[Bioc-devel] BiocStyle transition aftermath

[Andrzej Oleś]

Dear Bioconductor Developers,

overall the transition to the updated formatting went smooth considering
the number of packages using BiocStyle, and the different possible input
(.Rnw/.Rmd) and output formats (PDF/HTML).

However, we have identified some common issues with specifying author
information in Sweave/knitr (.Rnw) vignettes which lead to package build
errors or timeouts. The updated style loads the 'authblk' LaTeX package to
standardize the way of specifying author affiliations, but unfortunately
this approach is also more fragile than the default LaTeX macros. In
particular, the usual author separator ' \and' is not compatible with the
authblk's footnote mode used by BiocStyle.

The maintainers of the following packages are encouraged to review their
vignettes and ensure that '\author{}' does not contain any custom
formatting and meets the guidelines outlined in Section 2.1.2 "Authors and
affiliations" of the "Bioconductor LaTeX Style 2.0" vignette [1].

DiffBind
GMRP
groHMM
MBttest
MutationalPatterns
OncoScore
OperaMate
quantro
rCGH
RiboProfiling
sampleClassifier
TRONCO


Additionally, the following packages fail to build because their vignettes
contain some LaTeX customizations incompatible with the current version of
BiocStyle.

funtooNorm
Linnorm
NanoStringQCPro


Thank you for your understanding and cooperation.

Kind regards,
Andrzej Oleś

[1]
http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf

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