[Bioc-devel] warnings with BiocStyle pdf compilation

*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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The information in this e-mail is intended only for th...{{dropped:10}}

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 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}}