[Bioc-devel] BiocStyle2: issue with wide figure command

[Andrzej Oleś]

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.Geistlinger at 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 at wide {figure}{#1}
> l.761 \centering
>
> ! Undefined control sequence.
> \endfigure* ->\endfigure \unblockmargin
>                                         [1em]
> l.768 \end{figure*}
>
> ! Undefined control sequence.
> \\figure* [#1]->\blockmargin
>                              \@biocfloat at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Dr. Ludwig Geistlinger
> eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
>
>

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