Hi Ludwig, thank you! This sounds like an issue with your LaTeX distribution, in particular the package 'marginfix'. Please make sure that all the packages listed in the BiocStyle vignette under Appendix B "Attached LATEX packages" are installed, and possibly the up-to-date.
Best, Andrzej On Tue, Sep 12, 2017 at 11:03 PM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote: > 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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
