate code chunk calling 'BiocStyle::markdown' anymore o Functions facilitating the inclusion of document compilation date and package version in the .Rmd document header CHANGES IN VERSION 1.4.0 ------------------------ USER VISIBLE CHANGES o Support for markdown documents o Add \Githubpkg markup command CHANGES IN VERSION 1.2.0 ------------------------ USER VISIBLE CHANGES o Remove dependency on 'helvet' LaTeX package to allow for the same font both in Sweave and knitr o Improve package vignette by adding paragraphs about building vignettes and using bibliography o knitr chunk_opts error=FALSE by default, so failures during vignette processing are signaled to R CMD build and R CMD check o Name-mangle \comment mark-up to avoid conflicts with other LaTeX styles o Introduce \bioctitle to allow for full and short (header) titles o Add BiocStyle::latex option 'use.unsrturl=TRUE' to use the 'unsrturl' bibliography style by default BUG FIXES o Avoid use of 'titling' LaTeX package to circumvent the conflict w/ \footnote in \author CHANGES IN VERSION 1.0.0 ------------------------ USER VISIBLE CHANGES o Rename \Rpkg{} as \CRANpkg{} to reflect functionality BUG FIXES o Avoid option conflict with \usepackage{colors}