[Bioc-devel] warnings with BiocStyle pdf compilation
On Thu, May 9, 2019 at 5:12 AM Andrzej Ole? <andrzej.oles at 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 at 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}}