[Bioc-devel] warnings with BiocStyle pdf compilation

[Vincent Carey]

On Thu, May 9, 2019 at 5:12 AM Andrzej Oleś <andrzej.oles using gmail.com> wrote:

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

Hi Andrzej -- yes, the compilation seems fine.

Best regards
Vince


>
> 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
>>
>> --
>> The information in this e-mail is intended only for t...{{dropped:27}}