Yes, I was indeed sitting on an old Tex version. Upgrading to Tex Live 2017 fixed that.
Thanks, Ludwig > 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 âEnrichmentBrowser/DESCRIPTIONâ ... OK >> * preparing âEnrichmentBrowserâ: >> * 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 Oleà ⺠>> > >> > [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 >> >> > -- 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