[Bioc-devel] warnings with BiocStyle pdf compilation

[Andrzej Oleś]

Hi Vince,

thank you for your feedback. If the vignette compiles fine I wouldn't worry
too much about these warnings.

The first one "LaTeX Warning: You have requested package
`/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',
but the package provides `Bioconductor'." is related to the nonstandard
approach of specifying an external LaTeX package by file path rather than
by referring to a package from the local library by name. I haven't really
found a way around this, unfortunately.

The remaining warnings could be probably fixed by tweaks to
Bioconductor.sty, but as far as I can tell they doesn't seem to harm so I
wouldn't bother to much.

Cheers,
Andrzej

On Mon, May 6, 2019 at 9:42 PM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> *I don't often compile vignettes to pdf ... but a recent attempt led to:*
>
>
> *Warning message:*
>
> *LaTeX Warning: You have requested package
> `/Library/Frameworks/R.framework/Vers*
>
> *ions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',*
>
> *               but the package provides `Bioconductor'.*
>
> *Package geometry Warning: Over-specification in `h'-direction.*
>
> *    `width' (384.1122pt) is ignored.*
>
> *Package Fancyhdr Warning: \fancyhead's `E' option without twoside option
> is use*
>
> *less on input line 173. *
>
>
> *Any hints?  Must I update tex?*
>
>
> > sessionInfo()
>
> R Under development (unstable) (2019-03-18 r76245)
>
> 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/3.6/Resources/lib/libRblas.0.dylib
>
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>
> [1] BiocStyle_2.12.0 rmarkdown_1.12
>
>
> loaded via a namespace (and not attached):
>
>  [1] Rcpp_1.0.1         bookdown_0.9       digest_0.6.18      magrittr_1.5
>
>
>  [5] evaluate_0.13      stringi_1.4.3      startup_0.11.0     tools_3.6.0
>
>
>  [9] stringr_1.4.0      tinytex_0.12       xfun_0.6           yaml_2.2.0
>
>
> [13] compiler_3.6.0     BiocManager_1.30.4 htmltools_0.3.6    knitr_1.22
>
> --
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