[Bioc-devel] Failure to create PDF vignette with BiocStyle 2.4.1

[Vincent Carey]

I ran into this -- BiocStyle was modified by Andrzej to solve it.  I am now
at BiocStyle 2.5.39 and biocValid() does
not complain.  So try updating BiocStyle.

On Tue, Oct 3, 2017 at 9:29 PM, Stefan Mutter <Stefan.Mutter at sahmri.com>
wrote:

> Hi,
>
>
> I hope I am writing this to the right list.
>
>
> I am currently trying to author a vignette for a package, we will be
> submitting to Bioconductor. The PDF vignette creation fails inside a code
> block which I cannot explain. I have attached a small example that contains
> the same code block (the one labelled producesError) than my vignette and
> at least on my machine it reproduces the error.
>
>
> The process can create the .tex file, but fails in converting the .tex
> file to a pdf. The error message  in RStudio is:
>
>
> This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded
> format=pdflatex)
>
>  restricted \write18 enabled.
>
> entering extended mode
>
> Latexmk: Errors, so I did not complete making targets
>
> Collected error summary (may duplicate other messages):
>
>   pdflatex: Command for 'pdflatex' gave return code 256
>
> Latexmk: Use the -f option to force complete processing,
>
>  unless error was exceeding maximum runs of latex/pdflatex.
>
>
> The log file contains the following error:
>
>
> ! Undefined control sequence.
>
> <argument> ...{"MALE"}\NormalTok {] }\OperatorTok
>
>                                                   {==}\StringTok {
> }\DecValT...
>
> l.137 ...=}\StringTok{ }\DecValTok{1}\NormalTok{)}
>
>
> This points to a problem inside the code block with the which statement,
> but it is unclear to me how the which statement can be a problem?
>
>
> It would be really appreciated if you could help me.
>
>
> Cheers,
>
> Stefan
>
>
> My session info is:
>
> 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: /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>
> [1] Numero_0.99.0
>
>
> loaded via a namespace (and not attached):
>
>  [1] compiler_3.4.1  backports_1.1.1 BiocStyle_2.4.1 magrittr_1.5
> rprojroot_1.2
>
>  [6] htmltools_0.3.6 tools_3.4.1     yaml_2.1.14     Rcpp_0.12.13
> stringi_1.1.5
>
> [11] rmarkdown_1.6   knitr_1.17      stringr_1.2.0   digest_0.6.12
>  evaluate_0.10.1?
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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