Dear Andrzej, BiocStyle2 is a great piece of work and the new vignettes look really nice! Thank you!
However, I am having a problem with the widefigure (figure*) environment, which apparently only holds for my local installation, as the same vignette builds fine here: http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/ However, on my machine (- do I need to update any external dependencies?): Rdev CMD build EnrichmentBrowser * checking for file EnrichmentBrowser/DESCRIPTION ... OK * preparing EnrichmentBrowser: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Execution of 'texi2dvi' for 'EnrichmentBrowser.tex' failed. LaTeX errors: ! Undefined control sequence. \\figure* [#1]->\blockmargin \@biocfloat@wide {figure}{#1} l.761 \centering ! Undefined control sequence. \endfigure* ->\endfigure \unblockmargin [1em] l.768 \end{figure*} ! Undefined control sequence. \\figure* [#1]->\blockmargin \@biocfloat@wide {figure}{#1} l.1002 \begin{figure*}[!h] ! Undefined control sequence. \endfigure* ->\endfigure \unblockmargin [1em] l.1008 \end{figure*} Call: <Anonymous> -> texi2pdf -> texi2dvi Exectuion halted. Here is some information on the build environment, please let me know if I should provide additional information: > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocStyle_2.5.37 loaded via a namespace (and not attached): [1] compiler_3.4.1 backports_1.1.0 magrittr_1.5 rprojroot_1.2 [5] htmltools_0.3.6 tools_3.4.1 yaml_2.1.14 Rcpp_0.12.12 [9] stringi_1.1.5 rmarkdown_1.6 knitr_1.16 stringr_1.2.0 [13] digest_0.6.12 evaluate_0.10.1 Thanks, Ludwig > 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 OleÅ > > [1] > http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Dr. Ludwig Geistlinger eMail: ludwig.geistlin...@bio.ifi.lmu.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel