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

Stefan Mutter Stefan.Mutter at sahmri.com
Wed Oct 4 03:29:18 CEST 2017


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.



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


[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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