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NEWS
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NEWS
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CHANGES IN VERSION 2.30.0
------------------------
BUG FIXES
o Addressed issue where code chunks in HTML output did not have the
correct background colour
o Fixed incompatibility with ragged2e LaTeX package distributed in
TexLive 2023
(https://github.com/Bioconductor/BiocStyle/issues/105)
CHANGES IN VERSION 2.28.0
------------------------
BUG FIXES
o 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.
o Fixed problem including references in R Markdown documents when the
output format was BiocStyle::pdf_document
(https://github.com/Bioconductor/BiocStyle/issues/94)
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 <pre> 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}