CHANGES IN VERSION 2.24.0 ------------------------ BUG FIXES o Fixed incompatibility with recent versions of the longtable latex package when producing a PDF vignette. This bug manifested with the message 'LaTeX Error: Missing \begin{document}.' when attempting to knit. (https://github.com/Bioconductor/BiocStyle/issues/89) CHANGES IN VERSION 2.22.0 ------------------------ USER-VISIBLE CHANGES o Added section to HTML vignette regarding accessibility considerations when creating plots and figures. BUG FIXES AND IMPROVEMENTS TO HTML STYLE o Improved navigation for screen readers by adding role='link' and tabindex='0' to elements in the table of contents. TOC navigation can also be followed by pressing "Enter" when selected in addition to clicking with the cursor. o Addressed further styling issues for code blocks, introduced by changes in rmarkdown. This time re-introducing padding around
tags. CHANGES IN VERSION 2.20.0 ------------------------ o Addressed styling issues for output code blocks, introduced by changes in rmarkdown version 2.7.0 (https://github.com/Bioconductor/BiocStyle/issues/86) CHANGES IN VERSION 2.18.0 ------------------------ BUG FIXES o Fix issue where images created with the `fig.small=TRUE` chunk argument were not displayed in HTML output (https://github.com/Bioconductor/BiocStyle/issues/83). CHANGES IN VERSION 2.8.0 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Add 'relative_path' argument to 'pdf_document' o Add argument 'titlecaps' to 'html_document' o Defunct deprecated functions BUG FIXES o Fix a bug in generating navigation links which resulted in an empty document when there were no subsections to merge CHANGES IN VERSION 2.6.0 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Rename 'latex2', 'pdf_document2' and 'html_document2' to 'latex', 'pdf_document' and 'html_document', respectively o Rename argument to 'pdf_document' from 'use.unsrturl' to 'use_unsrturl' for consistency with rmarkdown naming scheme o Split figure/table captions on ". " rather than "." in order to minimize chances of hitting decimal point in numbers, etc. BUG FIXES AND IMPROVEMENTS TO PDF STYLE o Make knitr option 'fig.pos' functional in 'pdf_document' o Improve formatting of TOC chapter entries (https://github.com/Bioconductor/BiocStyle/issues/35) o Adjust width of non-floating figures according to the 'fig.wide'/'fig.small' setting (reported by Aaron Lun) o Robustify \texttt, e.g. by enabling backticks and fixing the substitution of control spaces o Update LaTeX code highlighting macros for pandoc output (reported by Vince Carey) o Silence spurious warning in 'latex()' emitted when the source file is missing a final EOL o Fix broken code in knitr hook adjusting page width o Include package version field in R Markdown documents even if they are missing an abstract (https://github.com/Bioconductor/BiocStyle/issues/29) o Correct way of enclosing non-floating figures in LaTeX 'adjustwidth' environment (https://github.com/Bioconductor/BiocStyle/issues/28) BUG FIXES AND IMPROVEMENTS TO HTML STYLE o Correct displaying of superscript text o Allow modifying table layout in 'knitr::kable' (https://github.com/Bioconductor/BiocStyle/issues/30) o Correct padding of nested lists, and indentation of document date and multi-line headings o Fix a bug in the function matching author affiliations (https://support.bioconductor.org/p/98155/) o Proper horizontal alignment of ggplotly graphics (https://support.bioconductor.org/p/97609/) o Fix compatibility with 'runtime: shiny' document option 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}