NEWS
BiocStyle 2.30.0
BUG FIXES
- Addressed issue where code chunks in HTML output did not have the
correct background colour
- Fixed incompatibility with ragged2e LaTeX package distributed in
TexLive 2023
(https://github.com/Bioconductor/BiocStyle/issues/105)
BiocStyle 2.28.0
BUG FIXES
- Addressed issue where, when using newer versions of Pandoc, footnotes
would appear at the bottom of HTML output rather than be moved to
the margin.
- Fixed problem including references in R Markdown documents when the
output format was BiocStyle::pdf_document
(https://github.com/Bioconductor/BiocStyle/issues/94)
BiocStyle 2.24.0
BUG FIXES
- 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)
BiocStyle 2.22.0
USER-VISIBLE CHANGES
- Added section to HTML vignette regarding accessibility considerations
when creating plots and figures.
BUG FIXES AND IMPROVEMENTS TO HTML STYLE
- 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.
- Addressed further styling issues for code blocks, introduced by changes
in rmarkdown. This time re-introducing padding around pre tags.
BiocStyle 2.20.0
- Addressed styling issues for output code blocks, introduced by changes
in rmarkdown version 2.7.0
(https://github.com/Bioconductor/BiocStyle/issues/86)
BiocStyle 2.18.0
BUG FIXES
- 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).
BiocStyle 2.8.0
SIGNIFICANT USER-VISIBLE CHANGES
- Add 'relative_path' argument to 'pdf_document'
- Add argument 'titlecaps' to 'html_document'
- Defunct deprecated functions
BUG FIXES
- Fix a bug in generating navigation links which resulted in an empty
document when there were no subsections to merge
BiocStyle 2.6.0
SIGNIFICANT USER-VISIBLE CHANGES
- Rename 'latex2', 'pdf_document2' and 'html_document2' to 'latex', 'pdf_document' and 'html_document', respectively
- Rename argument to 'pdf_document' from 'use.unsrturl' to 'use_unsrturl' for consistency with rmarkdown naming scheme
- 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
- Make knitr option 'fig.pos' functional in 'pdf_document'
- Improve formatting of TOC chapter entries (https://github.com/Bioconductor/BiocStyle/issues/35)
- Adjust width of non-floating figures according to the 'fig.wide'/'fig.small' setting (reported by Aaron Lun)
- Robustify \texttt, e.g. by enabling backticks and fixing the substitution of control spaces
- Update LaTeX code highlighting macros for pandoc output (reported by Vince Carey)
- Silence spurious warning in 'latex()' emitted when the source file is missing a final EOL
- Fix broken code in knitr hook adjusting page width
- Include package version field in R Markdown documents even if they are missing an abstract (https://github.com/Bioconductor/BiocStyle/issues/29)
- 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
- Correct displaying of superscript text
- Allow modifying table layout in 'knitr::kable' (https://github.com/Bioconductor/BiocStyle/issues/30)
- Correct padding of nested lists, and indentation of document date and multi-line headings
- Fix a bug in the function matching author affiliations (https://support.bioconductor.org/p/98155/)
- Proper horizontal alignment of ggplotly graphics (https://support.bioconductor.org/p/97609/)
- Fix compatibility with 'runtime: shiny' document option
BiocStyle 2.4.0
NEW FEATURES
- Vignette "Authoring R Markdown vignettes"
- R Markdown templates for 'pdf_document2' and 'html_document2'
- Standard way of specifying author affiliations
- Support for short title in R Markdown PDF output
- Argument 'relative.path' to 'latex2()' (https://support.bioconductor.org/p/90352/)
SIGNIFICANT USER-VISIBLE CHANGES
- Increase column width in order to accommodate 80 characters wide code chunks
- Separate caption title from description with newline
- Use canonical URL to link to CRAN packages (https://github.com/Bioconductor/BiocStyle/issues/24)
- Consistently number equations on right hand side across different output formats
- Numerous CSS tweaks
BUG FIXES AND IMPROVEMENTS
- Support for PDFs typeset with 9pt and 8pt font size
- Proper formatting of 'longtable' captions
- Fix to retain spaces in '\texttt'
- Replace carets "\^{}" by "\textasciicircum" to fix incompatibility with LaTeX 'soul' package used for inline code highlighting
- Patch to avoid overfull pages containing a float followed by a longtable
BiocStyle 2.2.0
NEW FEATURES
- New Bioconductor HTML Style. See package vignettes for details.
BUG FIXES AND IMPROVEMENTS to Bioconductor LaTeX Style 2
- Use '\path' for file names to allow long line breaks
- Load 'nowidow' LaTeX package to prevent widows and orphans
- Patch bug in 'titlesec' 2.10.1 (http://tex.stackexchange.com/q/299969/102422)
- Pass option ‘multiple' to ’footmisc' for better handling of consecutive footnotes
- Load 'marginfix' LaTeX package to prevent margin notes from overflowing the bottom margin
- Fix the issue with color spilling out on margin notes (https://github.com/Bioconductor/BiocStyle/issues/5)
- Use 'fig.asp' to override figure height (https://github.com/Bioconductor/BiocStyle/issues/4)
- Fix compatibility with the 'float' package, in particular the '[H]' placement specifier
- Load 'marginfix' LaTeX package to prevent margin notes from overflowing the bottom margin
- Enclose wide floats in '\blockmargin' and '\unblockmargin' to prevent footnotes from entering them
- Move the footnote mark inside margin notes
- Add vertical skip after margin phantoms of wide floats for better alignment of margin notes with paragraph text
- Fix concatenation of 'includes' reported in https://github.com/Bioconductor/BiocStyle/issues/8
- Stratify parnote mark definition depending on package version (https://github.com/Bioconductor/BiocStyle/issues/7)
- Capitalize default opening words in '\comment', '\warning' and '\fixme', and mention the optional argument in the vignette
BiocStyle 2.0.0
- New Bioconductor LaTeX Style. See package vignettes for details.
BiocStyle 1.8.0
- R Markdown templates for Bioconductor HTML and PDF documents
- Suggest 'rmarkdown' as the default engine for .Rmd documents
- Simplified use with 'rmarkdown' - no need to include a separate code chunk calling 'BiocStyle::markdown' anymore
- Functions facilitating the inclusion of document compilation date and package version in the .Rmd document header
BiocStyle 1.4.0
USER VISIBLE CHANGES
- Support for markdown documents
- Add \Githubpkg markup command
BiocStyle 1.2.0
USER VISIBLE CHANGES
- Remove dependency on 'helvet' LaTeX package to allow for the same font
both in Sweave and knitr
- Improve package vignette by adding paragraphs about building vignettes
and using bibliography
- knitr chunk_opts error=FALSE by default, so failures during vignette
processing are signaled to R CMD build and R CMD check
- Name-mangle \comment mark-up to avoid conflicts with other LaTeX styles
- Introduce \bioctitle to allow for full and short (header) titles
- Add BiocStyle::latex option 'use.unsrturl=TRUE' to use the 'unsrturl'
bibliography style by default
BUG FIXES
- Avoid use of 'titling' LaTeX package to circumvent the conflict w/
\footnote in \author
BiocStyle 1.0.0
USER VISIBLE CHANGES
- Rename \Rpkg{} as \CRANpkg{} to reflect functionality
BUG FIXES
- Avoid option conflict with \usepackage{colors}